🔥 #MESScience 3: Overview of Biology

in MES Science5 months ago (edited)

In #MESScience 3, I have uploaded a deep dive in all things mainstream biology. As stated last year in the Progress and Update video, I initially planned on just making a COVID and masks video. But the background genetic and molecular biology section got very large, so I decided to do that separately. Unlike mathematics, I had researched biology before, which is why I felt it important to first go over a very extensive overview video of all things mainstream biology. This is essentially a mini-course (or degree) compacted into one 48+ hour video. Buckle up!

The topics covered in this video are listed below with their time stamps.

  • 0:00 - Video Meta Data
    • 3:24 - MES Inline Commentary
    • 4:34 - Note on Wikipedia
  1. 6:20 - Overview of Biology
  2. 7:17 - Table of Contents
  3. 9:42 - Biology
    • 16:09 - Etymology [Origin/history of words]
    • 19:28 - History
    • Chemical basis
      • 36:55 - Atoms and molecules
      • 1:09:45 - Organic compounds
        • 1:11:39 - Carbohydrates / Saccharides
        • 1:16:15 - Acids and Bases
        • 1:35:46 - Important Chemistry Terms
        • 1:55:53 - Fats
        • 2:17:59 - Amino Acids
        • 2:34:34 - Nucleotides
      • 3:18:55 - Macromolecules
    • 3:36:24 - Cells
      • 3:50:03 - Cell structure
      • 4:55:14 - Metabolism
      • 5:33:10 - Cellular respiration
      • 7:02:17 - Photosynthesis
      • 7:45:43 - Cell signaling
      • 8:34:05 - Cell cycle
    • Genetics
      • 9:41:29 - Inheritance
      • 10:22:43 - DNA
      • 10:28:25 - Gene expression
      • 11:09:32 - Genomes
      • 11:42:17 - Biotechnology
      • 12:27:38 - Genes, development, and evolution
    • Evolution
      • 12:58:00 - Evolutionary processes
      • 13:07:46 - Speciation
      • 13:33:54 - Phylogenies
      • 13:52:48 - History of life
    • Diversity
      • 14:50:54 - Bacteria and Archaea
      • 15:49:37 - Protists
      • 15:52:56 - Plant diversity
      • 17:03:00 - Fungi
      • 17:31:07 - Animal diversity
      • 18:30:16 - Viruses
    • Plant form and function
      • 19:33:43 - Plant body
      • 20:28:06 - Plant nutrition and transport
      • 21:01:56 - Plant development
      • 21:25:49 - Plant reproduction
      • 21:34:27 - Plant responses
    • Animal form and function
      • 21:45:40 - Principles
      • 22:15:47 - Water and salt balance
      • 22:34:52 - Nutrition and digestion
      • 23:05:15 - Breathing
      • 1:00:09:05 - Circulation
      • 1:00:30:37 - Muscle and movement
      • 1:01:30:06 - Nervous system
      • 1:01:54:57 - Hormonal control
      • 1:02:46:25 - Animal reproduction
      • 1:02:52:41 - Animal development
      • 1:02:59:23 - Immune system
      • 1:03:55:46 - Animal behavior
    • Ecology
      • 1:04:00:40 - Ecosystems
      • 1:04:15:31 - Populations
      • 1:04:35:39 - Communities
      • 1:04:42:26 - Biosphere
      • 1:05:41:48 - Conservation
  4. 1:05:56:42 - Summary
  5. 2:00:35:23 - MES Science 4

Stay tuned for #MESScience Part 4...


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🔥#MESScience 3: Overview of Biology

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MES Inline Commentary

Note that I often provide inline commentary when referencing sources.

The types of commentary I use are listed below:

MES Note:Usually after a referenced paragraph.
[bold text in square brackets]Inline sentence commentary.
BoldSometimes bolded by me for emphasis but sometimes they are as referenced.
...Indicates transition of sentences / paragraphs between referenced text.
Figure:
Source:
References a figure outside of Wikipedia.
[sic]Indicates quote is copied as is, which includes any errors or spelling mistakes.

From Latin “sic erat scriptum” meaning “thus was it written”.

Note on Wikipedia

In this video and document, I will be referencing Wikipedia heavily throughout.

My research over the years has gained the insight that Wikipedia generally provides and maintains the “mainstream narrative of all things”.

What I mean by this is that if one were to want to know the position that most large universities, corporations, governments, or even the general public have then one can simply read up on Wikipedia on that particular topic.

Wikipedia has a structured system of publishing and modifying articles that relies almost exclusively upon the already existing large institutions. For example, if you were to find that there was a mistake in physics or that a “controversial” topic is wrongly reported, then you would first have to get an article written in, for example, the New York Times or a Scientific Journal, before being accepted on Wikipedia.

While this system prevents lots of inaccurate reporting from being published, it nonetheless keeps the existing power structure as the usual gatekeepers of knowledge.

I also like Wikipedia’s general uniformity in how topics are covered while including references to all sources used, thus it is my preferred destination for gathering “mainstream” information.

For actual truth, however, it requires personally analyzing each claim with complete disregard for all existing “authorities”.

Overview of Biology

In this video I will be going over an extensive overview of the mainstream science of biology, which is the study of life or living organisms and their interactions with each other and the environment at large.

The driving force for this particular video occurred when I was researching for a video on COVID-19 and masks, but the background biology information became too extensive.

Thus, it is only appropriate to first cover a video on the necessary background information and which will also serve as a good reference for future biology related videos that I plan to make.

In a similar way, I had gone through years of math courses, both at school and self-taught, before I even published any math videos.

Table of Contents

  • Video Meta Data
    • MES Inline Commentary
    • Note on Wikipedia
  1. Overview of Biology
  2. Table of Contents
  3. Biology
    • Etymology [Origin/history of words]
    • History
    • Chemical basis
      • Atoms and molecules
      • Organic compounds
        • Carbohydrates / Saccharides
        • Acids and Bases
        • Important Chemistry Terms
        • Fats
        • Amino Acids
        • Nucleotides
      • Macromolecules
    • Cells
      • Cell structure
      • Metabolism
      • Cellular respiration
      • Photosynthesis
      • Cell signaling
      • Cell cycle
    • Genetics
      • Inheritance
      • DNA
      • Gene expression
      • Genomes
      • Biotechnology
      • Genes, development, and evolution
    • Evolution
      • Evolutionary processes
      • Speciation
      • Phylogenies
      • History of life
    • Diversity
      • Bacteria and Archaea
      • Protists
      • Plant diversity
      • Fungi
      • Animal diversity
      • Viruses
    • Plant form and function
      • Plant body
      • Plant nutrition and transport
      • Plant development
      • Plant reproduction
      • Plant responses
    • Animal form and function
      • Principles
      • Water and salt balance
      • Nutrition and digestion
      • Breathing
      • Circulation
      • Muscle and movement
      • Nervous system
      • Hormonal control
      • Animal reproduction
      • Animal development
      • Immune system
      • Animal behavior
    • Ecology
      • Ecosystems
      • Populations
      • Communities
      • Biosphere
      • Conservation
  4. Summary
  5. MES Science 4

Biology

As per my usual starting point for information gathering, I first make sure to understand the mainstream narrative as given by Wikipedia.

The biology Wiki page is in fact very extensive on its own thus I will be covering this particular page for the most part, while I inject definitions and further clarification where needed.

https://en.wikipedia.org/wiki/Biology
Retrieved: 3 June 2021
Archive: https://archive.ph/1EwaV

Biology

Biology is the scientific study of life.[1][2][3] It is a natural science [science of nature] with a broad scope but has several unifying themes that tie it together as a single, coherent field.[1][2][3] For instance, all living organisms are made up of cells that process hereditary information encoded in genes, which can be transmitted to future generations. Another major theme is evolution, which explains the unity and diversity of life.[1][2][3] Finally, all living organisms require energy to move, grow, and reproduce, as well as to regulate their own internal environment.[1][2][3][4][5]

MES Note: Note the general biological breakdown:

Information → genes → cells → life

Biologists are able to study life at multiple levels of organization.[1] From the molecular biology of a cell to the anatomy [structure and parts of organisms] and physiology [functions and mechanism] of plants and animals, and evolution of populations.[1][6] Hence, there are multiple subdisciplines within biology, each defined by the nature of their research questions and the tools that they use.[7][8][9] Like other scientists, biologists use the scientific method to make observations, pose questions, generate hypotheses, perform experiments, and form conclusions about the world around them.[1]

MES Note:

image.png

The simplest unit in this hierarchy is the atom, like oxygen. Two or more atoms is a molecule, like a dioxide. Many small molecules may combine in a chemical reaction to make up a macromolecule, such as a phospholipid. Multiple macromolecules form a cell, like a club cell [formerly Clara cells, found in small airways of the lungs]. A group of cells functioning together as a tissue, for example, Epithelial tissue [lining of many organs and blood vessels]. Different tissues make up an organ, like a lung. Organs work together to form an organ system, such as the Respiratory System. All of the organ systems make a living organism, like a lion. A group of the same organism living together in an area is a population, such as a pride of lions. Two or more populations interacting with each other form a community, for example, lion and zebra populations interacting with each other. Communities interacting not only with each other but also with the physical environment encompass an ecosystem, such as the Savanna ecosystem. All of the ecosystems make up the biosphere, the area of life on Earth.

Life on Earth, which emerged before 3.7 billion years ago,[10] is immensely diverse. Biologists have sought to study and classify the various forms of life, from prokaryotic [cells without a nucleus] organisms such as archaea and bacteria to eukaryotic [cell with a nucleus] organisms such as protists, fungi, plants, and animals. These various living organisms contribute to the biodiversity of an ecosystem, where they play specialized roles in the cycling of nutrients and energy.

image.png
Biology deals with the study of life.

  • top: E. coli bacteria and gazelle
  • bottom: Goliath beetle and tree fern

Etymology [Origin/history of words]

"Biology" derives from the Ancient Greek words of βίος; romanized [conversion of writing to the Roman or Latin script] bíos meaning "life" and -λογία; romanized logía (-logy) meaning "branch of study" or "to speak".[11][12] Those combined make the Greek word βιολογία; romanized biología meaning biology. Despite this, the term βιολογία as a whole didn't exist in Ancient Greek. The first to borrow it was the English and French (biologie). Historically there was another term for "biology" in English, lifelore; it is rarely used today.

The Latin-language form of the term first appeared in 1736 when Swedish scientist Carl Linnaeus (Carl von Linné) used biologi in his Bibliotheca Botanica. It was used again in 1766 in a work entitled Philosophiae naturalis sive physicae: tomus III, continens geologian, biologian, phytologian generalis, by Michael Christoph Hanov, a disciple of Christian Wolff. The first German use, Biologie, was in a 1771 translation of Linnaeus' work. In 1797, Theodor Georg August Roose used the term in the preface of a book, Grundzüge der Lehre van der Lebenskraft. Karl Friedrich Burdach used the term in 1800 in a more restricted sense of the study of human beings from a morphological, physiological and psychological perspective (Propädeutik zum Studien der gesammten Heilkunst). The term came into its modern usage with the six-volume treatise Biologie, oder Philosophie der lebenden Natur (1802–22) by Gottfried Reinhold Treviranus, who announced:[13]

The objects of our research will be the different forms and manifestations of life, the conditions and laws under which these phenomena occur, and the causes through which they have been affected. The science that concerns itself with these objects we will indicate by the name biology [Biologie] or the doctrine of life [Lebenslehre].

History

Further information: History of biology

The earliest of roots of science, which included medicine, can be traced to ancient Egypt and Mesopotamia [modern day Iraq, Syria, Iran] in around 3000 to 1200 BCE.[14][15] Their contributions later entered and shaped Greek natural philosophy of classical antiquity.[14][15][16][17]

MES Note: Natural philosophy or philosophy of nature (from Latin philosophia naturalis) was the philosophical study of nature and the physical universe that was dominant before the development of modern science. It is considered to be the precursor of natural science.

The Scientific Revolution was a series of events that marked the emergence of modern science during the early modern period, when developments in mathematics, physics, astronomy, biology (including human anatomy) and chemistry transformed the views of society about nature.

image.png

Dates are approximate. Consult particular article for details.

In the history of Europe, the Middle Ages or medieval period lasted approximately from the 5th to the late 15th centuries.

The scientific method is an empirical [from experiments or observation] method of acquiring knowledge that has characterized the development of science since at least the 17th century (with notable practitioners in previous centuries).

image.png

The scientific method is often represented as an ongoing process. This diagram represents one variant, and there are many others.

Classical antiquity (also the classical era, classical period or classical age) is the period of cultural history between the 8th century BC and the 6th century AD centred on the Mediterranean Sea,[note 1] comprising the interlocking civilizations of ancient Greece and ancient Rome known as the Greco-Roman world.

image.png

Map of the Mediterranean Sea

Ancient Greek philosophers such as Aristotle (384–322 BCE) contributed extensively to the development of biological knowledge. His works such as History of Animals were especially important because they revealed his naturalist leanings, and later more empirical works that focused on biological causation and the diversity of life.

Scholars of the medieval Islamic world who wrote on biology included al-Jahiz (781–869), Al-Dīnawarī (828–896), who wrote on botany [plant biology],[19] and Rhazes (865–925) who wrote on anatomy [structure of organisms and their parts] and physiology [functions and mechanisms in living systems]. Medicine was especially well studied by Islamic scholars working in Greek philosopher traditions, while natural history drew heavily on Aristotelian thought, especially in upholding a fixed hierarchy of life.

image.png
Diagram of a fly from Robert Hooke's innovative Micrographia, 1665

Biology began to quickly develop and grow with Anton van Leeuwenhoek's dramatic improvement of the microscope. It was then that scholars discovered spermatozoa, bacteria, infusoria [a collective term for minute aquatic creatures] and the diversity of microscopic life. Investigations by Jan Swammerdam led to new interest in entomology [study of insects, 6 legged animals with exoskeletons] and helped to develop the basic techniques of microscopic dissection and staining.[20]

MES Note: Dissection (from Latin dissecare "to cut to pieces"; also called anatomization) is the dismembering of the body of a deceased animal or plant to study its anatomical structure.

image.png

Dissection of a pregnant rat in a biology class

Staining is a technique used to enhance contrast in samples, generally at the microscopic level.

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A stained histologic specimen, sandwiched between a glass microscope slide.

Histology,[help 1] also known as microscopic anatomy or microanatomy,[1] is the branch of biology which studies the microscopic anatomy of biological tissues.

A microscope slide is a thin flat piece of glass, typically 75 by 26 mm (3 by 1 inches) and about 1 mm thick, used to hold objects for examination under a microscope.

Advances in microscopy also had a profound impact on biological thinking. In the early 19th century, a number of biologists pointed to the central importance of the cell. Then, in 1838, Schleiden and Schwann began promoting the now universal ideas that (1) the basic unit of organisms is the cell and (2) that individual cells have all the characteristics of life, although they opposed the idea that (3) all cells come from the division of other cells. Thanks to the work of Robert Remak and Rudolf Virchow, however, by the 1860s most biologists accepted all three tenets of what came to be known as cell theory.[21][22]

MES Note: Some biologists consider non-cellular entities such as viruses as living organisms, thus disagree with the first tenet [principal assumption].

Meanwhile, taxonomy and classification became the focus of natural historians. Carl Linnaeus published a basic taxonomy for the natural world in 1735 (variations of which have been in use ever since), and in the 1750s introduced scientific names for all his species.[23] Georges-Louis Leclerc, Comte de Buffon, treated species as artificial categories and living forms as malleable—even suggesting the possibility of common descent. Although he was opposed to evolution, Buffon is a key figure in the history of evolutionary thought; his work influenced the evolutionary theories of both Lamarck and Darwin.[24]

MES Note: Common descent is a concept in evolutionary biology applicable when one species is the ancestor of two or more species later in time.

Count (feminine: countess) is a historical title of nobility in certain European countries, varying in relative status, generally of middling rank in the hierarchy of nobility.[1] The etymologically related English term "county" denoted the land owned by a count.

The word count came into English from the French comte, itself from Latin comes—in its accusative comitem—meaning “companion”, and later “companion of the emperor, delegate of the emperor”.

The accusative case is the grammatical form used to show a direct object of a verb.

image.png

Figure

Serious evolutionary thinking originated with the works of Jean-Baptiste Lamarck, who was the first to present a coherent theory of evolution.[26] He posited that evolution was the result of environmental stress on properties of animals, meaning that the more frequently and rigorously an organ was used, the more complex and efficient it would become, thus adapting the animal to its environment. Lamarck believed that these acquired traits could then be passed on to the animal's offspring, who would further develop and perfect them.[27]

MES Occult Note: Note the religious / occult theme of John the Baptist (Jean-Baptiste Lamarck) serving as a forerunner to Christ (Charles Darwin).

However, it was the British naturalist Charles Darwin, combining the biogeographical approach of Humboldt, the uniformitarian geology of Lyell, Malthus's writings on population growth, and his own morphological expertise and extensive natural observations, who forged a more successful evolutionary theory based on natural selection; similar reasoning and evidence led Alfred Russel Wallace to independently reach the same conclusions.[28][29] Darwin's theory of evolution by natural selection quickly spread through the scientific community and soon became a central axiom of the rapidly developing science of biology.

MES Note: Natural selection is the differential survival and reproduction of individuals due to differences in their phenotype, which is the set of observable characteristics or traits of an organism.

image.png
In 1842, Charles Darwin penned his first sketch of On the Origin of Species.[25]

The basis for modern genetics began with the work of Gregor Mendel, who presented his paper, "Versuche über Pflanzenhybriden" ("Experiments on Plant Hybridization"), in 1865,[30] which outlined the principles of biological inheritance, serving as the basis for modern genetics.[31] However, the significance of his work was not realized until the early 20th century when evolution became a unified theory as the modern synthesis reconciled Darwinian evolution with classical genetics.[32]

MES Note: The modern synthesis combines the Darwinian natural selection of variations in species with the classical genetics of mutation.

Mutation refers to small changes in individual characteristics.

Classical genetics is the branch of genetics based solely on visible results of reproductive acts.

Genetics is the study of genes, genetic variation, and heredity in organisms.

In the 1940s and early 1950s, a series of experiments by Alfred Hershey and Martha Chase pointed to DNA as the component of chromosomes that held the trait-carrying units that had become known as genes. A focus on new kinds of model organisms such as viruses and bacteria, along with the discovery of the double-helical structure of DNA by James Watson and Francis Crick in 1953, marked the transition to the era of molecular genetics. From the 1950s to the present times, biology has been vastly extended in the molecular domain. The genetic code was cracked by Har Gobind Khorana, Robert W. Holley and Marshall Warren Nirenberg after DNA was understood to contain codons.

MES Note: Some of the terms are defined below.

The genetic code is the set of rules used by living cells to translate information encoded within genetic material (codons) into proteins.

Codons are DNA or mRNA sequences of nucleotide triplets that contain genetic code.

Nucleotides are molecules that make up DNA and RNA.

Genetic material refers to DNA and RNA in general, both of which are biopolymers and classed as nucleic acids.

A genome is all the genetic material of an organism.

Finally, the Human Genome Project was launched in 1990 with the goal of mapping the general human genome. This project was essentially completed in 2003,[33] with further analysis still being published. The Human Genome Project was the first step in a globalized effort to incorporate accumulated knowledge of biology into a functional, molecular definition of the human body and the bodies of other organisms.

MES Note: The human genome is a complete set of nucleic acid sequences encoded as DNA within 23 chromosome pairs in cell nuclei (nuclear genome) and in a small DNA molecule found within individual mitochondria (mitochondrial genome).

There are over 3 billion base pairs in the human genome.

Chemical basis

Atoms and molecules

Further information: Chemistry

All living organisms are made up of matter and all matter is made up of elements.[34] Oxygen, carbon, hydrogen, and nitrogen are the four elements that account for 96% of all living organisms, with calcium, phosphorus, sulfur, sodium, chlorine, and magnesium accounting for the remaining 3.7%.[34] Different elements can combine to form compounds such as water, which is fundamental to life.[34] Life on Earth began from water and remained there for about three billions years prior to migrating onto land.[35] Matter can exist in different states as a solid, liquid, or gas.

MES Note: Matter is any substance that has mass and takes up space by having volume. All everyday objects that can be touched are ultimately composed of atoms, which are made up of interacting subatomic particles, and in everyday as well as scientific usage, "matter" generally includes atoms and anything made up of them, and any particles (or combination of particles) that act as if they have both rest mass [portion of mass independent from motion] and volume. However it does not include massless particles such as photons, or other energy phenomena or waves such as light.

image.png
Model of hydrogen bonds (1) between molecules of water

The smallest unit of an element [which still has all the properties of that substance] is an atom, which is composed of a nucleus and one or more electrons bound to the nucleus. The nucleus is made of one or more protons and a number of neutrons. Individual atoms can be held together by chemical bonds to form molecules and ionic compounds.[34] Common types of chemical bonds include ionic bonds, covalent bonds, and hydrogen bonds. Ionic bonding involves the electrostatic attraction between oppositely charged ions, or between two atoms with sharply different electronegativities,[36] and is the primary interaction occurring in ionic compounds. Ions are atoms (or groups of atoms) with an electrostatic charge. Atoms that gain electrons make negatively charged ions (called anions) whereas those that lose electrons make positively charged ions (called cations).

MES Note: Some of the terms are defined below.

Electrostatic attraction or repulsion is the experimentally determined force between electrically charged particles.

Electric charge is the physical property of matter that causes it to experience a force when placed in an electromagnetic field. Electric charge can be positive or negative (commonly carried by protons and electrons respectively). Like charges repel each other and unlike charges attract each other. An object with an absence of net charge is referred to as neutral.

image.png

Figure

An electromagnetic field (also EM field or EMF) is a classical (i.e. non-quantum) field produced by accelerating electric charges. The electromagnetic field propagates at the speed of light (in fact, this field can be identified as light) and interacts with charges and currents. The field can be viewed as the combination of an electric field and a magnetic field. The electric field is produced by stationary charges, and the magnetic field by moving charges (currents); these two are often described as the sources of the field. The force created by the electric field is much stronger than the force created by the magnetic field.

An electric field (sometimes E-field[1]) is the physical field that surrounds electrically charged particles and exerts force on all other charged particles in the field, either attracting or repelling them.

image.png

Effects of an electric field. The girl is touching an electrostatic generator, which charges her body with a high voltage [electric charge pressure]. Her hair, which is charged with the same polarity, is repelled by the electric field of her head and stands out from her head.

A magnetic field is a vector field [magnitude / direction assigned to points in space] that describes the magnetic influence on moving electric charges, electric currents,[1]: ch1 [2] and magnetic materials. A moving charge in a magnetic field experiences a force perpendicular to its own velocity and to the magnetic field. The term "magnetic field" is used for two distinct but closely related vector fields denoted by the symbols B and H.

Source: The magnetic field H might be thought of as the magnetic field produced by the flow of current in wires and the magnetic field B as the total magnetic field including also the contribution M made by the magnetic properties of the materials in the field.

image.png

The shape of the magnetic field produced by a horseshoe magnet is revealed by the orientation of iron filings sprinkled on a piece of paper above the magnet.

image.png

A portion of the vector field

image.png

Comparison of B, H and M inside and outside a cylindrical bar magnet.

The magnetization vector field M represents how strongly a region of material is magnetized.

image.png

A charged particle that is moving with velocity v in a magnetic field B will feel a magnetic force F. Since the magnetic force always pulls sideways to the direction of motion, the particle moves in a circle.

image.png

Left: the direction of magnetic field lines represented by iron filings sprinkled on paper placed above a bar magnet.
Right: compass needles point in the direction of the local magnetic field, towards a magnet's south pole and away from its north pole.

image.png

The magnetic pole model: two opposing poles, North (+) and South (−), separated by a distance d produce a H-field (lines).

MES True Science Note: The exact nature of electric charges and electromagnetism is unknown (publicly) as exemplified by the circular reasoning fallacy in their definitions.

“An electric charge is a property of matter that causes it to experience a force when placed in an electromagnetic field, which itself is produced by electric charges”.

What is a field? A field of what?

A good starting point, however, is to view charges as physical interactions of an aether and the resulting electromagnetic field as the propagation of the resulting disturbances of the aether, like the wakes behind a moving boat (except the boat itself can be seen as a void in the aether itself).

https://youtu.be/HywoX6UFOe8
Retrieved: 8 February 2022

image.png

Electronegativity, symbolized as χ, is the tendency for an atom of a given chemical element to attract shared electrons (or electron density) when forming a chemical bond.

The loosely defined term electropositivity is the opposite of electronegativity: it characterizes an element's tendency to donate valence [outer] electrons.

image.png

Figure: Electrons might be unevenly distributed within the bond due to a difference in electronegativity. For example, fluorine F, the most electronegative element, is covalently bonded with H, which has a considerably lower electronegativity. Within the bond, electrons will tend to spend more time around the, giving it a slightly negative charge. On the other hand, since the electrons are not spending as much time around the, it gets a slightly positive charge. This is a polar bond, with what we call a permanent dipole.

An ion is an atom or molecule with a net electrical charge. A cation is a positively charged ion with fewer electrons than protons[2] while an anion is a negatively charged ion with more electrons than protons.[3] Opposite electric charges are pulled towards one another by electrostatic force, so cations and anions attract each other and readily form ionic compounds.

Light or visible light is electromagnetic radiation within the portion of the electromagnetic spectrum that is perceived by the human eye.[1] Visible light is usually defined as having wavelengths in the range of 400–700 nanometres (nm) [1 billionth of a meter], between the infrared (with longer wavelengths) and the ultraviolet (with shorter wavelengths).[2][3] In physics, the term "light" may refer more broadly to electromagnetic radiation of any wavelength, whether visible or not.[4][5] In this sense, gamma rays, X-rays, microwaves and radio waves are also light. The primary properties of light are intensity, propagation direction, frequency or wavelength spectrum and polarization. Its speed in a vacuum, 299 792 458 metres a second (m/s), is one of the fundamental constants of nature.[6] Like all types of electromagnetic radiation, visible light propagates by massless elementary particles called photons that represents the quanta of electromagnetic field, and can be analyzed as both waves and particles.

The speed of light in vacuum, commonly denoted c, is a universal physical constant that is important in many areas of physics. Its exact value is defined as 299792458 metres per second (approximately 300000 km/s or 186000 mi/s).[Note 3] It is exact because, by a 1983 international agreement, a metre is defined as the length of the path travelled by light in vacuum during a time interval of 1⁄299792458 second. [Note the circular reasoning, once again.]

In physics, a quantum (plural quanta) is the minimum amount of any physical entity (physical property) involved in an interaction. The fundamental notion that a physical property can be "quantized" is referred to as "the hypothesis of quantization".[1] This means that the magnitude of the physical property can take on only discrete values consisting of integer multiples of one quantum. For example, a photon is a single quantum of light (or of any other form of electromagnetic radiation).

Source: https://peakd.com/hive-128780/@mes/applied-project-radiation-from-the-stars

Mainstream light quantization:

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Fractal Woman (YouTuber) light quantization:

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In physics, electromagnetic radiation (EMR) consists of waves of the electromagnetic (EM) field, propagating through space, carrying electromagnetic radiant energy.

Picture1.gif

A triangular prism dispersing a beam of white light. The longer wavelengths (red) and the shorter wavelengths (blue) are separated.

image.png

Photograph of a triangular prism, dispersing light

image.png

Electromagnetic spectrum with visible light highlighted

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A linearly polarized electromagnetic wave going in the x-axis, with E denoting the electric field and perpendicular B denoting magnetic field

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Representation of the electric field vector of a wave of circularly polarized electromagnetic radiation.

Polarization (also polarisation) is a property applying to transverse waves that specifies the geometrical orientation of the oscillations.[1][2][3][4][5] In a transverse wave, the direction of the oscillation is perpendicular [at 90 degrees] to the direction of motion of the wave.[4] A simple example of a polarized transverse wave is vibrations traveling along a taut string (see image); for example, in a musical instrument like a guitar string. Depending on how the string is plucked, the vibrations can be in a vertical direction, horizontal direction, or at any angle perpendicular to the string. In contrast, in longitudinal waves, such as sound waves in a liquid or gas, the displacement of the particles in the oscillation is always in the direction of propagation, so these waves do not exhibit polarization. Transverse waves that exhibit polarization include electromagnetic waves such as light and radio waves, gravitational waves,[6] and transverse sound waves (shear waves) in solids.

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Illustration of a simple (plane) transverse wave propagating through an elastic medium in the horizontal direction, with particles being displaced in the vertical direction. Only one layer of the material is shown

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Circular polarization on rubber thread, converted to linear polarization

Longitudinal waves are waves in which the vibration of the medium is parallel ("along") to the direction the wave travels and displacement of the medium is in the same (or opposite) direction of the wave propagation.

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Plane pressure pulse wave

Unlike ionic bonds, a covalent bond involves the sharing of electron pairs between atoms. These electron pairs and the stable balance of attractive and repulsive forces between atoms, when they share electrons, is known as covalent bonding.[37]

MES Note: Some of the terms are defined below.

Electron pairs consist of two electrons that occupy the same molecular orbital but have opposite spins.

A molecular orbital is a mathematical function describing the location and wave-like behavior of an electron in a molecule. This function can be used to calculate chemical and physical properties such as the probability of finding an electron in any specific region.

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Complete acetylene (H–C≡C–H) molecular orbital set. The left column shows MO's which are occupied in the ground state, with the lowest-energy orbital at the top. The white and grey line visible in some MO's is the molecular axis passing through the nuclei. The orbital wave functions are positive in the red regions and negative in the blue [that is, the mathematical function has a + or a – sign]. The right column shows virtual MO's which are empty in the ground state, but may be occupied in excited states.

Spin is an intrinsic form of angular momentum carried by elementary particles, and thus by composite particles (hadrons) and atomic nuclei. Spin is analogous to classical rotation but has peculiar properties such as elementary particles cannot be made to spin faster or slower even though the direction of spin can be changed.

A hydrogen bond is primarily an electrostatic force of attraction between a hydrogen atom which is covalently bound to a more electronegative atom or group such as oxygen [and another electronegative atom bearing a lone pair of electrons, deemed the hydrogen bond acceptor]. A ubiquitous [widespread] example of a hydrogen bond is found between water molecules. In a discrete water molecule, there are two hydrogen atoms and one oxygen atom. Two molecules of water can form a hydrogen bond between them. When more molecules are present, as is the case with liquid water, more bonds are possible because the oxygen of one water molecule has two lone pairs of electrons, each of which can form a hydrogen bond with a hydrogen on another water molecule.

MES Note: Note that hydrogen is made up a proton (positive charge), zero or some neutrons (no charge), and zero or more electrons (negative charge).

The most common isotope of hydrogen has 1 proton and 0 neutrons, termed “protium” but rarely used.

Isotopes refer to atoms with the same number of protons but different number of neutrons.

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Model of hydrogen bonds (1) between molecules of water

A partial charge is a non-integer charge value when measured in elementary charge units [charge of a proton and electron]. Partial charge is more commonly called net atomic charge. It is represented by the Greek lowercase letter 𝛿 [delta], namely 𝛿− or 𝛿+. Partial charges are created due to the asymmetric distribution of electrons in chemical bonds.

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AFM [Atomic Force Microscopy] image of napthalenetetracarboxylic diimide [a solid organic compound] molecules on silver-terminated silicon, interacting via hydrogen bonding, taken at 77 K [-196.15 °C].[1] ("Hydrogen bonds" in the top image are exaggerated by artifacts of the imaging technique.[2][3])

Chain termination is any chemical reaction that ceases the formation of reactive intermediates in a chain propagation step in the course of a polymerization [chain of repeating molecules], effectively bringing it to a halt.

In chemistry, a reactive intermediate or an intermediate is a short-lived, high-energy, highly reactive molecule. When generated in a chemical reaction, it will quickly convert into a more stable molecule.

Chain propagation (sometimes referred to as propagation) is a process in which a reactive intermediate is continuously regenerated during the course of a chemical chain reaction.

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Figure: Ionic Covalent and Hydrogen Bond

A metal (from Greek μέταλλον métallon, "mine, quarry, metal") is a material that, when freshly prepared, polished, or fractured, shows a lustrous [shining] appearance, and conducts electricity and heat relatively well.

In chemistry, a nonmetal is a chemical element that generally lacks a predominance of metallic properties; they range from colorless gases to shiny and refractory (high melting point) solids.

A metalloid is a type of chemical element which has a preponderance of properties in between, or that are a mixture of, those of metals and nonmetals. There is no standard definition of a metalloid and no complete agreement on which elements are metalloids. Despite the lack of specificity, the term remains in use in the literature of chemistry.

Organic compounds

Further information: Organic chemistry

With the exception of water, nearly all the molecules that make up each living organism contain carbon.[38][39] Carbon can form very long chains of interconnecting carbon–carbon bonds, which are strong and stable. The simplest form of an organic molecule is the hydrocarbon, which is a large family of organic compounds that are composed of hydrogen atoms bonded to a chain of carbon atoms. A hydrocarbon backbone can be substituted by other atoms. When combined with other elements such as oxygen, hydrogen, phosphorus, and sulfur, carbon can form many groups of important biological compounds such as sugars, fats, amino acids, and nucleotides.

MES Note: The backbone chain of a polymer is the longest series of covalently bonded atoms that together create the continuous chain of the molecule.

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Organic compounds such as glucose [a simple sugar, C6H12O6] are vital to living organisms


Carbohydrates / Saccharides

In this section I am taking a bit of break from the Biology Wikipedia page to go over some of the commonly mentioned compounds.

Sugar is the generic name for sweet-tasting, soluble, carbohydrates, many of which are used in food.

A carbohydrate is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogen–oxygen atom ratio of 2:1 (as in water) and thus with the empirical formula Cm(H2O)n (where m may or may not be different from n). However, not all carbohydrates conform to this precise stoichiometric definition, nor are all chemicals that do conform to this definition automatically classified as carbohydrates.

Stoichiometry refers to the relationship between the quantities of reactants and products before, during, and following chemical reactions.

Carbohydrate is a synonym of saccharide. The word saccharide comes from the Greek word σάκχαρον (sákkharon), meaning "sugar".

The empirical formula of a chemical compound is the simplest whole number ratio of atoms present in a compound.

Carbohydrates / saccharides are classified by the degree of polymerization, which is the number of monomeric units in a macromolecule.

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The names of the monosaccharides and disaccharides very often end in the suffix -ose, which was originally taken from glucose, from Ancient Greek γλεῦκος (gleûkos, “wine, must”), and is used for almost all sugars, e.g. fructose (fruit sugar), sucrose (cane or beet sugar), ribose, amylose, lactose (milk sugar), etc.

e.g., abbreviation for exempli gratia, a Latin phrase meaning "for example".

aka = “also known as”.

id est (i.e.), Latin for "that is" or "in other words"

Must (from the Latin vinum mustum, "young wine") is freshly crushed fruit juice (usually grape juice) that contains the skins, seeds, and stems of the fruit.

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Grapes being pressed to create must

Acids and Bases

An acid is a molecule or ion capable of either donating a proton (i.e., hydrogen ion, H+), known as a Brønsted–Lowry acid, or, capable of forming a covalent bond with an electron pair, known as a Lewis acid.[1]

The first category of acids are the proton donors, or Brønsted–Lowry acids. In the special case of aqueous solutions, proton donors form the hydronium ion H3O+ and are known as Arrhenius acids.

An aqueous solution is a solution in which the solvent [substance that dissolves the solute] is water.

The word acid is derived from the Latin acidus/acēre, meaning 'sour'.

There are three definitions in common use of the word base, known as Arrhenius bases [give OH- in water], Brønsted[-Lowry] bases [accepts protons], and Lewis bases [donates electron pair].

All definitions agree that bases are substances which react with acids as originally proposed by G.-F. Rouelle in the mid-18th century.

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Acid Base Reaction Theories as superset and subset models.

The Arrhenius model is for aqueous solutions, and the symbol H+ is interpreted as a shorthand for H3O+, because it is now known that a bare proton does not exist as a free species in aqueous solution.

Bases and acids are seen as chemical opposites because the effect of an acid is to increase the hydronium (H3O+) concentration in water, whereas bases reduce this concentration.

MES Memory Tool: Acids become more negative. Bases become more positive.

In the Arrhenius theory, acids are defined as substances that dissociate in aqueous solution to give H>sup>+ (hydrogen ions) [forming H3O+], while bases are defined as substances that dissociate in aqueous solution to give OH (hydroxide ions). This was the first modern definition of acids and bases. It was devised by Svante Arrhenius in 1984 which led to him receiving the Nobel Prize in Chemistry in 1903.

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Figure: An Arrhenius acid increases hydrogen ion concentration in water, while an Arrhenius base increases hydroxide ion concentration.

The Brønsted–Lowry theory (also called proton theory of acids and bases[1]) is an acid–base reaction theory which was proposed independently by Johannes Nicolaus Brønsted and Thomas Martin Lowry in 1923.[2][3] The fundamental concept of this theory is that when an acid and a base react with each other, the acid forms its conjugate base, and the base forms its conjugate acid by exchange of a proton (the hydrogen cation, or H+). This theory is a generalization of the Arrhenius theory.

The Lewis theory is a generalization of the Brønsted-Lowry theory. In 1923, Gilbert N. Lewis wrote: An acid substance is one which can employ an electron lone pair from another molecule in completing the stable group of one of its own atoms.

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Figure

In the Brønsted–Lowry theory acids and bases are defined by the way they react with each other, which allows for greater generality. The definition is expressed in terms of an equilibrium expression:

Acid + Base ⇌ Conjugate Base + Conjugate Acid

With an acid, HA, the equation can be written symbolically as:

HA + B ⇌ A- + HB+

The conjugate base is an acid with a hydrogen ion (proton) added to it.

The conjugate acid is a base with a hydrogen ion removed from it.

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Reaction of NH4 to NH3

“Conjugate” means related or joined together.

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Figure

In a chemical reaction, chemical equilibrium is the state in which both the reactants and products are present in concentrations which have no further tendency to change with time, so that there is no observable change in the properties of the system.[1] This state results when the forward reaction proceeds at the same rate as the reverse reaction. The reaction rates of the forward and backward reactions are generally not zero, but they are equal. Thus, there are no net changes in the concentrations of the reactants and products. Such a state is known as dynamic equilibrium.[2][3]

In chemistry, pH (denoting "potential of hydrogen" or "power of hydrogen")[1] is a scale used to specify the acidity or basicity of an aqueous solution. Acidic solutions (solutions with higher concentrations of H+ ions) are measured to have lower pH values than basic or alkaline [groups 1 and 2 in the periodic table] solutions.

The pH scale is [base-10] logarithmic [non-linear scale] and inversely indicates the concentration of hydrogen ions in the solution.

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The higher the pH the more exponentially [H3O+] decreases.

At 25 °C, solutions with a pH less than 7 are acidic [high H+], and solutions with a pH greater than 7 are basic [low H+].

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Figure 1: The pH values for several common materials.

“Milk of Magnesia” is a common laxative [help in pooping].

A detergent is a surfactant or a mixture of surfactants with cleansing properties in dilute [low concentration] solutions.

Surfactants are compounds that lower the surface tension (or interfacial tension) between two liquids, between a gas and a liquid, or between a liquid and a solid.

Surface tension is the tendency of liquid surfaces at rest to shrink into the minimum surface area possible.

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Figure

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Figure

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Figure: Periodic table of elements

Note the alkali metals (group 1) and alkaline-earth metals (group 2).

MES Occult Note: The most common isotope of carbon is Carbon-12 which has 6 protons, 6 neutrons, and 6 electrons, which raises interesting questions about:

  • The number 666.
  • The Biblical “Mark of the Beast”.
  • Carbon-based life
    • Carbon is a primary component of all life on Earth.
    • Carbon represents about 45-50% of all dry biomass.
  • Carbon Tax and Carbon Tax Credits are to be implemented worldwide soon to lower the world’s carbon output.
  • World population is supposedly an issue.

Let’s ask Bugs Bunny what he thinks…

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Acid strength is the tendency of an acid, symbolised by the chemical formula HA, to dissociate into a proton, H+, and an anion, A-.

The dissociation of a strong acid in solution is effectively complete, except in its most concentrated solutions.

HA + S → SH+ + A-

Where S represents a solvent molecule, most commonly is water.

A weak acid is only partially dissociated, with both the undissociated acid and its dissociation products being present, in solution, in equilibrium with each other.

HA + S ⇌ SH+ + A-

Acid strength is solvent-dependent.

Important Chemistry Terms

A moiety is a part of a molecule[1][2] that is given a name because it is identified as a part of other molecules as well.

A substituent is one or a group of atoms that replaces (one or more) hydrogen atoms on the parent chain [longest unbranched chain] of a hydrocarbon, thereby becoming a moiety in the resultant (new) molecule.

The terms substituent and functional group, as well as side chain and pendant group, are used almost interchangeably to describe those branches from the parent structure.

A functional group is a substituent or moiety in a molecule that causes the molecule's characteristic chemical reactions. The same functional group will undergo the same or similar chemical reactions regardless of the rest of the molecule's composition.[1][2] This enables systematic prediction of chemical reactions and behavior of chemical compounds and the design of chemical synthesis.

A side chain is a chemical group [substituent] that is attached to a core part of the molecule called the "main chain" or backbone.

The backbone chain of a polymer is the longest series of covalently bonded atoms that together create the continuous chain of the molecule.

A pendant group (sometimes spelled pendent) or side group is a group of atoms attached to a backbone chain of a long molecule, usually a polymer.

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For example, the phenyl groups [C6H5] are the pendant groups on a polystyrene chain.

A pendant is something suspended, like a piece of jewelry.

An open-chain compound or acyclic compound (Greek prefix "α", without and "κύκλος", cycle) is a compound with a linear structure, rather than a cyclic one.

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A saturated compound is a chemical compound (or ion) that resists addition reactions (two or more molecules combine to form a larger one).

Overall, saturated compounds are less reactive than unsaturated compounds.

Saturation is derived from the Latin word saturare, meaning 'to fill'.

A saturated organic compound has only single bonds between carbon atoms.

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A hydroxy or hydroxyl group is a functional group with the chemical formula -OH and composed of one oxygen atom covalently bonded to one hydrogen atom.

An alkane, is an acyclic saturated hydrocarbon. Alkanes have the general chemical formula CnH2n+2.

An alkyl is an alkane missing one hydrogen.

Acetyl is a moiety with chemical formula CH3CO.

The alkoxy group is an alkyl group singularly bonded to oxygen; thus R–O.

R is a generic placeholder, which may replace any portion of the formula as the author finds convenient.

An ester is a chemical compound derived from an acid (organic or inorganic) in which at least one –OH hydroxyl group is replaced by an –O– alkyl (alkoxy) group.

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Benzyl acetate [C9H10O2] contains a benzyloxy [C6H5-CH2-O] moiety (encircled with light orange). It also contains an ester functional group (in red), and an acetyl functional group (encircled with dark green). Other divisions can be made.

Pi bonds (π bonds) are covalent chemical bonds where two lobes of an orbital on one atom overlap two lobes of an orbital on another atom and this overlap occurs laterally.

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Electron atomic and molecular orbitals, showing a pi bond at the bottom right

Resonance, also called mesomerism, is a way of describing bonding in certain molecules or ions by the combination of several contributing structures (or forms) into a resonance hybrid.

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Contributing structures of the carbonate ion [CO32-]

This resonance can be summarized by a model with fractional bonds [dashed lines] and delocalized charges [2 electrons shared between 3 oxygens resulting in a net average charge of -2/3]:

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Delocalized electrons are electrons in a molecule, ion or solid metal that are not associated with a single atom or a covalent bond.

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Benzene [C6H6], with the delocalization of the electrons indicated by the circle.

Aromaticity is a property of cyclic (ring-shaped), planar (flat) structures with pi bonds in resonance (those containing delocalized electrons) that gives increased stability compared to other geometric or connective arrangements with the same set of atoms. Aromatic rings are very stable and do not break apart easily. Organic compounds that are not aromatic are classified as aliphatic compounds—they might be cyclic, but only aromatic rings have enhanced stability.

Hydrocarbons are divided into two classes: aromatic compounds and aliphatic compounds (from Greek aleiphar meaning fat or oil).

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[Aromatic] Two different resonance of benzene (top) combine to produce an average structure (bottom)

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Acyclic aliphatic/non-aromatic compound (butane [C4H10])

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Cyclic aliphatic/non-aromatic compound (cyclobutane (CH2)4)

An alkene is a hydrocarbon containing a carbon–carbon double bond.

A double bond is a covalent bond between two atoms involving four bonding electrons as opposed to two in a single bond.

An alkenyl group is the fragment, containing an open point of attachment on a carbon atom, that would form if a hydrogen atom bonded to a doubly bonded carbon is removed from the molecule of an alkene.

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Figure

An aryl is any functional group or substituent derived from an aromatic ring.

A carboxylic acid is an organic acid that contains a carboxyl group (C(=O)OH)[1] attached to an R-group. The general formula of a carboxylic acid is R−COOH or R−CO2H, with R referring to the alkyl, alkenyl, aryl, or other group.

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Structure of a carboxylic acid

Deprotonation of a carboxylic acid gives a carboxylate anion [R-COO- or R-CO2- or -CO2-]. The negative charge that is left after deprotonation of the carboxyl group is delocalized between the two electronegative oxygen atoms in a resonance structure.

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Equivalence of the resonance forms the delocalised form of a general carboxylate anion

A fatty acid is a carboxylic acid with a aliphatic chain, which is either saturated or unsaturated.

Fats

Fat usually means any ester of fatty acids, or a mixture of such compounds, most commonly those that occur in living beings or in food.

In other words, fat is a R-COOH compound in which at least one -OH has been replaced by an -O-R.

Glycerol (also called glycerine in British English or glycerin in American English) is a simple polyol compound with chemical formula is C3H8O3.

A polyol is an organic compound containing multiple hydroxyl [-OH] groups.

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Sample of glycerin

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Glycerol

A triglyceride (TG, triacylglycerol, TAG, or triacylglyceride) is an ester derived from glycerol and three fatty acids (from tri- and glyceride).

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Structure of a triglyceride

Glycerides, more correctly known as acylglycerols, are esters formed from glycerol and fatty acids, and are generally very hydrophobic [water-fearing].

Fat often refers specifically to triglycerides (triple esters of glycerol), that are the main components of vegetable oils and of fatty tissue in animals;[2] or, even more narrowly, to triglycerides that are solid or semisolid at room temperature, thus excluding oils.

Vegetable oils, or vegetable fats, are oils extracted from seeds or from other parts of fruits. Like animal fats, vegetable fats are mixtures of triglycerides.

Fat may also be used more broadly as a synonym of lipid—any substance of biological relevance, composed of carbon, hydrogen, or oxygen, that is insoluble in water but soluble in non-polar solvents.[1]

Although, lipids are defined more generally than fats, thus making fats a subgroup of lipids.

Polarity is a separation of electric charge leading to a molecule or its chemical groups having an electric dipole moment, with a negatively charged end and a positively charged end.

The electric dipole moment is a measure of the separation of positive and negative electrical charges within a system, that is, a measure of the system's overall polarity.

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A water molecule, a commonly used example of polarity. Two charges are present with a negative charge in the middle (red shade), and a positive charge at the ends (blue shade).

An oil is any nonpolar chemical substance that is a viscous [thick] liquid at ambient temperatures and is both hydrophobic (does not mix with water, literally "water fearing") and lipophilic (mixes with other oils, literally "fat loving"). Oils have a high carbon and hydrogen content and are usually flammable and surface active [surfactants].

The viscosity of a fluid is a measure of its resistance to deformation at a given rate. For liquids, it corresponds to the informal concept of "thickness": for example, syrup has a higher viscosity than water.

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A simulation of liquids with different viscosities. The liquid on the right has higher viscosity than the liquid on the left

Syrup or sirup (from Arabic: شراب‎; sharāb, beverage, wine and Latin: sirupus)[1] is a thick, viscous liquid consisting primarily of a solution of sugar in water, containing a large amount of dissolved sugars but showing little tendency to deposit crystals [aka remains a fluid solution].

The terms saturated vs unsaturated are often applied to the fatty acid constituents of fats.

A saturated fat is a type of fat in which the fatty acid chains have all single bonds [while unsaturated fat contain at least one double bond].

Many vegetable oils contain fatty acids with one (monounsaturated) or more (polyunsaturated) double bonds in them.

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One of the three side chains of this fat is described as unsaturated.

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Fat composition in different foods, as percentage of total fat.

Soap is a salt of a fatty acid[1] used in a variety of cleansing and lubricating products. In a domestic setting, soaps are surfactants usually used for washing, bathing, and other types of housekeeping. In industrial settings, soaps are used as thickeners [increasing viscosity], components of some lubricants [decrease friction], and precursors to catalysts [increasing reaction rate].

A salt is a chemical compound consisting of an ionic assembly of cations and anions.[1] Salts are composed of related numbers of cations (positively charged ions) and anions (negatively charged ions) so that the product is electrically neutral (without a net charge).

Adipose tissue, body fat, or simply fat is a loose connective tissue composed mostly of adipocytes.

Adipocytes, also known as lipocytes and fat cells, are the cells that primarily compose adipose tissue, specialized in storing energy as fat. There are two types of adipose tissue, white adipose tissue (WAT) and brown adipose tissue (BAT), which are also known as white and brown fat, respectively, and comprise two types of fat cells.

White fat cells contain a single large lipid droplet surrounded by a layer of cytoplasm, and are known as unilocular [1 cavity]. The nucleus is flattened and pushed to the periphery. A typical fat cell is 0.1 mm in diameter with some being twice that size, and others half that size. The fat stored is in a semi-liquid state, and is composed primarily of triglycerides, and cholesteryl ester [ester of cholesterol]. In healthy, non-overweight humans, white adipose tissue composes as much as 20% of the body weight in men and 25% in women. White adipose tissue is used for energy storage.

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Distribution of white adipose tissue in the human body.

Brown fat cells are polyhedral [polygonal flat faces, straight edges, sharp corners] in shape. Unlike white fat cells, these cells have considerable cytoplasm, with several lipid droplets scattered throughout, and are known as multilocular [multi-cavity] cells. The nucleus is round and, although eccentrically located, it is not in the periphery of the cell. The brown color comes from the large quantity of mitochondria. Brown fat, also known as "baby fat," is used to generate heat. Classification of brown fat refers to two distinct cell populations with similar functions. The first shares a common embryological origin with muscle cells [cardiac or smooth muscle cells], found in larger "classic" deposits. The second develops from white adipocytes that are stimulated by the sympathetic nervous system. These adipocytes are found interspersed in white adipose tissue and are also named 'beige' or 'brite' (for "brown in white"[2]).[3][4][5] Brown adipose tissue is especially abundant in newborns and in hibernating mammals.[6] It is also present and metabolically active in adult humans,[7][8] but its prevalence decreases as humans age.[9] Its primary function is thermoregulation.

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Brown adipose tissue in a woman shown in a FDG PET/CT exam

Fluorodeoxyglucose (18F) (INN), or fluorodeoxyglucose F 18 (USAN and USP), also commonly called fluorodeoxyglucose and abbreviated [18F]FDG, 18F-FDG or FDG, is a radiopharmaceutical, specifically a radiotracer, used in the medical imaging modality positron emission tomography (PET).

The positron or antielectron is the antiparticle or the antimatter counterpart of the electron.

In particle physics, every type of particle is associated with an antiparticle with the same mass but with opposite physical charges (such as electric charge).

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Source

Amino Acids

Ammonia is a compound of nitrogen and hydrogen with the formula NH3. It is a colourless gas with a distinct pungent [strong] smell.

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MES Note: The two dots are Lewis Dots and represent a lone pair of electrons.

Amines are compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are formally derivatives of ammonia, wherein one or more hydrogen atoms have been replaced by a substituent such as an alkyl or aryl group[4] (these may respectively be called alkylamines and arylamines; amines in which both types of substituent are attached to one nitrogen atom may be called alkylarylamines). Important amines include amino acids.

The substituent -NH2 is called an amino group.

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Amino acids are organic compounds that contain [charged] amino[1] (-NH3+)* [or -NH2+ in the case of proline] and carboxylate (-CO2-) functional groups, along with a side chain (R group) specific to each amino acid.

*Strictly ammonio, as amino refers to uncharged -NH2, but this term is almost never used.

The elements present in every amino acid are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N); in addition sulfur (S) is present in the side chains of cysteine and methionine, and selenium (Se) in the less common amino acid selenocysteine.

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Structure of a generic L-amino acid in the "neutral" form needed for defining a systematic name, without implying that this form actually exists in detectable amounts either in aqueous solution or in the solid state.

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Figure: d-and l-configurations of a chiral [“handed”] amino acid. R is the side chain of the amino acid.

A molecule or ion is called chiral if it cannot be superposed on its mirror image by any combination of rotations, translations, and some conformational changes [rotations on single bonds]. This geometric property is called chirality.[1][2][3][4] The terms are derived from Ancient Greek χείρ (cheir) 'hand'; which is the canonical [standard] example of an object with this property.

A chiral molecule or ion exists in two stereoisomers [same molecular formula, sequence of bonded atoms, but different 3D orientations of their atoms] that are mirror images of each other, called enantiomers; they are often distinguished as either "right-handed" or "left-handed" by their absolute configuration or some other criterion. The two enantiomers have the same chemical properties, except when reacting with other chiral compounds. They also have the same physical properties, except that they often have opposite optical activities [ability to rotate linear polarized light].

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Two enantiomers of a generic amino acid that are chiral

Dextrorotation and laevorotation (also spelled levorotation)[1][2][3] are terms used in chemistry and physics to describe the optical rotation of [linear or] plane-polarized light. From the point of view of the observer, dextrorotation refers to clockwise or right-handed rotation, and laevorotation refers to counterclockwise or left-handed rotation.[4][5] [D = R and L = Left]

The first word component dextro- comes from the Latin word dexter, meaning "right" (as opposed to left). Laevo- or levo- comes from the Latin laevus, meaning "left side".

The "D-" and "L-" prefixes are used to specify the enantiomer of chiral organic compounds in biochemistry.

Peptides (from Greek language πεπτός, peptós "digested”) are short chains of amino acids linked by peptide bonds (a type of covalent bond, involves release of water molecule).

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Peptide bond formation via dehydration reaction [loss of water from the reacting molecule or ion]

An oligopeptide, often just called peptide (oligo-, "a few"), consists of two to twenty amino acids and can include dipeptides, tripeptides, tetrapeptides, and pentapeptides.

A polypeptide is a longer, continuous, unbranched peptide chain.

A polypeptide that contains more than approximately fifty amino acids is known as a protein.

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Figure

Proteins consist of one or more polypeptides arranged in a biologically functional way, often bound to ligands such as coenzymes and cofactors, or to another protein or other macromolecule such as DNA or RNA, or to complex macromolecular assemblies.[6]

A ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. The etymology stems from [Latin] ligare, which means 'to bind'.

A biomolecule or biological molecule is a loosely used term for molecules present in organisms that are essential to one or more typically biological processes.

A coordination complex consists of a central atom or ion, which is usually metallic and is called the coordination centre, and a surrounding array of bound molecules or ions, that are in turn known as ligands or complexing agents.

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Cisplatin, PtCl2(NH3)2, is a coordination complex of platinum(II) with two chloride and two ammonia ligands.

A cofactor is a non-protein chemical compound or metallic ion that is required for an enzyme's activity as a catalyst (a catalyst is a substance that increases the rate of a chemical reaction).

Cofactors can be divided into two types: inorganic ions [lacks C-H bonds] and complex organic molecules called coenzymes.[1]

Polypeptides and proteins are often referred to being comprised of “amino acid residues”.

A residue is whatever that remains after a series of events.

In molecular biology, a residue refers to a specific monomer within a polymeric chain of a polysaccharide, protein, or nucleic acid [which has some discarded atoms during a condensation reaction].

The concept that suggested this term is presumably the nature of the condensation reaction by which such classes of monomeric building blocks, such as amino acids or monosaccharides, are strung together to form a polymeric chain, such as a peptide or a polysaccharide; some atoms, typically in the form of a water molecule, are discarded from each building block, leaving only a "residue" of the building block, that ends up in the finished product.

A residue might be one amino acid [minus the discarded atoms] in a polypeptide or one monosaccharide in a starch molecule.

A condensation reaction is the combination of two molecules to form a single molecule, usually with the loss of a small molecule such as water.

A protein sequence or protein primary structure is the linear sequence of amino acids in a peptide or protein.

By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end.

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Nucleotides

Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth. Nucleotides are obtained in the diet and are also synthesized from common nutrients by the liver.[1]

A polynucleotide molecule is a biopolymer composed of 13 or more[1] nucleotide monomers covalently bonded in a chain.

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This nucleotide contains the five-carbon sugar deoxyribose (at center), a nucleobase called adenine (upper right), and one phosphate group (left).

Phosphoric acid, also known as orthophosphoric acid or phosphoric(V) acid, is a weak acid with the chemical formula H3PO4. The pure compound is a colorless solid.

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Structural formula of phosphoric acid, showing dimensions
A picometer (pm) is 1/trillionth of a meter.

1 pm = 1 x 10-12 m

A phosphate is an anion, salt, functional group or ester derived from a phosphoric acid.

It most commonly means orthophosphate, a derivative of orthophosphoric acid H3PO4.

The phosphate or orthophosphate ion [PO4]3− is derived from phosphoric acid by the removal of three protons H+.

Removal of one or two protons gives the dihydrogen phosphate ion [H2PO4] and the hydrogen phosphate ion [HPO4]2−, respectively.

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Stereo [3D] skeletal formula of phosphate [anion]

Free phosphate anions in solution are called inorganic phosphate, generally denoted Pi, and at physiological (homeostatic or steady internal conditions) pH primarily consists of a mixture of [HPO4]2- and [H2PO4]- ions.

A nucleoside consists simply of a nucleobase (also termed a nitrogenous base) and a five-carbon sugar (ribose or deoxyribose).

Ribose has the chemical formula C5H10O5.

Deoxyribose has the chemical formula C5H10O4.

Deoxy sugars[1] are sugars that have had a hydroxyl [-OH] group replaced with a hydrogen atom [H]. [aka loss of an oxygen atom].

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Figure: The difference between ribose and deoxyribose is the presence of a 2'OH

Note that the carbon atoms are labeled from 1’ to 5’.

Nucleobases, also known as nitrogenous bases or often simply bases, are nitrogen-containing biological compounds that form nucleosides, which, in turn, are components of nucleotides, with all of these monomers constituting the basic building blocks of nucleic acids. The ability of nucleobases to form base pairs and to stack one upon another leads directly to long-chain helical structures such as ribonucleic acid (RNA) and deoxyribonucleic acid (DNA).

Five nucleobases—adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U)—are called primary or canonical. They function as the fundamental units of the genetic code, with the bases A, G, C, and T being found in DNA while A, G, C, and U are found in RNA.

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Purine nucleobases are fused-ring molecules.

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Pyrimidine nucleobases are simple ring molecules.

A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, "Watson–Crick" base pairs (guanine–cytosine and adenine–thymine)[1] allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence.[2] The complementary nature of this based-paired structure provides a redundant copy of the genetic information encoded within each strand of DNA.

Complementarity is the base principle of DNA replication and transcription [DNA to RNA] as it is a property shared between two DNA or RNA sequences, such that when they are aligned antiparallel [parallel but reverse directions] to each other, the nucleotide bases at each position in the sequences will be complementary, much like looking in the mirror and seeing the reverse of things.

Adenine and guanine are purines, while thymine, cytosine and uracil are pyrimidines. Purines are larger than pyrimidines. Both types of molecules complement each other and can only base pair with the opposing type of nucleobase. In nucleic acid, nucleobases are held together by hydrogen bonding, which only works efficiently between adenine and thymine [or adenine and uracil in RNA] and between guanine and cytosine. The base complement A = T shares two hydrogen bonds, while the base pair G ≡ C has three hydrogen bonds. All other configurations between nucleobases would hinder double helix formation. DNA strands are oriented in opposite directions, they are said to be antiparallel.

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Match up between two DNA bases (adenine and thymine) showing hydrogen bonds (dashed lines) holding them together

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Match up between two DNA bases (guanine and cytosine) showing hydrogen bonds (dashed lines) holding them together

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Figure: Uracil - Adenine base pairing in RNA

Nucleic acids are biopolymers, or large biomolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). If the sugar is ribose, the polymer is RNA; if the sugar is the ribose derivative deoxyribose, the polymer is DNA.

Nucleic acids are naturally occurring chemical compounds that serve as the primary information-carrying molecules in cells and makeup the genetic material.

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Nucleic acids RNA (left) and DNA (right).

Deoxyribonucleic acid (DNA) is a molecule composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses. DNA and ribonucleic acid (RNA) are nucleic acids.

A large part of DNA (more than 98% for humans) is non-coding, meaning that these sections do not serve as patterns for protein sequences.

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The structure of the DNA double helix. The atoms in the structure are colour-coded by element and the detailed structures of two base pairs are shown in the bottom right.

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Location of eukaryote [organisms whose cells have a nucleus enclosed with a nuclear envelope] nuclear DNA [DNA contained within each cell nucleus (nDNA)] within the chromosomes [long DNA molecule with part or all of the genetic material of an organism]

Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes.

Like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA, RNA is found in nature as a single strand folded onto itself, rather than a paired double strand.

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A hairpin loop from a pre-mRNA. Highlighted are the nucleobases (green) and the ribose-phosphate backbone (blue). This is a single strand of RNA that folds back upon itself.

A nucleic acid sequence is a succession of bases signified by a series of a set of five different letters that indicate the order of nucleotides within a DNA (using GACT) or RNA (GACU) molecule.

By convention, sequences are usually presented from the 5' end to the 3' end.

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A furanose (sugar-ring) molecule with carbon atoms labeled using standard notation. The 5′ is upstream; the 3′ is downstream. DNA and RNA are synthesized in the 5′ to 3′ direction.

Nucleic acids can only be synthesized in vivo [on whole, living organisms] in the 5′-to-3′ direction, as the polymerases that assemble various types of new strands generally rely on the energy produced by breaking nucleoside triphosphate bonds to attach new nucleoside monophosphates to the 3′-hydroxyl (-OH) group, via a phosphodiester bond.

A polymerase is an enzyme that synthesizes long chains of polymers or nucleic acids.

Enzymes are proteins that act as biological catalysts (biocatalysts). Catalysts accelerate chemical reactions.

A phosphodiester bond occurs when exactly two of the hydroxyl groups in phosphoric acid react with hydroxyl groups on other molecules to form two ester bonds.

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Diagram of phosphodiester bonds (PO43−) between three nucleotides.

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Structural elements of three nucleotides—where one-, two- or three-phosphates are attached to the nucleoside (in yellow, blue, green) at center: 1st, the nucleotide termed as a nucleoside monophosphate is formed by adding a phosphate (in red); 2nd, adding a second phosphate forms a nucleoside diphosphate; 3rd, adding a third phosphate results in a nucleoside triphosphate. + The nitrogenous base (nucleobase) is indicated by "Base" and "glycosidic bond" (sugar bond). All five primary, or canonical, bases—the purines and pyrimidines—are sketched at right (in blue).

A glycosidic bond or glycosidic linkage is a type of covalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate.

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In the DNA segment shown, the 5′ to 3′ directions are down the left strand and up the right strand

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The following DNA sequences illustrate pair double-stranded patterns. By convention, the top strand is written from the 5' end to the 3' end; thus, the bottom strand is written 3' to 5'.

A base-paired DNA sequence:

ATCGATTGAGCTCTAGCG
TAGCTAACTCGAGATCGC

The corresponding RNA sequence, in which uracil is substituted for thymine in the RNA strand:

AUCGAUUGAGCUCUAGCG
UAGCUAACUCGAGAUCGC

Adenosine triphosphate (ATP) is an organic compound and hydrotrope that provides energy to drive many processes in living cells, such as muscle contraction, nerve impulse propagation, condensate [class of non-membrane organelles inside cells] dissolution, and chemical synthesis. Found in all known forms of life, ATP is often referred to as the "molecular unit of currency" of intracellular (inside cells) energy transfer. When consumed in metabolic processes [life-sustaining chemical reactions], it converts either to adenosine diphosphate (ADP) or to adenosine monophosphate (AMP). Other processes regenerate ATP so that the human body recycles its own body weight equivalent in ATP each day.[3]

ATP is also a precursor to DNA and RNA, and is used as a coenzyme.

From the perspective of biochemistry, ATP is classified as a nucleoside triphosphate, which indicates that it consists of three components: a nitrogenous base (adenine), the sugar ribose, and the triphosphate.

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Structure of adenosine triphosphate (ATP)

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Figure: Chemical structure of ATP, ADP and AMP

A hydrotrope is a compound that solubilizes hydrophobic compounds in aqueous solutions by means other than micellar solubilization.

Micellar solubilization (solubilization) is the process of incorporating the solubilizate (the component that undergoes solublization) into or onto micelles.

A micelle or micella (plural micelles or micellae, respectively) is an aggregate (or supramolecular assembly) of surfactant molecules dispersed in a liquid, forming a colloidal suspension (also known as associated colloidal system[4]).

A supramolecular assembly is a complex of molecules held together by noncovalent bonds.

A colloid is a mixture in which one substance of microscopically dispersed insoluble particles are suspended throughout another substance.

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Schematic of micellar solubilization of fatty substance in water with the use of a dispersant [substance to improve separation of particles in a mixture, such as a surfactant]

Typically, hydrotropes consist of a hydrophilic part and a hydrophobic part (similar to surfactants), but the hydrophobic part is generally too small to cause spontaneous self-aggregation.

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Source


Back to the Wikipedia page on Biology:


Macromolecules

Further information: Macromolecule and Biochemistry

Molecules such as sugars, amino acids, and nucleotides can act as single repeating units called monomers to form chain-like molecules called polymers via a chemical process called condensation.[40] For example, amino acids can form polypeptides whereas nucleotides can form strands of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). Polymers make up three of the four macromolecules [very large molecules] (polysaccharides, lipids, proteins, and nucleic acids) that are found in all living organisms.

MES Note:

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The Major Macromolecules [DNA should have deoxyribose not ribose]

Each macromolecule plays a specialized role within any given cell. Some polysaccharides, for instance, can function as storage material that can be hydrolyzed [chemical bonds broken by water] to provide cells with sugar. Lipids are the only class of macromolecules that are not made up of polymers and the most biologically important lipids are fats, phospholipids, and steroids.[40]

MES Note: Phospholipids, also known as phosphatides,[1] are a class of lipids whose molecule has a hydrophilic [attracted to water] "head" containing a phosphate group, and two hydrophobic [not attracted to water] "tails" derived from fatty acids, joined by a glycerol [multiple -OH] molecule.

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Phospholipid arrangement in cell membranes.

Lumen is the inside space of a tubular structure, such as an artery or intestine.

A steroid is a biologically active organic compound [and a type of lipid] with four rings arranged in a specific molecular configuration. Steroids have two principal biological functions: as important components of cell membranes which alter membrane fluidity; and as signaling molecules.

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Structure of cholestane, a steroid with 27 carbon atoms, its core ring system (ABCD) is composed of 17 carbon atoms.

Membrane fluidity refers to the viscosity of the lipid bilayer of a cell membrane.

The lipid bilayer (or phospholipid bilayer) is a thin polar membrane [positive charge on one side and negative on the other] made of two layers of lipid molecules.

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The three main structures phospholipids form in solution; the liposome (a closed bilayer), the micelle and the bilayer.

Proteins are the most diverse of the macromolecules, which include enzymes, transport proteins, large signaling molecules, antibodies, and structural proteins. Finally, nucleic acids store, transmit, and express hereditary information.[40]

MES Note: An antibody (Ab), also known as an immunoglobulin (Ig),[1] is a large, Y-shaped protein used by the immune system to identify and neutralize foreign objects such as pathogenic bacteria and viruses. The antibody recognizes a unique molecule of the pathogen [organism that can produce disease], called an antigen [Ag or “antibody generator”].[2][3]

To allow the immune system to recognize millions of different antigens, the antigen-binding sites at both tips of the antibody come in an equally wide variety. In contrast, the remainder of the antibody is relatively constant. It only occurs in a few variants, which define the antibody's class or isotype: IgA, IgD, IgE, IgG, or IgM.

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Each antibody binds to a specific antigen; an interaction similar to a lock and key.

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The (a) primary, (b) secondary, (c) tertiary, and (d) quaternary structures of a hemoglobin protein. [pleated = folded; heme = precursor to hemoglobin; globular = spherical, ball, globe]

MES Note: Hemoglobin (Hb or Hgb) is the iron-containing oxygen-transport metalloprotein (contains a metal ion cofactor) in the red blood cells (also called erythrocytes).

Red blood cells (RBCs), also referred to as red cells,[1] red blood corpuscles (in humans or other animals not having nucleus in red blood cells), haematids, erythroid cells or erythrocytes (from Greek erythros for "red" and kytos for "hollow vessel", with -cyte translated as "cell" in modern usage), are the most common type of blood cell and the vertebrate's [class of animals with backbones] principal means of delivering oxygen (O2) to the body tissues—via blood flow through the circulatory system.[2]

Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function.

The structure of these molecules may be considered at any of several length scales ranging from the level of individual atoms to the relationships among entire protein subunits [individual protein molecules that assemble with other protein molecules to form a protein complex].

A protein complex or multiprotein complex is a group of two or more associated polypeptide chains. Protein complexes are a form of quaternary structure.

This useful distinction among scales is often expressed as a decomposition of molecular structure into four levels: primary, secondary, tertiary, and quaternary.

The scaffold [support structure] for this multiscale organization of the molecule arises at the secondary level, where the fundamental structural elements are the molecule's various hydrogen bonds.

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Histones are proteins that act as spools around which DNA winds to create structural units called nucleosomes.

Cells

Further information: Cell (biology)

Cell theory states that cells are the fundamental units of life, that all living things are composed of one or more cells, and that all cells arise from preexisting cells through cell division.[41] Most cells are very small, with diameters ranging from 1 to 100 micrometers [um or µm = 1/millionth of a meter] and are therefore only visible under a light or electron microscope.[42] There are generally two types of cells: eukaryotic cells, which contain a nucleus, and prokaryotic cells, which do not. Prokaryotes are single-celled organisms such as bacteria, whereas eukaryotes can be single-celled or multicellular. In multicellular organisms, every cell in the organism's body is derived ultimately from a single cell in a fertilized egg.

MES Note: Fertilisation or fertilization (see spelling differences), also known as generative fertilisation, syngamy and impregnation,[1] is the fusion of gametes to give rise to a new individual organism or offspring and initiate its development.

The cycle of fertilisation and development of new individuals is called sexual reproduction.

Processes such as insemination [introduction of sperm into a female’s reproductive system] or pollination [transfer of pollen (which produce gametes) from a male part of a plant to a female part] which happen before the fusion of gametes are also sometimes informally called fertilization.[2]

A gamete is a haploid cell that fuses with another haploid cell during fertilization in organisms that reproduce sexually.[1]

Gametes are an organism's reproductive cells, also referred to as sex cells.[2]

In species that produce two morphologically distinct types of gametes, and in which each individual produces only one type, a female is any individual that produces the larger type of gamete—called an ovum— and a male produces the smaller type—called a sperm.

Morphology is a branch of biology dealing with the study of the form and structure of organisms and their specific structural features.

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Sperm and ovum fusing

Ploidy is the number of complete sets of chromosomes in a cell. Sets of chromosomes refer to the number of maternal [mother] and paternal [father] chromosome copies, respectively, in each homologous chromosome pair, which chromosomes naturally exist as. Somatic cells [non-sex cells], tissues, and individual organisms can be described according to the number of sets of chromosomes present (the "ploidy level"): monoploid (1 set), diploid (2 sets), triploid (3 sets), tetraploid (4 sets), pentaploid (5 sets), hexaploid (6 sets), heptaploid[2] or septaploid[3] (7 sets), etc. The generic term polyploid is often used to describe cells with three or more chromosome sets.

A couple of homologous chromosomes, or homologs, are a set of one maternal and one paternal chromosome that pair up with each other inside a cell during fertilization.

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A haploid set that consists of a single complete set of chromosomes (equal to the monoploid set), as shown in the picture above, must belong to a diploid species. If a haploid set consists of two sets, it must be of a tetraploid (four sets) species.[1]

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Figure

Haploid has two related definitions:

(1) A cell with half the number of sets of chromosomes found in the somatic cells (general cells of the body and not sex cells).
(2) A cell with one and only one set of chromosomes, and synonymous with the term monoploid.

A zygote is a eukaryotic cell formed by a fertilization event between two gametes.

The zygote's genome is a combination of the DNA in each gamete, and contains all of the genetic information necessary to form a new individual.

An egg is the organic vessel containing the zygote in which an embryo develops until it can survive on its own, at which point the animal hatches. An egg results from fertilization of an egg cell [or ovum].

An embryo is the early stage of development of a multicellular organism. A newly developing human is typically referred to as an embryo until the ninth week after conception, when it is then referred to as a fetus. In other multicellular organisms, the word "embryo" can be used more broadly to any early developmental or life cycle stage prior to birth or hatching.

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A male human embryo, seven weeks old or nine weeks' gestational age

Gestational age is a measure of the age of a pregnancy which is taken from the beginning of the woman's last menstrual period (LMP).

Menstruation (also known as a period and many other colloquial [casual, informal] terms) is the regular discharge of blood and mucosal tissue from the inner lining of the uterus [endometrium] through the vagina.

A mucous membrane or mucosa is a membrane that lines various cavities in the body and covers the surface of internal organs.

The uterus (from Latin "uterus", plural uteri) or womb is the main female hormone-responsive, secondary sex organ of the reproductive system in humans and most other mammals. Things occurring in the uterus are described with the term in utero. It is within the uterus that the fetus develops during gestation.

Gestation is the period of development during the carrying of an embryo, and later fetus, inside viviparous animals (the embryo develops within the parent).

A hormone is any member of a class of signaling molecules in multicellular organisms, that are transported to distant organs to regulate physiology and behavior.[1]

A sex organ (or reproductive organ) is any part of an animal or plant that is involved in sexual reproduction. The reproductive organs together constitute the reproductive system. In animals, the testis in the male, and the ovary in the female, are called the primary sex organs.[1][pages needed] All others are called secondary sex organs, divided between the external sex organs—the genitals or genitalia, visible at birth in both sexes—and the internal sex organs.

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Uterus and uterine tubes.

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Figure: The period occurs every 21 to 35 days.

A follicle is a small spherical or vase-like group of cells enclosing a cavity in which some other structure grows or other material is contained.

Cell structure

Further information: Animal cell and Plant cell

Every cell is enclosed within a cell membrane that separates its cytoplasm [all the material inside a eukaryotic cell except the cell nucleus] from the extracellular space [outside of the cells].[43] A cell membrane consists of a lipid bilayer [two layers of lipids], including cholesterols [a type of lipid] that sit between phospholipids to maintain their fluidity at various temperatures. Cell membranes are semipermeable, allowing small molecules such as oxygen, carbon dioxide, and water to pass through while restricting the movement of larger molecules and charged particles such as ions.[44] Cell membranes also contains [sic] membrane proteins, including integral membrane proteins that go across the membrane serving as membrane transporters, and peripheral proteins that loosely attach to the outer side of the cell membrane, acting as enzymes shaping the cell.[45] Cell membranes are involved in various cellular processes such as cell adhesion [interact and attach to neighboring cells], storing electrical energy [by maintaining a voltage or electric charge difference between the inside and outside of the cell] and cell signalling [ability to receive, process, and transmit signals with its environment and with itself] and serve as the attachment surface for several extracellular structures such as a cell wall [surrounds cell membrane of some cells], glycocalyx [generally fuzzy hair-like attachments surrounding some cell], and cytoskeleton [provides shape and mechanical resistance to deformation within and surrounding a cell].

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Structure of an animal cell depicting various organelles [subunit within a cell, analogous to organs in a body]

MES Note: Diagram of a typical animal cell. Organelles are labelled as follows:

(1) Nucleolus [largest structure in the nucleus, produces ribosomes]

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Electron micrograph of part of a HeLa cell.

HeLa is an immortal cell line used in scientific research. It is the oldest and most commonly used human cell line.[1] The line is named after and derived from cervical cancer cells taken on February 8, 1951,[2] from Henrietta Lacks, a 31-year-old African-American mother of five, who died of cancer on October 4, 1951.[3] The cell line was found to be remarkably durable and prolific, which allows it to be used extensively in scientific study.[4][5]

The cells from Lacks's cancerous cervical tumor were taken without her knowledge or consent, which was common practice at the time.[6] Cell biologist George Otto Gey found that they could be kept alive,[7] and developed a cell line. Previously, cells cultured from other human cells would only survive for a few days. Cells from Lacks's tumor behaved differently.

An immortalised cell line is a population of cells from a multicellular organism which would normally not proliferate indefinitely but, due to mutation [alteration of a nucleotide sequence of a genome], have evaded normal cellular senescence [cessation of cell division] and instead can keep undergoing division. The cells can therefore be grown for prolonged periods in vitro [in the lab; in vivo = in living organism]. The mutations required for immortality can occur naturally or be intentionally induced for experimental purposes.

(2) Nucleus [contains all of the cell’s genome except for mitochondrial DNA (and plastid DNA in plants)]

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An electron micrograph of a cell nucleus, showing the darkly stained nucleolus

A plastid is a membrane-bound organelle[1] found in the cells of plants, algae, and some other eukaryotic organisms.

(3) Ribosome [found floating in the cytoplasm or attached to the rough endoplasmic reticulum (dots as part of 5), synthesizes protein from mRNA (messenger RNA)]

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Figure

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Figure 1: Electron microscopy image of simultaneous transcription [copying segment of DNA into RNA] and translation [synthetize mRNA into specific amino acid chain]. The image shows bacterial DNA and its associated mRNA transcripts, each of which is occupied by ribosomes. (Adapted from O. L. Miller et al., Science 169:392, 1970.):

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Figure 3.4.13.4.1: An electron micrograph of polysomes [group of ribosomes] held together with mRNA. Image courtesy of Alexander Rich.

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Figure: Rough endoplasmic reticulum with ribosomes on the surface (mammal neuron, CNS [central nervous system]), transmission electron micrograph (TEM).

A neuron or nerve cell is an electrically excitable cell that communicates with other cells via specialized connections called synapses.

In biology, the nervous system is a highly complex part of an animal that coordinates its actions and sensory information by transmitting signals to and from different parts of its body.

The central nervous system (CNS) is the part of the nervous system consisting primarily of the brain and spinal cord.

(4) Vesicle [structure consisting of liquid or cytoplasm enclosed by a lipid bilayer]

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Sarfus [optical microscope imaging technique] image of lipid vesicles.

(5) Rough endoplasmic reticulum [RER, synthesizes certain lipids such as cholesterol, contains ribosomes]

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Micrograph of rough endoplasmic reticulum network around the nucleus (shown in lower right-hand side of the picture). Dark small circles in the network are mitochondria [and possibly other organelles].

(6) Golgi apparatus (or "Golgi body") [packages proteins into membrane-bound vesicles inside the cell before they are sent to their destination]

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Micrograph of Golgi apparatus, visible as a stack of semicircular black rings near the bottom. Numerous circular vesicles can be seen in proximity to the organelle.

(7) Cytoskeleton [complex dynamic network of interlinking protein filaments (long chains of protein) present in the cytoplasm of all cells]

In eukaryotes, it is composed of three main components, microfilaments, intermediate filaments and microtubules, and these are all capable of rapid growth or disassembly dependent on the cell's requirements.

Microfilaments, also called actin filaments, are protein filaments in the cytoplasm of eukaryotic cells that form part of the cytoskeleton. Microfilaments are usually about 7 nm in diameter and made up of two strands of actin.

Actin is a family of globular [spherical] multi-functional proteins that form microfilaments in the cytoskeleton, and the thin filaments in muscle fibrils [Rod-like organelle of a muscle cell]. It can be present as either a free monomer called G-actin (globular) or as part of a linear polymer microfilament called F-actin (filamentous).

Intermediate filaments (IFs) are cytoskeletal structural components found in the cells of vertebrates, and many invertebrates. Intermediate filaments are composed of a family of related proteins sharing common structural and sequence features. The diameter of intermediate filaments [10 nm] is now commonly compared to actin microfilaments (7 nm) and microtubules (25 nm).

Microtubules are polymers of tubulin that form part of the cytoskeleton and provide structure and shape to eukaryotic cells. The outer diameter of a microtubule is between 23 and 27 nm[2] while the inner diameter is between 11 and 15 nm.

Tubulin in molecular biology can refer either to the tubulin protein superfamily of globular proteins, or one of the member proteins of that superfamily. α- and β-tubulins polymerize into microtubules, a major component of the eukaryotic cytoskeleton.

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The eukaryotic cytoskeleton. Actin filaments are shown in red, and microtubules composed of beta tubulin are in green.

  • Blue: nucleus stained with DAPI [fluorescent stain that binds strongly to adenine-thymine-rich regions in DNA]
    -Green: Tubulin (microtubles) stained with antibody Bodipy FL goat anti-mouse IgG (Indirect fluorescent antibody stain)
  • Red: F-Actin stained with Texas Red X-Phalloidin

Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation.

Immunoglobulin G (IgG) is a type of antibody. Representing approximately 75% of serum antibodies in humans, IgG is the most common type of antibody found in blood circulation.

Serum is the fluid and solute component of blood which does not play a role in clotting.[1] It may be defined as blood plasma without the clotting factors, or as blood with all cells and clotting factors removed.

Blood plasma is a yellowish liquid component of blood that holds the blood cells, proteins and other constituents of whole blood in suspension. It makes up about 55% of the body's total blood volume.

Coagulation, also known as clotting, is the process by which blood changes from a liquid to a gel, forming a blood clot.

(8) Smooth endoplasmic reticulum [SER, functions in synthesis of certain lipids such as cholesterol, does not contain ribosomes, produces steroid hormones, detoxification]

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Electron micrograph showing smooth ER (arrow) in mouse tissue, at 110,510× magnification.

(9) Mitochondrion [generate most of the cell’s supply of adenosine triphosphate (ATP) for chemical energy, has its own genome (mitogenome)]

Chemical energy is the energy of chemical substances [held in chemical bonds] that is released when they undergo a chemical reaction and transform into other substances.

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Two mitochondria from mammalian lung tissue displaying their matrix and membranes as shown by electron microscopy

Mammals (from Latin mamma, 'breast') are a group of vertebrate animals constituting the class Mammalia and characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or hair, and three middle ear bones.

A mammary gland is an exocrine gland in humans and other mammals that produces milk to feed young offspring.

A gland is a group of cells[1] in an animal's body that synthesizes substances (such as hormones) for release into the bloodstream (endocrine gland) or into cavities inside the body or its outer surface (exocrine gland).

(10) Vacuole [membrane-bound organelle filled mainly with water containing inorganic and organic molecules such as enzymes in solution, and certain cases includes solids which have been engulfed]

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Figure: This is a micrograph of a plant cell. Can you see the clear, white organelles, which are the vacuoles? The cytoplasm appears very granular in this image.

(11) Cytosol [Crowded solution of many different types of molecules dissolved in water that occupies up to 30% of the cytoplasm by volume]

https://youtu.be/TptsLsxc2lQ

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Picture of cytosol, showing microtubules (light blue), actin filaments (dark blue), ribosomes (yellow and purple), soluble proteins (light blue), kinesin (red) [protein that can move along the cytoplasm of animal cells], small molecules (white) and RNA (pink).

(12) Lysosome [membrane-bound spherical organelle that contains enzymes that can break down many kinds of biomolecules]

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TEM views of various vesicular compartments. Lysosomes are denoted by "Ly". They are dyed dark due to their acidity; in the center of the top image, a Golgi Apparatus can be seen, distal from the cell membrane relative to the lysosomes.

The terms proximal (from Latin proximus 'nearest') and distal (from Latin distare 'to stand away from') are used to describe parts of a feature that are close to or distant from the main mass of the body, respectively.

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Anatomical directional reference [caudal is from Latin caudum; tail]

Anatomy (Greek anatomē, 'dissection') is the branch of biology concerned with the study of the structure of organisms and their parts.

(13) Centriole [cylindrical organelle composed mainly of a protein called tubulin, typically made up of 9 sets of short microtubule triplets]

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The structure of the centrosome

The centrosome (Latin centrum 'center' + Greek sōma 'body') (also called cytocenter[1]) is an organelle that serves as the main microtubule organizing center (MTOC) of the animal cell, as well as a regulator of cell-cycle progression. The centrosome provides structure for the cell. Centrosomes are composed of two centrioles arranged at right angles to each other, and surrounded by a dense, highly structured[8] mass of protein termed the pericentriolar material (PCM).

The microtubule-organizing center (MTOC) is a structure found in eukaryotic cells from which microtubules emerge.

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A mother and daughter centriole, attached orthogonally

Before DNA replication, cells contain two centrioles, an older mother centriole, and a younger daughter centriole. During cell division, a new centriole grows at the proximal end of both mother and daughter centrioles. After duplication, the two centriole pairs (the freshly assembled centriole is now a daughter centriole in each pair) will remain attached to each other orthogonally until mitosis. At that point the mother and daughter centrioles separate dependently on an enzyme called separase.[28] The two centrioles in the centrosome are tied to one another. The mother centriole has radiating appendages at the distal end of its long axis and is attached to its daughter at the proximal end. Each daughter cell formed after cell division will inherit one of these pairs. Centrioles start duplicating when DNA replicates.

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Mitosis divides the chromosomes in a cell nucleus.

DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule.

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DNA replication: The double helix is un'zipped' and unwound, then each separated strand (turquoise) acts as a template for replicating a new partner strand (green). Nucleotides (bases) are matched to synthesize the new partner strands into two new double helices.

The cell cycle, or cell-division cycle, is the series of events that take place in a cell that cause it to divide into two daughter cells. These events include the duplication of its DNA (DNA replication) and some of its organelles, and subsequently the partitioning of its cytoplasm and other components into two daughter cells in a process called cell division.

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Life cycle of the cell

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Centrosome (shown by arrow) next to nucleus

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Electron micrograph of a centriole from a mouse embryo.

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3D rendering of centrioles

(14) Cell Membrane [separates and protects the interior of the cell from the outside environment; also known as plasma membrane or cytoplasmic membrane]

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Illustration of a Eukaryotic cell membrane

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A micrograph from a Transmission Electron Micrograph [sic] showing a lipid vesicle. The two dark bands are the two leaflets [individual units of the phospholipids; akin to leaflets of a leaf] comprising the bilayer. Similar images taken in the 1950s and 1960s confirmed the bilayer nature of the cell membrane

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Pinnate [feather-like arrangement] leaf of an Acacia [type of plant] with 10 leaflets

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Figure 4-3: Lipid bilayers in cells are asymmetric. In mammalian cells, the major lipids in the outer leaflet are sphingomyelin (SM), glycosphingolipid (GSL), phosphatidylcholine (PC), cholesterol, and some phosphatidylethanolamine (PE). The inner leaflet’s major lipids are PE, phosphatidylserine (PS), phosphatidylinositol (PI), cholesterol, and some PC. SOURCE: London (2014). Reproduced with permission from Erwin London. [Exofacial means facing away from a cell]

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Figure 2: A neuromuscular junction [type of synapse] in C. elegans [tiny 1 mm long transparent worm]. The lipid bilayer of the plasma membrane is less than 5nm but the individual leaflets of the bilayer can be resolved. (photo Shigeki Watanabe and Erik Jorgensen)

Within the cytoplasm of a cell, there are many biomolecules such as proteins and nucleic acids.[46] In addition to biomolecules, eukaryotic cells have specialized structures called organelles that have their own lipid bilayers or are spatially units. These organelles include the cell nucleus, which contains a cell's genetic information, or mitochondria, which generates adenosine triphosphate (ATP) to power cellular processes. Other organelles such as endoplasmic reticulum and Golgi apparatus play a role in the synthesis and packaging of proteins, respectively. Biomolecules such as proteins can be engulfed by lysosomes, another specialized organelle.

Plant cells have additional organelles that distinguish them from animal cells such as a cell wall, chloroplasts, and vacuole.

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Structure of a plant cell

MES Note: Most mature plant cells have one large vacuole that typically occupies more than 30% of the cell's volume, and that can occupy as much as 80% of the volume for certain cell types and conditions.

The fluid in the vacuole is called the cell sap and serves as storage of materials and provides mechanical support to the cell.

The tonoplast is the vacuole membrane.

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The anthocyanin-storing vacuoles [vacuoles containing water-soluble pigments] of Rhoeo spathacea, a spiderwort [a type of wildflower]

A pigment is a colored material that is completely or nearly insoluble in water.[1] In contrast, dyes are typically soluble, at least at some stage in their use.

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Pigments for sale at a market stall in Goa, India.

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A wide variety of wavelengths (colors) encounter a pigment. This pigment absorbs red and green light, but reflects blue—creating the color blue.

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Sunlight encounters Rosco R80 "Primary Blue" pigment. The product of the source spectrum and the reflectance spectrum of the pigment results in the final spectrum, and the appearance of blue.

White light is how the eye perceives many wavelengths at once.

A cell wall is a structural layer surrounding some types of cells, just outside the cell membrane.

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Figure

Plants are mainly multicellular organisms, predominantly photosynthetic eukaryotes of the kingdom Plantae.

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The hierarchy of biological classification's eight major taxonomic ranks [categorization ranks]. A kingdom contains one or more phyla. Intermediate minor rankings are not shown.

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The major ranks: domain, kingdom, phylum, class, order, family, genus, and species, applied to the red fox, Vulpes vulpes.

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Figure 3: Taxonomy of Humans. Source: Biology Online.

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Figure [typo: should be “high forehead”]

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Figure

Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration [reactions and processes in breaking down nutrients into ATP and then releasing waste products], can later be released to fuel the organism's metabolic activities.

Chloroplasts are organelles that conduct photosynthesis, where the photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in the energy-storage molecules ATP and NADPH while freeing oxygen from water in plant and algal [informal term for a diverse group of photosynthetic eukaryotic organisms that typically live underwater] cells.

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Seen through a microscope, chlorophyll is concentrated within organisms in structures called chloroplasts – shown here grouped inside plant cells.

Metabolism

Further information: Metabolism and Bioenergetics

All cells require energy to sustain cellular processes. Energy is the capacity to do work, which, in thermodynamics, can be calculated using Gibbs free energy.

MES Note: In thermodynamics, work performed by a system is energy transferred by the system to its surroundings, by a mechanism through which the system can spontaneously exert macroscopic forces on its surroundings. In the surroundings, through suitable passive linkages, the work can lift a weight, for example.

MES Subtle Note: Note the circular reasoning: Energy is the capacity to do work while work is the energy transferred by a system exerting forces on its surroundings.

Gibbs free energy or Gibbs energy is a measure of thermodynamic potential energy.

Thermodynamics is a branch of physics that deals with heat, work, and temperature, and their relation to energy, radiation, and physical properties of matter. Traditionally, thermodynamics has recognized three fundamental laws, simply named by an ordinal [counting] identification, the first law, the second law, and the third law.[1][2][3] A more fundamental statement was later labelled as the zeroth law, after the first three laws had been established.

The zeroth law of thermodynamics defines thermal equilibrium and forms a basis for the definition of temperature: If two systems are each in thermal equilibrium with a third system, then they are in thermal equilibrium with each other. Two physical systems are in thermal equilibrium if there is no net flow of thermal energy between them when they are connected by a path permeable to heat.

The first law of thermodynamics states that, when energy passes into or out of a system (as work, heat, or matter), the system's internal energy changes in accord with the law of conservation of energy. The law of conservation of energy states that the total energy of an isolated system is constant; energy can be transformed from one form to another, but can be neither created nor destroyed. For a thermodynamic process without transfer of matter, the first law is often formulated[1][nb 1]

∆U = Q – W,

where U denotes the change in the internal energy of a closed system, Q denotes the quantity of energy supplied to the system as heat, and W denotes the amount of thermodynamic work done by the system on its surroundings.

The second law of thermodynamics states that in a natural thermodynamic process, the sum of the entropies [measure of disorder] of the interacting thermodynamic systems never decreases. Another form of the statement is that heat does not spontaneously pass from a colder body to a warmer body.

The third law of thermodynamics states that a system's entropy approaches a constant value as the temperature approaches absolute zero. With the exception of non-crystalline solids (glasses) the entropy of a system at absolute zero is typically close to zero.

Classical thermodynamics considers three main kinds of thermodynamic processes: (1) changes in a system, (2) cycles in a system, and (3) flow processes.

Entropy is a scientific concept, as well as a measurable physical property that is most commonly associated with a state of disorder, randomness, or uncertainty.

A crystal or crystalline solid is a solid material whose constituents (such as atoms, molecules, or ions) are arranged in a highly ordered microscopic structure, forming a crystal lattice that extends in all directions.

Glass is a non-crystalline [or amorphous], often transparent solid, that has widespread practical, technological, and decorative use in, for example, window panes, tableware, and optics.

Absolute zero is the lowest limit of the thermodynamic temperature scale, a state at which the enthalpy and entropy of a cooled ideal gas reach their minimum value, taken as zero kelvins. The fundamental particles of nature have minimum vibrational motion, retaining only quantum mechanical, zero-point energy-induced particle motion. The theoretical temperature is determined by extrapolating the ideal gas law; by international agreement, absolute zero is taken as −273.15 degrees on the Celsius scale (International System of Units),[1][2] which equals −459.67 degrees on the Fahrenheit scale (United States customary units or Imperial units).

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Zero kelvins (−273.15 °C) is defined as absolute zero.

Enthalpy is a property of a thermodynamic system, and is defined as the sum of the system's internal energy and the product of its pressure and volume.

The ideal gas law, also called the general gas equation, is the equation of state of a hypothetical ideal gas. It is a good approximation of the behavior of many gases under many conditions, although it has several limitations.

The ideal gas law is often written in an empirical form:

PV = nRT

where P, V and R are the pressure, volume and temperature; n is the amount of substance; and R is the ideal gas constant [relates average kinetic energy of gas particles with temperature].

Zero-point energy (ZPE) is the lowest possible energy that a quantum mechanical system may have. Unlike in classical mechanics, quantum systems constantly fluctuate in their lowest energy state.

According to the first law of thermodynamics, energy is conserved, i.e., cannot be created or destroyed. Hence, chemical reactions in a cell do not create new energy but are involved instead in the transformation and transfer of energy.[47] Nevertheless, all energy transfers lead to some loss of usable energy, which increases entropy (or state of disorder) as stated by the second law of thermodynamics. As a result, living organisms such as cells require continuous input of energy to maintain a low state of entropy. In cells, energy can be transferred as electrons during redox (reduction–oxidation) reactions, stored in covalent bonds, and generated by the movement of ions (e.g., hydrogen, sodium, potassium) across a membrane.

MES Note: Redox (reduction–oxidation) is a type of chemical reaction in which the oxidation states of atoms are changed.

The oxidation state, sometimes referred to as oxidation number, describes the degree of oxidation (loss of electrons) of an atom in a chemical compound. Conceptually, the oxidation state, which may be positive, negative or zero, is the hypothetical charge that an atom would have if all bonds to atoms of different elements were 100% ionic, with no covalent component. This is never exactly true for real bonds.

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Figure: The oxidation number of an element or neutral compound is zero. Otherwise, the total charge is ionic charge.

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Figure

Oxidation is the loss of electrons or an increase in the oxidation state of an atom, an ion, or of certain atoms in a molecule.

Reduction is the gain of electrons or a decrease in the oxidation state of an atom, an ion, or of certain atoms in a molecule (a reduction in oxidation state).

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Figure 11: A reducing agent reduces other substances and loses electrons; therefore, its oxidation state increases. An oxidizing agent oxidizes other substances and gains electrons; therefore, its oxidation state decreases.

Gaining electrons = decreasing oxidation state.
Losing electrons = increasing oxidation state.

A reducing agent increases oxidation state by losing electrons.
An oxidatizing agent decreases oxidation state by gaining electrons.

Many reactions in organic chemistry are redox reactions due to changes in oxidation states but without distinct electron transfer. For example, during the combustion of wood with molecular oxygen [O2], the oxidation state of carbon atoms in the wood increases and that of oxygen atoms decreases as carbon dioxide and water are formed. The oxygen atoms undergo reduction, formally gaining electrons, while the carbon atoms undergo oxidation, losing electrons. Thus oxygen is the oxidizing agent and carbon is the reducing agent in this reaction.[4]

Combustion, or burning,[1] is a high-temperature exothermic redox chemical reaction between a fuel (the reductant) and an oxidant [oxidizing agent], usually atmospheric oxygen, that produces oxidized, often gaseous products, in a mixture termed as smoke. Combustion does not always result in fire, because a flame is only visible when substances undergoing combustion vapourise, but when it does, a flame is a characteristic indicator of the reaction.

Smoke is a collection of airborne particulates and gases[3] emitted when a material undergoes combustion or pyrolysis [thermal decomposition without oxygen], together with the quantity of air that is entrained or otherwise mixed into the mass.

Particulates – also known as atmospheric aerosol particles, atmospheric particulate matter, particulate matter (PM), or suspended particulate matter (SPM) – are microscopic particles of solid or liquid matter suspended in the air. The term aerosol commonly refers to the particulate/air mixture, as opposed to the particulate matter alone.

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This diagram shows types, and size distribution in micrometres (μm) [0.001 mm], of atmospheric particulate matter.

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Figure: Exothermic [energy is released] Reaction

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Figure: Combustion of methane gas.

Carbon: Oxidation state increases; loses more electrons.
Oxygen: Oxidation state decreases, gains more electrons.

O increases C’s oxidation state.
C decreases O’s oxidation state.

C is a reducer.
O is an oxidizer.

Although oxidation reactions are commonly associated with the formation of oxides [contains at least one oxygen atom and one other element] from oxygen molecules, oxygen is not necessarily included in such reactions, as other chemical species can serve the same function.

Redox reactions can occur relatively slowly, as in the formation of rust [iron (Fe) oxide], or much more rapidly, as in the case of burning fuel.

Rust is an iron oxide, a usually reddish-brown oxide formed by the reaction of iron and oxygen in the catalytic presence of water or air moisture.

Iron oxides are chemical compounds composed of iron and oxygen.

Oxygen is the quintessential [perfect example] oxidizer.

Metabolism is the set of life-sustaining chemical reactions in organisms. The three main purposes of metabolism are: the conversion of food to energy to run cellular processes; the conversion of food/fuel to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; and the elimination of metabolic wastes [toxic remains that can’t be further used by the organism]. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolic reactions may be categorized as catabolic – the breaking down of compounds (for example, the breaking down of glucose to pyruvate by cellular respiration); or anabolic – the building up (synthesis) of compounds (such as proteins, carbohydrates, lipids, and nucleic acids). Usually, catabolism releases energy, and anabolism consumes energy.

MES Note: Pyruvic acid (CH3COCOOH) is the simplest of the alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the conjugate base, CH3COCOO, is an intermediate in several metabolic pathways throughout the cell.

A ketone is a functional group with the structure R2C=O, where R can be a variety of carbon-containing substituents.

A metabolic pathway is a linked series of chemical reactions occurring within a cell.

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Example of an enzyme-catalysed exothermic reaction

MES Note: Activation energy is the minimum amount of energy that must be provided for compounds to result in a chemical reaction. For a chemical reaction to proceed at a reasonable rate, the temperature of the system should be high enough such that there exists an appreciable number of molecules with translational energy equal to or greater than the activation energy.

The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, each step being facilitated by a specific enzyme. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy that will not occur by themselves, by coupling them to spontaneous reactions that release energy. Enzymes act as catalysts – they allow a reaction to proceed more rapidly without being consumed by it – by reducing the amount of activation energy needed to convert reactants into products. Enzymes also allow the regulation of the rate of a metabolic reaction, for example in response to changes in the cell's environment or to signals from other cells.

MES Note: Fermentation is a metabolic process that produces chemical changes in organic substrates through the action of enzymes. In biochemistry, it is narrowly defined as the extraction of energy from carbohydrates in the absence of oxygen. In food production, it may more broadly refer to any process in which the activity of microorganisms brings about a desirable change to a foodstuff or beverage.[1] The science of fermentation is known as zymology [from Greek “the workings of fermentation”].

Some countries list a legal definition of food, often referring them with the word foodstuff.

A substrate is typically the chemical species being observed in a chemical reaction, which reacts with a reagent to generate a product.

Cellular respiration

Further information: Cellular respiration and Fermentation

Cellular respiration is a set of metabolic reactions and processes that take place in the cells of organisms to convert chemical energy from nutrients into adenosine triphosphate (ATP), and then release waste products.[48] The reactions involved in respiration are catabolic reactions, which break large molecules into smaller ones, releasing energy because weak high-energy bonds, in particular in molecular oxygen [dioxygen, O2],[49] are replaced by stronger bonds in the products. Respiration is one of the key ways a cell releases chemical energy to fuel cellular activity. The overall reaction occurs in a series of biochemical steps, some of which are redox reactions. Although cellular respiration is technically a combustion reaction, it clearly does not resemble one when it occurs in a living cell because of the slow, controlled release of energy from the series of reactions.

MES Note:

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Basic overview of energy and human life.

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Respiration in a eukaryotic cell

Sugar in the form of glucose [C6H12O6] is the main nutrient used by animal and plant cells in respiration. Cellular respiration involving oxygen is called aerobic respiration, which has four stages: glycolysis, citric acid cycle (or Krebs cycle), electron transport chain, and oxidative phosphorylation.[50]

Glycolysis is a metabolic process that occurs in the cytoplasm whereby glucose is converted into two pyruvates [CH3COCOO], with two net molecules of ATP being produced at the same time.[50]

MES Note: The overall process of glycolysis is:

Glucose + 2 NAD+ + 2 ADP + 2 Pi → 2 pyruvate + 2 NADH + 2 H+ + 2 ATP

Nicotinamide adenine dinucleotide (NAD) is a coenzyme central to metabolism. Found in all living cells, NAD is called a dinucleotide because it consists of two nucleotides joined through their phosphate groups. One nucleotide contains an adenine nucleobase and the other nicotinamide. NAD exists in two forms: an oxidized [lost an electron] and reduced [gains an electron] form, abbreviated as NAD+ and NADH (H for hydrogen) respectively. The NAD+ addition sign reflects the formal charge on one of its nitrogen atoms; this species is actually a singly charged anion — carrying a (negative) ionic charge of 1 — under conditions of physiological pH. NADH, in contrast, is a doubly charged anion.

NADH is carrying a charged hydrogen molecule with two electrons (H-) thus the charges cancel. That is, NAD+ + H- = NADH, with no net charge on the nitrogen atom.

A formal charge (F.C. or q) in the covalent view of bonding, is the charge assigned to an atom in a molecule, assuming that electrons in all chemical bonds are shared equally between atoms, regardless of relative electronegativity.

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Formal charges in ozone [O3] and the nitrate [NO3-] anion

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Figure: Formal charge [The neutral atom is when the net charge is 0]

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Figure

A valence electron is an electron in the outer shell associated with an atom, and that can participate in the formation of a chemical bond if the outer shell is not closed [no unpaired electrons]; in a single covalent bond, both atoms in the bond contribute one valence electron in order to form a shared pair.

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Four covalent bonds. Carbon has four valence electrons and here a valence of four. Each hydrogen atom has one valence electron and is univalent.

The valence or valency of an element is the measure of its combining capacity with other atoms when it forms chemical compounds or molecules.

An electron shell may be thought of as an orbit followed by electrons around an atom's nucleus. The closest shell to the nucleus is called the "1 shell" (also called the "K shell"), followed by the "2 shell" (or "L shell"), then the "3 shell" (or "M shell"), and so on farther and farther from the nucleus. The shells correspond to the principal quantum numbers (n = 1, 2, 3, 4 ...) or are labeled alphabetically with the letters used in X-ray notation (K, L, M, …). Each shell can contain only a fixed number of electrons: The first shell can hold up to two electrons, the second shell can hold up to eight (2 + 6) electrons, the third shell can hold up to 18 (2 + 6 + 10) and so on. The general formula is that the nth shell can in principle hold up to 2(n2) electrons. Each shell consists of one or more subshells, and each subshell consists of one or more atomic orbitals.

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Figure

Source: However, one orbital can hold only a maximum of two electrons. These electrons are in the same energy level, but different from each other according to their spin. They always have opposite spins. When electrons are filled into the orbitals, they are filled according to the Hund’s Rule. This rule indicates that every orbital in a subshell is singly occupied with electrons before any orbital is doubly coupled.

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Figure 3: Shapes of d Orbitals

The above image shows the shapes of d orbitals. Since one d subshell is composed of 5 orbitals, the above image shows the 5 different shapes of these orbitals.

Each orbital in an atom is characterized by a set of values of the three quantum numbers n, ℓ, and ml, which respectively correspond to the electron's energy, angular momentum, and an angular momentum vector component (the magnetic quantum number). Alternative to the magnetic quantum number, the orbitals are often labeled by the associated harmonic polynomials (e.g. xy, x2−y2) [spherical mathematical functions]. Each such orbital can be occupied by a maximum of two electrons, each with its own projection of spin ms. The simple names s orbital, p orbital, d orbital, and f orbital refer to orbitals with angular momentum quantum number ℓ = 0, 1, 2, and 3 respectively.

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Figure

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Atomic orbitals of the electron in a hydrogen atom at different energy levels. The probability of finding the electron is given by the color, as shown in the key at upper right.

The azimuthal quantum number is a quantum number for an atomic orbital that determines its orbital angular momentum and describes the shape of the orbital. The azimuthal quantum number is the second of a set of quantum numbers that describe the unique quantum state of an electron (the others being the principal quantum number, the magnetic quantum number, and the spin quantum number). It is also known as the orbital angular momentum quantum number, orbital quantum number or second quantum number, and is symbolized as ℓ (pronounced ell).

Quantum numbers describe values of conserved quantities in the dynamics of a quantum system.

The magnetic quantum number distinguishes the orbitals available within a subshell.

The spin quantum number is a quantum number (designated ms) which describes the intrinsic angular momentum (or spin angular momentum, or simply spin) of an electron or other particle.

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The shapes of the five orbitals occupied in nitrogen. The two colours show the phase or sign of the wave function in each region. From left to right: 1s, 2s (cutaway to show internal structure), 2px, 2py, 2pz.

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Figure AT3.2: A sine wave, showing phase and nodal properties

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Skeletal formula of the oxidized form [NAD+]

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The redox reactions of nicotinamide adenine dinucleotide.

Niacinamide or Nicotinamide (NAM) is a form of vitamin B3 found in food and used as a dietary supplement and medication. Chemical formula is C6H6N2O.

Vitamin B3 is a vitamin family that includes three forms or vitamers: nicotinamide (niacinamide), niacin (nicotinic acid), and nicotinamide riboside.[1] All three forms of vitamin B3 are converted within the body to nicotinamide adenine dinucleotide (NAD).

A vitamin is an organic molecule (or a set of molecules closely related chemically, i.e. vitamers) that is an essential micronutrient which an organism needs in small quantities for the proper functioning of its metabolism. Essential nutrients cannot be synthesized in the organism, either at all or not in sufficient quantities, and therefore must be obtained through the diet. Vitamin C [C6H8O6] can be synthesized by some species but not by others; it is not a vitamin in the first instance but is in the second.

Vitamins occur in a variety of related forms known as vitamers.

Each pyruvate is then oxidized into acetyl-CoA [acetyl (CH3CO) coenzyme A] by the pyruvate dehydrogenase complex [complex of 3 enzymes], which also generates NADH [a coenzyme] and carbon dioxide [CO2]. Acetyl-CoA enters the citric acid cycle, which takes places inside the mitochondrial matrix.

MES Note: The citric acid cycle (CAC) – also known as the TCA cycle (tricarboxylic acid cycle) or the Krebs cycle[1][2] – is a series of chemical reactions to release stored energy through the oxidation [loss of electrons] of acetyl-CoA derived from carbohydrates, fats, and proteins.

Acetyl-CoA (acetyl coenzyme A) is a molecule that participates in many biochemical reactions in protein, carbohydrate and lipid metabolism.[2] Its main function is to deliver the acetyl group to the citric acid cycle (Krebs cycle) to be oxidized for energy production.

In the mitochondrion, the matrix is the space within the inner membrane.

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Components of a typical mitochondrion

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Figure 1: This electr4on micrograph shows a mitochondrion as viewed with a transmission electron microscope. This organelle has an outer membrane and an inner membrane. The inner membrane contains folds, called cristae, which increase its surface area. The space between the two membranes is called the intermembrane space, and the space inside the inner membrane is called the mitochondrial matrix. ATP synthesis takes place on the inner membrane. (credit: modification of work by Matthew Britton; scale-bar data from Matt Russell)

At the end of the cycle, the total yield from 1 glucose (or 2 pyruvates) is 6 NADH, 2 FADH2, and 2 ATP molecules. Finally, the next stage is oxidative phosphorylation, which in eukaryotes, occurs in the mitochondrial cristae.

MES Note: Oxidative phosphorylation or electron transport-linked phosphorylation or terminal oxidation is the metabolic pathway in which cells use enzymes to oxidize nutrients, thereby releasing the chemical energy stored within the nutrients in order to produce adenosine triphosphate (ATP).

Flavin adenine dinucleotide (FAD) is a redox-active coenzyme associated with various proteins, which is involved with several enzymatic reactions in metabolism. FAD can exist in four redox states, which are the flavin-N(5)-oxide, quinone, semiquinone, and hydroquinone.[1] FAD is converted between these states by accepting or donating electrons. FAD, in its fully oxidized form, or quinone form, accepts two electrons and two protons to become FADH2 (hydroquinone form). The semiquinone (FADH·) [note the dot indicating it is a free radical] can be formed by either reduction of FAD or oxidation of FADH2 by accepting or donating one electron and one proton, respectively. Some proteins, however, generate and maintain a superoxidized form, the flavin-N(5)-oxide. FAD is an aromatic ring system, whereas FADH2 is not.[12] This means that FADH2 is significantly higher in energy, without the stabilization through resonance that the aromatic structure provides. FADH2 is an energy-carrying molecule, because, once oxidized it regains aromaticity and releases the energy represented by this stabilization.

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Different redox states of FAD

Oxidative phosphorylation comprises the electron transport chain, which is a series of four protein complexes that transfer electrons from one complex to another, thereby releasing energy from NADH and FADH2 that is coupled to the pumping of protons (hydrogen ions) across the inner mitochondrial membrane (chemiosmosis), which generates a proton motive force.[50]

MES Note: Chemiosmosis is the movement of ions across a semipermeable membrane bound structure, down their electrochemical gradient. An example of this would be the formation of adenosine triphosphate (ATP) by the movement of hydrogen ions (H+) across a membrane during cellular respiration or photosynthesis.

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An ion gradient has potential energy and can be used to power chemical reactions when the ions pass through a channel [pore-forming membrane proteins] (red).

The proton-motive force (PMF) is the measure of the potential energy stored as a combination of proton and voltage (electrical potential) gradients across a membrane.

Voltage, electric potential difference, electric pressure or electric tension is the difference in electric potential between two points, which (in a static electric field) is defined as the work needed per unit of charge to move a test charge between the two points.

A test particle, or test charge, is an idealized model of an object whose physical properties (usually mass, charge, or size) are assumed to be negligible except for the property being studied, which is considered to be insufficient to alter the behavior of the rest of the system. In simulations with electric fields the most important characteristics of a test particle is its electric charge and its mass. In this situation it is often referred to as a test charge.

Energy from the proton motive force drives the enzyme ATP synthase to synthesize more ATPs by phosphorylating ADPs.

MES Note: ATP synthase is a protein that catalyzes the formation of the energy storage molecule adenosine triphosphate (ATP) using adenosine diphosphate (ADP) and inorganic phosphate (Pi).

Phosphorylation of a molecule is the attachment of a phosphoryl group.

A phosphoryl group is the chemical ion or radical: P+O32−, containing phosphorus and oxygen. This process and its inverse, dephosphorylation, are critical for many cellular processes in biology.

In biochemistry, dephosphorylation is the removal of a phosphate (PO43-) group from an organic compound by hydrolysis.

Hydrolysis (from Ancient Greek hydro- 'water', and lysis 'to unbind') is any chemical reaction in which a molecule of water breaks one or more chemical bonds.

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A free radical is an atom, molecule, or ion that has at least one unpaired valence electron.

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The hydroxyl radical contains one unpaired electron

The transfer of electrons terminates with molecular oxygen being the final electron acceptor.

If oxygen were not present, pyruvate would not be metabolized by cellular respiration but undergoes a process of fermentation. The pyruvate is not transported into the mitochondrion but remains in the cytoplasm, where it is converted to waste products that may be removed from the cell. This serves the purpose of oxidizing the electron carriers so that they can perform glycolysis again and removing the excess pyruvate. Fermentation oxidizes NADH to NAD+ so it can be re-used in glycolysis.

MES Note:

Post-Glycolysis Processes

The overall process of glycolysis is:

Glucose + 2 NAD+ + 2 ADP + 2 Pi → 2 pyruvate + 2 NADH + 2 H+ + 2 ATP

If glycolysis were to continue indefinitely, all of the NAD+ would be used up, and glycolysis would stop. To allow glycolysis to continue, organisms must be able to oxidize NADH back to NAD+. How this is performed depends on which external electron acceptor is available.

One method of doing this is to simply have the pyruvate do the oxidation; in this process, pyruvate is converted to lactate (the conjugate base of lactic acid [CH3CH(OH)COOH]) in a process called lactic acid fermentation:

Pyruvate + NADH + H+ → lactate + NAD+

This process occurs in the bacteria involved in making yogurt (the lactic acid causes the milk to curdle [thicken]). This process also occurs in animals under hypoxic (or partially anaerobic) conditions, found, for example, in overworked muscles that are starved of oxygen. In many tissues, this is a cellular last resort for energy; most animal tissue cannot tolerate anaerobic conditions for an extended period of time.

Anaerobic means "living, active, occurring, or existing in the absence of free oxygen", as opposed to aerobic which means "living, active, or occurring only in the presence of oxygen."

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Figure

In the absence of oxygen, fermentation prevents the buildup of NADH in the cytoplasm and provides NAD+ for glycolysis. This waste product varies depending on the organism. In skeletal muscles [muscles connected to bones], the waste product is lactic acid [CH3CH(OH)COOH]. This type of fermentation is called lactic acid fermentation. In strenuous [intense] exercise, when energy demands exceed energy supply, the respiratory chain cannot process all of the hydrogen atoms joined by NADH. During anaerobic [without oxygen] glycolysis, NAD+ regenerates when pairs of hydrogen combine with pyruvate to form lactate [conjugate base of lactic acid]. Lactate formation is catalyzed by lactate dehydrogenase [enzyme] in a reversible reaction. Lactate can also be used as an indirect precursor for liver glycogen. During recovery, when oxygen becomes available, NAD+ attaches to hydrogen from lactate to form ATP.

MES Note: Glycogen is a multibranched polysaccharide of glucose that serves as a form of energy storage in animals,[2] fungi, and bacteria.[3] The polysaccharide structure represents the main storage form of glucose in the body.

Due to the way glycogen is synthesised, every glycogen granule has at its core a glycogenin [enzyme] protein.

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Schematic two-dimensional cross-sectional view of glycogen: A core protein of glycogenin is surrounded by branches of glucose units. The entire globular granule may contain around 30,000 glucose units.[1]

Glycogen functions as one of two forms of energy reserves, glycogen being for short-term and the other form being triglyceride stores in adipose tissue (i.e., body fat) for long-term storage. In humans, glycogen is made and stored primarily in the cells of the liver and skeletal muscle.

The liver is an organ only found in vertebrates which detoxifies various metabolites, synthesizes proteins and produces biochemicals necessary for digestion and growth.

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The human liver is located in the upper right abdomen [midsection of the body]

In yeast [singled cell eukaryotes, type of fungus], the waste products are ethanol and carbon dioxide. This type of fermentation is known as alcoholic or ethanol fermentation. The ATP generated in this process is made by substrate-level phosphorylation, which does not require oxygen.

MES Note: Ethanol is a simple alcohol with the chemical formula C2H6O.

In chemistry, alcohol is an organic compound that carries at least one hydroxyl functional group (−OH) bound to a saturated carbon atom.[2] The term alcohol originally referred to the primary alcohol ethanol (ethyl alcohol), which is used as a drug and is the main alcohol present in alcoholic drinks.

Substrate-level phosphorylation is a metabolism reaction that results in the production of ATP or GTP by the transfer of a phosphate [or phosphoryl] group from a substrate [chemical substance being observed] directly to ADP or GDP.

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Substrate-level phosphorylation exemplified with the conversion of ADP to ATP

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Figure: [Oxidative phosphorylation (top) vs substrate-level phosphorylation (bottom)]

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Figure

Guanosine-5'-triphosphate (GTP) is a purine nucleoside triphosphate. It is one of the building blocks needed for the synthesis of RNA during the transcription [copying a DNA segment into RNA] process. It also has the role of a source of energy or an activator of substrates in metabolic reactions, like that of ATP, but more specific. It is used as a source of energy for protein synthesis and gluconeogenesis.

Guanosine diphosphate, abbreviated GDP, is a [purine] nucleoside diphosphate.

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GTP vs GDP

Gluconeogenesis (GNG) is a metabolic pathway that results in the generation of glucose from certain non-carbohydrate carbon substrates. It is a ubiquitous process, present in plants, animals, fungi, bacteria, and other microorganisms. In vertebrates, gluconeogenesis occurs mainly in the liver and, to a lesser extent, in the kidneys.

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Simplified gluconeogenesis pathway (as occurs in humans). Acetyl-CoA derived from fatty acids (dotted lines) may be converted to pyruvate to a minor extent under conditions of fasting.

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Ethanol fermentation: (1) A glucose molecule is broken down via glycolysis, yielding two pyruvate molecules. The energy released by these exothermic reactions is used to phosphorylate two ADP molecules, yielding two ATP molecules, and to reduce two molecules of NAD+ to NADH. (2) The two pyruvate molecules are broken down, yielding two acetaldehyde [or ethanal, CH3CHO] molecules and giving off two molecules of carbon dioxide. (3) The two molecules of NADH reduce the two acetaldehyde molecules to two molecules of ethanol; this converts NAD+ back into NADH.

Anaerobic respiration is respiration using electron acceptors other than molecular oxygen (O2). Although oxygen is not the final electron acceptor, the process still uses a respiratory electron transport chain.[1]

Anaerobic cellular respiration and fermentation generate ATP in very different ways, and the terms should not be treated as synonyms. Cellular respiration (both aerobic and anaerobic) uses highly reduced chemical compounds such as NADH and FADH2 (for example produced during glycolysis and the citric acid cycle) to establish an electrochemical gradient (often a proton gradient) across a membrane. This results in an electrical potential or ion concentration difference across the membrane. The reduced chemical compounds are oxidized by a series of respiratory integral membrane proteins with sequentially increasing reduction potentials, with the final electron acceptor being oxygen (in aerobic respiration) or another chemical substance (in anaerobic respiration). A proton motive force drives protons down the gradient (across the membrane) through the proton channel of ATP synthase. The resulting current drives ATP synthesis from ADP and inorganic phosphate.

Fermentation, in contrast, does not use an electrochemical gradient. Fermentation instead only uses substrate-level phosphorylation to produce ATP. The electron acceptor NAD+ is regenerated from NADH formed in oxidative steps of the fermentation pathway by the reduction of oxidized compounds. These oxidized compounds are often formed during the fermentation pathway itself, but may also be external.

Photosynthesis

Further information: Photosynthesis

Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that can later be released to fuel the organism's metabolic activities via cellular respiration. This chemical energy is stored in carbohydrate molecules, such as sugars, which are synthesized from carbon dioxide and water.[51][52][53] In most cases, oxygen is also released as a waste product. Most plants, algae [large group of photosynthetic eukaryotic organisms], and cyanobacteria perform photosynthesis, which is largely responsible for producing and maintaining the oxygen content of the Earth's atmosphere, and supplies most of the energy necessary for life on Earth.[54]

MES Note: An atmosphere (from the greek words ἀτμός (atmos), meaning 'vapour', and σφαῖρα (sphaira), meaning 'ball' or 'sphere'[1][2]) is a layer or a set of layers of gases surrounding a planet or other material body, that is held in place by the gravity of that body.

Atmosphere → Atom Sphere

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Visualisation of composition by volume of Earth's atmosphere. Water vapour is not included as it is highly variable. Each tiny cube (such as the one representing krypton) has one millionth of the volume of the entire block.

Photosynthesis has four stages: Light absorption, electron transport, ATP synthesis, and carbon fixation.[50] Light absorption is the initial step of photosynthesis whereby light energy is absorbed by chlorophyll pigments attached to proteins in the thylakoid membranes.

MES Note: Thylakoids are membrane-bound compartments inside chloroplasts and cyanobacteria [type of bacteria that obtain energy via photosynthesis]. They are the site of the light-dependent reactions of photosynthesis. Thylakoids consist of a thylakoid membrane surrounding a thylakoid lumen. Chloroplast thylakoids frequently form stacks of disks referred to as grana (singular: granum). Grana are connected by intergranal/stromal thylakoids, which join granum stacks together as a single functional compartment.

The thylakoid membrane is the site of the light-dependent reactions of photosynthesis with the photosynthetic pigments embedded directly in the membrane. It is an alternating pattern of dark and light bands measuring each 1 nanometre.[3]

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Thylakoids (dark green) inside a chloroplast

Stroma is the part of a tissue or organ with a structural or connective role.

Stroma, in botany [study of plants], refers to the colorless fluid surrounding the grana within the chloroplast.

Granum are stacks of thylakoids.

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Thylakoid structures

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Scanning transmission electron microscope (STEM) imaging of thylakoid membranes 10-nm-thick STEM tomographic slice from a lettuce chloroplast. Grana stacks are interconnected by unstacked stromal thylakoids, called “stroma lamellae”. Scalebar = 200 nm.

Absorption of electromagnetic radiation is how matter (typically electrons bound in atoms) takes up a photon's energy — and so transforms electromagnetic energy into internal energy of the absorber (for example, thermal energy).[1] A notable effect is attenuation, or the gradual reduction of the intensity of light waves as they propagate through a medium.

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An overview of electromagnetic radiation absorption. This example discusses the general principle using visible light as a specific example. A white light source — emitting light of multiple wavelengths — is focused on a sample (the pairs of complementary colors [opposite colors, cancel when combined or mixed, highest relative contrast, such as black and white] are indicated by the yellow dotted lines). Upon striking the sample, photons that match the energy gap of the molecules present (green light in this example) are absorbed, exciting the molecules. Other photons are transmitted unaffected and, if the radiation is in the visible region (400–700 nm), the transmitted light appears as the complementary color (here red) [green-red are opposites, when green is absorbed, reddish color is observed]. By recording the attenuation [loss of intensity] of light for various wavelengths, an absorption spectrum can be obtained.

Contrast is the difference in luminance [light intensity] or colour that makes an object (or its representation in an image or display) distinguishable.

The absorbed light energy is used to remove electrons from a donor (water) to a primary electron acceptor, a quinone [oxidized derivative of aromatic compounds] designated as Q. In the second stage, electrons move from the quinone primary electron acceptor through a series of electron carriers until they reach a final electron acceptor, which is usually the oxidized form of NADP+, which is reduced to NADPH, a process that takes place in a protein complex called photosystem I (PSI). The transport of electrons is coupled to the movement of protons (or hydrogen) from the stroma to the thylakoid membrane, which forms a pH gradient across the membrane as hydrogen becomes more concentrated in the lumen than in the stroma. This is analogous to the proton-motive force generated across the inner mitochondrial membrane in aerobic respiration.[50]

MES Note: Nicotinamide adenine dinucleotide phosphate, abbreviated NADP+, is a cofactor used in anabolic reactions [building up of molecules], such as the Calvin cycle and lipid and nucleic acid syntheses, which require NADPH as a reducing agent. It is used by all forms of cellular life.[1]

NADPH is the reduced form of NADP+.

NADP+ differs from NAD+ by the presence of an additional phosphate group.

During the third stage of photosynthesis, the movement of protons down their concentration gradients from the thylakoid lumen to the stroma through the ATP synthase is coupled to the synthesis of ATP by that same ATP synthase.[50]

MES Note: Molecular diffusion, often simply called diffusion, is the thermal motion of all (liquid or gas) particles at temperatures above absolute zero.

Molecules tend to move from high to low concentrations.

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Diffusion from a microscopic and macroscopic point of view.

The NADPH and ATPs generated by the light-dependent reactions in the second and third stages, respectively, provide the energy and electrons to drive the synthesis of glucose by fixing atmospheric carbon dioxide into existing organic carbon compounds, such as ribulose bisphosphate (RuBP) in a sequence of light-independent (or dark) reactions called the Calvin cycle.[55]

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Photosynthesis changes sunlight into chemical energy, splits water to liberate O2, and fixes CO2 into sugar.

MES Note: Carbon fixation or сarbon assimilation is the process by which inorganic carbon (particularly in the form of carbon dioxide) is converted to organic compounds by living organisms. The compounds are then used to store energy and as structure for other biomolecules. Carbon is primarily fixed through photosynthesis, but some organisms use a process called chemosynthesis in the absence of sunlight.

Chemosynthesis is the biological conversion of one or more carbon-containing molecules (usually carbon dioxide or methane) and nutrients into organic matter using the oxidation of inorganic compounds (e.g., hydrogen gas, hydrogen sulfide [H2S]) or ferrous [containing iron] ions as a source of energy, rather than sunlight, as in photosynthesis.

The Calvin cycle, light-independent reactions, bio synthetic phase, dark reactions, or photosynthetic carbon reduction (PCR) cycle[1] of photosynthesis are the chemical reactions that convert carbon dioxide and other compounds into glucose.

Cell signaling

Further information: Cell signaling

Cell communication (or signaling) is the ability of cells to receive, process, and transmit signals with its environment and with itself.[56][57] Signals can be non-chemical such as light, electrical impulses, and heat, or chemical signals (or ligands) that interact with receptors, which can be found embedded in the cell membrane of another cell or located deep inside a cell.[58][57] There are generally four types of chemical signals: autocrine, paracrine, juxtacrine, and hormones.[58]

In autocrine signaling, the ligand [molecules or ions that bind to a central atom forming a complex] affects the same cell that releases it. Tumor [abnormal/excessive tissue growth] cells, for example, can reproduce uncontrollably because they release signals that initiate their own self-division.

In paracrine signaling, the ligand diffuses to nearby cells and affect them. For example, brain cells called neurons release ligands called neurotransmitters that diffuse across a synaptic cleft [small space between neurons] to bind with a receptor on an adjacent cell such as another neuron or muscle cell.

MES Note: A synapse[2] is a structure that permits a neuron (or nerve cell) to pass an electrical or chemical signal to another neuron or to the target effector cell.

Chemical synapses are biological junctions through which neurons' signals can be sent to each other and to non-neuronal cells such as those in muscles or glands. Chemical synapses are not the only type of biological synapse: electrical and immunological synapses also exist. Without a qualifier, however, "synapse" commonly refers to a chemical synapse.

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"The connection linking neuron to neuron is the synapse. Signal flows in one direction, from the presynaptic neuron to the postsynaptic neuron via the synapse which acts as a variable attenuator." [5] In brief, the direction of the signal flow determines the prefix for the involved synapses.[5]

An attenuator is an electronic device that reduces the power [rate of energy transfer] of a signal without appreciably distorting its waveform.

In juxtacrine signaling, there is direct contact between the signaling and responding cells.

Finally, hormones are ligands that travel through the circulatory systems of animals or vascular systems of plants to reach their target cells.

MES Note: The circulatory system, also called the cardiovascular system or the vascular [channels for conveying fluid] system, is an organ system that permits blood to circulate and transport nutrients (such as amino acids and electrolytes), oxygen, carbon dioxide, hormones, and blood cells to and from the cells in the body to provide nourishment and help in fighting diseases, stabilize temperature and pH, and maintain homeostasis.

Homeostasis is the state of steady internal, physical, and chemical conditions maintained by living systems.

An electrolyte is a substance that produces an electrically conducting solution when dissolved in a polar solvent, such as water. The dissolved electrolyte separates into cations and anions, which disperse uniformly through the solvent. Electrically, such a solution is neutral. If an electric potential is applied to such a solution, the cations of the solution are drawn to the electrode [conductor in contact with a nonmetallic part of the circuit] that has an abundance of electrons, while the anions are drawn to the electrode that has a deficit of electrons.

The cardiovascular (from Latin words meaning "heart" and "vessel") system comprises the blood, heart, and blood vessels.[3] It includes the pulmonary circulation, a "loop" through the lungs where blood is oxygenated; and the systemic circulation, a "loop" through the rest of the body to provide oxygenated blood. The cardiovascular systems of humans are closed, meaning that the blood never leaves the network of blood vessels.

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The human circulatory system (simplified). Red indicates oxygenated blood carried in arteries [from the heart]. Blue indicates deoxygenated blood carried in veins [to the heart]. Capillaries, which join the arteries and veins, and the lymphatic vessels are not shown.

The lymphatic system, or lymphoid system, is an organ system in vertebrates that is part of the circulatory system and the immune system. It is made up of a large network of lymph, lymphatic vessels, lymph nodes, lymphatic or lymphoid organs, and lymphoid tissues.[1][2] The vessels carry a clear fluid called lymph (the Latin word lympha refers to the deity of fresh water, "Lympha")[3] towards the heart.
Unlike the cardiovascular system, the lymphatic system is not a closed system. The human circulatory system processes an average of 20 litres of blood per day through capillary filtration, which removes plasma from the blood. Roughly 17 litres of the filtered blood is reabsorbed directly into the blood vessels, while the remaining three litres are left in the interstitial fluid [fluid between the blood vessels and cells]. One of the main functions of the lymphatic system is to provide an accessory return route to the blood for the surplus three litres.

Wikipedia Note: During filming, Wikipedia changed the article to read: The lymphatic system, or lymphoid system, is an organ system in vertebrates that is part of the immune system, and complementary to the circulatory system.

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Human lymphatic system

The spleen is an organ found in all vertebrates. Similar in structure to a large lymph node, it acts primarily as a blood filter. It removes old red blood cells and holds a reserve of blood, which can be valuable in case of hemorrhagic shock [insufficient blood to tissues], and also recycles iron.

Lymph (from Latin, lympha meaning "water"[1]) is the fluid that flows through the lymphatic system, a system composed of lymph vessels (channels) and intervening lymph nodes [small kidney shaped-organs] whose function, like the venous system, is to return fluid from the tissues to the central circulation. At the origin of the fluid-return process, interstitial fluid—the fluid between the cells in all body tissues[2]—enters the lymph capillaries. This lymphatic fluid is then transported via progressively larger lymphatic vessels through lymph nodes, where substances are removed by tissue lymphocytes [type of white blood cell, which are part of the immune system] and circulating lymphocytes are added to the fluid, before emptying ultimately into the right or the left subclavian vein, where it mixes with central venous blood [deoxygenated blood]. Because it is derived from interstitial fluid, with which blood and surrounding cells continually exchange substances, lymph undergoes continual change in composition. It is generally similar to blood plasma, which is the fluid component of blood. Lymph returns proteins and excess interstitial fluid to the bloodstream. Lymph also transports fats from the digestive system to the blood. In vertebrates, complementary to the circulatory system is the lymphatic system. This system carries excess plasma filtered from the capillaries as interstitial fluid between cells, away from the body tissues in an accessory route to return the excess fluid back to the blood circulation as lymph.[5] The passage of lymph takes much longer than that of blood.[6] The lymphatic system is a subsystem that is essential for the functioning of the blood circulatory system; without it the blood would become depleted of fluid. The lymphatic system works together with the immune system.[7] Unlike the closed circulatory system, the lymphatic system is an open system. Some sources describe it as a secondary circulatory system.

The subclavian vein is a paired large vein, one on either side of the body, that is responsible for draining blood from the upper extremities, allowing this blood to return to the heart.

Lymph capillaries or lymphatic capillaries are tiny, thin-walled microvessels located in the spaces between cells (except in the central nervous system and non-vascular tissues) which serve to drain and process extracellular fluid [more specifically, interstitial fluid].

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A simplified illustration of a capillary network

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Diagram showing the formation of lymph from interstitial fluid (labeled here as "Tissue fluid"). Note how the tissue fluid is entering the blind ends of interstitial fluid

An arteriole is a small-diameter blood vessel in the microcirculation that extends and branches out from an artery and leads to capillaries.[1] Arterioles have muscular walls (usually only one to two layers of smooth muscle cells) and are the primary site of vascular resistance. The greatest change in blood pressure and velocity of blood flow occurs at the transition of arterioles to capillaries.

A venule is a very small blood vessel in the microcirculation that allows blood to return from the capillary beds to drain into the larger blood vessels, the veins.

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Illustration of blood vessels including artery, arteriole, capillaries, vein and venule.

Interstitial fluid is the body fluid between blood vessels and cells,[7] containing nutrients from capillaries [small blood vessels connecting arteries and veins] by diffusion and holding waste products discharged out by cells due to metabolism.

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The distribution of the total body water in mammals between the intracellular compartment [within cells] and the extracellular compartment [outside of cells], which is, in turn, subdivided into interstitial fluid and smaller components, such as the blood plasma, the cerebrospinal fluid [surrounds the brain and spinal cord] and lymph [makes up a small % of the interstitial fluid]

In lean healthy adult men, the total body water is about 60% (60–67%) of the total body weight; it is usually slightly lower in women (52-55%).[2][3] The exact percentage of fluid relative to body weight is inversely proportional to the percentage of body fat.

A lymph node, or lymph gland,[1] is a kidney-shaped organ of the lymphatic system, and the adaptive immune system. A large number of lymph nodes are linked throughout the body by the lymphatic vessels. They are major sites of lymphocytes that include B and T cells. Lymph nodes are important for the proper functioning of the immune system, acting as filters for foreign particles including cancer cells, but have no detoxification function.

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Diagram showing major parts of a lymph node.

Once a ligand binds with a receptor, it can influence the behavior of another cell, depending on the type of receptor. For instance, neurotransmitters that bind with an inotropic receptor [ion-channel protein] can alter the excitability [ease of response] of a target cell. Other types of receptors include protein kinase receptors (e.g., receptor for the hormone insulin) and G protein-coupled receptors. Activation of G protein-coupled receptors can initiate second messenger cascades. The process by which a chemical or physical signal is transmitted through a cell as a series of molecular events is called signal transduction.

MES Note: A kinase is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates.

A protein kinase is a kinase which selectively modifies other proteins by covalently adding phosphates to them (phosphorylation) as opposed to kinases which modify lipids, carbohydrates, or other molecules.

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General scheme of kinase function

Insulin (from Latin insula, 'island') is a peptide hormone produced by beta cells of the pancreatic islets; it is considered to be the main anabolic hormone of the body.[7] It regulates the metabolism of carbohydrates, fats and protein by promoting the absorption of glucose from the blood into liver, fat and skeletal muscle cells.[8]

Peptide hormones or protein hormones are hormones whose molecules are peptides or proteins, respectively. The latter have longer amino acid chain lengths than the former.

The pancreatic islets or islets of Langerhans are the regions of the pancreas that contain its endocrine (hormone-producing) cells.

The pancreas is an organ of the digestive system and endocrine system of vertebrates. In humans, it is located in the abdomen behind the stomach and functions as a gland. The pancreas is a mixed or heterocrine gland, i.e. it has both an endocrine and a digestive exocrine function.[2] 99% of the pancreas is exocrine and 1% is endocrine.[3][4][5][6] As an endocrine gland, it functions mostly to regulate blood sugar levels, secreting the hormones insulin, glucagon, somatostatin, and pancreatic polypeptide. As a part of the digestive system, it functions as an exocrine gland secreting pancreatic juice into the duodenum through the pancreatic duct. This juice contains bicarbonate [HCO3-], which neutralizes acid entering the duodenum from the stomach; and digestive enzymes, which break down carbohydrates, proteins, and fats in food entering the duodenum from the stomach.

Pancreatic juice is a liquid secreted by the pancreas,[1] which contains a number of digestive enzymes, including trypsinogen, chymotrypsinogen, elastase, carboxypeptidase, pancreatic lipase, nucleases and amylase.

The pancreatic duct, or duct of Wirsung (also, the major pancreatic duct due to the existence of an accessory pancreatic duct), is a duct joining the pancreas to the common bile duct. This supplies it with pancreatic juice from the exocrine pancreas, which aids in digestion.

The common bile duct, sometimes abbreviated as CBD,[2] is a duct in the gastrointestinal tract of organisms that have a gallbladder.

In vertebrates, the gallbladder, also known as the cholecyst, is a small hollow organ where bile is stored and concentrated before it is released into the small intestine.

Bile (from Latin bilis), or gall, is a dark-green-to-yellowish-brown fluid produced by the liver of most vertebrates that aids the digestion of lipids in the small intestine. In humans, bile is produced continuously by the liver (liver bile) and stored and concentrated in the gallbladder. After eating, this stored bile is discharged into the duodenum.

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Pancreatic islets are groups of cells found within the pancreas that release hormones

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A pancreatic islet from a mouse in a typical position, close to a blood vessel; insulin in red, nuclei in blue.

Visualised using immunofluorescent microscopy. Colours: red = insulin antibody, blue = DAPI = nuclei, green unspecific anti-mouse secondary antibody (stains mostly intercellular matrix) Dimension: real width 326µm Generated in the Solimena lab, Paul Langerhans Institute Dresden.

Immunofluorescence is a technique used for light microscopy with a fluorescence microscope and is used primarily on microbiological samples. This technique uses the specificity of antibodies to their antigen to target fluorescent dyes to specific biomolecule targets within a cell, and therefore allows visualization of the distribution of the target molecule through the sample.

G protein-coupled receptors (GPCRs are cell surface receptors that detect molecules outside the cell and activate cellular responses.

G proteins, also known as guanine nucleotide-binding proteins, are a family of proteins that act as molecular switches inside cells, and are involved in transmitting signals from a variety of stimuli outside a cell to its interior.

Second messengers are intracellular signaling molecules released by the cell in response to exposure to extracellular signaling molecules—the first messengers.

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Signal transduction pathways that lead to a cellular response

Apoptosis is programmed cell death vs necrosis is traumatic cell death.

Cell cycle

Further information: Cell cycle

The cell cycle is a series of events that take place in a cell that cause it to divide into two daughter cells. These events include the duplication of its DNA and some of its organelles, and the subsequent partitioning of its cytoplasm into two daughter cells in a process called cell division.[59]

In eukaryotes (i.e., animal, plant, fungal, and protist cells), there are two distinct types of cell division: mitosis and meiosis.[60] Mitosis is part of the cell cycle, in which replicated chromosomes are separated into two new nuclei. Cell division gives rise to genetically identical cells in which the total number of chromosomes is maintained. In general, mitosis (division of the nucleus) is preceded by the S stage of interphase (during which the DNA is replicated) and is often followed by telophase and cytokinesis; which divides the cytoplasm, organelles and cell membrane of one cell into two new cells containing roughly equal shares of these cellular components. The different stages of mitosis all together define the mitotic phase of an animal cell cycle—the division of the mother cell into two genetically identical daughter cells.[61] The cell cycle is a vital process by which a single-celled fertilized egg develops into a mature organism, as well as the process by which hair, skin, blood cells, and some internal organs are renewed. After cell division, each of the daughter cells begin the interphase of a new cycle.

MES Note: A chromosome is a long DNA molecule with part or all of the genetic material of an organism.

A chromatid is one half of a duplicated chromosome, during the Synthesis (S) phase, and occurring between Gap 1 and Gap 2 phases in the Interphase portion of the Cell Cycle.

A sister chromatid refers to the identical copies (chromatids) formed by the DNA replication of a chromosome, with both copies joined together by a common centromere.

The centromere is the specialized DNA sequence of a chromosome that links a pair of sister chromatids (a dyad).

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The paternal (blue) chromosome and the maternal (pink) chromosome are homologous chromosomes. Following chromosomal DNA replication, the blue chromosome is composed of two identical sister chromatids and the pink chromosome is composed of two identical sister chromatids. In mitosis, the sister chromatids separate into the daughter cells, but are now referred to as chromosomes (rather than chromatids) much in the way that one child is not referred to as a single twin.

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Figure: Mitosis in an animal cell (phases ordered counter-clockwise). [Furrow = groove]

Chromatin is a complex of DNA and protein found in eukaryotic cells.[1] The primary function is to package long DNA molecules into more compact, denser structures. This prevents the strands from becoming tangled and also plays important roles in reinforcing the DNA during cell division preventing DNA damage and regulating gene expression and DNA replication.

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Basic units of chromatin structure

Histones are proteins that act as spools around which DNA winds to create structural units called nucleosomes.

A nucleosome is the basic structural unit of DNA packaging in eukaryotes. The structure of a nucleosome consists of a segment of DNA wound around eight histone proteins[1] and resembles thread wrapped around a spool. The nucleosome is the fundamental subunit of chromatin. Each nucleosome is composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones, which are known as a histone octamer. Each histone octamer is composed of two copies each of the histone proteins H2A, H2B, H3, and H4.

Myosins are a superfamily of motor proteins best known for their roles in muscle contraction and in a wide range of other motility processes in eukaryotes.

Motor proteins are a class of molecular motors that can move along the cytoplasm of animal cells.

Motility is the ability of an organism to move independently, using metabolic energy.

Molecular motors are natural (biological) or artificial molecular machines that are the essential agents of movement in living organisms. In general terms, a motor is a device that consumes energy in one form and converts it into motion or mechanical work; for example, many protein-based molecular motors harness the chemical free energy released by the hydrolysis of ATP in order to perform mechanical work.[1] In terms of energetic efficiency, this type of motor can be superior to currently available man-made motors. One important difference between molecular motors and macroscopic motors is that molecular motors operate in the thermal bath, an environment in which the fluctuations due to thermal noise are significant.

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A ribosome is a biological machine that utilizes protein dynamics

Proteins are generally thought to adopt unique structures determined by their amino acid sequences. However, proteins are not strictly static objects, but rather populate ensembles of (sometimes similar) conformations.

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Mitosis divides the chromosomes in a cell nucleus.

The spindle apparatus (or mitotic spindle) refers to the cytoskeletal structure of eukaryotic cells that forms during cell division to separate sister chromatids between daughter cells.

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This diagram depicts the organization of a typical mitotic spindle found in animal cells. Chromosomes are attached to kinetochore microtubules via a multiprotein complex called the kinetochore. The microtubules that aren’t connect to a kinetochore are called astral microtubules.

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Figure: Polar Microtubules: Spindle microtubules that do not attach to the chromosomes are called polar microtubules. They overlap at the spindle midzone and push the spindle poles apart via motor proteins, contributing to cell elongation. [Interdigitation = interlocking]

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Figure

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Micrograph showing condensed chromosomes in blue, kinetochores in pink, and microtubules in green during metaphase of mitosis.

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Human chromosomes during metaphase

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Stages of early mitosis in a vertebrate cell with micrographs of chromatids

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Animation: Label-free live cell imaging of Mesenchymal [connective tissue] Stem Cells [can change / differentiate into another cell type] undergoing mitosis

Most human cells are produced by mitotic cell division. Important exceptions include the gametes – sperm and egg cells – which are produced by meiosis.

In contrast to mitosis, meiosis results in four haploid daughter cells by undergoing one round of DNA replication followed by two divisions.[62] Homologous chromosomes are separated in the first division (meiosis I), and sister chromatids are separated in the second division (meiosis II).

Both of these cell division cycles are used in the process of sexual reproduction at some point in their life cycle. Both are believed to be present in the last eukaryotic common ancestor.

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In meiosis, the chromosomes duplicate and the homologous chromosomes exchange genetic information during meiosis I. The daughter cells divide again in meiosis II to form haploid gametes.

MES Note:

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Figure: Comparison of Meiotic and Mitotic Processes

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Figure: Meiotic versus Mitotic

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Figure [allele = gene variant]

A gene (from genos[1] (Greek) meaning generation[2] or birth[1] or gender) is a basic unit of heredity and a sequence of nucleotides in DNA that encodes the synthesis of a gene product, either RNA or protein.

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A gene is a region of DNA that encodes function. A chromosome consists of a long strand of DNA containing many genes. A human chromosome can have up to 500 million base pairs of DNA with thousands of genes.

The term allele (modern formation from Greek ἄλλος állos, "other")[1] [2] [3] denotes the variant of a given gene. In genetics it is normal for genes to show deviations or diversity − all alleles together make up the set of genetic information that defines a gene.

Synapsis is the pairing of two chromosomes that occurs during meiosis. It allows matching-up of homologous pairs prior to their segregation, and possible chromosomal crossover between them.

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Synapsis during Meiosis. The circled area is the part where synapsis occurs, where the two chromatids meet before crossing over

Chromosomal crossover, or crossing over, is the exchange of genetic material during sexual reproduction between two homologous chromosomes' non-sister chromatids that results in recombinant chromosomes.

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Crossing over occurs between prophase I and metaphase I and is the process where two homologous non-sister chromatids pair up with each other and exchange different segments of genetic material to form two recombinant chromosome sister chromatids. It can also happen during mitotic division,[1] which may result in loss of heterozygosity . Crossing over is important for the normal segregation of chromosomes during meiosis.[2] Crossing over also accounts for genetic variation, because due to the swapping of genetic material during crossing over, the chromatids held together by the centromere are no longer identical. So, when the chromosomes go on to meiosis II and separate, some of the daughter cells receive daughter chromosomes with recombined alleles. Due to this genetic recombination, the offspring have a different set of alleles and genes than their parents do. In the diagram, genes B and b are crossed over with each other, making the resulting recombinants after meiosis Ab, AB, ab, and aB.

Loss of heterozygosity (LOH) is a cross chromosomal event that results in loss of the entire gene and the surrounding chromosomal region. [Loss of genetic diversity]

A diploid organism is heterozygous at a gene locus when its cells contain two different alleles (one wild-type [typical form] allele and one mutant [non-standard] allele) of a gene.

A bivalent is one pair of chromosomes (sister chromatids) in a tetrad. A tetrad is the association of a pair of homologous chromosomes (4 sister chromatids) physically held together by at least one DNA crossover. This physical attachment allows for alignment and segregation of the homologous chromosomes in the first meiotic division.

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A bivalent

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Figure: A tetrad

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Figure: Source: Tortora, GJ (2008). Principles of Anatomy and Physiology. 12th ED.

Cytokinesis is the part of the cell division process during which the cytoplasm of a single eukaryotic cell divides into two daughter cells.

Prokaryotes (i.e., archaea [simpler and evolutionarily older than bacteria] and bacteria) can also undergo cell division (or binary fission [division into two parts]). Unlike the processes of mitosis and meiosis in eukaryotes, binary fission takes [sic] in prokaryotes takes place without the formation of a spindle apparatus on the cell. Before binary fission, DNA in the bacterium is tightly coiled. After it has uncoiled and duplicated, it is pulled to the separate poles of the bacterium as it increases the size to prepare for splitting. Growth of a new cell wall begins to separate the bacterium (triggered by FtsZ polymerization and "Z-ring" formation).[63]

MES Note: FtsZ (Filamenting temperature-sensitive mutant Z) is a protein that assembles into a ring at the future site of bacterial cell division (also called the Z ring).

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The Z-ring forms from smaller subunits of FtsZ filaments. These filaments may pull on each other and tighten to divide the cell.

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Super-resolution image of Z-rings (green) at different stages of constriction in two E. coli cells.

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Figure

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Figure: S. aureus cells

The new cell wall (septum) fully develops, resulting in the complete split of the bacterium. The new daughter cells have tightly coiled DNA rods, ribosomes, and plasmids.

MES Note: A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. In nature, plasmids often carry genes that benefit the survival of the organism and confer selective advantage such as antibiotic resistance.

Extrachromosomal DNA (abbreviated ecDNA) is any DNA that is found off the chromosomes, either inside or outside the nucleus of a cell. Most DNA in an individual genome is found in chromosomes contained in the nucleus.

Antimicrobial resistance (AMR) occurs when microbes evolve mechanisms that protect them from the effects of antimicrobials.

An antimicrobial is an agent that kills microorganisms or stops their growth.[1] Antimicrobial medicines can be grouped according to the microorganisms they act primarily against. For example, antibiotics are used against bacteria, and antifungals are used against fungi.

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Illustration of a bacterium [singular] showing chromosomal DNA and plasmids (Not to scale)

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Electron micrograph of a DNA fiber bundle, presumably of a single bacterial chromosome loop

Genetics

Inheritance

Further information: Genetics, Mendelian inheritance, and Classical genetics

Genetics is the scientific study of inheritance.[64][65][66] Mendelian inheritance, specifically, is the process by which genes and traits are passed on from parents to offspring.[31] It was formulated by Gregor Mendel, based on his work with pea plants in the mid-nineteenth century. Mendel established several principles of inheritance. The first is that genetic characteristics, which are now called alleles [gene variants], are discrete and have alternate forms (e.g., purple vs. white or tall vs. dwarf), each inherited from one of two parents. Based on his law of dominance and uniformity, which states that some alleles are dominant while others are recessive; an organism with at least one dominant allele will display the phenotype [observable traits] of that dominant allele.[67] Exceptions to this rule include penetrance and expressivity.[31]

MES Note: An allele (modern formation from Greek ἄλλος állos, "other")[1][2][3] is one of two, or more, forms of a given gene variant.

Dominance is the phenomenon of one variant (allele) of a gene on a chromosome masking or overriding the effect of a different variant of the same gene on the other copy of the chromosome.[1][2] The first variant is termed dominant and the second recessive.

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Autosomal dominant and autosomal recessive inheritance, the two most common Mendelian inheritance patterns. An autosome is any chromosome other than a sex chromosome.

Note that the carrier parents carry the recessive genes but are not affected unless both gene copies are recessive.

Penetrance in genetics is the proportion of individuals carrying a particular variant (or allele) of a gene (the genotype) that also express an associated trait (the phenotype). In medical genetics, the penetrance of a disease-causing mutation is the proportion of individuals with the mutation who exhibit clinical symptoms among all individuals with such mutation. For example, if a mutation in the gene responsible for a particular autosomal dominant disorder has 95% penetrance, then 95% of those with the mutation will develop the disease, while 5% will not.

MES Insight: This raises the question of what the actual causation is…

The genotype of an organism is its complete set of genetic material.[1] However, the term is often used to refer to a single gene or set of genes, such as the genotype for eye color.

Expressivity is the degree to which a phenotype is expressed by individuals having a particular genotype. Expressivity is related to the intensity of a given phenotype; it differs from penetrance, which refers to the proportion of individuals with a particular genotype that actually express the phenotype.

Mendel noted that during gamete formation, the alleles for each gene segregate from each other so that each gamete carries only one allele for each gene, which is stated by his law of segregation. Heterozygotic individuals produce gametes with an equal frequency of two alleles.

MES Note: Zygosity is the degree to which both copies of a chromosome or gene have the same genetic sequence. In other words, it is the degree of similarity of the alleles in an organism.

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Homozygous and heterozygous

Finally, Mendel formulated the law of independent assortment, which states that genes of different traits can segregate independently during the formation of gametes, i.e., genes are unlinked. An exception to this rule would include traits that are sex-linked. Test crosses can be performed to experimentally determine the underlying genotype of an organism with a dominant phenotype.[68]

MES Note: Sex linked describes the sex-specific patterns of inheritance and presentation when a gene mutation (allele) is present on a sex chromosome (allosome) rather than a non-sex chromosome (autosome). In humans, these are termed X-linked recessive, X-linked dominant and Y-linked. The inheritance and presentation of all three differ depending on the sex of both the parent and the child. This makes them characteristically different from autosomal dominance and recessiveness.

A sex chromosome (also referred to as an allosome, heterotypical chromosome, gonosome, or heterochromosome,[1][2] or idiochromosome[3]) is a chromosome that differs from an ordinary autosome in form, size, and behavior. The human sex chromosomes, a typical pair of mammal allosomes, determine the sex of an individual created in sexual reproduction. Autosomes differ from allosomes because autosomes appear in pairs whose members have the same form but differ from other pairs in a diploid cell, whereas members of an allosome pair may differ from one another and thereby determine sex.

An autosome is any chromosome that is not a sex chromosome.[1] The members of an autosome pair in a diploid cell have the same morphology, unlike those in allosome pairs which may have different structures. The DNA in autosomes is collectively known as atDNA or auDNA.[2] For example, humans have a diploid genome that usually contains 22 pairs of autosomes and one allosome pair (46 chromosomes total). The autosome pairs are labeled with numbers (1–22 in humans) roughly in order of their sizes in base pairs, while allosomes are labelled with their letters. By contrast, the allosome pair consists of two X chromosomes in females or one X and one Y chromosome in males. Unusual combinations of XYY, XXY, XXX, XXXX, XXXXX or XXYY, among other combinations, are known to occur and usually cause developmental abnormalities.

The X chromosome is one of the two sex-determining chromosomes (allosomes) in many organisms, including mammals (the other is the Y chromosome), and is found in both males and females. The X chromosome in humans spans more than 153 million base pairs.

The Y chromosome is normally the sex-determining chromosome in many species, since it is the presence or absence of Y that determines the male or female sex of offspring produced in sexual reproduction. In mammals, the Y chromosome contains the gene SRY [sex-determining region Y protein], which triggers male development. The DNA in the human Y chromosome is composed of about 59 million base pairs.[5] The Y chromosome is passed only from father to son.

The XY sex-determination system is a sex-determination system used to classify many mammals, including humans, some insects (Drosophila), some snakes, some fish (guppies), and some plants (Ginkgo tree). In this system, the sex of an individual is determined by a pair of sex chromosomes. Females have two of the same kind of sex chromosome (XX), and are called the homogametic sex. Males have two different kinds of sex chromosomes (XY), and are called the heterogametic sex.

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Drosophila [fruit flies] sex-chromosomes

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Dioecy (Greek: διοικία "two households"; adjective [modifies a noun] form: dioecious) is a characteristic of a species, meaning that it has distinct individual organisms that produce male or female gametes, either directly (in animals) or indirectly (in seed plants) [male plants produces pollen which contains gametes]. Dioecious reproduction is biparental reproduction. Dioecy has costs, since only about half the population directly produces offspring.

Humans are diploid organisms, normally carrying two complete sets of chromosomes in their somatic cells: two copies of paternal and maternal chromosomes, respectively, in each of the 23 homologous pairs of chromosomes that humans normally have. This results in two homologous pairs within each of the 23 homologous pairs, providing a full complement of 46 chromosomes.

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Graphical representation of the idealized human diploid karyotype [ordering of chromosome pairs], showing the organization of the genome into chromosomes. This drawing shows both the female (XX) and male (XY) versions of the 23rd chromosome pair. Chromosomes are shown aligned at their centromeres. The mitochondrial DNA is not shown.

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Figure: The figure shows karyogram [ordering from a micrograph] for human male. where you can see set of 23 pairs of homologous chromosomes.

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Karyogram of human male using Giemsa staining [nucleic acid stain]

X-linked recessive inheritance is a mode of inheritance in which a mutation in a gene on the X chromosome causes the phenotype to be always expressed in males (who are necessarily homozygous [or hemizygous] for the gene mutation because they have one X and one Y chromosome) and in females who are homozygous for the gene mutation, see zygosity. Females with one copy of the mutated gene are carriers.

A chromosome in a diploid organism is hemizygous when only one copy is present. For organisms in which the male is heterogametic, such as humans, almost all X-linked genes are hemizygous in males with normal chromosomes, because they have only one X chromosome and few of the same genes are on the Y chromosome.

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X-linked recessive inheritance

X-linked dominant inheritance, sometimes referred to as X-linked dominance, is a mode of genetic inheritance by which a dominant gene is carried on the X chromosome.

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X-linked dominant inheritance

Y linkage, also known as holandric inheritance (from Ancient Greek ὅλος hólos, "whole" + ἀνδρός andrós, "male"),[1] describes traits that are produced by genes located on the Y chromosome. It occurs only in males.

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Y-linked inheritance

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Pedigree [ancestry] tree showing the inheritance of a Y-linked trait

A Punnett square can be used to predict the results of a test cross. The chromosome theory of inheritance, which states that genes are found on chromosomes, was supported by Thomas Morgans's experiments with fruit flies, which established the sex linkage between eye color and sex in these insects.[69] In humans and other mammals (e.g., dogs), it is not feasible or practical to conduct test cross experiments. Instead, pedigrees, which are genetic representations of family trees,[70] are used instead to trace the inheritance of a specific trait or disease through multiple generations.[71]

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Punnett square depicting a cross between two pea plants heterozygous for purple (B) and white (b) blossoms.

MES Note: In a test cross, the individual in question is bred with another individual that is homozygous for the recessive trait and the offspring of the test cross are examined.

The Punnett square is a square diagram that is used to predict the genotypes of a particular cross or breeding experiment. It is named after Reginald C. Punnett, who devised the approach in 1905.

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Punnett squares [square diagram for predicting genotypes] showing typical test crosses and the two potential outcomes. The individual in question may either be heterozygous, in which half the offspring would be heterozygous and half would be homozygous recessive, or homozygous dominant, in which all the offspring would be heterozygous.

DNA

Further information: DNA

Deoxyribonucleic acid (DNA) is a molecule composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic hereditary information. The two DNA strands are known as polynucleotides as they are composed of monomers called nucleotides.[72][73] Each nucleotide is composed of one of four nitrogenous bases (cytosine [C], guanine [G], adenine [A] or thymine [T]), a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone.

MES Note: The backbone chain of a polymer is the longest series of covalently bonded atoms that together create the continuous chain of the molecule.

It is the sequence of these four bases along the backbone that encodes genetic information. Bases of the two polynucleotide strands are bound together by hydrogen bonds, according to base pairing rules (A with T and C with G), to make double-stranded DNA.

The bases are divided into two groups: pyrimidines and purines. In DNA, the pyrimidines are thymine and cytosine whereas the purines are adenine and guanine. The two strands of DNA run in opposite directions to each other and are thus antiparallel. DNA is replicated once the two strands separate.

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Bases lie between two spiraling DNA strands.

A gene is a unit of heredity that corresponds to a region of DNA that influences the form or function of an organism in specific ways. DNA is found as linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. A chromosome is an organized structure consisting of DNA and histones. The set of chromosomes in a cell and any other hereditary information found in the mitochondria, chloroplasts, or other locations is collectively known as a cell's genome. In eukaryotes, genomic DNA is localized in the cell nucleus, or with small amounts in mitochondria and chloroplasts.[74] In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the nucleoid.[75]

MES Note:

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Diagram of a typical prokaryotic cell

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Figure: Electron Micrograph of Escherichia coli

A flagellum (pl. flagella) is a hairlike appendage that protrudes from a wide range of microorganisms termed as flagellates.

The genetic information in a genome is held within genes, and the complete assemblage of this information in an organism is called its genotype.[76] Genes encode the information needed by cells for the synthesis of proteins, which in turn play a central role in influencing the final phenotype of the organism.

Gene expression

Further information: Gene expression

Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. The process is summarized in the central dogma of molecular biology first formulated by Francis Crick in 1958.[77][78][79]

MES Note: A gene product is the biochemical material, either RNA or protein, resulting from expression of a gene. A measurement of the amount of gene product is sometimes used to infer how active a gene is. Abnormal amounts of gene product can be correlated with disease-causing alleles, such as the overactivity of oncogenes which can cause cancer.

A non-coding RNA (ncRNA) is an RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene.

The central dogma of molecular biology is an explanation of the flow of genetic information within a biological system. It is often stated as "DNA makes RNA, and RNA makes protein",[1] although this is not its original meaning. It was first stated by Francis Crick in 1957,[2][3] then published in 1958:[4][5]

The Central Dogma. This states that once "information" has passed into protein it cannot get out again. In more detail, the transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein may be possible, but transfer from protein to protein, or from protein to nucleic acid is impossible. Information means here the precise determination of sequence, either of bases in the nucleic acid or of amino acid residues in the protein.

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Information flow in biological systems

Gene expression is the most fundamental level at which a genotype gives rise to a phenotype, i.e., observable trait. The genetic information stored in DNA represents the genotype, whereas the phenotype results from the synthesis of proteins that control an organism's structure and development, or that act as enzymes catalyzing specific metabolic pathways. A large part of DNA (e.g., >98% in humans) is non-coding meaning that these sections do not serve as patterns for protein sequences.

MES Note: The amount of non-coding DNA varies greatly among species. Often, only a small percentage of the genome is responsible for coding proteins, but an increasing percentage is being shown to have regulatory functions. When there is much non-coding DNA, a large proportion appears to have no biological function, as predicted in the 1960s. Since that time, this non-functional portion has controversially been called "junk DNA". [Functional DNA estimates range widely from some being between 8 to 15% and others as greater than 80%.]

It was originally suggested that over 98% of the human genome does not encode protein sequences, while 20% of a typical prokaryote genome is non-coding.[3] In 2013, a new "record" for the most efficient eukaryotic genome was discovered with Utricularia gibba, a bladderwort plant that has only 3% non-coding DNA and 97% of coding DNA.

In eukaryotes, genome size, and by extension the amount of non-coding DNA, is not correlated to organism complexity, an observation known as the C-value enigma.[17] For example, the genome of the unicellular Polychaos dubium (formerly known as Amoeba dubia) has been reported to contain more than 200 times the amount of DNA in humans.[18] The pufferfish Takifugu rubripes genome is only about one eighth the size of the human genome, yet seems to have a comparable number of genes; approximately 90% of the Takifugu genome is non-coding DNA.[16] Therefore, most of the difference in genome size is not due to variation in amount of coding DNA, rather, it is due to a difference in the amount of non-coding DNA.[19]

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Utricularia gibba has only 3% non-coding DNA.[15]

Messenger RNA (mRNA) strands are created using DNA strands as a template in a process called transcription, where DNA bases are exchanged for their corresponding bases except in the case of thymine (T), for which RNA substitutes uracil (U).[80] Under the genetic code, these mRNA strands specify the sequence of amino acids within proteins in a process called translation, which occurs in ribosomes. This process is used by all life—eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea), and utilized by viruses—to generate the macromolecular machinery for life. Gene products are often proteins, but in non-protein-coding genes such as transfer RNA (tRNA) and small nuclear RNA (snRNA), the product is a functional non-coding RNA.[81][82]

MES Note: A transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA[1]) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes),[2] that serves as the physical link between the mRNA and the amino acid sequence of proteins.

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The interaction of tRNA and mRNA in protein synthesis.

Small nuclear RNA (snRNA) is a class of small RNA molecules that are found within the cell nucleus in eukaryotic cells.

Small RNA are polymeric RNA molecules that are less than 200 nucleotides in length, and are usually non-coding.

PNAS: Historically, it has been understood that for gene expression in eukaryotes, each messenger RNA encodes a single protein. With the recent development of technologies to sequence full-length transcripts en masse, we have discovered hundreds of examples in two species of green algae where two, three, or more proteins are translated from a single transcript. These “polycistronic” transcripts are found in diverse species throughout the green algal lineage, which highlights their biological importance. We have leveraged these findings to coexpress [express together] pairs of genes on polycistronic transcripts in vitro [in the lab], which should facilitate efforts to engineer algae for research and industrial applications. The term “polycistronic” describes the situation in which two (bicistronic/dicistronic), three (tricistronic), or more separate proteins are encoded on a single molecule of messenger RNA (mRNA). In prokaryotes, polycistronic expression is common.

A cistron is an alternative term for "gene".

NIH: Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship

Conclusions: “We need to unlearn our misconception of the gene, accepting its polycistronic nature, to strive for a better understanding of the genomic complexity underlying physiological and pathological mechanisms.”

All steps in the gene expression process can be regulated, including the transcription [DNA to RNA], RNA splicing, translation [RNA to proteins], and post-translational modification of a protein.

MES Note: RNA splicing, in molecular biology, is a form of RNA processing in which a newly made precursor messenger RNA (pre-mRNA) transcript is transformed into a mature messenger RNA (mRNA). It works by removing introns (non-coding regions of RNA) and so joining together exons (coding regions).

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Introns are removed and exons joined together in the process of RNA splicing.

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Simple illustration of exons and introns in pre-mRNA [the py-py-py indicates a region of high pyrimidines, C and U]

The polypyrimidine tract is a region of pre-messenger RNA (mRNA) that promotes the assembly of the spliceosome, the protein complex specialized for carrying out RNA splicing during the process of post-transcriptional modification. The region is rich with pyrimidine nucleotides, especially uracil, and is usually 15–20 base pairs long, located about 5–40 base pairs before the 3' end of the intron to be spliced.

snRNPs (pronounced "snurps"), or small nuclear ribonucleoproteins, are RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs.

Note that a “lariat” or lasso is a loop of rope used to catch horses.

A precursor mRNA (pre-mRNA) is a type of primary transcript that becomes a messenger RNA (mRNA) after processing [or post-transcriptional modification]. Pre-mRNA is synthesized from a DNA template in the cell nucleus by transcription. Pre-mRNA comprises the bulk of heterogeneous nuclear RNA (hnRNA). Once pre-mRNA has been completely processed, it is termed "mature messenger RNA", or simply "messenger RNA". The term hnRNA is often used as a synonym for pre-mRNA, although, in the strict sense, hnRNA may include nuclear RNA transcripts that do not end up as cytoplasmic mRNA.

Post-transcriptional modification or co-transcriptional modification is a set of biological processes common to most eukaryotic cells by which an RNA primary transcript is chemically altered following transcription from a gene to produce a mature, functional RNA molecule that can then leave the nucleus and perform any of a variety of different functions in the cell.

A primary transcript is the single-stranded ribonucleic acid (RNA) product synthesized by transcription of DNA, and processed to yield various mature RNA products such as mRNAs, tRNAs, and rRNAs.

Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes.

Ribozymes (ribonucleic acid enzymes) are RNA molecules that have the ability to catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes.

Mature messenger RNA, often abbreviated as mature mRNA is a eukaryotic RNA transcript that has been spliced and processed and is ready for translation in the course of protein synthesis. Unlike the eukaryotic RNA immediately after transcription known as precursor messenger RNA, mature mRNA consists exclusively of exons [coding regions] and has all introns [non-coding regions] removed.

Post-translational modification (PTM) refers to the covalent and generally enzymatic modification of proteins following protein biosynthesis.

Protein biosynthesis (or protein synthesis) is a core biological process, occurring inside cells, balancing the loss of cellular proteins (via degradation or export) through the production of new proteins.

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Protein biosynthesis starting with transcription and post-transcriptional modifications in the nucleus. Then the mature mRNA is exported to the cytoplasm where it is translated. The polypeptide chain then folds and is post-translationally modified.

Regulation of gene expression gives control over the timing, location, and amount of a given gene product (protein or ncRNA) present in a cell and can have a profound effect on cellular structure and function.

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The extended central dogma of molecular biology includes all the processes involved in the flow of genetic information.

MES Note: A DNA polymerase is a member of a family of enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates, the molecular precursors of DNA.

RNA polymerase (abbreviated RNAP or RNApol, and officially DNA-directed (dependent) RNA polymerase), is an enzyme that synthesizes RNA from a DNA template.

RNA-dependent RNA polymerase (RdRp) or RNA replicase is an enzyme that catalyzes the replication of RNA from an RNA template.

A reverse transcriptase (RT) is an enzyme used to generate complementary DNA (cDNA) from an RNA template, a process termed reverse transcription.

The sense of a nucleic acid molecule, particularly of a strand of DNA or RNA, refers to the nature of the roles of the strand and its complement in specifying a sequence of amino acids. Depending on the context, sense may have slightly different meanings. For example, DNA is positive-sense if an RNA version of the same sequence is translated or translatable into protein, negative-sense if not.

Because of the complementary nature of base-pairing between nucleic acid polymers, a double-stranded DNA molecule will be composed of two strands with sequences that are reverse complements of each other. To help molecular biologists specifically identify each strand individually, the two strands are usually differentiated as the "sense" strand and the "antisense" strand. An individual strand of DNA is referred to as positive-sense (also positive (+) or simply sense) if its nucleotide sequence corresponds directly to the sequence of an RNA transcript which is translated or translatable into a sequence of amino acids (provided that any thymine bases in the DNA sequence are replaced with uracil bases in the RNA sequence). The other strand of the double-stranded DNA molecule is referred to as negative-sense (also negative (−) or antisense), and is reverse complementary to both the positive-sense strand and the RNA transcript. It is actually the antisense strand that is used as the template from which RNA polymerases construct the RNA transcript, but the complementary base-pairing by which nucleic acid polymerization occurs means that the sequence of the RNA transcript will look identical to the sense strand, apart from the RNA transcript's use of uracil instead of thymine.

Sometimes the phrases coding strand and template strand are encountered in place of sense and antisense, respectively, and in the context of a double-stranded DNA molecule the usage of these terms is essentially equivalent. However, the coding/sense strand need not always contain a code that is used to make a protein; both protein-coding and non-coding RNAs may be transcribed. [Note the confusion: some definitions have coding/sense as translatable into protein and others as simple transcribable to RNA.]

Source: The term template strand refers to the sequence of DNA that is copied during the synthesis of mRNA. The opposite strand (that is, the strand with a base sequence directly corresponding to the mRNA sequence) is called the coding strand or the mRNA-like strand because the sequence corresponds to the codons that are translated into protein.

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Position of the template and coding strands during transcription.

An RNA sequence that is complementary to an endogenous mRNA transcript is sometimes called "antisense RNA". In other words, it is a non-coding strand complementary to the coding sequence of RNA.

Endogenous substances and processes are those that originate from within a system such as an organism, tissue, or cell.[1]

Exogenous substances and processes contrast with endogenous ones, such as drugs, which originate from outside of the organism.

Genomes

Further information: Genomes, Genomics, and Proteomics

A genome is an organism's complete set of DNA, including all of its genes.[83] Sequencing and analysis of genomes can be done using high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes.[84][85][86]

MES Note: In general terms, throughput is the rate of production or the rate at which something is processed.

DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine.

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An example of the results of automated chain-termination DNA sequencing.

Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex.

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Early bioinformatics—computational alignment of experimentally determined sequences of a class of related proteins.

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Map of the human X chromosome (from the National Center for Biotechnology Information website) [Exact source: https://www.ncbi.nlm.nih.gov/genome/gdv/]

An ideogram or ideograph is a graphic symbol that represents an idea or concept or specific words / phrases.

Gene mapping describes the methods used to identify the locus of a gene and the distances between genes.[2] Gene mapping can also describe the distances between different sites within a gene.

The essence of all genome mapping is to place a collection of molecular markers onto their respective positions on the genome. Molecular markers come in all forms. Genes can be viewed as one special type of genetic markers in the construction of genome maps, and mapped the same way as any other markers.

There are two distinctive types of "Maps" used in the field of genome mapping: genetic maps and physical maps. While both maps are a collection of genetic markers and gene loci,[3] genetic maps' distances are based on the genetic linkage information, while physical maps use actual physical distances usually measured in number of base pairs.

In genetics, a locus (plural loci) is a specific, fixed position on a chromosome where a particular gene or genetic marker is located.

A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species.

Genetic linkage is the tendency of DNA sequences that are close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction. Two genetic markers that are physically near to each other are unlikely to be separated onto different chromatids during chromosomal crossover, and are therefore said to be more linked than markers that are far apart. In other words, the nearer two genes are on a chromosome, the lower the chance of recombination between them, and the more likely they are to be inherited together. Markers on different chromosomes are perfectly unlinked. Genetic linkage is the most prominent exception to Gregor Mendel's Law of Independent Assortment.

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Chicks atop a picture of a genetic map of a chicken. The chicken genome has 39 pairs of chromosomes, whereas the human genome contains 23 pairs

A molecular marker is a molecule contained within a sample taken from an organism (biological markers) or other matter. It can be used to reveal certain characteristics about the respective source. DNA, for example, is a molecular marker containing information about genetic disorders and the evolutionary history of life.

Many genes encode more than one protein, with posttranslational modifications increasing the diversity of proteins within a cell. A cell's proteome is its entire set of proteins expressed by its genome.[87]

MES Note:

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General schema [framework] showing the relationships of the genome, transcriptome, proteome, and metabolome (lipidome) in the total interactome of a cell.

The interactome is the whole set of molecular interactions in a particular cell.

The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells.

A metabolite is an intermediate or end product of metabolism. The term metabolite is usually used for small molecules.

The metabolome refers to the complete set of small-molecule chemicals found within a biological sample.

The lipidome refers to the totality of lipids.

The genomes of prokaryotes are small, compact, and diverse. In contrast, the genomes of eukaryotes are larger and more complex such as having more regulatory sequences and much of its genome are made up of non-coding DNA sequences for functional RNA (rRNA, tRNA, and mRNA) or regulatory sequences.

MES Note: A regulatory sequence is a segment of a nucleic acid molecule which is capable of increasing or decreasing the expression of specific genes within an organism.

A non-coding RNA (ncRNA) is an RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-coding RNAs include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs) [primary component of ribosomes], as well as small RNAs such as microRNAs [miRNA], siRNAs [small interfering RNA], piRNAs [Piwi-interacting RNA], snoRNAs [small nucleolar RNA], snRNAs [small nuclear], exRNAs [extracellular RNA], scaRNAs [small Cajal body-specific RNA] and the long ncRNAs such as Xist and HOTAIR.

The number of non-coding RNAs within the human genome is unknown; however, recent transcriptomic and bioinformatic studies suggest that there are thousands of them.[1][2][3][4][5][6] Many of the newly identified ncRNAs have not been validated for their function.[7] It is also likely that many ncRNAs are non functional (sometimes referred to as junk RNA), and are the product of spurious [dubious/unnecessary] transcription.[8][9] Non-coding RNAs are thought to contribute to diseases including cancer and Alzheimer's.

Alzheimer's disease (AD) is a neurodegenerative disease that usually starts slowly and progressively worsens.[2] It is the cause of 60–70% of cases of dementia.[2] The most common early symptom is difficulty in remembering recent events.

Neurodegeneration is the progressive loss of structure or function of neurons, which may ultimately involve cell death.

Dementia manifests as a set of related symptoms, which usually surface when the brain is damaged by injury or disease.[4] The symptoms involve progressive impairments to memory, thinking, and behavior, which negatively impact a person's ability to function and carry out everyday activities. Aside from memory impairment and a disruption in thought patterns, the most common symptoms include emotional problems, difficulties with language, and decreased motivation.

Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts.

Most of the above listed functional non-coding RNA deal with regulation of expression.

Cajal bodies (CBs) also coiled bodies, are spherical nuclear bodies of 0.3–1.0 µm in diameter found in the nucleus of proliferative cells like embryonic cells and tumor cells, or metabolically active cells like neurons.

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The roles of non-coding RNAs in the central dogma of molecular biology: Ribonucleoproteins are shown in red, non-coding RNAs in blue. Note: in spliceosome snRNA is used [mDNA = messenger DNA, uDNA = ? (see note below), rDNA = ribosomal DNA, tDNA = transfer DNA]

A ribonucleoprotein (RNP) is a complex of ribonucleic acid and RNA-binding protein.

Nascent means coming or having recently come into existence.

Transfer-messenger RNA (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties.

Source: In bacteria, trans-translation is the main rescue system, freeing ribosomes stalled on defective messenger RNAs. This mechanism is driven by small protein B (SmpB) and transfer-messenger RNA (tmRNA), a hybrid RNA known to have both a tRNA-like and an mRNA-like domain.

In molecular biology, Small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs.

uDNA Note: I couldn’t find any relevant definition for uDNA. I am assuming it relates to the different types of snRNPs that join the spliceosome, which are labeled as U1, U2, U4, U5, and U6.

At least five different kinds of snRNPs join the spliceosome to participate in splicing. They can be visualized by gel electrophoresis and are known individually as: U1, U2, U4, U5, and U6. Their snRNA components are known, respectively, as: U1 snRNA, U2 snRNA, U4 snRNA, U5 snRNA, and U6 snRNA.

Gel electrophoresis is a method for separation and analysis of macromolecules (DNA, RNA and proteins) and their fragments, based on their size and charge.

The genomes of various model organisms such as arabidopsis [flowering plant], fruit fly, mice, nematodes [type of worm], and yeast have been sequenced. The sequencing of the entire human genome has yielded practical applications such as DNA fingerprinting, which can be used for paternity testing and forensics.

MES Note: A model organism (often shortened to model) is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workings of other organisms.

DNA profiling (also called DNA fingerprinting) is the process of determining an individual's DNA characteristics. DNA analysis intended to identify a species, rather than an individual, is called DNA barcoding.

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Human reference genome data, by chromosome

Pseudogenes are nonfunctional segments of DNA that resemble functional genes. Most arise as superfluous copies of functional genes, either directly by DNA duplication or indirectly by reverse transcription of an mRNA transcript. Pseudogenes are usually identified when genome sequence analysis finds gene-like sequences that lack regulatory sequences needed for transcription or translation, or whose coding sequences are obviously defective due to frameshifts or premature stop codons.

A frameshift mutation (also called a framing error or a reading frame shift) is a genetic mutation caused by indels (insertions or deletions) of a number of nucleotides in a DNA sequence that is not divisible by three. Due to the triplet nature of gene expression by codons, the insertion or deletion can change the reading frame (the grouping of the codons), resulting in a completely different translation from the original.

A stop codon (or termination codon) is a codon (nucleotide triplet within messenger RNA) that signals the termination of the translation process of the current protein.

In medicine, sequencing of the entire human genome has allowed for the identification of mutations that cause tumors as well as genes that cause a specific genetic disorder.[87]

MES Note: A mutation is an alteration in the nucleotide sequence of the genome of an organism, virus, or extrachromosomal DNA.[1] Mutations result from errors during DNA or viral replication, mitosis, or meiosis or other types of damage to DNA (such as by exposure to ultraviolet radiation), which then may undergo error-prone repair, cause an error during other forms of repair,[3][4] or cause an error during replication (translesion synthesis). Mutations may also result from insertion or deletion of segments of DNA due to mobile genetic elements.

Mobile genetic elements (MGEs) sometimes called selfish genetic elements[1] are a type of genetic material that can move around within a genome, or that can be transferred from one species or replicon to another. MGEs are found in all organisms. In humans, approximately 50% of the genome is thought to be MGEs.

A replicon is a DNA molecule or RNA molecule, or a region of DNA or RNA, that replicates from a single origin of replication.

Wikipedia update after filming: A replicon is the entire region of DNA that is independently replicated from a single origin of replication. A bacterial chromosome contains a single origin, and therefore the whole bacterial chromosome is a replicon. The chromosomes of archaea and eukaryotes can have multiple origins of replication, and so their chromosomes may consist of several replicons.

The origin of replication (also called the replication origin) is a particular sequence in a genome at which replication is initiated.

A genetic disorder is a health problem caused by one or more abnormalities in the genome.

Biotechnology

Further information: Biotechnology and Molecular biology

Biotechnology is the use of cells or living organisms to develop products for humans.[88] It includes tools such as recombinant DNA, which are DNA molecules formed by laboratory methods of genetic recombination such as molecular cloning, which bring together genetic material from multiple sources, creating sequences that would otherwise not be found in a genome. Other tools include the use of genomic libraries, DNA microarrays, expression vectors, synthetic genomics, and CRISPR gene editing.[88][89]

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Construction of recombinant DNA, in which a foreign DNA fragment is inserted into a plasmid vector.

MES Note: Genetic recombination (also known as genetic reshuffling) is the exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent. In eukaryotes, genetic recombination during meiosis can lead to a novel set of genetic information that can be passed on from the parents to the offspring. Most recombination is naturally occurring.

Molecular cloning is a set of experimental methods in molecular biology that are used to assemble recombinant DNA molecules and to direct their replication within host organisms.[1] The use of the word cloning refers to the fact that the method involves the replication of one molecule to produce a population of cells with identical DNA molecules. Molecular cloning generally uses DNA sequences from two different organisms: the species that is the source of the DNA to be cloned, and the species that will serve as the living host for replication of the recombinant DNA. Molecular cloning methods are central to many contemporary areas of modern biology and medicine.

In molecular cloning, a vector is a DNA molecule used as a vehicle to artificially carry foreign genetic material into another cell.

Annealing, in genetics, means for complementary sequences [anti-parallel mirrors of each other] of single-stranded DNA or RNA to pair by hydrogen bonds to form a double-stranded polynucleotide.

A restriction enzyme, restriction endonuclease, or restrictase is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites.

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Diagram of molecular cloning using bacteria and plasmids.

DNA ligase is a specific type of enzyme, a ligase, (EC 6.5.1.1) that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond.

A genomic library is a collection of the total genomic DNA from a single organism.

A DNA microarray (also commonly known as DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome.

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Video: How to use a microarray for genotyping. The video shows the process of extracting genotypes from a human spit sample using microarrays. Genotyping is a major use of DNA microarrays, but with some modifications they can also be used for other purposes such as measurement of gene expression and epigenetic markers.

In biology, epigenetics is the study of heritable phenotype changes that do not involve alterations in the DNA sequence.

Genotyping is the process of determining differences in the genetic make-up (genotype) of an individual by examining the individual's DNA sequence using biological assays and comparing it to another individual's sequence or a reference sequence. Traditionally genotyping is the use of DNA sequences to define biological populations by use of molecular tools. It does not usually involve defining the genes of an individual.

A bioassay is an analytical method to determine the concentration or potency of a substance by its effect on living animals or plants (in vivo), or on living cells or tissues (in vitro).

An expression vector, otherwise known as an expression construct, is usually a plasmid or virus designed for gene expression in cells. The vector is used to introduce a specific gene into a target cell, and can commandeer the cell's mechanism for protein synthesis to produce the protein encoded by the gene. Expression vectors are the basic tools in biotechnology for the production of proteins.

Vectors are also components of the current COVID-19 vaccines using mRNA vectors to get the body to produce the supposed “coronavirus spike protein”.

Synthetic genomics is a nascent field of synthetic biology that uses aspects of genetic modification on pre-existing life forms, or artificial gene synthesis to create new DNA or entire lifeforms. Synthetic genomics is unlike genetic modification in the sense that it does not use naturally occurring genes in its life forms. It may make use of custom designed base pair series, though in a more expanded and presently unrealized sense synthetic genomics could utilize genetic codes that are not composed of the two base pairs of DNA that are currently used by life.

Synthetic biology (SynBio) is a multidisciplinary area of research that seeks to create new biological parts, devices, and systems, or to redesign systems that are already found in nature.

Artificial gene synthesis, or gene synthesis, refers to a group of methods that are used in synthetic biology to construct and assemble genes from nucleotides de novo. Unlike DNA synthesis in living cells, artificial gene synthesis does not require template DNA, allowing virtually any DNA sequence to be synthesized in the laboratory.

De novo synthesis refers to the synthesis of complex molecules from simple molecules such as sugars or amino acids, as opposed to recycling after partial degradation.

De novo is a Latin phrase, literally translating to "from the new", but implying "anew", "from scratch", or "from the beginning."

Genetic engineering, also called genetic modification or genetic manipulation, is the direct manipulation of an organism's genes using biotechnology.

CRISPR (which is an acronym for clustered regularly interspaced short palindromic repeats) is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea.[2] These sequences are derived from DNA fragments of bacteriophages that had previously infected the prokaryote. They are used to detect and destroy DNA from similar bacteriophages during subsequent infections.

A palindrome is a word, number, phrase, or other sequence of characters which reads the same backward as forward, such as madam or racecar.

A bacteriophage, also known informally as a phage, is a virus that infects and replicates within bacteria and archaea.

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Structural model at atomic resolution of bacteriophage T4[1] [Å = angstrom = 10-10 m = 10 billionth of a meter]

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Bacteriophage P22, a member of the Podoviridae by morphology due to its short, non-contractile tail

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In this electron micrograph of bacteriophages attached to a bacterial cell, the viruses are the size and shape of coliphage T1

Cas9 (CRISPR associated protein 9, formerly called Cas5, Csn1, or Csx12) is a protein which plays a vital role in the immunological defense of certain bacteria against DNA viruses and plasmids, and is heavily utilized in genetic engineering applications. Its main function is to cut DNA and thereby alter a cell's genome. It is an enzyme that uses CRISPR sequences as a guide to recognize and cleave [cut so as to separate] specific strands of DNA that are complementary to the CRISPR sequence. Cas9 enzymes together with CRISPR sequences form the basis of a technology known as CRISPR-Cas9 that can be used to edit genes within organisms.

CRISPR gene editing (pronounced "crisper") is a genetic engineering technique by which the genomes of living organisms may be modified. It is based on a simplified version of the bacterial CRISPR-Cas9 antiviral defense system. By delivering the Cas9 nuclease complexed with a synthetic guide RNA (gRNA) into a cell, the cell's genome can be cut at a desired location, allowing existing genes to be removed and/or new ones added in vivo (in living organisms).[1]

A nuclease is an enzyme capable of cleaving the phosphodiester bonds between nucleotides of nucleic acids.

A phosphodiester bond occurs when exactly two of the hydroxyl groups [-OH] in phosphoric acid [H3PO4] react with hydroxyl groups on other molecules to form two ester [-OH is replaced by -O-R] bonds.

Guide RNA (gRNA) is a piece of RNAs that function as guides for RNA- or DNA-targeting enzymes, which they form complexes with.

A protein–ligand complex is a complex of a protein bound with a ligand[2] that is formed following molecular recognition between proteins that interact with each other or with various other molecules.

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CRISPR-Cas9

dsDNA = double stranded DNA.

A protospacer adjacent motif (PAM) is a 2–6-base pair DNA sequence immediately following the DNA sequence targeted by the Cas9 nuclease in the CRISPR bacterial adaptive immune system.[1]

The canonical [typical] PAM is the sequence 5'-NGG-3', where "N" is any nucleobase followed by two guanine ("G") nucleobases.

The 5’ and 3’ refer to the directionality of a strand of nucleic acid.

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A furanose (sugar-ring) molecule with carbon atoms labeled using standard notation. The 5′ is upstream; the 3′ is downstream. DNA and RNA are synthesized in the 5′ to 3′ direction.

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In the DNA segment shown, the 5′ to 3′ directions are down the left strand and up the right strand

Many of these tools have wide applications such as creating medically useful proteins, or improving plant cultivation [preparing and growing plants] and animal husbandry [animals raised for food and other products]. [88] Human insulin, for example, was the first medicine to be made using recombinant DNA technology [produced either in yeast or E. coli bacteria]. Other approaches such as pharming can produce large quantities of medically useful products through the use of genetically modified organisms.[88]

MES Note: Pharming, a portmanteau [blend of words] of "farming" and "pharmaceutical", refers to the use of genetic engineering to insert genes that code for useful pharmaceuticals into host animals or plants that would otherwise not express those genes, thus creating a genetically modified organism (GMO).[1][2] Pharming is also known as molecular farming, molecular pharming[3] or biopharming.[4]

A medication (also referred to as medicament, medicine, pharmaceutical drug, medicinal drug or simply drug) is a drug used to diagnose, cure, treat, or prevent disease.

A drug is any chemical substance that causes a change in an organism's physiology or psychology when consumed.

Genes, development, and evolution

Further information: Evolutionary developmental biology

Development is the process by which a multicellular organism (plant or animal) goes through a series of changes, starting from a single cell, and taking on various forms that are characteristic of its life cycle.[90] There are four key processes that underlie development: Determination, differentiation, morphogenesis, and growth.

Determination sets the developmental fate of a cell, which becomes more restrictive during development.

Differentiation is the process by which specialized cells [are formed] from less specialized cells such as stem cells.[91][92] Stem cells are undifferentiated or partially differentiated cells that can differentiate into various types of cells and proliferate indefinitely to produce more of the same stem cell.[93] Cellular differentiation dramatically changes a cell's size, shape, membrane potential [difference in electrical potential / charge concentration between the interior and exterior of a cell], metabolic activity, and responsiveness to signals, which are largely due to highly controlled modifications in gene expression and epigenetics. With a few exceptions, cellular differentiation almost never involves a change in the DNA sequence itself.[94] Thus, different cells can have very different physical characteristics despite having the same genome.

MES Note: In biology, epigenetics is the study of heritable phenotype changes that do not involve alterations in the DNA sequence.

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Epigenetic mechanisms

A methyl group is derived by from methane (CH4) by removing 1 hydrogen, thus containing the chemical formula -CH3.

Chromatin is a complex of DNA and protein found in eukaryotic cells.

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Source: Histone tails protrude from the histones.

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Source: Chromatin modification. Enzymes can add negative acetyl groups (-COCH3) to histone tails. Histone acetylation loosens chromatin structure, making the DNA accessible to transcription. Such chromatin modifications may be passed to future generations of cells in a process called epigenetic inheritance.

An autoimmune disease is a condition arising from an abnormal immune response to a functioning body part.

Diabetes mellitus (DM), commonly known as just diabetes, is a group of metabolic disorders characterized by a high blood sugar level over a prolonged period of time.

Cancer is a group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body.

Morphogenesis, or development of body form, is the result of spatial differences in gene expression.[90] Specially, the organization of differentiated tissues into specific structures such as arms or wings, which is known as pattern formation, is governed by morphogens, signaling molecules that move from one group of cells to surrounding cells, creating a morphogen gradient as described by the French flag model.

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Model of concentration gradient building up; fine yellow-orange outlines are cell boundaries.[105]

MES Note: In the French flag model, the French flag is used to represent the effect of a morphogen on cell differentiation: a morphogen affects cell states based on concentration, these states are represented by the different colors of the French flag: high concentrations activate a "blue" gene, lower concentrations activate a "white" gene, with "red" serving as the default state in cells below the necessary concentration threshold.

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The flag of France is a three-colored triband

Apoptosis, or programmed cell death, also occurs during morphogenesis, such as the death of cells between digits [fingers and toes] in human embryonic development, which frees up individual fingers and toes. Expression of transcription factor genes can determine organ placement in a plant and a cascade of transcription factors themselves can establish body segmentation in a fruit fly.[90]

MES Note: Syndactyly is a condition wherein two or more digits are fused together.

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Figure: Syndactyly of the human hand (Flatt, 1994)

A transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence.

Cell growth refers to an increase in the total mass of a cell, including both cytoplasmic, nuclear and organelle volume.[1] Cell growth occurs when the overall rate of cellular biosynthesis is greater than the overall rate of cellular degradation. Cell growth is not to be confused with cell division or the cell cycle, which are distinct processes that can occur alongside cell growth during the process of cell proliferation, where a cell, known as the "mother cell", grows and divides to produce two "daughter cells".[1] Importantly, cell growth and cell division can also occur independently of one another.

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Cell division, growth & proliferation [note that mass increases with cell proliferation]

A small fraction of the genes in an organism's genome called the developmental-genetic toolkit control the development of that organism. These toolkit genes are highly conserved among phyla, meaning that they are ancient and very similar in widely separated groups of animals. Differences in deployment of toolkit genes affect the body plan and the number, identity, and pattern of body parts. Among the most important toolkit genes are the Hox genes. Hox genes determine where repeating parts, such as the many vertebrae of snakes, will grow in a developing embryo or larva.[95]

MES Note: A larva (plural larvae) is a distinct juvenile form many animals undergo before metamorphosis into adults.

Metamorphosis is a biological process by which an animal physically develops after birth or hatching, involving a conspicuous [obvious] and relatively abrupt change in the animal's body structure through cell growth and differentiation.

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Figure

Variations in the toolkit may have produced a large part of the morphological evolution of animals. The toolkit can drive evolution in two ways.

A toolkit gene can be expressed in a different pattern, as when the beak of Darwin's large ground-finch [a type of bird] was enlarged by the BMP gene [bone morphogenetic proteins, stimulates cell proliferation],[96] or when snakes lost their legs as Distal-less (Dlx) genes [morphological transcription genes] became under-expressed or not expressed at all in the places where other reptiles continued to form their limbs.[97]

Or, a toolkit gene can acquire a new function, as seen in the many functions of that same gene, distal-less, which controls such diverse structures as the mandible [lower jawbone] in vertebrates,[98][99] legs and antennae in the fruit fly,[100] and eyespot pattern in butterfly wings.[101]

Given that small changes in toolbox genes can cause significant changes in body structures, they have often enabled convergent or parallel evolution.

MES Note: Convergent evolution is the independent evolution of similar features in species of different periods or epochs in time.

Divergent evolution or divergent selection is the accumulation of differences between closely related populations within a species, leading to speciation [become distinct species].

Parallel evolution is the similar development of a trait in distinct species that are not closely related, but share a similar original trait in response to similar evolutionary pressure.

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Evolution at an amino acid position. In each case, the left-hand species changes from incorporating alanine (A) at a specific position within a protein in a hypothetical common ancestor deduced from comparison of sequences of several species, and now incorporates serine (S) in its present-day form. The right-hand species may undergo divergent, parallel, or convergent evolution at this amino acid position relative to that of the first species.

Evolution

Evolutionary processes

Further information: Evolution and Evolutionary biology

A central organizing concept in biology is that life changes and develops through evolution, which is the change in heritable characteristics of populations over successive generations.[102][103] Evolution is now used to explain the great variations of life on Earth. The term evolution was introduced into the scientific lexicon by Jean-Baptiste de Lamarck in 1809,[104] and fifty years later Charles Darwin and Alfred Russel Wallace formulated the theory of evolution by natural selection.[105][106][107][108] According to this theory, individuals differ from each other with respect to their heritable traits, resulting in different rates of survival and reproduction. As a results [sic], traits that are better adapted to their environment are more likely to be passed on to subsequent generations.[109][110]

Darwin was not aware of Mendel's work of inheritance and so the exact mechanism of inheritance that underlie natural selection was not well-understood[111] until the early 20th century when the modern synthesis reconciled Darwinian evolution with classical genetics, which established a neo-Darwinian [any combination of natural selection and genetics] perspective of evolution by natural selection.[112] This perspective holds that evolution occurs when there are changes in the allele frequencies within a population of interbreeding organisms. In the absence of any evolutionary process acting on a large random mating population, the allele frequencies will remain constant across generations as described by the Hardy–Weinberg principle.[113]

MES Note:

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Several major ideas about evolution came together in the population genetics of the early 20th century to form the modern synthesis, including genetic variation, natural selection, and Mendelian [gene] inheritance.

Allele frequency, or gene frequency, is the relative frequency of an allele (variant of a gene) at a particular locus in a population, expressed as a fraction or percentage.[1] Specifically, it is the fraction of all chromosomes in the population that carry that allele.

In population genetics, the Hardy–Weinberg principle, also known as the Hardy–Weinberg equilibrium, model, theorem, or law, states that allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences.

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Natural selection for darker traits.

Another process that drives evolution is genetic drift, which is the random fluctuations of allele frequencies within a population [due to random sampling] from one generation to the next.[114] When selective forces are absent or relatively weak, allele frequencies are equally likely to drift upward or downward at each successive generation because the alleles are subject to sampling error.[115] This drift halts when an allele eventually becomes fixed, either by disappearing from the population or replacing the other alleles entirely. Genetic drift may therefore eliminate some alleles from a population due to chance alone.

MES Note: Sampling errors are incurred when the statistical characteristics of a population are estimated from a subset, or sample, of that population.

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Figure

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Figure

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Figure

A population bottleneck or genetic bottleneck is a sharp reduction in the size of a population due to environmental events such as famines, earthquakes, floods, fires, disease, and droughts; or human activities such as specicide [large scale elimination of a species], widespread violence or intentional culling, and human population planning.

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Population bottleneck followed by recovery or extinction

In biology, culling is the process of segregating organisms from a group according to desired or undesired characteristics. In animal breeding, it is the process of removing or segregating animals from a breeding stock based on specific trait.

Speciation

Further information: Speciation

Speciation is the process of splitting one lineage into two lineages that evolve independently from each other.[116] For speciation to occur, there has to be reproductive isolation.[116]

MES Note: The mechanisms of reproductive isolation are a collection of evolutionary mechanisms, behaviors and physiological processes critical for speciation. They prevent members of different species from producing offspring, or ensure that any offspring are sterile. These barriers maintain the integrity of a species by reducing gene flow between related species.

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Gene flow is the transfer of alleles from one population to another population through immigration of individuals.

Reproductive isolation can result from incompatibilities between genes as described by Bateson–Dobzhansky–Muller model.

MES Note: The Bateson-Dobzhansky-Muller model, also known as Dobzhansky–Muller model, is a model of the evolution of genetic incompatibility, important in understanding the evolution of reproductive isolation during speciation and the role of natural selection in bringing it about. It describes the negative [incompatible] epistatic interactions that occur between genes with a different evolutionary history. These genetic incompatibilities can occur when populations are hybridising.

Epistasis is a phenomenon in genetics in which the effect of a gene mutation is dependent on the presence or absence of mutations in one or more other genes, respectively termed modifier genes. In other words, the effect of the mutation is dependent on the genetic background in which it appears.

Hybrid incompatibility is a phenomenon in plants and animals, wherein most offspring produced by the mating of two different species are not viable or are unable to reproduce. Examples of hybrids include mules [male donkey + female horse] and ligers [male lion + female tiger] from the animal world, and subspecies of the Asian rice crop Oryza sativa from the plant world.

A hybrid is the offspring resulting from combining the qualities of two organisms of different breeds, varieties, species or genera [plural for genus] through sexual reproduction.

Hybrid inviability is a post-zygotic barrier [occurring after fertilization or mating], which reduces a hybrid's capacity to mature into a healthy, fit adult.[1] The relatively low health of these hybrids relative to pure-breed individuals prevents gene flow between species. Thus, hybrid inviability acts as an isolating mechanism, limiting hybridization and allowing for the differentiation of species.

Purebreds are "cultivated varieties" [bred for desired traits] of an animal species achieved through the process of selective breeding. When the lineage of a purebred animal is recorded, that animal is said to be "pedigreed". Purebreds breed true-to-type which means the progeny of like-to-like purebred parents will carry the same phenotype, or observable characteristics of the parents.

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Figure: In the ancestral population the genotype is AABB. When two populations become isolated from each other, new mutations can arise. In one population A evolves into a, and in the other B evolves into b. When the two populations hybridise it is the first time a and b interact with each other. When these alleles are incompatible, we speak of Dobzhansky–Muller incompatibilities.

Reproductive isolation also tends to increase with genetic divergence. Speciation can occur when there are physical barriers that divide an ancestral species, a process known as allopatric speciation.[116] In contrast, sympatric speciation occurs in the absence of physical barriers.

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Comparison of allopatric, peripatric, parapatric and sympatric speciation

MES Note: Peripatric speciation describes when a new species is formed from an isolated peripheral population.[1]:105 Since peripatric speciation resembles allopatric speciation, in that populations are isolated and prevented from exchanging genes, it can often be difficult to distinguish between them.[2] Nevertheless, the primary characteristic of peripatric speciation proposes that one of the populations is much smaller than the other.

In parapatric speciation, two subpopulations of a species evolve reproductive isolation from one another while continuing to exchange genes.

Polymorphism[1] is the occurrence of two or more clearly different morphs or forms, also referred to as alternative phenotypes, in the population of a species.

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Light-morph jaguar

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Dark-morph or melanistic [having melanin, natural pigments] jaguar (about 6% of the South American population)

Pre-zygotic isolation [occurring before fertilization or mating] such as mechanical, temporal, behavioral, habitat, and gametic isolations can prevent different species from hybridizing.[116]

MES Note: Examples of each type of isolation is listed below.

Mechanical isolation: Mating pairs may not be able to couple successfully if their genitals are not compatible.

Temporal isolation: Difference in the time of sexual maturity or flowering.

The different mating rituals of animal species creates extremely powerful reproductive barriers, termed sexual or behavior isolation, that isolate apparently similar species in the majority of the groups of the animal kingdom. In dioecious species, males and females have to search for a partner, be in proximity to each other, carry out the complex mating rituals and finally copulate [male introduces sperm into the female] or release their gametes into the environment in order to breed.

Habitat isolation: Physical barriers, or seasonal travel opposite of other similar species.

Gametic isolations: Gamete incompatibility, or inability to produce hybrid offspring despite the gametes being found in the same time and place.

The term habitat summarises the array of resources, physical and biotic factors that are present in an area, such as to support the survival and reproduction of a particular species.

Similarly, post-zygotic isolations [occurring after fertilization or mating] can result in hybridization being selected against due to the lower viability of hybrids or hybrid infertility (e.g., mule [hybrid of a horse and donkey]). Hybrid zones can emerge if there were to be incomplete reproductive isolation between two closely related species.

MES Note: Mules [male donkey (jack) + female horse (mare)] and hinnies [male horse (stallion) + female donkey (jenny)] have 63 chromosomes, a mixture of the horse's 64 and the donkey's 62. The different structure and number usually prevents the chromosomes from pairing up properly and creating successful embryos, rendering most mules infertile.

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Mule

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Hinny

A hybrid zone exists where the ranges of two interbreeding species or diverged intraspecific lineages meet and cross-fertilize.

Intraspecificity (literally within species), or being intraspecific, describes behaviors, biochemical variations and other issues within individuals of a single species.

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Figure

Phylogenies

Further information: PhylogeneticsPhylogenetics and Biodiversity

A phylogeny is an evolutionary history of a specific group of organisms or their genes.[117] A phylogeny can be represented using a phylogenetic tree, which is a diagram showing lines of descent among organisms or their genes. Each line drawn on the time axis of a tree represents a lineage [continuous series] of descendants of a particular species or population. When a lineage divides into two, it is represented as a node (or split) on the phylogenetic tree. The more splits there are over time, the more branches there will be on the tree, with the common ancestor of all the organisms in that tree being represented by the root of that tree. Phylogenetic trees may portray the evolutionary history of all life forms, a major evolutionary group (e.g., insects), or an even smaller group of closely related species. Within a tree, any group of species designated by a name is a taxon (e.g., humans, primates, mammals, or vertebrates) and a taxon that consists of all its evolutionary descendants is a clade. Closely related species are referred to as sister species and closely related clades are sister clades.

MES Note: A clade (from Ancient Greek: κλάδος, klados, "branch"), also known as a monophyletic group or natural group,[3] is a group of organisms that are monophyletic – that is, composed of a common ancestor and all its lineal descendants [lineage] - on a phylogenetic tree.

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Cladogram (family tree) of a biological group. The last common ancestor is the vertical line stem at the bottom. The blue and red subgroups are clades [monophyletic]; each shows its common ancestor stem at the bottom of the subgroup branch. The green subgroup is not a clade; it is a paraphyletic group, because it excludes the blue branch which has descended from the same common ancestor. The green subgroup together with the blue one forms a clade again.

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Phylogenetic tree showing the domains of bacteria, archaea, and eukaryotes [based on rRNA genes]

Phylogenetic trees are the basis for comparing and grouping different species.[117] Different species that share a feature inherited from a common ancestor are described as having homologous features. Homologous features may be any heritable traits such as DNA sequence, protein structures, anatomical features, and behavior patterns. A vertebral column [backbone] is an example of a homologous feature shared by all vertebrate animals.

MES Note: Homology is similarity due to shared ancestry between a pair of structures or genes in different taxa [plural of taxon].

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The principle of homology: The biological relationships (shown by colours) of the bones in the forelimbs of vertebrates were used by Charles Darwin as an argument in favor of evolution.

Traits that have a similar form or function but were not derived from a common ancestor are described as analogous features.

Phylogenies can be reconstructed for a group of organisms of primary interests, which are called the ingroup. A species or group that is closely related to the ingroup but is phylogenetically outside of it is called the outgroup, which serves a reference point in the tree. The root of the tree is located between the ingroup and the outgroup.[117]

MES Note:

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A simple cladogram showing the evolutionary relationships between four species: A, B, C, and D. Here, Species A is the outgroup, and Species B, C, and D form the ingroup.

A cladogram (from Greek clados "branch" and gramma "character") is a diagram used in cladistics [categorization into clades] to show relations among organisms.

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Two seemingly different, though identical, cladograms, illustrating the idea that neither shape, nor a particular arrangement of the terminal branches really matters.

When phylogenetic trees are reconstructed, multiple trees with different evolutionary histories can be generated. Based on the principle of Parsimony (or Occam's razor), the tree that is favored is the one with the fewest evolutionary changes needed to be assumed over all traits in all groups. Computational algorithms can be used to determine how a tree might have evolved given the evidence.[117]

MES Note: Parsimony means spareness and is also referred to as the Rule of Simplicity.

Occam's razor, Ockham's razor, Ocham's razor, or the principle of parsimony or law of parsimony is the problem-solving principle that "entities should not be multiplied beyond necessity",[1][2] sometimes inaccurately paraphrased as "the simplest explanation is usually the best one."[3] The idea is attributed to English Franciscan friar William of Ockham (c.  1287–1347), a scholastic philosopher and theologian who used a preference for simplicity to defend the idea of divine miracles. This philosophical razor advocates that when presented with competing hypotheses about the same prediction, one should select the solution with the fewest assumptions,[4] and that this is not meant to be a way of choosing between hypotheses that make different predictions.

In philosophy, a razor is a principle or rule of thumb that allows one to eliminate ("shave off") unlikely explanations for a phenomenon, or avoid unnecessary actions.

Phylogeny provides the basis of biological classification, which is based on Linnaean taxonomy that was developed by Carl Linnaeus in the 18th century.[117] This classification system is rank-based, with the highest rank being the domain followed by kingdom, phylum, class, order, family, genus, and species.[117] All living organisms can be classified as belonging to one of three domains: Archaea (originally Archaebacteria); bacteria (originally eubacteria), or eukarya (includes the protist, fungi, plant, and animal kingdoms).[118] A binomial nomenclature is used to classify different species. Based on this system, each species is given two names, one for its genus and another for its species.[117] For example, humans are Homo sapiens, with Homo being the genus and ***sapiens ***being the species. By convention, the scientific names of organisms are italicized, with only the first letter of the genus capitalized.[119][120]

History of life

Further information: History of life

The history of life on Earth traces the processes by which organisms have evolved from the earliest emergence of life to present day. Earth formed about 4.5 billion years ago and all life on Earth, both living and extinct, descended from a last universal common ancestor that lived about 3.5 billion years ago.[121][122]

MES Note: Common descent is a concept in evolutionary biology applicable when one species is the ancestor of two or more species later in time. All living beings are in fact descendants of a unique ancestor commonly referred to as the last universal common ancestor (LUCA) of all life on Earth, according to modern evolutionary biology.

The last universal common ancestor or last universal cellular ancestor (LUCA), also called the last universal ancestor (LUA), is the most recent population of organisms from which all organisms now living on Earth have a common descent—the most recent common ancestor of all current life on Earth.

The most recent common ancestor (MRCA), last common ancestor (LCA), or concestor[note 1] of a set of organisms is the most recent individual from which all the organisms of the set are descended.

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Figure: Schematic diagrams of a three-domain (a) and two-domain (b) tree. “LUCA” refers to the last universal common ancestor while the “MRCA” of all Archaea is the most recent common ancestor of the Archaea. In a each of the three domains is monophyletic. In b, the MRCA of the Archaea is an ancestor of all of the Eukaryotes as well making the Archaean domain paraphyletic. Thus some Archaea are more closely related to the Eukaryotes than they are to some other Archaea

The similarities among all known present-day species indicate that they have diverged through the process of evolution from their common ancestor.[123] Biologists regard the ubiquity [widespread occurrence] of the genetic code as evidence of universal common descent for all bacteria, archaea, and eukaryotes.[124][10][125][126]

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MES Note: The Late Heavy Bombardment (LHB), or lunar cataclysm, is a hypothesized event thought to have occurred approximately 4.1 to 3.8 billion years (Ga) ago,[1]

A glacial period (alternatively glacial or glaciation) is an interval of time (thousands of years) within an ice age that is marked by colder temperatures and glacier advances. Interglacials, on the other hand, are periods of warmer climate between glacial periods.

A glacier is a persistent body of dense ice that is constantly moving under its own weight.

An ice age is a long period of reduction in the temperature of Earth's surface and atmosphere, resulting in the presence or expansion of continental and polar ice sheets [greater than 50,000 km2] and alpine [mountainous] glaciers.

The Oxygen Crisis or Great Oxidation Event (GOE), sometimes also called the Great Oxygenation Event, was a time period when the Earth's atmosphere and the shallow ocean first experienced a rise in oxygen, approximately 2.4–2.0 Ga (billion years ago) during the Paleoproterozoic era, and resulting in many existing species on Earth to die out.

The Ediacaran biota is a taxonomic period classification that consists of all life forms that were present on Earth during the Ediacaran Period (c. 635–541 Mya). These were composed of enigmatic [mysterious] tubular and frond-shaped [a frond is a large, divided leaf], mostly sessile [lacks self-locomotion], organisms.

Tetrapods (from Greek τετρα- tetra- 'four' and πούς poús 'foot') are four-limbed animals.

The Cambrian explosion or Cambrian radiation[1] was an event approximately 541 million years ago when practically all major animal phyla started appearing in the fossil record.

A fossil (from Classical Latin: fossilis, literally 'obtained by digging')[1] is any preserved remains, impression, or trace of any once-living thing from a past geological age.

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Figure: Chronostratigraphic chart

A Global Boundary Stratotype Section and Point (GSSP) is an internationally agreed upon reference point on a stratigraphic section which defines the lower boundary of a stage on the geologic time scale.

A Global Standard Stratigraphic Age, abbreviated GSSA, is a chronological reference point and criterion in the geologic record used to define the boundaries (an internationally sanctioned benchmark point) between different geological periods, epochs or ages on the overall geologic time scale in a chronostratigraphically useful rock layer.

Chronostratigraphy is the branch of stratigraphy that studies the ages of rock strata in relation to time.

Stratigraphy is a branch of geology concerned with the study of rock layers (strata) and layering (stratification).

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Strata in Cafayate (Argentina)

Microbial mats [multi-layered sheets] of coexisting bacteria and archaea were the dominant form of life in the early Archean Epoch and many of the major steps in early evolution are thought to have taken place in this environment.[127] The earliest evidence of eukaryotes dates from 1.85 billion years ago,[128][129] and while they may have been present earlier, their diversification accelerated when they started using oxygen in their metabolism. Later, around 1.7 billion years ago, multicellular organisms began to appear, with differentiated cells performing specialised functions.[130]

Algae-like multicellular land plants are dated back even to about 1 billion years ago,[131] although evidence suggests that microorganisms formed the earliest terrestrial ecosystems [ecosystems on land], at least 2.7 billion years ago.[132] Microorganisms are thought to have paved the way for the inception of land plants in the Ordovician period. Land plants were so successful that they are thought to have contributed to the Late Devonian extinction event.[133]

MES Note: The Late Devonian extinction refers to one or more extinction events in the Late Devonian Epoch, which collectively represent one of five largest mass extinction events in the history of life on Earth.

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Comparison of the three episodes of extinction in the Late Devonian (Late D) to other mass extinction events in Earth's history. Plotted is the extinction intensity, calculated from marine genera [plural of genus].

The Permian–Triassic (P-T, P-Tr)[3][4] extinction event, also known as the End-Permian Extinction[5] and colloquially [or informally] as the Great Dying,[6] formed the boundary between the Permian and Triassic geologic periods, as well as between the Paleozoic and Mesozoic eras, approximately 251.9 million years ago. It is the Earth's most severe known extinction event, with the extinction of 57% of biological families, 83% of genera, 81% of marine species[8][9][10] and 70% of terrestrial vertebrate species.[11] It was the largest known mass extinction of insects. There is evidence for one to three distinct pulses, or phases, of extinction.[11][12][13][14] The scientific consensus is that the causes of extinction were elevated temperatures and widespread oceanic anoxia [depletion of dissolved oxygen] and ocean acidification [decreasing pH] due to the large amounts of carbon dioxide that were emitted by the eruption of the Siberian Traps [large region of volcanic rock in Siberia, Russia resulting from volcanic activity].[15] It has also been proposed that the burning of hydrocarbon deposits, including oil and coal, by the Siberian Traps and emissions of methane by methanogenic microorganisms contributed to the extinction.[16][17]

Methanogens are microorganisms that produce methane as a metabolic byproduct in hypoxic conditions.

Hypoxia refers to low oxygen conditions.

Ediacara biota appear during the Ediacaran period,[134] while vertebrates, along with most other modern phyla originated about 525 million years ago during the Cambrian explosion.[135] During the Permian period, synapsids [mammals and similar animals], including the ancestors of mammals, dominated the land,[136] but most of this group became extinct in the Permian–Triassic extinction event 252 million years ago.[137] During the recovery from this catastrophe, archosaurs [reptiles group: birds and crocodilians] became the most abundant land vertebrates;[138] one archosaur group, the dinosaurs, dominated the Jurassic and Cretaceous periods.[139]

MES Note: Archosauria (lit. 'ruling reptiles') is a clade of diapsids, with birds and crocodilians as the only living representatives. Archosaurs are broadly classified as reptiles, in the cladistic sense of [the] term which includes birds.

Diapsids ("two arches") are a group of amniote tetrapods [4 limbed vertebrates] that developed two holes (temporal fenestra) in each side of their skulls about 300 million years ago during the late Carboniferous period.

An infratemporal fenestra, also called the lateral temporal fenestra or simply temporal fenestra, is an opening in the skull behind the orbit in some animals. An opening in front of the eye sockets, conversely, is called an antorbital fenestra. Both of these openings reduced the weight of the skull. Infratemporal fenestrae are commonly (although not universally) seen in the fossilized skulls of dinosaurs.

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The lateral temporal fenestra in relation to the other skull openings in the dinosaur Massospondylus.

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Diagram of the diapsid skull with temporal openings, unlike in Anapsida

An anapsid is an amniote whose skull lacks one or more skull openings (fenestra) near the temples.

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Anapsid skull

The temple is a juncture where four skull bones fuse together: the frontal, parietal, temporal, and sphenoid.

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Location of temple

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Human skull

Reptiles, as most commonly defined, are the animals in the class Reptilia, a paraphyletic grouping comprising all amniotes except synapsids (mammals and their extinct relatives) and Aves (birds).

Crocodilia (or Crocodylia) is an order of mostly large, predatory, semiaquatic reptiles, known as crocodilians. The order Crocodilia includes the true crocodiles (family Crocodylidae), the alligators and caimans (family Alligatoridae), and the gharial and false gharial (family Gavialidae). Although the term 'crocodiles' is sometimes used to refer to all of these, crocodilians is a less ambiguous vernacular [common, informal] term for members of this group.

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Figure

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Figure

After the Cretaceous–Paleogene extinction event [asteroid impact hypothesis] 66 million years ago killed off the non-avian dinosaurs,[140] mammals increased rapidly in size and diversity.[141] Such mass extinctions may have accelerated evolution by providing opportunities for new groups of organisms to diversify.[142]

MES Note: The Cretaceous–Paleogene (K–Pg) extinction event[a] (also known as the Cretaceous–Tertiary (K–T) extinction)[b] was a sudden mass extinction of three-quarters of the plant and animal species on Earth,[2][3][4] approximately 66 million years ago. With the exception of some ectothermic species such as sea turtles and crocodilians, no tetrapods weighing more than 25 kilograms (55 pounds) survived. As originally proposed in 1980[7] by a team of scientists led by Luis Alvarez and his son Walter, it is now generally thought that the K–Pg extinction was caused by the impact of a massive comet or asteroid 10 to 15 km (6 to 9 mi) wide,[8][9] 66 million years ago,[3] which devastated the global environment, mainly through a lingering impact winter which halted photosynthesis in plants and plankton.

An ectotherm (from the Greek ἐκτός (ektós) "outside" and θερμός (thermós) "heat") is an organism in which internal physiological sources of heat are of relatively small or of quite negligible importance in controlling body temperature.[1] Such organisms (for example frogs) rely on environmental heat sources,[2] which permit them to operate at very economical metabolic rates.

Asteroids are made up of metals and rocky material, while comets are made up of ice, dust and rocky material. Comets which approach the Sun lose material with each orbit because some of their ice melts and vaporizes to form a tail.

An impact winter is a hypothesized period of prolonged cold weather due to the impact of a large asteroid or comet on the Earth's surface. If an asteroid were to strike land or a shallow body of water, it would eject an enormous amount of dust, ash, and other material into the atmosphere, blocking the radiation from the Sun. This would cause the global temperature to decrease drastically.

Britannica: TV shows such as The Flintstones depict humans and dinosaurs living together in harmony. But that’s just fiction, right? Actually, not quite. The dinosaurs the earliest humans lived among were not the huge lumbering lizards we most commonly think of when we see the word. Those had been extinct for almost 66 million years before the first humans began to make their mark. The dinosaurs that comingled with our ancient ancestors were modern birds—the closest natural relatives to the extinct dinosaurs—which means that we live with dinosaurs too.

Diversity

Bacteria and Archaea

Further information: Bacteria, Archaea, and Microbiology

Bacteria are a type of cell that constitute a large domain of prokaryotic microorganisms. Typically a few micrometers in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste,[143] and the deep biosphere of the earth's crust.

MES Note: Bacteria, common noun bacteria, singular bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell.

A hot spring, hydrothermal spring, or geothermal spring is a spring produced by the emergence of geothermally heated groundwater onto the surface of the Earth. The groundwater is heated either by shallow bodies of magma (molten rock) or by circulation through faults to hot rock deep in the Earth's crust. In either case, the ultimate source of the heat is radioactive decay of naturally occurring radioactive elements in the Earth's mantle, the layer beneath the crust.

Hot spring water often contains large amounts of dissolved minerals. The chemistry of hot springs ranges from acid sulfate [SO42-] springs with a pH as low as 0.8, to alkaline chloride [containing chlorine, Cl] springs saturated with silica [oxide (containing O) of silicon, Si], to bicarbonate springs saturated with carbon dioxide and carbonate minerals.

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The internal structure of Earth

Basalt is an aphanitic [very fine grained] extrusive igneous rock formed from the rapid cooling of low-viscosity lava rich in magnesium and iron exposed at or very near the surface of a rocky planet or moon.

Extrusive rock refers to the mode of igneous volcanic rock formation in which hot magma from inside the Earth flows out (extrudes) onto the surface as lava or explodes violently into the atmosphere to fall back as pyroclastics [ejected rock] or tuff [ejected ash].[1] In contrast, intrusive rock refers to rocks formed by magma which cools below the surface.[2] The main effect of extrusion is that the magma can cool much more quickly in the open air or under seawater, and there is little time for the growth of crystals.[3] Sometimes, a residual portion of the matrix fails to crystallize at all, instead becoming a natural glass or obsidian [naturally occurring volcanic glass].

Igneous rock (derived from the Latin word ignis meaning fire), or magmatic rock, is formed through the cooling and solidification of magma or lava.

Granite is a coarse-grained (phaneritic) intrusive igneous rock composed mostly of [high silica containing minerals] quartz, alkali feldspar, and plagioclase.

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Figure: Intrusive Igneous rock "Granite" - cooled slowly within the Earth (left); Extrusive Igneous rock “Basalt” erupted from volcanoes

The asthenosphere (Ancient Greek: ἀσθενός [asthenos] meaning "without strength", and thus "weak", and σφαίρα [sphaira] meaning "sphere") is the highly viscous, mechanically weak,[1] and ductile [deformable without fracturing] region of the upper mantle of Earth.

Earth's mantle is a layer of silicate rock [containing silicon (Si) and oxygen (O)] between the crust and the outer core.

The hydrosphere (from Greek ὕδωρ hydōr, "water"[1] and σφαῖρα sphaira, "sphere"[2]) is the combined mass of water found on, under, and above the surface of a planet.

An atmosphere (Greek: ἀτμός atmos + σφαῖρα sphaira, sphere of vapour) is a layer of gas or layers of gases that envelope a planet.

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Grand Prismatic Spring and Midway Geyser Basin in Yellowstone National Park

Radioactive decay (also known as nuclear decay, radioactivity, radioactive disintegration or nuclear disintegration) is the process by which an unstable atomic nucleus loses energy by radiation [of particles and photons].

Radioactive waste is a type of hazardous waste that contains radioactive material.

The biosphere (from Greek βίος bíos "life" and σφαῖρα sphaira "sphere"), also known as the ecosphere (from Greek οἶκος oîkos "environment" and σφαῖρα), is the worldwide sum of all ecosystems.

The deep biosphere is the part of the biosphere that resides below the first few meters of the surface.

Bacteria also live in symbiotic [co-existing together] and parasitic [symbiotic but one organism is harmed by the other] relationships with plants and animals. Most bacteria have not been characterised, and only about 27 percent of the bacterial phyla have species that can be grown [microbial culture] in the laboratory.[144]

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Bacteria – Gemmatimonas aurantiaca (-=1 Micrometer)

Archaea constitute the other domain of prokaryotic cells and were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom), a term that has fallen out of use.[145] Archaeal cells have unique properties separating them from the other two domains, Bacteria and Eukaryota. Archaea are further divided into multiple recognized phyla. Archaea and bacteria are generally similar in size and shape, although a few archaea have very different shapes, such as the flat and square cells of Haloquadratum walsbyi.[146] Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes,[147] including archaeols.

MES Note: An ether group contains an oxygen atom connected to two alkyl or aryl groups. They have the general formula R–O–R′, where R and R′ represent the alkyl or aryl groups.

An alkyl is an alkane missing one hydrogen.

An alkane is an acyclic saturated hydrocarbon.

An aryl is any functional group or substituent derived from an aromatic ring.

An ether lipid implies an ether bridge [connections between molecules] between an alkyl group (a lipid) and an unspecified alkyl or aryl group, not necessarily glycerol.

Archaeol is one of the main core membrane lipids of archaea.

Archaea use more energy sources than eukaryotes: these range from organic compounds, such as sugars, to ammonia [a colorless gas, NH3], metal ions or even hydrogen gas. Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species of archaea fix carbon, but unlike plants and cyanobacteria, no known species of archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or budding; unlike bacteria, no known species of Archaea form endospores.

MES Note: Asexual reproduction is a type of reproduction that does not involve the fusion of gametes or change in the number of chromosomes. The offspring that arise by asexual reproduction from either unicellular or multicellular organisms inherit the full set of genes of their single parent. Asexual reproduction is the primary form of reproduction for single-celled organisms such as archaea and bacteria.

Fragmentation in multicellular or colonial organisms is a form of asexual reproduction or cloning, where an organism is split into fragments. Each of these fragments develop into mature, fully grown individuals that are clones of the original organism.

Budding is a type of asexual reproduction in which a new organism develops from an outgrowth or bud due to cell division at one particular site.

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Saccharomyces cerevisiae [yeast: single celled fungi; eukaryote] reproducing by budding

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Figure

A spore is a unit of sexual or asexual reproduction that may be adapted for dispersal and for survival, often for extended periods of time, in unfavourable conditions. Spores form part of the life cycles of many plants, algae, fungi and protozoa.[1] Bacterial spores [endospores] are not part of a sexual cycle but are resistant structures used for survival under unfavourable conditions.

An endospore [bacterial spore] is a dormant, tough, and non-reproductive structure produced by some bacteria in the phylum Firmicutes. It is a stripped-down, dormant form to which the bacterium can reduce itself. Endospore formation is usually triggered by a lack of nutrients. Endospores enable bacteria to lie dormant for extended periods, even centuries. There are many reports of spores remaining viable over 10,000 years, and revival of spores millions of years old has been claimed.

Dormancy is a period in an organism's life cycle when growth, development, and (in animals) physical activity are temporarily stopped. This minimizes metabolic activity and therefore helps an organism to conserve energy.

Protozoa (also protozoan, plural protozoans) is an informal term for a group of single-celled eukaryotes, either free-living or parasitic, that feed on organic matter such as other microorganisms or organic tissues and debris.

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Archaea – Halobacteria

The first observed archaea were extremophiles, living in extreme environments, such as hot springs and salt lakes with no other organisms. Improved molecular detection tools led to the discovery of archaea in almost every habitat, including soil, oceans, and marshlands. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet.

MES Note: An extremophile (from Latin extremus meaning "extreme" and Greek philiā (φιλία) meaning "love") is an organism that is able to live (or in some cases thrive) in extreme environments, i.e. environment that make survival challenging such as due to extreme temperature, radiation, salinity, or pH level.

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Graphic breakdown of water salinity, defining freshwater, brackish water, saltwater, and brine water.

An estuary is a partially enclosed coastal body of brackish water with one or more rivers or streams flowing into it, and with a free connection to the open sea.[1]

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Mattole River [California, USA] estuary

A mangrove is a shrub or small tree that grows in coastal saline or brackish water.

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Mangroves are adapted to saline conditions.

An aquifer is an underground layer of water-bearing permeable rock [porous rock], rock fractures or unconsolidated materials (gravel, sand, or silt).

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Figure: A graphic representation of particle size and surface area.

A swamp is a forested wetland.

A wetland is a distinct ecosystem that is flooded by water, either permanently or seasonally, where oxygen-free processes prevail.

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A freshwater swamp in Florida, United States

A marsh is a wetland that is dominated by herbaceous rather than woody plant species.

A woody plant is a plant that produces wood as its structural tissue and thus has a hard stem. In cold climates, woody plants further survive winter or dry season above ground, as opposite to herbaceous plants that die back to the ground until spring.

Herbaceous plants are vascular plants that have no persistent woody stems above ground.

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A marsh along the edge of a small river

Plankton are the diverse collection of organisms found in water (or air) that are unable to propel themselves against a current (or wind).[1][2] The individual organisms constituting plankton are called plankters.[3] In the ocean, they provide a crucial source of food to many small and large aquatic organisms.

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Part of the contents of one dip of a hand net. The image contains diverse planktonic organisms, ranging from photosynthetic cyanobacteria and diatoms [major group of algae] to many different types of zooplankton [plankton that can’t produce its own food (heterotrophic)], including both holoplankton (permanent residents of the plankton) and meroplankton (temporary residents of the plankton, e.g., fish eggs, crab larvae, worm larvae).

Archaea are a major part of Earth's life. They are part of the microbiota of all organisms. In the human microbiome, they are important in the gut [gastrointestinal tract], mouth, and on the skin.[148] Their morphological, metabolic, and geographical diversity permits them to play multiple ecological roles: carbon fixation; nitrogen cycling; organic compound turnover [or recycling]; and maintaining microbial symbiotic and syntrophic communities, for example.[149]

MES Note: Microbiota are "ecological communities of commensal [co-existing without harming others], symbiotic and pathogenic microorganisms"[2][3] found in and on all multicellular organisms studied to date from plants to animals. Microbiota include bacteria, archaea, protists, fungi and viruses.[4] Microbiota have been found to be crucial for immunologic, hormonal and metabolic homeostasis of their host.

The term microbiome describes either the collective genomes of the microorganisms that reside in an environmental niche [suitable fit] or the microorganisms themselves.

The gastrointestinal tract [tract = system/region of related organs] (GI tract, GIT, digestive tract, alimentary canal [alimentary = relating to nutrition; canal = waterway channel]) is the tract from the mouth to the anus which includes all the organs of the digestive system in humans and other animals. Food taken in through the mouth is digested to extract nutrients and absorb energy, and the waste expelled as feces.

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Upper and lower human gastrointestinal tract

Syntrophy, synthrophy,[1] or cross-feeding (from Greek syn meaning together, trophe meaning nourishment) is the phenomenon of one species living off the metabolic products of another species.

The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into multiple chemical forms as it circulates among atmosphere, terrestrial, and marine ecosystems.

A biogeochemical cycle is the pathway by which a chemical substance cycles (is turned over or moves through) the biotic [living] and the abiotic [non-living] compartments of Earth.

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Global cycling of reactive nitrogen [Tg / year = million tons / year]

Anthropogeny is the study of human origins. Anthropogenic = "human" + "generating".

The Haber process,[1] also called the Haber–Bosch process, is an artificial nitrogen fixation process and is the main industrial procedure for the production of ammonia [NH3] today.

Nitrogen fixation is a chemical process by which molecular nitrogen (N2), with a strong triple covalent bond, in the air is converted into ammonia (NH3) or related nitrogenous compounds, typically in soil or aquatic systems [1] but also in industry.

Denitrification is a microbially facilitated process where nitrate (NO3) is reduced and ultimately produces molecular nitrogen (N2) [which is a gas] through a series of intermediate gaseous nitrogen oxide products.

NO x  is a generic term for the [mono-]nitrogen oxides that are most relevant for air pollution, namely nitric oxide (NO) and nitrogen dioxide (NO2 ). These gases contribute to the formation of smog and acid rain.

Smog, or smoke fog, is a type of intense air pollution.

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Smog and sunny day within 10-day interval in Fanhe, China

Acid rain is rain or any other form of precipitation that is unusually acidic, meaning that it has elevated levels of hydrogen ions (low pH). Most water, including the water we drink, has a neutral pH that exists between 6.5-8.5, but acid rain has a pH level lower than this and ranges from 4-5 on average.[1][2] The more acidic the acid rain is, the lower its pH is.[2] Acid rain can have harmful effects on plants, aquatic animals, and infrastructure. Acid rain is caused by emissions of sulphur dioxide [SO2] and nitrogen oxide [NOx], which react with the water molecules in the atmosphere to produce acids.

Reactive nitrogen ("Nr") is a term used for a variety of nitrogen compounds that support growth directly or indirectly. Representative species include the gases nitrogen oxides (NOx), ammonia (NH3), nitrous oxide (N2O), as well as the anion nitrate (NO3−). Although required for life, nitrogen is stored in the biosphere in an unreactive ("unfixed") form N2, which supports only a few life forms. Reactive nitrogen is however "fixed" and is readily converted into protein, which supports life, leading to depletion of oxygen in fresh waters by eutrophication.[1] Nr is removed from the biosphere via Denitrification.

Eutrophication is the process by which an entire body of water, or parts of it, becomes progressively enriched with minerals and nutrients, particularly nitrogen and phosphorus. It has also been defined as "nutrient-induced increase in phytoplankton productivity".

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  1. Excess nutrients are applied to the soil.
  2. Some nutrients leach into the soil and later drain into surface water.
  3. Some nutrients run off over the ground into the body of water.
  4. The excess nutrients cause an algal bloom.
  5. The algal bloom reduces light penetration.
  6. The plants beneath the algal bloom die because they cannot get sunlight to perform photosynthesis.
  7. Eventually, the algal bloom dies and sinks to the bottom of the lake. Bacterial communities begin to decompose the remains, using up oxygen for respiration.
  8. The decomposition causes the water to become depleted of oxygen if the water body is not regularly mixed vertically. Larger life forms, such as fish die.

An algal bloom or algae bloom is a rapid increase or accumulation in the population of algae in freshwater or marine water systems.

Source: NPK on a fertilizer package stands for nitrogen [N], phosphorus [P], and potassium [K], the three nutrients that compose complete fertilizers. While the description of the fertilizer may not expressly say "NPK," you will see a series of three numbers, often separated by dashes. These numbers correspond, respectively, to the percentage of nitrogen, phosphorus, and potassium in that fertilizer. For example, if you purchase a 10-pound bag fertilizer labeled 5-10-5, it contains 5 percent nitrogen, 10 percent phosphorus, and 5 percent potassium by weight. The remaining 80 percent of the bag's weight is comprised of minor nutrients or fillers.

Phytoplankton are the autotrophic (self-feeding) components of the plankton community and a key part of ocean and freshwater ecosystems. The name comes from the Greek words φυτόν (phyton), meaning 'plant', and πλαγκτός (planktos), meaning 'wanderer' or 'drifter'.

An autotroph or primary producer is an organism that produces complex organic compounds (such as carbohydrates, fats, and proteins) using carbon from simple substances such as carbon dioxide,[1] generally using energy from light (photosynthesis) or inorganic chemical reactions (chemosynthesis).

Protists

Further information: Protist and Protistology

Protists are eukaryotic organism [sic] that is not an animal, plant, or fungus. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor),[150] the exclusion of other eukaryotes means that protists do not form a natural group, or clade.[a] So some protists may be more closely related to animals, plants, or fungi than they are to other protists; however, like algae, invertebrates, or protozoans, the grouping is used for convenience.[151]

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Diversity of protists

The taxonomy of protists is still changing. Newer classifications attempt to present monophyletic groups based on morphological (especially ultrastructural [structure visible beyond optical light microscope]),[152][153][154] biochemical (chemotaxonomy [classification based on chemical compounds]) [155][156] and DNA sequence (molecular research) information.[157][158] Because protists as a whole are paraphyletic, new systems often split up or abandon the kingdom, instead treating the protist groups as separate lines of eukaryotes.

Plant diversity

Further information: Botany, Plant, Algae, Non-vascular plant, Vascular plant, and Spermatophyte

Plants are mainly multicellular organisms, predominantly photosynthetic eukaryotes of the kingdom Plantae. Botany is the study of plant life, which would exclude fungi and some algae. Botanists have studied approximately 410,000 species of land plants of which some 391,000 species are vascular plants (including approximately 369,000 species of flowering plants),[159] and approximately 20,000 are bryophytes.[160]

MES Note: Vascular plants (from Latin vasculum: duct), also known as Tracheophyta (the tracheophytes, from Greek τραχεῖα ἀρτηρία trācheia artēria 'windpipe' + φυτά phutá 'plants'[citation needed]), form a large group of plants (c. 300,000 accepted known species)[5] that are defined as land plants with lignified tissues (the xylem) for conducting water and minerals throughout the plant. They also have a specialized non-lignified tissue (the phloem) to conduct [transport] products of photosynthesis.

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Phloem (orange) transports products of photosynthesis to various parts of the plant.

Lignin is a class of complex organic polymers that form key structural materials in the support tissues of most plants.[1] Lignins are particularly important in the formation of cell walls, especially in wood and bark [outermost layers of stems and roots], because they lend rigidity and do not rot easily. Chemically, lignins are polymers made by cross-linking phenolic [-OH bonded directly to an aromatic hydrocarbon group] precursors.

Wood is a porous and fibrous structural tissue found in the stems and roots of trees and other woody plants. It is an organic material – a natural composite of cellulose fibers that are strong in tension and embedded in a matrix of lignin that resists compression.

Cellulose is an organic compound with the formula (C6H10O5)n, a polysaccharide consisting of a linear chain of several hundred to many thousands of glycosidically linked glucose units. Cellulose is an important structural component of the primary cell wall of green plants, many forms of algae and the oomycetes [distinct fungus-like eukaryotic microorganisms]. Some species of bacteria secrete it to form biofilms [many microbes sticking to each other and often a surface].[5] Cellulose is the most abundant organic polymer on Earth.[6] The cellulose content of cotton fiber is 90%, that of wood is 40–50%, and that of dried hemp is approximately 57%.

A glycosidic bond or glycosidic linkage is a type of covalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate.

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The flowering plants, also known as Angiospermae, meaning hidden seeds in Greek, are the most diverse group of land plants with 64 orders, 416 families, approximately 13,000 known genera and 300,000 known species. They are seed-producing plants, have flowers, and produce fruits that contain the seeds. Etymologically, "angiosperm" literally means a plant that produces seeds within an enclosure; in other words, a fruiting plant.

A flower is the reproductive structure found in flowering plants.

A fruit is the seed-bearing structure in flowering plants that is formed from the ovary after flowering.

In the flowering plants, an ovary is a part of the female reproductive organ of the flower. It is an enlarged basal [forming the base] portion of the pistil, the female organ of a flower. The ovary contains ovules, which develop into seeds upon fertilization. The ovary itself will mature into a fruit, either dry or fleshy, enclosing the seeds.

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Figure: how flowering plants reproduce: Reproduction in flowering plants begins with pollination, the transfer of pollen from anther to stigma on the same flower or to the stigma of another flower on the same plant (self-pollination) or from the anther on one plant to the stigma of another plant (cross-pollination). Once the pollen grain lodges on the stigma, a pollen tube grows from the pollen grain to an ovule. Two sperm nuclei [hence called double fertilization] then pass through the pollen tube. One of them unites with the egg nucleus and produces a zygote. The other sperm nucleus unites with two polar nuclei to produce an endosperm nucleus. The fertilized ovule develops into a seed.

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Figure: Self-pollination and cross-pollination

A seedling is a young sporophyte developing out of a plant embryo from a seed.

A sporophyte is the diploid multicellular stage in the life cycle of a plant or alga [singular of algae].

In flowering plants, the sporophyte comprises the whole multicellular body except the pollen and embryo sac [contained in the ovule].

Bryophytes are a hypothetical taxonomic division containing three groups of non-vascular land plants (embryophytes): the liverworts, hornworts and mosses. Bryophytes produce enclosed reproductive structures (gametangia and sporangia), but they do not produce flowers or seeds. They reproduce via spores.[5] [Flowering plants also reproduce via spores.]

There are two kinds of reproductive cells produced by flowers. Microspores, which will divide to become pollen grains, are the "male" cells.[15] The "female" cells called megaspores, which will divide to become the egg cell (megagametogenesis), are contained in the ovule.

In biology, a biological life cycle (or just life cycle or lifecycle when the biological context is clear) is a series of changes in form that an organism undergoes, returning to the starting state. In some organisms, different "generations" of the species succeed each other during the life cycle. For plants and many algae, there are two multicellular stages, and the life cycle is referred to as alternation of generations. Life cycles that include sexual reproduction involve alternating haploid (n) and diploid (2n) stages, i.e., a change of ploidy is involved. To return from a diploid stage to a haploid stage, meiosis must occur. In regard to changes of ploidy, there are 3 types of cycles:

  • haplontic life cycle — the haploid stage is multicellular and the diploid stage is a single cell, meiosis is "zygotic".
  • diplontic life cycle — the diploid stage is multicellular and haploid gametes are formed, meiosis is "gametic".
  • haplodiplontic life cycle (also referred to as diplohaplontic, diplobiontic, or dibiontic life cycle) — multicellular diploid and haploid stages occur, meiosis is "sporic".

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Zygotic meiosis

A zoospore is a motile asexual spore that uses a flagellum [hair like appendages] for locomotion.

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Gametic meiosis

Oogenesis, ovogenesis, or oögenesis is the differentiation of the ovum (egg cell) into a cell competent to further develop when fertilized.[2] It is developed from the primary oocyte by maturation. Oogenesis is initiated in the embryonic stage.

A polar body is a small haploid cell that is formed at the same time as an egg cell during oogenesis, but generally does not have the ability to be fertilized. They frequently die and disintegrate by apoptosis, but in some cases remain and can be important in the life cycle of the organism.

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Sporic meiosis [Rhizomes are below ground stems that grow horizontally]

The cycles differ in when mitosis (growth) occurs. Zygotic meiosis and gametic meiosis have one mitotic stage: mitosis occurs during the n phase in zygotic meiosis and during the 2n phase in gametic meiosis. Therefore, zygotic and gametic meiosis are collectively termed "haplobiontic" (single mitotic phase, not to be confused with haplontic). Sporic meiosis, on the other hand, has mitosis in two stages, both the diploid and haploid stages, termed "diplobiontic" (not to be confused with diplontic).

Life cycles of plants and algae with alternating haploid and diploid multicellular stages are referred to as diplohaplontic (the equivalent terms haplodiplontic, diplobiontic and dibiontic are also in use, as is describing such an organism as having a diphasic ontogeny[5] [origination and development of an individual]). Life cycles, such as those of animals, in which there is only a diploid multicellular stage are referred to as diplontic. Life cycles in which there is only a haploid multicellular stage are referred to as haplontic.

Source: Three types of life cycles can be distinguished on account of the timing of the mitoses, in the haploid and/or diploid phase:

  • Haplontic: In haplonts the mitoses only occur in haploid cells. This can result in the formation of single haploid cells or a multicellular haploid organism. The haplontic life forms produce the gametes through mitosis. After fertilization a zygote is formed: this cell is the only diploid cell in the entire life cycle. It is thus that same zygotic cell that later undergoes meiosis. A haploid life cycle is found in most fungi and in some green algae like Chlamydomonas.
  • Diplontic: In diplonts mitotic divisions only occur in diploid cells. Gametes (arisen through meiosis) are the only occurance of the haploid phase. The diploid zygote formed after fertilization can however divide mitotically. This process results in the production of a multicellular diploid organism or in the production of many diploid single cells. Animals, for example, belong to the diplonts.
  • Haplo-diplontic: In haplo-diplonts the mitoses occur in both diploid and haploid cells. Such organisms go during their life cycle through a phase in which they are multicellular and haploid (the gametophyte), and a phase in which they are multicellular and diploid (the sporophyte). The phenomenon is called "alternation of generation". This haplo-diplontic type of cycle is found in all land plants and in many algae.

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Figure

Alternation of generations (also known as metagenesis or heterogenesis)[1] is the type of life cycle that occurs in those plants and algae in the Archaeplastida [often synonymous with the Kingdom Plantae] and the Heterokontophyta [group of protists] that have distinct haploid sexual and diploid asexual stages. In these groups, a multicellular haploid gametophyte with n chromosomes alternates with a multicellular diploid sporophyte with 2n chromosomes, made up of n pairs. A mature sporophyte produces haploid spores by meiosis, a process which reduces the number of chromosomes to half, from 2n to n. This cycle, from gametophyte to sporophyte (or equally from sporophyte to gametophyte), is the way in which all land plants and many algae undergo sexual reproduction. The relationship between the sporophyte and gametophyte varies among different groups of plants. In those algae which have alternation of generations, the sporophyte and gametophyte are separate independent organisms, which may or may not have a similar appearance. In liverworts, mosses and hornworts, the sporophyte is less well developed than the gametophyte and is largely dependent on it. Although moss and hornwort sporophytes can photosynthesise, they require additional photosynthate [resulting products from photosynthesis, usually sugars] from the gametophyte to sustain growth and spore development and depend on it for supply of water, mineral nutrients and nitrogen.[2][3] By contrast, in all modern vascular plants the gametophyte is less well developed than the sporophyte, although their Devonian ancestors had gametophytes and sporophytes of approximately equivalent complexity.[4] In ferns the gametophyte is a small flattened autotrophic prothallus [term for the gametophyte of ferns] on which the young sporophyte is briefly dependent for its nutrition. In flowering plants, the reduction of the gametophyte is much more extreme; it consists of just a few cells which grow entirely inside the sporophyte.

Source: Kingdom Archaeplastida is a taxonomic group comprised of land plants, green algae, red algae, and glaucophytes [small group of freshwater unicellular algae]. It is sometimes used in synonymous to Plantae. However, the stricter use of the term Plantae is one that which includes only the land plants and green algae. Archaeplastida is more general in including the red algae and the glaucophytes.

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Diagram showing the alternation of generations between a diploid sporophyte (bottom) and a haploid gametophyte (top)

The gametophyte is the sexual phase in the life cycle of plants and algae. It develops sex organs that produce gametes, haploid sex cells that participate in fertilization to form a diploid zygote which has a double set of chromosomes.

In heterosporic plants [most plants], there are two distinct kinds of gametophytes. Because the two gametophytes differ in form and function, they are termed heteromorphic, from hetero- "different" and morph "form". The egg-producing gametophyte is known as a megagametophyte, because it is typically larger, and the sperm producing gametophyte is known as a microgametophyte. Gametophytes which produce egg and sperm on separate plants are termed dioicous, while those that produce both eggs and sperm on the same gametophyte are termed monoicous.

Heterospory is the production of spores of two different sizes and sexes by the sporophytes of land plants. The smaller of these, the microspore, is male and the larger megaspore is female.

Pollen is a powdery substance consisting of pollen grains which are male microgametophytes of seed plants, which produce male gametes (sperm cells).

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Pollen from a variety of common plants: sunflower (Helianthus annuus, small spiky sphericals, colorized pink), morning glory (Ipomoea purpurea, big sphericals with hexagonal cavities, colorized mint green), hollyhock (Sildalcea malviflora, big spiky sphericals, colorized yellow), lily (Lilium auratum, bean shaped, colorized dark green), primrose (Oenothera fruticosa, tripod shaped, colorized red) and castor bean (Ricinus communis, small smooth sphericals, colorized light green). The image is magnified some x500, so the bean shaped grain in the bottom left corner is about 50 μm long.

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Pollen Tube Diagram [Diploid spore produces 4 haploid microspores, which produce pollen]

Pollen itself is not the male gamete.[3] It is a gametophyte, something that could be considered an entire organism, which then produces the male gamete. Each pollen grain contains vegetative (non-reproductive) cells (only a single cell in most flowering plants but several in other seed plants) and a generative (reproductive) cell. In flowering plants the vegetative tube cell produces the pollen tube, and the generative cell divides to form the two sperm nuclei.

In angiosperms [flowering plants], the megagametophyte is reduced to only a few nuclei and cells, and is sometimes called the embryo sac. A typical embryo sac contains seven cells and eight nuclei, one of which is the egg cell. Two nuclei [termed polar nuclei] fuse with a sperm nucleus to form the endosperm, which becomes the food storage tissue in the seed.

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Figure: Liverworts, hornworts, and mosses are modern bryophytes. Liverworts are named for the liver-shaped leaves of some species. Hornworts are named for their horn-like sporophytes.

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Diversity of plants

Algae is a large and diverse group of photosynthetic eukaryotic organisms. Included organisms range from unicellular microalgae [microscopic algae invisible to the naked eye], such as Chlorella, Prototheca and the diatoms, to multicellular forms, such as the giant kelp, a large brown alga. Most are aquatic and autotrophic and lack many of the distinct cell and tissue types, such as stomata, xylem and phloem, which are found in land plants. The largest and most complex marine algae are called seaweeds, while the most complex freshwater forms are the Charophyta.

MES Note:

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Figure

A mycorrhiza (from Greek μύκης mýkēs, "fungus", and ῥίζα rhiza, "root"; pl. mycorrhizae, mycorrhiza or mycorrhizas[1]) is a mutual symbiotic association between a fungus and a plant.

A plant cuticle is a protecting film covering the epidermis of leaves, young shoots and other aerial plant organs without periderm [the outer layer of bark]. It consists of lipid and hydrocarbon polymers impregnated with wax, and is synthesized exclusively by the epidermal cells.

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Water beads on the waxy cuticle of kale leaves

Waxes are a diverse class of organic compounds that are lipophilic , malleable [deformable] solids near ambient temperatures.

Lipophilicity (from Greek λίπος "fat" and φίλος "friendly"), refers to the ability of a chemical compound to dissolve in fats, oils, lipids, and non-polar solvents.

An autotroph or primary producer is an organism that produces complex organic compounds (such as carbohydrates, fats, and proteins) using carbon from simple substances such as carbon dioxide,[1] generally using energy from light (photosynthesis) or inorganic chemical reactions (chemosynthesis).

A heterotroph (from Ancient Greek ἕτερος héteros "other" and τροφή trophḗ "nutrition") is an organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly plant or animal matter.

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Cycle between autotrophs and heterotrophs. Autotrophs use light, carbon dioxide (CO2), and water to form oxygen and complex organic compounds, mainly through the process of photosynthesis (green arrow). Both types of organisms use such compounds via cellular respiration to both generate ATP and again form CO2 and water (two red arrows).

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Nannochloropsis microalgae

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Fucus serratus [a type of seaweed]

A stoma (from Greek στόμα, "mouth", plural "stomata"), also called a stomate (plural "stomates") is a pore, found in the epidermis of leaves, stems, and other organs, that controls the rate of gas exchange.

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Figure: Magnified leaf stomata - schematic (opened and closed)

Nonvascular plants are plants without a vascular system consisting of xylem and phloem. Instead, they may possess simpler tissues that have specialized functions for the internal transport of water. Vascular plants, on the other hand, are a large group of plants (c. 300,000 accepted known species)[161] [c. refers to circa, Latin for “around” or approximately] that are defined as land plants with lignified tissues (the xylem) for conducting water and minerals throughout the plant.[162] They also have a specialized non-lignified tissue (the phloem) to conduct products of photosynthesis. Vascular plants include the clubmosses, horsetails, ferns, gymnosperms (including conifers) and angiosperms (flowering plants).

Seed plants (or spermatophyte) comprise five divisions, four of which are grouped as gymnosperms and one is angiosperms. Gymnosperms includes conifers, cycads, Ginkgo, and gnetophytes. Gymnosperm seeds develop either on the surface of scales or leaves, which are often modified to form cones, or solitary [containing a single seed] as in yew, Torreya, Ginkgo.[163]

MES Note: The term gymnosperm comes from the composite word in Greek: γυμνόσπερμος (γυμνός, gymnos, 'naked' and σπέρμα, sperma, 'seed'), literally meaning 'naked seeds'. The name is based on the unenclosed condition of their seeds (called ovules in their unfertilized state). The non-encased condition of their seeds contrasts with the seeds and ovules of flowering plants (angiosperms), which are enclosed within an ovary.

A conifer cone (in formal botanical usage: strobilus, plural strobili) is an organ on plants in the division Pinophyta (conifers) that contains the reproductive structures. The familiar woody cone is the female cone, which produces seeds. The male cone, which produces pollen, is usually herbaceous and much less conspicuous [obvious to the eye] even at full maturity.

A pine is any conifer in the genus Pinus of the family Pinaceae.

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Figure: Pine cones

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Figure: Types of seeds

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Figure: Gymnosperm naked seeds

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A mature female Coulter pine (Pinus coulteri) cone, the heaviest pine cone

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Figure: Open male pollen cones below new needle bundles (late May)

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Horsetails [equisetum]

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Unidentified fern at Cambridge Botanic Garden

Angiosperms are the most diverse group of land plants, with 64 orders, 416 families, approximately 13,000 known genera and 300,000 known species.[161] Like gymnosperms, angiosperms are seed-producing plants. They are distinguished from gymnosperms by having characteristics such as flowers, endosperm within their seeds, and production of fruits that contain the seeds.

Fungi

Further information: Fungus and Mycology

Fungi are eukaryotic organisms that include microorganisms such as yeasts and molds, as well as the more familiar mushrooms. A characteristic that places fungi in a different kingdom from plants, bacteria, and some protists is chitin in their cell walls.

MES Note: A mould (UK, NZ, AU, ZA, IN, CA, IE) or mold (US) is a fungus that grows in the form of multicellular filaments called hyphae.[1][2] In contrast, fungi that can adopt a single-celled growth habit are called yeasts.

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A time-lapse animation of a peach decaying. The frames were taken approximately 12 hours apart over a period of six days.

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Yeast of the species Saccharomyces cerevisiae

A mushroom or toadstool is the fleshy, spore-bearing fruiting body of a fungus, typically produced above ground, on soil, or on its food source.

The sporocarp (also known as fruiting body, fruit body or fruitbody) of fungi is a multicellular structure on which spore-producing structures are borne.

Chitin (C8H13O5N)n) is a long-chain polymer of N-acetylglucosamine, an amide derivative of glucose. This polysaccharide is a primary component of cell walls in fungi, the exoskeletons of arthropods, such as crustaceans [crabs, lobsters, etc.] and insects, the radulae [“tongue with teeth”] of molluscs [snails, octopus, etc.], cephalopod beaks [jaws of squid, octopus, etc.] , and the scales of fish and skin of lissamphibians [frogs, etc.], [1] making it the second most abundant polysaccharide in nature,[2] behind only cellulose.

An amide, also known as an organic amide or a carboxamide, is a compound with the general formula RC(=O)NR′R″, where R, R', and R″ represent organic groups or hydrogen atoms.

The radula (plural radulae or radulas)[1] is an anatomical structure used by mollusks for feeding, sometimes compared to a tongue.[2] It is a minutely toothed, chitinous ribbon, which is typically used for scraping or cutting food before the food enters the esophagus [food pipe].

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Figure

Fungi, like animals, are heterotrophs; they acquire their food by absorbing dissolved molecules, typically by secreting digestive enzymes [breakdown polymers into smaller building blocks] into their environment. Fungi do not photosynthesize. Growth is their means of mobility, except for spores (a few of which are flagellated [having whip-like appendages]), which may travel through the air or water. Fungi are the principal decomposers in ecological systems.

MES Note: Decomposers are organisms that break down dead or decaying organisms; they carry out decomposition, a process possible by only certain kingdoms, such as fungi.

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Fungi acting as decomposers of a fallen tree branch

Decomposition is the process by which dead organic substances are broken down into simpler organic or inorganic matter such as carbon dioxide, water, simple sugars and mineral salts

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A rotten apple after it fell from a tree

These and other differences place fungi in a single group of related organisms, named the Eumycota (true fungi or Eumycetes), which share a common ancestor (from a monophyletic group). This fungal group is distinct from the structurally similar myxomycetes (slime molds) and oomycetes (water molds).

MES Note: Slime mold or slime mould is an informal name given to several kinds of unrelated eukaryotic organisms that can live freely as single cells, but can aggregate together to form multicellular reproductive structures.

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Slime mold growing out of a bin of wet paper

Oomycota or oomycetes form a distinct phylogenetic lineage of fungus-like eukaryotic microorganisms. The oomycetes are also often referred to as water molds (or water moulds), although the water-preferring nature which led to that name is not true of most species, which are terrestrial [land] pathogens.

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Asexual (A: sporangia, B: zoospores, C: chlamydospores) and sexual (D: oospores) reproductive structures of Phytophthora infestans (Peronosporales [pathogenic water molds])

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Diversity of fungi. Clockwise from top left: Amanita muscaria, a basidiomycete; Sarcoscypha coccinea [could also be S. austriaca?], an ascomycete; bread covered in mold; chytrid; Aspergillus conidiophore.

MES Note: Ascomycota is a phylum of the kingdom Fungi that, together with the Basidiomycota, forms the subkingdom Dikarya.

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Figure

Due to similar physical appearances and sometimes overlapping distributions, S. coccinea has often been confused with S. occidentalis, S. austriaca [see the later picture], and S. dudleyi.

Most fungi are inconspicuous [not easy to notice] because of the small size of their structures, and their cryptic lifestyles in soil or on dead matter.

MES Note: In ecology, crypsis is the ability of an animal or a plant[1] to avoid observation or detection by other animals.

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Hiding

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Revealing itself

Cryptic behavior. Mossy leaf-tailed gecko (Uroplatus sikorae) Montagne d’Ambre, Madagascar, showing the camouflage disguise using the dermal flap [flaps of skin across the full body].

The sporocarp (also known as fruiting body, fruit body or fruitbody) of fungi is a multicellular structure on which spore-producing structures are borne. The sporocarp of a basidiomycete is known as a basidiocarp or basidiome, while the fruitbody of an ascomycete is known as an ascocarp.

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Ascocarp of Sarcoscypha austriaca [or S. coccinea??]

Fungi include symbionts of plants, animals, or other fungi and also parasites. They may become noticeable when fruiting, either as mushrooms or as molds. Fungi perform an essential role in the decomposition of organic matter and have fundamental roles in nutrient cycling and exchange in the environment.

MES Note: A biogeochemical cycle is a pathway by which a chemical substance is turned over or moves through the biotic [living] (biosphere) and the abiotic [non-living] (lithosphere, atmosphere, and hydrosphere) compartments of Earth.

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Examples of major processes.

Assimilation (biology) is the conversion of nutrient into the fluid or solid substance of the body, by the processes of digestion and absorption.

Flora is all the plant life present in a particular region or time.

Fauna is all of the animal life present in a particular region or time.

A lithosphere (Ancient Greek: λίθος [líthos] for "rocky", and σφαίρα [sphaíra] for "sphere") is the rigid,[1] outermost shell of a terrestrial-type planet [rocky planet, composed mainly of metals].

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Earth cutaway from center to surface, the lithosphere comprising the crust and lithospheric mantle (detail not to scale)

The fungus kingdom encompasses an enormous diversity of taxa [plural of taxon] with varied ecologies, life cycle strategies, and morphologies ranging from unicellular aquatic chytrids to large mushrooms. However, little is known of the true biodiversity of Kingdom Fungi, which has been estimated at 2.2 million to 3.8 million species.[164] Of these, only about 148,000 have been described,[165] with over 8,000 species known to be detrimental [causing harm] to plants and at least 300 that can be pathogenic to humans.[166]

Animal diversity

Further information: Zoology, Sponge, Invertebrate, and Vertebrate

Animals are multicellular eukaryotic organisms that form the kingdom Animalia. With few exceptions, animals consume organic material, breathe oxygen, are able to move, can reproduce sexually, and grow from a hollow sphere of cells, the blastula, during embryonic development.

MES Note: Blastulation is the stage in early animal embryonic development that produces the blastula.[1] The blastula (from Greek βλαστός (blastos meaning sprout) is a hollow sphere of cells (blastomeres) surrounding an inner fluid-filled cavity (the blastocoel).[1][2] Embryonic development begins with a sperm fertilizing an egg cell to become a zygote, which undergoes many cleavages [division of cells in the early embryo] to develop into a ball of cells called a morula. Only when the blastocoel is formed does the early embryo become a blastula. The blastula precedes the formation of the gastrula in which the germ layers of the embryo form.[3]

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Blastulation: 1 - morula, 2 - blastula.

Gastrulation is a phase early in the embryonic development of most animals, during which the blastula (a single-layered hollow sphere of cells) is reorganized into a multilayered structure known as the gastrula.

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Gastrulation occurs when a blastula, made up of one layer, folds inward and enlarges to create a gastrula. This diagram is color-coded: ectoderm, blue; endoderm, green; blastocoel (the yolk sack), yellow; and archenteron (the gut), purple.

A germ layer is a primary layer of cells that forms during embryonic development. Germ layers eventually give rise to all of an animal’s tissues and organs through the process of organogenesis.

The gastrula has either two or three layers (the germ layers). In all vertebrates, these progenitor cells differentiate into all adult tissues and organs.

A progenitor cell is a biological cell that, like a stem cell, has a tendency to differentiate into a specific type of cell, but is already more specific than a stem cell and is pushed to differentiate into its "target" cell.[1] The most important difference between stem cells and progenitor cells is that stem cells can replicate indefinitely, whereas progenitor cells can divide only a limited number of times. Controversy about the exact definition remains and the concept is still evolving.

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Gastrulation of a diploblast: The formation of germ layers from a (1) blastula to a (2) gastrula. Some of the ectoderm cells (orange) move inward forming the endoderm (red).

Diploblasty is a condition of the blastula in which there are two primary germ layers: the ectoderm and endoderm. Simpler animals, such as sea sponges, have one germ layer and lack true tissue organization. All the more complex animals (from flat worms to humans) are triploblastic with three germ layers (a mesoderm as well as ectoderm and endoderm). The mesoderm allows them to develop true organs.

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Figure

Over 1.5 million living animal species have been described—of which around 1 million are insects—but it has been estimated there are over 7 million animal species in total. They have complex interactions with each other and their environments, forming intricate food webs.

MES Note: A food web is the natural interconnection of food chains and a graphical representation of what-eats-what in an ecological community.

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A freshwater aquatic food web. The blue arrows show a complete food chain (algae → daphnia → gizzard shad → largemouth bass → great blue heron)

A food chain is a linear network of links in a food web starting from producer organisms (such as grass or trees which use radiation from the Sun to make their food) and ending at an apex predator species (like grizzly bears or killer whales), detritivores (like earthworms or woodlice), or decomposer species (such as fungi or bacteria).

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Food chain in a Swedish lake. Osprey feed on northern pike, which in turn feed on perch which eat bleak which eat crustaceans

An apex predator, also known as an alpha predator or top predator, is a predator at the top of a food chain, without natural predators.

Predation is a biological interaction where one organism, the predator, kills and eats another organism, its prey.

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The great white shark (bottom) was originally considered the apex predator of the ocean; however, the killer whale (top) has proven to be a predator of the shark.

Detritivores (also known as detrivores, detritophages, detritus feeders, or detritus eaters) are heterotrophs that obtain nutrients by consuming [eating] detritus (decomposing plant and animal parts as well as feces).

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Earthworms are soil-dwelling detritivores.

Decomposers are organisms that break down dead or decaying organisms; they carry out decomposition, a process possible by only certain kingdoms, such as fungi.

The terms detritivore and decomposer are often used interchangeably, but they describe different organisms. Detritivores are usually arthropods and help in the process of remineralization. Detritivores perform the first stage of remineralization, by fragmenting the dead plant matter, allowing decomposers to perform the second stage of remineralization.

In biogeochemistry, remineralisation (or remineralization) refers to the breakdown or transformation of organic matter (those molecules derived from a biological source) into its simplest inorganic forms.

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Figure

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Diversity of animals.

From top to bottom:

  • First column: Echinoderm, cnidaria, bivalve, tardigrade, crustacean, and arachnid.
  • Second column: Sponge, insect, mammal, bryozoa, acanthocephala, and flatworm.
  • Third column: Cephalopod, annelid, tunicate, fish, bird, and phoronida

Sponges, the members of the phylum Porifera, are a basal Metazoa (animal) clade as a sister of the Diploblasts [also called Eumetazoa].[167][168][169][170][171] They are multicellular organisms that have bodies full of pores and channels allowing water to circulate through them, consisting of jelly-like mesohyl sandwiched between two thin layers of cells.

MES Note: In phylogenetics, basal is the direction of the base (or root) of a rooted phylogenetic tree or cladogram.

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Figure

The mesohyl, formerly known as mesenchyme or as mesoglea, is the gelatinous matrix within a sponge. The mesohyl is composed of the following main elements: collagen, fibronectin-like [high-molecular weight glycoprotein] molecules, galectin [specific sugar binding proteins], and a minor component, dermatopontin [non-collagen structural protein].

Collagen is the main structural protein in the extracellular matrix found in the body's various connective tissues. As the main component of connective tissue, it is the most abundant protein in mammals,[1] making up from 25% to 35% of the whole-body protein content. It is mostly found in connective tissue such as cartilage, bones, tendons, ligaments, and skin.

Connective tissue is one of the four basic types of animal tissue, along with epithelial tissue, muscle tissue, and nervous tissue. It develops from the mesoderm. Connective tissue is found in between other tissues everywhere in the body, including the nervous system.

Epithelial tissue or epithelium is a thin, continuous, protective layer of compactly packed cells with little intercellular matrix. Epithelial tissues line the outer surfaces of organs and blood vessels throughout the body, as well as the inner surfaces of cavities in many internal organs. An example is the epidermis, the outermost layer of the skin.

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Types of epithelium

Cartilage (cartilaginous tissue) is a resilient and smooth elastic tissue, rubber-like padding that covers and protects the ends of long bones at the joints and nerves, and is a structural component of the rib cage, the ear, the nose, the bronchial tubes [conducting air in lungs], the intervertebral discs, and many other body components. It is not as hard and rigid as bone, but it is much stiffer and much less flexible than muscle.

A tendon or sinew is a tough, high-tensile-strength band of dense fibrous connective tissue that connects muscle to bone.

A ligament is the fibrous connective tissue that connects bones to other bones.

Skin is the layer of usually soft, flexible outer tissue covering the body of a vertebrate animal, with three main functions: protection, regulation, and sensation.[1]

In biology, the extracellular matrix (ECM) is a three-dimensional network consisting of extracellular macromolecules and minerals, such as collagen, enzymes, glycoproteins and hydroxyapatite [naturally occurring mineral, (Ca5PO4)3(OH)] that provide structural and biochemical support to surrounding cells.

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A stove-pipe sponge

The majority (~97%) of animal species are invertebrates,[172] which are animals that neither possess nor develop a vertebral column (commonly known as a backbone or spine), derived from the notochord. This includes all animals apart from the subphylum Vertebrata. Familiar examples of invertebrates include arthropods (insects, arachnids [spiders, scorpions, etc.], crustaceans, and myriapods [millipedes, centipedes, etc.]), mollusks [of the phylum mollusca] (chitons, snail, bivalves, squids, and octopuses), annelid (earthworms and leeches), and cnidarians (hydras, jellyfishes, sea anemones, and corals). Many invertebrate taxa have a greater number and variety of species than the entire subphylum of Vertebrata.[173]

MES Note: The vertebral column, also known as the backbone or spine, is part of the axial skeleton. The vertebral column is the defining characteristic of a vertebrate in which the notochord (a flexible rod of uniform composition) found in all chordates has been replaced by a segmented series of bone: vertebrae separated by intervertebral discs.[1] The vertebral column houses the spinal canal, a cavity that encloses and protects the spinal cord. There are about 50,000 species of animals that have a vertebral column.[2] The human vertebral column is one of the most-studied examples.

The axial skeleton is the part of the skeleton that consists of the bones of the head and trunk [central or core] of a vertebrate.

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Diagram of the axial skeleton

The hyoid is anchored by muscles from the anterior [front], posterior [back] and inferior [down] directions, and aids in tongue movement and swallowing. It is the only bone in the human body that is not connected to any other bones nearby.

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Position of hyoid bone (shown in red)

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Shape of hyoid bone.

In the vertebrate spinal column, each vertebra (plural vertebrae) is an irregular bone with a complex structure composed of bone and some hyaline cartilage, the proportions of which vary according to the segment of the backbone and the species of vertebrate.

Hyaline cartilage is the glass-like (hyaline) but translucent cartilage found on many joint surfaces. It is also most commonly found in the ribs, nose, larynx, and trachea.

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Comparisons of 1. opacity, 2. translucency, and 3. transparency; behind each panel is a star.

An intervertebral disc (or intervertebral fibrocartilage) lies between adjacent vertebrae in the vertebral column. Intervertebral discs consist of an outer fibrous ring, the anulus fibrosus disci intervertebralis, which surrounds an inner gel-like center, the nucleus pulposus.

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Intervertebral disc

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Figure

A foramen is an open hole in animals.

In anatomy, the notochord is a flexible rod formed of a material similar to cartilage. If a species has a notochord at any stage of its life cycle, it is, by definition, a chordate.

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Figure

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Figure: Pharyngeal arches, pouches, and clefts [the 5th arch is not shown because it either quickly regresses after formation or doesn’t form at all]

In the embryonic development of vertebrates, pharyngeal pouches form on the endodermal side between the pharyngeal arches. The pharyngeal grooves (or clefts) form the lateral ectodermal surface of the neck region to separate the arches.
The pouches line up with the clefts,[1] and these thin segments become gills in fish.

A gill is a respiratory organ that many aquatic organisms use to extract dissolved oxygen from water and to excrete carbon dioxide.

The pharyngeal arches, also known as visceral arches, are structures seen in the embryonic development of vertebrates that are recognisable precursors for many structures.

A pharyngeal groove (or branchial groove, or pharyngeal cleft[1]) is made up of ectoderm unlike its counterpart the pharyngeal pouch on the endodermal side.

The dorsal hollow nerve cord is a hollow cord dorsal to the notochord. It is formed from a part of the ectoderm that rolls, forming the hollow tube. This is important, as it distinguishes chordates from other animal phyla, such as Annelids [ringed worms] and Arthropods [having exoskeletons, such as insects, etc.], which have solid, ventral tubes. Dorsal means the "back" side, as opposed to ventral which is the "belly" side of an organism.

The pharynx (plural: pharynges) is the part of the throat behind the mouth and nasal cavity, and above the oesophagus and trachea (the tubes going down to the stomach and the lungs).

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Head and Neck Overview

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Conducting passages of the human respiratory system

The larynx, commonly called the voice box, is an organ in the top of the neck involved in breathing, producing sound and protecting the trachea against food aspiration [suction into airway].

The spinal canal (or vertebral canal or spinal cavity) is the canal that contains the spinal cord within the vertebral column.

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The body cavities.

The spinal cord is a long, thin, tubular structure made up of nervous tissue, which extends from the medulla oblongata in the brainstem to the lumbar region of the vertebral column. It encloses the central canal of the spinal cord, which contains cerebrospinal fluid. The brain and spinal cord together make up the central nervous system (CNS).

The medulla oblongata or simply medulla is a long stem-like structure which makes up the lower part of the brainstem.

The brainstem (or brain stem) is the posterior stalk-like part of the brain that connects the cerebrum [largest part of the brain] with the spinal cord.

In tetrapod anatomy, lumbar is an adjective that means of or pertaining to the abdominal segment of the torso [or trunk].

Cerebrospinal fluid (CSF) is a clear, colorless body fluid found within the tissue that surrounds the brain and spinal cord of all vertebrates.

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The spinal cord (in yellow) connects the brain to nerves throughout the body.

In contrast, vertebrates comprise all species of animals within the subphylum Vertebrata (chordates with backbones). Vertebrates represent the overwhelming majority of the phylum Chordata, with currently about 69,963 species described.[174] Vertebrates include such groups as jawless fishes, jawed vertebrates such as cartilaginous fishes (sharks, rays, and ratfish), bony fishes, tetrapods such as amphibians, reptiles, birds and mammals.

MES Note: Amphibians are ectothermic [internal heat generation is very low], tetrapod vertebrates of the class Amphibia. They inhabit a wide variety of habitats, with most species living within terrestrial [land], fossorial [underground, via digging], arboreal [on trees] or freshwater aquatic ecosystems. Thus amphibians typically start out as larvae living in water, but some species have developed behavioural adaptations to bypass this.

Viruses

Further information: Virus and Virology

Viruses are submicroscopic infectious agents that replicate inside the living cells of organisms.[175] Viruses infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea.[176][177] More than 6,000 virus species have been described in detail.[178] Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity.[179][180]

MES Note: Submicroscopic = too small to be seen even with a [light] microscope.

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Bacteriophages [infects bacteria and archaea] attached to a bacterial cell wall.

When infected, a host cell is forced to rapidly produce thousands of identical copies of the original virus. When not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent particles, or virions, consisting of the genetic material (DNA or RNA), a protein coat called capsid, and in some cases an outside envelope of lipids. The shapes of these virus particles range from simple helical and icosahedral forms to more complex structures. Most virus species have virions too small to be seen with an optical microscope, as they are one-hundredth the size of most bacteria.

MES Note: An icosahedron is a polyhedron with 20 faces.

A polyhedron (plural polyhedra or polyhedrons) is a three-dimensional shape with flat polygonal faces, straight edges and sharp corners or vertices.

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Convex regular icosahedron

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Figure

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Structure of tobacco mosaic virus [TMV]: RNA coiled in a helix of repeating protein sub-units

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Transmission electron micrograph of TMV particles negative stained [background stained instead of the specimen] to enhance visibility at 160,000× magnification

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Structure of icosahedral adenovirus. Electron micrograph with an illustration to show shape

Transmission electron microscopy (TEM) is a microscopy technique in which a beam of electrons is transmitted through a specimen to form an image.

An electron microscope is a microscope that uses a beam of accelerated electrons as a source of illumination. As the wavelength of an electron can be up to 100,000 times shorter than that of visible light photons, electron microscopes have a higher resolving power than light microscopes and can reveal the structure of smaller objects. A scanning transmission electron microscope has achieved better than 50 pm [1 pm = 1 trillionth of a meter] resolution in annular dark-field imaging [ADF] mode[1] and magnifications of up to about 10,000,000× whereas most light microscopes are limited by diffraction to about 200 nm resolution and useful magnifications below 2000×.

1 picometer (pm) is equal to 10-12 m or 1 trillionth of a meter.

Annular dark-field imaging is a method of mapping samples in a scanning transmission electron microscope (STEM). These images are formed by collecting scattered electrons with an annular dark-field detector.

An annulus (plural annuli or annuluses) is the region between two concentric [having a common center] circles.

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An annulus

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Figure

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A modern transmission electron microscope

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Diagram of a transmission electron microscope

Materials to be viewed under an electron microscope may require processing to produce a suitable sample. The technique required varies depending on the specimen and the analysis required. One technique is staining which involves using heavy metals such as lead, uranium or tungsten to scatter imaging electrons and thus give contrast between different structures, since many (especially biological) materials are nearly "transparent" to electrons.

Note that all images of organisms under an electron microscope are of dead organisms due to the high energy of electrons and preparation process, which kill the organisms.

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An insect coated in gold for viewing with a scanning electron microscope

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Figure

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Figure

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The origins of viruses in the evolutionary history of life are unclear: some may have evolved from plasmids—pieces of DNA that can move between cells—while others may have evolved from bacteria. In evolution, viruses are an important means of horizontal gene transfer, which increases genetic diversity in a way analogous to sexual reproduction.[181] Because viruses possess some but not all characteristics of life, they have been described as "organisms at the edge of life",[182] and as self-replicators.[183]

MES Note: Horizontal gene transfer (HGT) or lateral gene transfer (LGT)[1][2][3] is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction).[4] HGT is an important factor in the evolution of many organisms.

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Tree of life showing vertical and horizontal gene transfers

Viruses can spread in many ways. One transmission pathway is through disease-bearing organisms known as vectors: for example, viruses are often transmitted from plant to plant by insects that feed on plant sap [fluid transported in xylem and phloem of plants], such as aphids [sap-sucking insects]; and viruses in animals can be carried by blood-sucking insects [such as mosquitos].

Influenza viruses [“the flu”] are spread by coughing and sneezing. Norovirus and rotavirus, common causes of viral gastroenteritis [inflammation of the gastrointestinal tract – the stomach and intestine], are transmitted by the faecal–oral route, passed by hand-to-mouth contact or in food or water.

MES Note: The fecal–oral route (also called the oral–fecal route or orofecal route) describes a particular route of transmission of a disease wherein pathogens in fecal particles pass from one person to the mouth of another person.

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The "F-diagram" (feces, fingers, flies, fields, fluids, food), showing pathways of fecal–oral disease transmission. The vertical blue lines show barriers: toilets, safe water, hygiene and handwashing.

Viral infections in animals provoke an immune response that usually eliminates the infecting virus. Immune responses can also be produced by vaccines, which confer an artificially acquired immunity to the specific viral infection.

MES Note: An immune response is a reaction which occurs within an organism for the purpose of defending against foreign invaders. These invaders include a wide variety of different microorganisms including viruses, bacteria, parasites, and fungi which could cause serious problems to the health of the host organism if not cleared from the body. There are two distinct aspects of the immune response, the innate and the adaptive [or acquired], which work together to protect against pathogens. The innate branch—the body's first reaction to an invader—is known to be a non-specific and quick response to any sort of pathogen. On the other hand, the adaptive branch is the body's immune response which is catered against specific antigens and thus, it takes longer to activate the components involved.

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Figure

A vaccine is a biological preparation that provides active acquired immunity to a particular infectious disease.[1] A vaccine typically contains an agent that resembles a disease-causing microorganism and is often made from weakened or killed forms of the microbe, its toxins, or one of its surface proteins. The agent stimulates the body's immune system to recognize the agent as a threat, destroy it, and to further recognize and destroy any of the microorganisms associated with that agent that it may encounter in the future. Vaccines can be prophylactic (to prevent or ameliorate [make better] the effects of a future infection by a natural or "wild" pathogen), or therapeutic (to fight a disease that has already occurred, such as cancer).

Immunity is the capability of multicellular organisms to resist harmful microorganisms.

A viral vector vaccine is a vaccine that uses a viral vector to deliver genetic material coding for a desired antigen into the recipient's host cells. This process can be performed inside a living organism (in vivo) or in cell culture (in vitro). Viruses have evolved specialized molecular mechanisms to efficiently transport their genomes inside the cells they infect. Delivery of genes or other genetic material by a vector is termed transduction and the infected cells are described as transduced. Molecular biologists first harnessed this machinery in the 1970s. Viral vector vaccines use a modified version of one virus as a vector to deliver to a cell a nucleic acid coding for an antigen for another infectious agent. Viral vector vaccines do not cause infection with either the virus used as the vector, or the source of the antigen. The genetic material it delivers does not integrate into a person's genome. As of April 2021, six viral vector vaccines have been authorized for use in humans in at least one country: four COVID-19 vaccines and two Ebola vaccines.

Viral vectors are tools commonly used by molecular biologists to deliver genetic material into cells.

An mRNA vaccine is a type of vaccine that uses a copy of a molecule called messenger RNA (mRNA) to produce an immune response.[1] The vaccine delivers molecules of antigen-encoding mRNA into immune cells, which use the designed mRNA as a blueprint to build foreign protein that would normally be produced by a pathogen (such as a virus) or by a cancer cell. These protein molecules stimulate an adaptive immune response that teaches the body to identify and destroy the corresponding pathogen or cancer cells.[1] The mRNA is delivered by a co-formulation of the RNA encapsulated in lipid nanoparticles [essentially a tiny ball of fat] that protect the RNA strands and help their absorption into the cells. Among the COVID-19 vaccines are a number of RNA vaccines under development to combat the COVID-19 pandemic and some have been approved or have received emergency use authorization in some countries. For example, the Pfizer-BioNTech vaccine is approved for use in adults, while the Moderna mRNA vaccine has emergency use authorization in the US.

DNA vaccines work by injecting genetically engineered plasmid containing the DNA sequence encoding the antigen(s) against which an immune response is sought, so the cells directly produce the antigen, thus causing a protective immunological response.[3] Some cells of the immune system that recognize the proteins expressed will mount an attack against these proteins and cells expressing them. Because these cells live for a very long time, if the pathogen that normally expresses these proteins is encountered at a later time, they will be attacked instantly by the immune system. DNA vaccines have theoretical advantages over conventional vaccines, including the "ability to induce a wider range of types of immune response". One potential advantage of DNA vaccines is that they are very easy to produce and store. In August 2021, Indian authorities gave emergency approval to ZyCoV-D [a COVID-19 vaccine]. Developed by Cadila Healthcare, it is the first DNA vaccine approved for humans.

Electroporation, or electropermeabilization, is a microbiology technique in which an electrical field is applied to cells in order to increase the permeability of the cell membrane, allowing chemicals, drugs, electrode arrays or DNA to be introduced into the cell (also called electrotransfer).

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Figure [from April 2020]

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[From April 2020]

Plant form and function

Plant body

Further information: Plant morphology, Plant anatomy, and Plant physiology

The plant body is made up of organs that can be organized into two major organ systems: a root system and a shoot system.[184] The root system anchors the plants into place. The roots themselves absorb water and minerals and store photosynthetic products. The shoot system is composed of stem, leaves, and flowers. The stems hold and orient the leaves to the sun, which allow the leaves to conduct photosynthesis. The flowers are shoots that have been modified for reproduction. Shoots are composed of phytomers, which are functional units [carries out specific instructions] that consist of a node carrying one or more leaves, internode, and one or more buds [undeveloped or embryonic shoots].

MES Note: A plant shoot consists of any plant stem together with its appendages, leaves and lateral buds, flowering stems, and flower buds.

A bud is an undeveloped or embryonic shoot.

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Root and shoot systems in a eudicot.

MES Note: The apical (Terminal) bud of a plant is the primary growing point located at the apex (tip) of the stem. It is the dominant bud, since it can cause all the Axillary (lateral) buds below them to remain dormant.

A taproot is a large, central, and dominant root from which other roots sprout laterally.

Vegetative shoots consist of stems and leaves.

The stamen (plural stamina or stamens) is the pollen-producing reproductive organ of a flower. A stamen typically consists of a stalk called the filament and an anther which contains microsporangia.

A sporangium (pl. sporangia)[2] (modern Latin, from Greek σπόρος (sporos), 'spore' + ἀγγεῖον (angeion), 'vessel') is an enclosure in which spores are formed.

Microsporangia are sporangia that produce microspores that give rise to male gametophytes when they germinate.

Microspores are land plant spores that develop into male gametophytes, whereas megaspores develop into female gametophytes.

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Stamens of a Hippeastrum with white filaments and prominent anthers carrying pollen

Gynoecium (from Ancient Greek γυνή (gyne, "woman") and οἶκος (oikos, "house")) is most commonly used as a collective term for the parts of a flower that produce ovules and ultimately develop into the fruit and seeds. The gynoecium may consist of one or more separate pistils. A pistil typically consists of an expanded basal portion called the ovary, an elongated section called a style and an apical structure that receives pollen called a stigma.

A carpel is the female reproductive part of the flower —composed of ovary, style, and stigma— and usually interpreted as modified leaves that bear structures called ovules, inside which egg cells ultimately form.

If a gynoecium has a single carpel, it is called monocarpous. If a gynoecium has multiple, distinct (free, unfused) carpels, it is apocarpous. If a gynoecium has multiple carpels "fused" into a single structure, it is syncarpous. A syncarpous gynoecium can sometimes appear very much like a monocarpous gynoecium.

The pistils of a flower are considered to be composed of one or more carpels. A pistil may consist of one carpel (with its ovary, style and stigma); or it may comprise several carpels joined together to form a single ovary, the whole unit called a pistil. The gynoecium may present as one or more uni-carpellate pistils or as one multi-carpellate pistil. (The number of carpels is denoted by terms such as tricarpellate (three carpels).)

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Figure 2: Pistil a. 3 Simple Pistils, b. 1 Compound Pistil, c. 1 Pistil

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Figure: Carpel and Pistil

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Figure

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Cross-section through the ovary of Narcissus showing multiple connate [united] carpels (a compound pistil) fused along the placental line where the ovules form in each locule [small cavity]

In flowering plants, placentation is the attachment of ovules inside the ovary.

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Flower of Magnolia × wieseneri [a hybrid flower] showing the many pistils making up the gynoecium in the middle of the flower

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A syncarpous gynoecium in context. The gynoecium (whether composed of a single carpel or multiple "fused" carpels) is typically made up of an ovary, style, and stigma as in the center of the flower.

A plant body has two basic patterns (apical–basal [top-bottom] and radial axes [laterally]) that been established during embryogenesis [process after fertilization to produce a fully developed plant embryo].[184] Cells and tissues are arranged along the apical-basal axis from root to shoot whereas the three tissue systems (dermal, ground, and vascular) that make up a plant's body are arranged concentrically around its radial axis.[184]

The dermal tissue system forms the epidermis (or outer covering) of a plant, which is usually a single cell layer that consists of cells that have differentiated into three specialized structures: stomata for gas exchange in leaves, trichomes (or leaf hair) for protection against insects and solar radiation, and root hairs for increased surface areas and absorption of water and nutrients.

MES Note:

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Figure: Magnified leaf stomata - schematic (opened and closed)

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Flower bud of a Capsicum pubescens plant, with many trichomes

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Figure: Root hair phenotypes of L. japonicus wild-type Gifu (left), Ljrhl1-1 mutant (center), and Ljrhl1-2 mutant (right) lines. Six-day-old seedlings are shown. Note the emerging difference in root length between wild-type and mutant plants.

The ground tissue makes up virtually all the tissue that lies between the dermal and vascular tissues in the shoots and roots. It consists of three cell types: Parenchyma, collenchyma, and sclerenchyma cells.

MES Note:

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Figure

Palisade cells are plant cells located on the leaves, right below the epidermis and cuticle. In simpler terms, they are known as leaf cells. They are vertically elongated, a different shape from the spongy mesophyll cells beneath them. The chloroplasts in these cells absorb a major portion of the light energy used by the leaf. Palisade cells contain the largest number of chloroplasts per cell, which makes them the primary site of photosynthesis in the leaves of those plants that contain them, converting the energy in light to the chemical energy of carbohydrates. Beneath the palisade mesophyll are the spongy mesophyll cells, which also perform photosynthesis. They are irregularly shaped cells that have many intercellular spaces that allow the passage of gases. There are also guard cells that allow the gases to exchange. The guard cells are collectively known as a stoma derived from the Greek word meaning mouth and plural stomata.

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Cross section of a leaf showing various ground tissue types

Most of the interior of the leaf between the upper and lower layers of epidermis is a parenchyma (ground tissue) or chlorenchyma tissue called the mesophyll (Greek for "middle leaf").

Source: Despite countless sites and other resources saying otherwise, Mesophyll is not a tissue technically speaking. It's just a place, a specific area. Or you can even think of it as the set of all tissues in a given area. And that given area is easy to define: the "filling" of the leaf, between the upper and lower epidermis. According to Mauseth (2012), that with Raven is my favourite book on Botany:

Mesophyll: All tissues of a leaf except the epidermis.

Actually, this is easy to see if you understand the Greek origin of the term: μέσος, meaning "in the middle", and φύλλον, meaning "leaf". Therefore, mesophyll means "in the middle of the leaf". In a common, regular leaf, most of the mesophyll is made of parenchyma, be it palisade or spongy. As I said before several sources treat these terms (mesophyll and parenchyma) as synonyms, but they are not.

Finally, the vascular tissues are made up of two constituent tissues: xylem and phloem. The xylem is made up two of conducting cells called tracheids and vessel elements whereas the phloem is characterized by the presence of sieve tube elements and companion cells.[184]

MES Note: The tracheids and vessel elements are dead, hollow cells specialized to conduct water from the root. Tracheids have tapered ends with pits, while vessel elements have perforated ends [having holes] to allow water transport.

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Figure

Sieve elements are specialized cells that are important for the function of phloem, which is a highly organized tissue that transports organic compounds made during photosynthesis. Sieve elements are the major conducting cells in phloem. Sieve elements typically lack a nucleus and contain none to a very small number of ribosomes.[2] The two types of sieve elements, sieve tube members and sieve cells, have different structures. Sieve tube members are shorter and wider with greater area for nutrient transport while sieve cells tend to be longer and narrower with smaller area for nutrient transport. Although the function of both of these kinds of sieve elements is the same, sieve cells are found in gymnosperms, non-flowering vascular plants, while sieve tube members are found in angiosperms, flowering vascular plants.

The main functions of sieve tube members include maintaining cells and transporting necessary molecules with the help of companion cells.[6] The sieve tube members are living cells (which do not contain a nucleus) that are responsible for transporting carbohydrates throughout the plant.[7] Sieve tube members are associated with companion cells, which are cells that combine with sieve tubes to create the sieve element-companion cell complex. This allows for supply and maintenance of the plant cells and for signaling between distant organs within the plant.[6] Sieve tube members do not have ribosomes or a nucleus and thus need companion cells to help them function as transport molecules. Companion cells provide sieve tube members with proteins necessary for signaling and ATP in order to help them transfer molecules between different parts of the plant. It is the companion cells that helps transport carbohydrates from outside the cells into the sieve tube elements.[8] The companion cells also allow for bidirectional flow.[2]

The metabolic functioning of sieve-tube members depends on a close association with the companion cells, a specialized form of parenchyma cell. All of the cellular functions of a sieve-tube element are carried out by the (much smaller) companion cell, a typical nucleate [contains a cell nucleus] plant cell except the companion cell usually has a larger number of ribosomes and mitochondria.

Sieve tube members tend to be found largely in angiosperms.[1] They are very long and have horizontal end walls containing sieve plates. Sieve plates contain sieve pores which can regulate the size of the openings in the plates with changes in the surroundings of the plants.

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Sieve tube members form a sieve tube which have sieve plates between them to transport nutrients. The companion cells shown contain a nucleus which can synthesize additional protein for cell signaling. The bidirectional flow of nutrients is shown with the double arrow.

Sieve cells are long, conducting cells in the phloem that do not form sieve tubes. The major difference between sieve cells and sieve tube members is the lack of sieve plates in sieve cells.[1] They have a very narrow diameter and tend to be longer in length than sieve tube elements as they are generally associated with albuminous cells [specialized parenchyma cells].[4] Similar to how Sieve Tube members are associated with companion cells, sieve cells are flanked [situated at the sides] with albuminous cells in order to aid in transporting organic material. Albuminous cells have long, unspecialized areas with ends that overlap with those of other sieve cells and contain nutrients and store food in order to nourish tissues.[7] They enable the sieve cells to be connected to parenchyma, functional tissue in the organs, which helps to stabilize the tissue and transport nutrients. Sieve cells are also associated with gymnosperms because they lack the companion cell and sieve member complexes that angiosperms have.

Sieve elements elongate cells containing sieve areas on their walls. Pores on sieve areas allow for cytoplasmic connections to neighboring cells, which allows for the movement of photosynthetic material and other organic molecules necessary for tissue function.

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Figure: Schematic drawing of phloem sieve element end wall types. Some angiosperm species have a transverse-oriented end wall covered by a single sieve area (SA) (simple), while others have inclined end walls with, typically, between two and 20 sieve areas (compound). Gymnosperms have highly inclined end walls with, typically, between 12 and 30 sieve areas. While in angiosperms sieve areas on the end walls are different from lateral sieve areas (LSA), there is no distinct difference between sieve areas in gymnosperms. SP, sieve pore.

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Figure

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Figure: Conductive cells of vascular plants: sieve elements. A. Types of sieve elements. B,C. Sieve tube members. Sieve plates consist of one or more sieve areas at the end-wall junction of two sieve tube members; the pores of a sieve plate, however, are significantly larger than are those of sieve areas located on the side wall (Figure 4.6C). Both sieve cells and sieve tube members have parenchyma cells associated with them. Parenchyma cells associated with sieve cells are called albuminous cells; those associated with sieve tube members are called companion cells.

Callose is a plant polysaccharide and it is produced to act as a temporary cell wall in response to stimuli such as stress or damage.

Plant nutrition and transport

Further information: Vascular plant § Nutrient distribution

Like all other organisms, plants are primarily made up of water and other molecules containing elements that are essential to life.[185] The absence of specific nutrients (or essential elements), many of which have been identified in hydroponic experiments, can disrupt plant growth and reproduction.

MES Note: An essential nutrient is a nutrient required for normal physiological function that cannot be synthesized in the body – either at all or in sufficient quantities – and thus must be obtained from a dietary source.

Hydroponics[1] is a type of horticulture and a subset of hydroculture which involves growing plants (usually crops) without soil, by using mineral nutrient solutions in an aqueous solvent.

Horticulture is the art of cultivating plants in gardens to produce food and medicinal ingredients, or for comfort and ornamental purposes.

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NASA researcher checking hydroponic onions (center), Bibb lettuces (left), and radishes (right)

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Water plant-cultivated crocus.

Passive sub-irrigation, also known as passive hydroponics, semi-hydroponics, or hydroculture,[43] is a method wherein plants are grown in an inert porous medium that transports water and fertilizer to the roots by capillary action from a separate reservoir as necessary, reducing labor and providing a constant supply of water to the roots.

Source: What is hydroculture? The term “hydroponics” is familiar to most people. Hydroponics involves growing plants in a liquid growing medium solution. Hydroponics has become quite popular in recent years, particularly in the growth of vegetables like lettuce and tomatoes. Hydroculture is similar to hydroponics in many ways but has a key difference – instead of using a nutrient solution containing water as a growing medium, it uses an inorganic solid growing medium (or inert). The inert growing medium is usually rock-based, typically something called “expanded clay aggregates.” Hydroculture is sometimes called “passive hydroponics,” meaning the plants grow without soil, bark or peat moss.

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Figure: Passive Hydroponics: There is no electricity used as well as no pumps and wick needed.

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Figure: The “wick” of Wick & Grow™ is a simple little string inserted into the bottom of the pot that allows plants to drink up water from a reservoir in the base of the container. Like a straw, the plants’ roots use the wick to take sips of water when the plant is thirsty.

Aquatic plants [or water plants] are plants that have adapted to living in aquatic environments (saltwater or freshwater).

Capillary action (sometimes capillarity, capillary motion, capillary effect, or wicking) is the process of a liquid flowing in narrow spaces without the assistance of, or even in opposition to, external forces like gravity. The effect can be seen in the drawing up of liquids between the hairs of a paint-brush. It occurs because of intermolecular forces between the liquid and surrounding solid surfaces. If the diameter of the tube is sufficiently small, then the combination of surface tension (which is caused by cohesion within the liquid) and adhesive forces between the liquid and container wall act to propel the liquid. With some pairs of materials, such as mercury and glass, the intermolecular forces within the liquid exceed those between the solid and the liquid, so a convex meniscus forms and capillary action works in reverse.

The meniscus (plural: menisci, from the Greek for "crescent", after Giacomo Meniscus (1449-1512), a Venetian physician and friend of Leonardo da Vinci[1]) is the curve in the upper surface of a liquid close to the surface of the container or another object, caused by surface tension. It can be either concave or convex, depending on the liquid and the surface.

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A: The bottom of a concave meniscus. B: The top of a convex meniscus.

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Capillary action of water (polar) compared to mercury (non-polar), in each case with respect to a polar surface such as glass (≡Si–OH)

Intermolecular forces (IMF) (or secondary forces) are the forces which mediate interaction between molecules, including forces of attraction or repulsion which act between atoms and other types of neighboring particles, e.g. atoms or ions. Intermolecular forces are weak relative to intramolecular forces – the forces which hold a molecule together. For example, the covalent bond, involving sharing electron pairs between atoms, is much stronger than the forces present between neighboring molecules.

The majority of plants are able to obtain these nutrients from solutions that surrounds their roots in the soil.[185] Continuous leaching and harvesting of crops can deplete [reduce] the soil of its nutrients, which can be restored with the use of fertilizers.

MES Note: In agriculture, leaching is the loss of water-soluble plant nutrients from the soil, due to rain and irrigation.

Harvesting is the process of gathering a ripe crop from the fields.

Agriculture is the practice of cultivating [growing] plants and livestock [domesticated animals].

Irrigation is the artificial process of applying controlled amounts of water to land to assist in the production of crops,[1] but also to grow landscape plants and lawns, where it may be known as watering.

A crop is a plant or animal product that can be grown and harvested extensively for profit or subsistence [food, clothing, shelter].

A fertilizer (American English) or fertiliser (British English) is any material of natural or synthetic origin that is applied to soil or to plant tissues to supply plant nutrients.

Domestication is a sustained multi-generational relationship in which one group of organisms assumes a significant degree of influence over the reproduction and care of another group to secure a more predictable supply of resources from that second group.[1] The domestication of plants and animals was a major cultural innovation ranked in importance with the conquest of fire, the manufacturing of tools, and the development of verbal language.

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Dogs and sheep were among the first animals to be domesticated.

Carnivorous plants such as Venus flytraps are able to obtain nutrients by digesting other arthropods whereas parasitic plants such as mistletoes can parasitize other plants for water and nutrients.

MES Note: A carnivore, or meat-eater (Latin, caro, genitive [modifying another word] carnis, meaning meat or "flesh" and vorare meaning "to devour"), is an animal whose food and energy requirements derive solely from animal tissues (mainly muscle, fat and other soft tissues) whether through hunting or scavenging.

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A closing trap

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Video: A time lapse showing Venus flytrap catching prey

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European mistletoe (Viscum album) attached to a common aspen (Populus tremula)

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The xylem (blue) transports water and minerals from the roots upwards whereas the phloem (orange) transports carbohydrates between organs.

Plants need water to conduct photosynthesis, transport solutes between organs, cool their leaves by evaporation, and maintain internal pressures that support their bodies.[185] Water is able to diffuse in and out of plant cells by osmosis. The direction of water movement across a semipermeable membrane is determined by the water potential across that membrane.[185]

MES Note: Diffusion is the net movement of anything (for example, atoms, ions, molecules, energy) from a region of higher concentration to a region of lower concentration. Diffusion is driven by a gradient [difference] in concentration.

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Some particles are dissolved in a glass of water. At first, the particles are all near one top corner of the glass. If the particles randomly move around ("diffuse") in the water, they eventually become distributed randomly and uniformly from an area of high concentration to an area of low concentration.

Osmosis is the spontaneous net movement or diffusion of solvent molecules through a selectively permeable membrane from a region of high water potential [potential energy / pressure] (region of lower solute concentration) to a region of low water potential (region of higher solute concentration),[2] in the direction that tends to equalize the solute concentrations on the two sides.

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The process of osmosis over a semi-permeable membrane. The blue dots represent particles driving the osmotic gradient.

The mechanism of osmosis is not straight-forward but may be due to a lowering of water/solvent pressure with increased solute; thus the solvent moves until the pressure is in equilibrium.

Water is able to diffuse across a root cell's membrane through aquaporins whereas solutes are transported across by the membrane by ion channels and pumps.

MES Note: Aquaporins, also called water channels, are proteins that form pores [small openings] in the membrane of biological cells, mainly facilitating transport of water between cells.

Ion channels are pore-forming membrane proteins that allow ions to pass through the channel pore.

In biology, a transporter is a transmembrane protein that moves ions (or other small molecules) across a biological membrane to accomplish many different biological functions including, cellular communication, maintaining homeostasis, energy production, etc.[1] Active transporters or ion pumps are transporters that convert energy from various sources—including adenosine triphosphate (ATP), sunlight, and other redox reactions—to potential energy by pumping an ion up its concentration gradient.

A transmembrane protein (TP) is a type of integral membrane protein that spans the entirety of the cell membrane.

An integral membrane protein (IMP) is a type of membrane protein that is permanently attached to the biological membrane. All transmembrane proteins are IMPs, but not all IMPs are transmembrane proteins.

In vascular plants, water and solutes are able to enter the xylem, a vascular tissue [conducting tissue], by way of an apoplast and symplast. Once in the xylem, the water and minerals are distributed upward by transpiration from the soil to the aerial parts of the plant.[162][185]

MES Note: Inside a plant, the apoplast is the space outside the plasma membrane [but within cell wall] within which material can diffuse freely.

The symplast of a plant is the inner side of the plasma membrane in which water and low-molecular-weight solutes can freely diffuse.

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The apoplastic and symplastic pathways

Transpiration is the process of water movement through a plant and its evaporation from aerial parts, such as leaves, stems and flowers. Water is necessary for plants but only a small amount of water taken up by the roots is used for growth and metabolism. The remaining 97–99.5% is lost by transpiration and guttation.

Guttation is the exudation of drops of xylem sap on the tips or edges of leaves of some vascular plants, such as grasses, and a number of fungi. Guttation is not to be confused with dew, which condenses [phase change from gas to liquid] from the atmosphere onto the plant surface. Guttation generally happens during the night time.

An exudate is a fluid emitted by an organism through pores or a wound, a process known as exuding or exudation.[1] Exudate is derived from exude, "to ooze",[2] from the Latin exsūdāre, "to (ooze out) sweat" (ex- "out" and sūdāre "to sweat").

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Guttation on a strawberry leaf

In contrast, the phloem, another vascular tissue, distributes carbohydrates (e.g., sucrose) and other solutes such as hormones by translocation from a source (e.g., mature leaf or root) in which they were produced to a sink (e.g., root, flower, or developing fruit) in which they will be used and stored.[185] Sources and sinks can switch roles, depending on the amount of carbohydrates accumulated or mobilized for the nourishment of other organs.

MES Note:

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The process of translocation within the phloem

Plant development

Further information: Plant development

Plant development is regulated by environmental cues [signals] and the plant's own receptors, hormones, and genome.[186] Moreover, they have several characteristics that allow them to obtain resources for growth and reproduction such as meristems, post-embryonic organ formation, and differential growth.

MES Note: The meristem is a type of tissue found in plants. It consists of undifferentiated cells (meristematic cells) capable of cell division. Cells in the meristem can develop into all the other tissues and organs that occur in plants. These cells continue to divide until a time when they get differentiated and then lose the ability to divide.

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Tunica-Corpus model of the apical meristem (growing tip). The epidermal (L1) and subepidermal (L2) layers form the outer layers called the tunica [named after a tunic, i.e. coat]. The inner L3 layer is called the corpus. Cells in the L1 and L2 layers divide in a sideways fashion, which keeps these layers distinct, whereas the L3 layer divides in a more random fashion.

In biology, tissue is a cellular organizational level between cells and a complete organ.

Development begins with a seed, which is an embryonic plant [contains the embryo] enclosed in a protective outer covering. Most plant seeds are usually dormant, a condition in which the seed's normal activity is suspended.[186] Seed dormancy may last weeks, months, years, and even centuries. Dormancy is broken once conditions are favorable for growth, and the seed will begin to sprout [grow], a process called germination.

MES Note: Germination is the process by which an organism grows from a seed or spore. The term is applied to the sprouting of a seedling from a seed of an angiosperm or gymnosperm, the growth of a sporeling from a spore, such as the spores of fungi, ferns, bacteria, and the growth of the pollen tube from the pollen grain of a seed plant.

Sprouting is the natural process by which seeds or spores germinate and put out shoots, and already established plants produce new leaves or buds or other newly developing parts[example needed] experience further growth.

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Sunflower time lapse with soil. cross section, showing how the roots and the upper part of the plant grow

Imbibition is the first step in germination, whereby water is absorbed by the seed. Once water is absorbed, the seed undergoes metabolic changes whereby enzymes are activated and RNA and proteins are synthesized. Once the seed germinates, it obtains carbohydrates, amino acids, and small lipids that serve as building blocks for its development. These monomers are obtained from the hydrolysis of starch, proteins, and lipids that are stored in either the cotyledons or endosperm. Germination is completed once embryonic roots called radicle have emerged from the seed coat. At this point, the developing plant is called a seedling and its growth is regulated by its own photoreceptor proteins and hormones.[186]

MES Note: A cotyledon ("seed leaf" from Latin cotyledon[1]) is a significant part of the embryo within the seed of a plant, and is defined as "the embryonic leaf in seed-bearing plants, one or more of which are the first to appear from a germinating seed." Species with one cotyledon are called monocotyledonous ("monocots"). Plants with two embryonic leaves are termed dicotyledonous ("dicots").

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Comparison of a monocot and dicot sprouting. The visible part of the monocot plant (left) is actually the first true leaf produced from the meristem; the cotyledon itself remains within the seed

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Figure

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Note that a “kernel” is broadly a synonym for “seed”.

The endosperm is a tissue produced inside the seeds of most of the flowering plants following double fertilization.

Bran, also known as miller's bran, is the hard outer layers of cereal grain.

The germ of a cereal is the reproductive part that germinates to grow into a plant;[1] it is the embryo[2] of the seed.

A cereal is any grass [a type of flowering plant] cultivated (grown) for the edible components of its grain (botanically, a type of fruit called a caryopsis), composed of the endosperm, germ, and bran.

The seed coat in the mature seed can be a paper-thin layer (e.g. peanut) or something more substantial (e.g. thick and hard in a coconut), or fleshy as in the pomegranate.

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Seed coat of pomegranate

Unlike animals in which growth is determinate, i.e., ceases when the adult state is reached, plant growth is indeterminate as it is an open-ended process that could potentially be lifelong.[184] Plants grow in two ways: primary and secondary. In primary growth, the shoots and roots are formed and lengthened. The apical meristem produces the primary plant body, which can be found in all seed plants. During secondary growth, the thickness of the plant increases as the lateral meristem [surrounds the established stem of a plant and grow latterly] produces the secondary plant body, which can be found in woody eudicots [clade of flowering plants that are dicots] such as trees and shrubs. Monocots do not go through secondary growth.[184] The plant body is generated by a hierarchy of meristems. The apical meristems in the root and shoot systems give rise to primary meristems (protoderm, ground meristem, and procambium), which in turn, give rise to the three tissue systems (dermal, ground, and vascular).

MES Note:

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Figure

The meristem cells mature into three primary meristems:

  • protoderm gives rise to dermal tissues (epidermis).
  • procambium gives rise to vascular tissues.
    • It also produces the vascular cambium, and cork cambium, secondary meristems.
    • Vascular cambium produces secondary xylem inwards, and secondary phloem outwards.
    • Cork cambium is one of the many layers of bark.
  • ground meristem gives rise to ground tissues.

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Figure

Vascular tissue is a complex conducting tissue, formed of more than one cell type, found in vascular plants.

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Cross section of celery stalk, showing vascular bundles, which include both phloem and xylem.

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Figure

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Figure

The ground tissue of plants includes all tissues that are neither dermal nor vascular.

Plant reproduction

Further information: Plant reproduction

Most angiosperms (or flowering plants) engage in sexual reproduction.[187]

MES Note: Sexual reproduction is a type of reproduction that involves a complex life cycle in which a gamete (such as a sperm or egg cell) with a single set of chromosomes (haploid) combines with another to produce a zygote that develops into an organism composed of cells with two sets of chromosomes (diploid).

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In the first stage of sexual reproduction, "meiosis", the number of chromosomes is reduced from a diploid number (2n) to a haploid number (n). During "fertilisation", haploid gametes come together to form a diploid zygote, and the original number of chromosomes is restored.

Their flowers are organs that facilitate reproduction, usually by providing a mechanism for the union of sperm with eggs. Flowers may facilitate two types of pollination: self-pollination and cross-pollination. Self-pollination occurs when the pollen from the anther is deposited on the stigma of the same flower, or another flower on the same plant. Cross-pollination is the transfer of pollen from the anther of one flower to the stigma of another flower on a different individual of the same species. Self-pollination happened [sic] in flowers where the stamen and carpel mature at the same time, and are positioned so that the pollen can land on the flower’s stigma [such as via wind]. This pollination does not require an investment from the plant to provide nectar and pollen as food for pollinators.[188]

MES Note: A pollinator is an animal that moves pollen from the male anther of a flower to the female stigma of a flower.

Nectar is a sugar-rich liquid produced by plants in glands called nectaries or nectarines, either within the flowers with which it attracts pollinating animals, or by extrafloral nectaries, which provide a nutrient source to animal mutualists [interaction where all benefit], which in turn provide herbivore protection [protection against plant eaters].

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An Australian painted lady [a type of butterfly] feeding on a flower's nectar

Extrafloral nectaries (also known as extranuptial nectaries) are specialised nectar-secreting plant glands that develop outside of flowers and are not involved in pollination, generally on the leaf or petiole [connects leaf to the stem] (foliar nectaries) and often in relation to the leaf venation.

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Stem showing internode and nodes plus leaf petioles

Venation is the pattern of veins in the blade of a leaf. The veins consist of vascular tissues which are important for the transport of food and water.

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A leaf with laminar [smooth, layered organization] structure and pinnate [feather like arrangement] venation

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Reproduction and development in sporophytes

Plant responses

Further information: Plant perception (physiology) and Plant defense against herbivory § Chemical defenses

Like animals, plants produce hormones in one part of its body to signal cells in another part to respond. The ripening of fruit and loss of leaves in the winter are controlled in part by the production of the gas ethylene [CH2=CH2, acts naturally as a plant hormone] by the plant. Stress from water loss, changes in air chemistry, or crowding by other plants can lead to changes in the way a plant functions. These changes may be affected by genetic, chemical, and physical factors.

MES Note: Ripening is a process in fruits that causes them to become more palatable. In general, fruit becomes sweeter, less green, and softer as it ripens. Climacteric fruits ripen after harvesting and so some fruits for market are picked green (e.g. bananas and tomatoes).

The climacteric is a stage of fruit ripening associated with increased ethylene production and a rise in cellular respiration.

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Figure 1.4: Phases in respiration in a ripening climacteric and non-climacteric fruit. Note, in a climacteric fruit, ethylene production is typically very low prior to the pre-climacteric minimum and increases rapidly as the respiratory climacteric occurs.

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Figure

To function and survive, plants produce a wide array of chemical compounds not found in other organisms. Because they cannot move, plants must also defend themselves chemically from herbivores, pathogens and competition from other plants. They do this by producing toxins and foul-tasting or smelling chemicals. Other compounds defend plants against disease, permit survival during drought, and prepare plants for dormancy, while other compounds are used to attract pollinators or herbivores to spread ripe seeds.

MES Note: A toxin is a harmful substance produced within living cells or organisms;[1][2] synthetic toxicants created by artificial processes are thus excluded.

Many plant organs contain different types of photoreceptor proteins [light-sensitive proteins], each of which reacts very specifically to certain wavelengths of light.[189] The photoreceptor proteins relay information such as whether it is day or night, duration of the day, intensity of light available, and the source of light. Shoots generally grow towards light, while roots grow away from it, responses known as phototropism and skototropism, respectively. They are brought about by light-sensitive pigments like phototropins and phytochromes and the plant hormone auxin.[190] Many flowering plants bloom [grow flowers] at the appropriate time because of light-sensitive compounds that respond to the length of the night, a phenomenon known as photoperiodism.

MES Note:

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The light from the lamp (1.) functions as a detectable change in the plant's environment. As a result, the plant exhibits a reaction of phototropism--directional growth (2.) toward the light stimulus.

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Auxin distribution controls phototropism. 1. Sunlight strikes the plant from directly above. Auxin (pink dots) encourages growth straight up. 2, 3, 4. Sunlight strikes the plant at an angle. Auxin is concentrated on one side, encouraging growth at an angle from the preceding stem.

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Daisies (Bellis perennis) facing the sun after opening in the morning, and they follow the sun through the day

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Video: Daisies following the sun

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Figures: Why sunflowers move with the sun

In addition to light, plants can respond to other types of stimuli. For instance, plants can sense the direction of gravity to orient themselves correctly. They can respond to mechanical stimulation.[191]

Animal form and function

Principles

Further information: Zoology, Anatomy, and Physiology

The cells in each animal body are bathed in interstitial fluid, which make up the cell's environment. This fluid and all its characteristics (e.g., temperature, ionic composition) can be described as the animal's internal environment, which is in contrast to the external environment that encompasses the animal's outside world.[192]

MES Note: Interstitial fluid is the body fluid between blood vessels and cells,[7] containing nutrients from capillaries [small blood vessels connecting arteries and veins] by diffusion and holding waste products discharged out by cells due to metabolism.

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A simplified illustration of a capillary network

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The distribution of the total body water in mammals between the intracellular compartment [within cells] and the extracellular compartment [outside of cells], which is, in turn, subdivided into interstitial fluid and smaller components, such as the blood plasma, the cerebrospinal fluid [surrounds the brain and spinal cord] and lymph [makes up a small % of the interstitial fluid]

In lean healthy adult men, the total body water is about 60% (60–67%) of the total body weight; it is usually slightly lower in women (52-55%).[2][3] The exact percentage of fluid relative to body weight is inversely proportional to the percentage of body fat.

Animals can be classified as either regulators or conformers. Animals such as mammals and birds are regulators as they are able to maintain a constant internal environment such as body temperature despite their environments changing. These animals are also described as homeotherms as they exhibit thermoregulation by keeping their internal body temperature constant. In contrast, animals such as fishes and frogs are conformers as they adapt their internal environment (e.g., body temperature) to match their external environments. These animals are also described as poikilotherms [highly variable internal temperature] or ectotherms [internal heat generation is very low] as they allow their body temperatures to match their external environments. In terms of energy, regulation is more costly than conformity as an animal expands more energy to maintain a constant internal environment such as increasing its basal metabolic rate, which is the rate of energy consumption.[192] Similarly, homeothermy is more costly than poikilothermy.

MES Note: Thermoregulation is the ability of an organism to keep its body temperature within certain boundaries, even when the surrounding temperature is very different. A thermoconforming organism, by contrast, simply adopts the surrounding temperature as its own body temperature, thus avoiding the need for internal thermoregulation.

Homeothermy, homothermy or homoiothermy[1] is thermoregulation that maintains a stable internal body temperature regardless of external influence. This internal body temperature is often, though not necessarily, higher than the immediate environment[2] (from Greek ὅμοιος homoios "similar" and θέρμη thermē "heat"). Homeothermy is one of the three types of thermoregulation in warm-blooded animal species. Homeothermy's opposite is poikilothermy. A poikilotherm is an organism that does not maintain a fixed internal temperature but rather fluctuates based on their environment and physical behaviour.[3] Homeotherms are not necessarily endothermic. Some homeotherms may maintain constant body temperatures through behavioral mechanisms alone, i.e., behavioral thermoregulation. Many reptiles use this strategy. For example, desert lizards are remarkable in that they maintain near-constant activity temperatures that are often within a degree or two of their lethal critical temperatures. The only known living homeotherms are birds and mammals.

Source: Many lizards behaviorally regulate body temperatures within a narrow range by shuttling between sun and shade or hot and cold microenvironments to alter heat flux, by modifying posture to alter surface areas exposed to heat sources or sinks, and regulating activity times.

An endotherm (from Greek ἔνδον endon "within" and θέρμη thermē "heat") is an organism that maintains its body at a metabolically favorable temperature, largely by the use of heat released by its internal bodily functions instead of relying almost purely on ambient heat. Such internally generated heat is mainly an incidental product of the animal's routine metabolism, but under conditions of excessive cold or low activity an endotherm might apply special mechanisms adapted specifically to heat production. Examples include special-function muscular exertion such as shivering, and uncoupled oxidative metabolism such as within brown adipose tissue [body fat]. Only birds and mammals are extant universally endothermic groups of animals. Certain lamnid sharks, tuna and billfishes are also endothermic. In common parlance [way of speaking], endotherms are characterized as "warm-blooded". The opposite of endothermy is ectothermy, although in general, there is no absolute or clear separation between the nature of endotherms and ectotherms.

Shivering (also called shuddering) is a bodily function in response to cold and extreme fear in warm-blooded animals. When the core body temperature drops, the shivering reflex is triggered to maintain homeostasis. Skeletal muscles begin to shake in small movements, creating warmth by expending energy.

An uncoupler or uncoupling agent is a molecule that disrupts oxidative phosphorylation in prokaryotes and mitochondria or photophosphorylation in chloroplasts and cyanobacteria by dissociating the reactions of ATP synthesis from the electron transport chain. The result is that the cell or mitochondrion expends energy to generate a proton motive force, but the proton motive force is dissipated before the ATP synthase can recapture this energy and use it to make ATP. Uncouplers are capable of transporting protons through mitochondrial and lipid membranes.

Many terrestrial ectotherms are poikilothermic.[2] However some ectotherms remain in temperature-constant environments to the point that they are actually able to maintain a constant internal temperature (i.e. are homeothermic). It is this distinction that often makes the term "poikilotherm" more useful than the vernacular [common, informal] "cold-blooded", which is sometimes used to refer to ectotherms more generally.

Basal metabolic rate (BMR) is the rate of energy expenditure per unit time by endothermic animals at rest.

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Source: Pacific bluefin tuna are top predators renowned for their epic migrations across the Pacific Ocean. They are also unique amongst bony fish as they are warm bodied (endothermic) and are capable of elevating their core body temperature up to 20°C above that of the surrounding water. They are also capable of diving down below 1000 m into much colder water which affects the temperature of their heart. Dr Holly Shiels at the university's Faculty of Life Sciences says: "When tunas dive down to cold depths their body temperature stays warm but their heart temperature can fall by 15°C within minutes. The heart is chilled because it receives blood directly from the gills which mirrors water temperature. This clearly imposes stress upon the heart but it keeps beating, despite the temperature change. In most other animals the heart would stop."

Homeostasis is the stability of an animal's internal environment, which is maintained by negative feedback loops.[192][193]

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Negative feedback is necessary for maintaining homeostasis such as keeping body temperature constant.

MES Note: Negative feedback work against stimulus while positive feedback reinforces stimulus.

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The body size of terrestrial animals [land animals] vary across different species but their use of energy does not scale linearly according to their size.[192] Mice, for example, are able to consume three times more food than rabbits in proportion to their weights as the basal metabolic rate per unit weight in mice is greater than in rabbits.[192] Physical activity can also increase an animal's metabolic rate. When an animal runs, its metabolic rate increases linearly with speed.[192] However, the relationship is non-linear in animals that swim or fly. When a fish swims faster, it encounters greater water resistance and so its metabolic rates increases exponential.[192] Alternatively, the relationship of flight speeds and metabolic rates is U-shaped in birds.[192] At low flight speeds, a bird must maintain a high metabolic rates [sic] to remain airborne. As it speeds up its flight, its metabolic rate decreases with the aid of air rapidly flows over its wings. However, as it increases in its speed even further, its high metabolic rates rises again due to the increased effort associated with rapid flight speeds. Basal metabolic rates can be measured based on an animal's rate of heat production.

MES Note:

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Figure: Cost of Exercise Rate of O2 consumption as a function of forward speed for (A) people running, (B) fish swimming, and (C) birds flying. [200 m/min = 12 km/hour = 7.46 mph]

Water and salt balance

Further information: Osmoregulation and Urinary system

An animal's body fluids have three properties: osmotic pressure, ionic composition, and volume.[194] Osmotic pressures determine the direction of the diffusion of water (or osmosis), which moves from a region where osmotic pressure (total solute concentration) is low to a region where osmotic pressure (total solute concentration) is high. Aquatic animals are diverse with respect to their body fluid compositions and their environments. For example, most invertebrate animals in the ocean have body fluids that are isosmotic [same osmotic pressure, hence no osmotic flow] with seawater.

In contrast, ocean bony fishes [fish that have skeletons] have body fluids that are hyposmotic [has lower concentration of solutes (salt)] to seawater [resulting in water loss]. Finally, freshwater animals have body fluids that are hyperosmotic [has greater concentration of solutes (salt)] to fresh water.

MES Note: Saltwater fish live in a natural environment where the levels of salt are much higher than they have in their bodies. Because salt is an agent that attracts and draws out water, the surrounding salt water draws water from inside the fish so they must constantly drink water to replace the lost water in their system. The process of water being drawn out of the body by the surrounding water of higher salt levels is known as osmosis. Both saltwater fish and freshwater fish rely on osmosis and diffusion to keep their tissues in healthy condition.

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Typical ions that can be found in an animal's body fluids are sodium [Na], potassium [K], calcium [Ca], and chloride [Cl].

The volume of body fluids can be regulated by excretion. Vertebrate animals have kidneys, which are excretory organs made up of tiny tubular structures called nephrons, which make urine from blood plasma. The kidneys' primary function is to regulate the composition and volume of blood plasma by selectively removing material from the blood plasma itself. The ability of xeric [dry-land] animals such as kangaroo rats [rats that hop like kangaroos] to minimize water loss by producing urine that is 10-20 times concentrated than their blood plasma allows them to adapt in desert [dry barren areas, hostile for living conditions] environments that receive very little precipitation [water fall, rain, snow, etc.].[194]

MES NOTE: Excretion is a process in which metabolic waste is eliminated from an organism. In vertebrates this is primarily carried out by the lungs, kidneys, and skin.[1] This is in contrast with secretion, where the substance may have specific tasks after leaving the cell. Excretion is an essential process in all forms of life. For example, in mammals, urine is expelled through the urethra, which is part of the excretory system. In unicellular organisms, waste products are discharged directly through the surface of the cell.

The excretory system is a passive biological system that removes excess, unnecessary materials from the body fluids of an organism, so as to help maintain internal chemical homeostasis and prevent damage to the body.

Urine is a liquid by-product [secondary product] of metabolism in humans and in many other animals. Urine flows from the kidneys through the ureters to the urinary bladder. Urination results in urine being excreted from the body through the urethra.

The urethra (from Greek οὐρήθρα – ourḗthrā) is a tube that connects the urinary bladder to the urinary meatus [opening urethra] for the removal of urine from the body of both females and males.

The urinary meatus, also known as the external urethral orifice, is the opening of the urethra.

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The urethra transports urine from the bladder to the outside of the body. This image shows (a) a female urethra and (b) a male urethra.

The ureters are tubes made of smooth muscle that propel urine from the kidneys to the urinary bladder.

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The ureters are tubes that carry urine and connect the kidneys to the bladder.

The kidneys are two reddish-brown bean-shaped organs found in vertebrates.

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The kidneys lie behind the abdomen, and act to filter blood to create urine.

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A CT scan [computer tomography via x-rays] of the abdomen showing the [cross-section top view] position of the kidneys.

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Figure: A healthy kidney

The nephron is the minute or microscopic structural and functional unit of the kidney.

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Diagram (left) of a long juxtamedullary nephron and (right) of a short cortical nephron. The left nephron is labelled with six named nephron segments. Also labelled is the collecting duct, mislabelled the "collection duct"; it is the last part of the nephron.

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Nutrition and digestion

Further information: Nutrition, Digestion, and Digestive system

Animals are heterotrophs as they feed on other living organisms to obtain energy and organic compounds.[195] They are able to obtain food in three major ways such as targeting visible food objects, collecting tiny food particles, or depending on microbes for critical food needs. The amount of energy stored in food can be quantified based on the amount of heat (measured in calories or kilojoules) emitted when the food is burnt in the presence of oxygen.

MES Note: The calorie is a unit of energy defined as the amount of heat needed to raise the temperature of a quantity of water by one degree.

For historical reasons, two main definitions of calorie are in wide use. The small calorie or gram calorie (usually denoted cal) is the amount of heat needed to raise the temperature of one gram of water by one degree Celsius (or one kelvin).[1][2] The large calorie, food calorie, or kilocalorie (Cal, Calorie or kcal), most widely used in nutrition,[3] is the amount of heat needed to cause the same increase in one kilogram of water.[4] Thus, 1 kilocalorie (kcal) = 1000 calories (cal).

Calorie relates directly to the metric system, and therefore to the SI system [International System of Units]. The SI unit of energy is the joule. One calorie is defined as exactly 4.184 J, and one Calorie (kilocalorie) is 4184 J [or 4.184 kilojoules (kJ)].

If an animal were to consume food that contains an excess amount of chemical energy, it will store most of that energy in the form of lipids [fat] for future use and some of that energy as glycogen for more immediate use (e.g., meeting the brain's energy needs).[195] The molecules in food are chemical building blocks that are needed for growth and development. These molecules include nutrients [macronutrients] such as carbohydrates, fats, and proteins. Vitamins and minerals (e.g., calcium [Ca], magnesium [Mg], sodium [Na], and phosphorus [P]) are also essential.

MES Note: A vitamin is an organic molecule that is an essential micronutrient which an organism needs in small quantities for the proper functioning of its metabolism. Essential nutrients cannot be synthesized in the organism, either at all or not in sufficient quantities, and therefore must be obtained through the diet. Vitamin C [C6H8O6] can be synthesized by some species but not by others; it is not a vitamin in the first instance but is in the second. The term vitamin does not include the three other groups of essential nutrients: minerals, essential fatty acids, and essential amino acids.[2] Most vitamins are not single molecules, but groups of related molecules called vitamers.

In the context of nutrition, a mineral is a chemical element required as an essential nutrient by organisms to perform functions necessary for life.[1][2][3] However, the four major structural elements in the human body by weight (oxygen, hydrogen, carbon, and nitrogen), are usually not included in lists of major nutrient minerals (nitrogen is considered a "mineral" for plants, as it often is included in fertilizers). These four elements compose about 96% of the weight of the human body, and major minerals (macrominerals) and minor minerals (also called trace elements) compose the remainder.

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Figure: Illustration of the makeup of the human body.

In geology and mineralogy, a mineral or mineral species is, broadly speaking, a solid chemical compound with a fairly well-defined chemical composition and a specific crystal structure [orderly, repeating structure] that occurs naturally in pure form.

The digestive system, which typically consist of a tubular tract that extends from the mouth to the anus, is involved in the breakdown (or digestion) of food into small molecules as it travels down peristaltically through the gut lumen shortly after it has been ingested. These small food molecules are then absorbed into the blood from the lumen, where they are then distributed to the rest of the body as building blocks (e.g., amino acids) or sources of energy (e.g., glucose).[195]

MES Note: Peristalsis is a radially symmetrical contraction and relaxation of muscles that propagates in a wave down a tube.

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A simplified image showing peristalsis

Ingestion is the consumption of a substance by an organism.

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Different digestive systems in marine fishes

MES Note: Many fish have a number of small outpocketings, also called pyloric caeca, along their intestine. Their purpose is to increase the overall surface area of the digestive epithelium, therefore optimizing the absorption of sugars, amino acids, and dipeptides, among other nutrients.

The gizzard, also referred to as the ventriculus, gastric mill, and gigerium, is an organ found in the digestive tract of some animals, including archosaurs (pterosaurs [extinct flying lizards], crocodiles, alligators, dinosaurs, birds), earthworms, some gastropods [snails and slugs], some fish, and some crustaceans. This specialized stomach constructed of thick muscular walls is used for grinding up food, often aided by particles of stone or grit [sand or gravel].

In addition to their digestive tracts, vertebrate animals have accessory glands such as a liver and pancreas as part of their digestive systems.[195] The processing of food in these animals begins in the foregut, which includes the mouth, esophagus, and stomach. Mechanical digestion of food starts in the mouth with the esophagus serving as a passageway for food to reach the stomach, where it is stored and disintegrated (by the stomach's acid) for further processing. Upon leaving the stomach, food enters into the midgut, which is the first part of the intestine (or small intestine in mammals) and is the principal site of digestion and absorption [of nutrients]. Food that does not get absorbed are stored as indigestible waste (or feces) in the hindgut, which is the second part of the intestine (or large intestine in mammals). The hindgut then completes the reabsorption of needed water and salt prior to eliminating the feces from the rectum [final portion of the large intestine to your a-hole].[195]

MES Note: The small intestine or small bowel is an organ in the gastrointestinal tract where most of the absorption of nutrients from food takes place. It lies between the stomach and large intestine, and receives bile and pancreatic juice through the pancreatic duct to aid in digestion.

The large intestine, also known as the large bowel, is the last part of the gastrointestinal tract and of the digestive system in vertebrates. Water is absorbed here and the remaining waste material is stored in the rectum as feces before being removed by defecation.

The rectum is the final straight portion of the large intestine in humans and some other mammals, and the gut in others.

Defecation (or defaecation) is the final act of digestion, by which organisms eliminate a solid, semisolid, or liquid waste material known as feces from the digestive tract via the anus.

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Diagram showing the small intestine and surrounding structures

The duodenum is the first section of the small intestine, the jejunum is the second part, and the ileum is the final section of the small intestine.

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The sigmoid colon (or pelvic colon) is the part of the large intestine that is closest to the rectum and anus.

The appendix (or vermiform appendix; also cecal [or caecal] appendix; vermix; or vermiform process) is a finger-like, blind-ended tube connected to the cecum, from which it develops in the embryo. The cecum is a pouch-like structure of the large intestine, located at the junction of the small and the large intestines. The term "vermiform" comes from Latin and means "worm-shaped." The appendix used to be considered a vestigial organ, but this view has changed over the past decades.[clarify][1] Research suggests that the appendix may serve an important purpose. In particular, it may serve as a reservoir for beneficial gut bacteria.

In the context of human evolution, human vestigiality involves those traits (such as organs or behaviors) occurring in humans that have lost all or most of their original function through evolution. Although structures called vestigial often appear functionless, a vestigial structure may retain lesser functions or develop minor new ones. In some cases, structures once identified as vestigial simply had an unrecognized function. Vestigal organs are sometimes called rudimentary organs. The examples of human vestigiality are numerous, including the anatomical (such as the human tailbone, wisdom teeth, and inside corner of the eye), the behavioral (goose bumps and palmar grasp reflex), and molecular (pseudogenes). Many human characteristics are also vestigial in other primates and related animals.

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Figure: Tailbone [or coccyx]

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Figure: If you watch a cat blink, you will see a white membrane cross its eye – that is called its third eyelid. It is quite a rare thing in mammals, but common in birds, reptiles, and fish. Humans have a remnant (but non-working) third eyelid (you can see it in the picture above). It has become quite small in humans.

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Goosebumps on a human

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Infant grasping adult finger

Palmar grasp reflex (or grasp reflex) is a primitive and involuntary reflex found in infants of humans and most primates. Biologists have found that the reflex is significantly more frequent in infants of fur carrying primate species. It is theorized that the grasping reflex evolved as it is essential to survival in species, usually primates, where the young are carried in the fur. The infant's ability to grasp onto a mother's fur allows the mother to keep the infant with her while foraging [searching] for food or moving from one place to another.

Breathing

Further information: Respiratory system

The respiratory system consists of specific organs and structures used for gas exchange in animals and plants. The anatomy and physiology that make this happen varies greatly, depending on the size of the organism, the environment in which it lives and its evolutionary history. In land animals the respiratory surface is internalized as linings of the lungs.[196] Gas exchange in the lungs occurs in millions of small air sacs; in mammals and reptiles these are called alveoli, and in birds they are known as atria. These microscopic air sacs have a very rich blood supply, thus bringing the air into close contact with the blood.[197] These air sacs communicate with the external environment via a system of airways, or hollow tubes, of which the largest is the trachea [windpipe], which branches in the middle of the chest into the two main [or primary] bronchi. These enter the lungs where they branch into progressively narrower secondary and tertiary bronchi that branch into numerous smaller tubes, the bronchioles. In birds the bronchioles are termed parabronchi. It is the bronchioles, or parabronchi that generally open into the microscopic alveoli in mammals and atria in birds. Air has to be pumped from the environment into the alveoli or atria by the process of breathing which involves the muscles of respiration.

MES Note: Respiration is the movement of oxygen from the outside environment to the cells within tissues, and the removal of carbon dioxide in the opposite direction.

Breathing (or ventilation) is the process of moving air out and in the lungs to facilitate gas exchange with the internal environment, mostly to flush out carbon dioxide and bring in oxygen.

In precise usage, the words breathing and ventilation are hyponyms, not synonyms, of respiration; but this prescription is not consistently followed, even by most health care providers, because the term respiratory rate (RR) is a well-established term in health care, even though it would need to be consistently replaced with ventilation rate if the precise usage were to be followed.

Hyponymy (from Greek ὑπό, hupó, "under", and ὄνυμα, ónuma, "name") is a semantic relation between a hyponym denoting a subtype and a hypernym or hyperonym denoting a supertype.

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The lungs are the primary organs of the respiratory system in humans and most animals including a few fish, and some snails.

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In anatomy, a nasal concha, plural conchae), also called a nasal turbinate or turbinal,[1][2] is a long, narrow, curled shelf of bone that protrudes into the breathing passage of the nose in humans and various animals. The conchae are shaped like an elongated seashell, which gave them their name (Latin concha from Greek κόγχη). A concha is any of the scrolled spongy bones of the nasal passages in vertebrates.

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The human lungs flank the heart and great vessels in the chest cavity

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Figure: Gross Anatomy of the Lungs

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Conducting passages of the human respiratory system

The larynx, commonly called the voice box, is an organ in the top of the neck involved in breathing, producing sound and protecting the trachea against food aspiration [suction into airways].

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The bronchi are conducting passages for air found in the lungs.

The pulmonary veins are the veins that transfer oxygenated blood from the lungs to the heart.

A pulmonary artery is an artery in the pulmonary circulation that carries deoxygenated blood from the right side of the heart to the lungs.

Veins are blood vessels in humans, and most other animals that carry blood towards the heart. Most veins carry deoxygenated blood from the tissues back to the heart; exceptions are the pulmonary and umbilical veins, both of which carry oxygenated blood to the heart. In contrast to veins, arteries carry blood away from the heart.

An artery (plural arteries) (from Greek ἀρτηρία (artēríā) 'windpipe, artery')[1] is a blood vessel in humans and most other animals that takes blood away from the heart to one or more parts of the body (tissues, lungs, brain etc.). Most arteries carry oxygenated blood; the two exceptions are the pulmonary and the umbilical arteries, which carry deoxygenated blood to the organs that oxygenate it (lungs and placenta, respectively).

The umbilical vein is a vein present during fetal development that carries oxygenated blood from the placenta into the growing fetus.

The umbilical artery is a paired artery (with one for each half of the body) that is found in the abdominal and pelvic regions. In the fetus, it extends into the umbilical cord. The umbilical arteries supply deoxygenated blood from the fetus to the placenta. Although this blood is typically referred to as deoxygenated, it is important to note that this blood is fetal systemic arterial blood and will have the same amount of oxygen and nutrients as blood distributed to the other fetal tissues.

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Fetal circulation; the umbilical vein is the large, red vessel at the far left. The umbilical arteries are purple and wrap around the umbilical vein.

In placental mammals, the umbilical cord (also called the navel string,[1] birth cord or funiculus umbilicalis) is a conduit between the developing embryo or fetus and the placenta. During prenatal development [fertilization to birth], the umbilical cord is physiologically and genetically part of the fetus and (in humans) normally contains two arteries (the umbilical arteries) and one vein (the umbilical vein), buried within Wharton's jelly [a gelatinous substance within the umbilical cord].

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Cross section of the umbilical cord.

The allantois (plural allantoides or allantoises) is a hollow sac-like structure filled with clear fluid that forms part of a developing amniote's [tetrapod vertebrates] conceptus (which consists of all embryonic and extra-embryonic tissues). It helps the embryo exchange gases and handle liquid waste.

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Umbilical cord of a three-minute-old baby. A medical clamp has been applied.

The placenta is a temporary fetal organ that plays critical roles in facilitating nutrient, gas and waste exchange between the physically separate maternal and fetal circulations, and is an important endocrine organ producing hormones that regulate both maternal and fetal physiology during pregnancy. The placenta connects to the fetus via the umbilical cord.

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Placenta

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The fetal circulatory system includes three shunts [ductus venosus, ductus arteriosus, foramen ovale] to divert blood from undeveloped and partially functioning organs, as well as blood supply to and from the placenta.

A shunt is a hole or passage allowing fluid to move from one part of the body to another.

The [human] heart has four chambers, two upper atria, the receiving chambers, and two lower ventricles, the discharging chambers.

The inferior vena cava is a large vein that carries the deoxygenated blood from the lower and middle body into the right atrium of the heart.

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The heart, showing valves, arteries and veins. The white arrows show the normal direction of blood flow.

The aorta is the main and largest artery in the human body, originating from the left ventricle of the heart and extending down to the abdomen, where it splits into two smaller arteries (the common iliac arteries). The aorta distributes oxygenated blood to all parts of the body through the systemic circulation.[1]

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Schematic view of the aorta and its segments

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Branches of the aorta

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Animated schematic of the hearts and circulatory systems of a fetus and its mother – red and blue represent oxygenated and deoxygenated blood, respectively (animation) [note that this diagram does not provide detail regarding the umbilical cord and the 3 shunts that bypass the non-functioning / developing organs]

The venae cavae (from the Latin for "hollow veins", singular "vena cava")[2] are two large veins (great vessels) that return deoxygenated blood from the body into the heart. In humans they are the superior vena cava and the inferior vena cava, and both empty into the right atrium.

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Blood circulation around alveoli

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Alveolar sacs and capillaries [small blood vessels].

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Anatomy of the respiratory system, showing the trachea and both lungs and their lobes and airways. Lymph nodes and the diaphragm are also shown. Oxygen is inhaled into the lungs and passes through the thin membranes of the alveoli and into the bloodstream (see inset).

The muscles of respiration are those muscles that contribute to inhalation and exhalation, by aiding in the expansion and contraction of the thoracic cavity [chamber protected by the rib cage]. The diaphragm and, to a lesser extent, the intercostal muscles drive respiration during quiet breathing. The elasticity of these muscles is crucial to the health of the respiratory system and to maximize its functional capabilities.

The thoracic cavity (or chest cavity) is the chamber of the body of vertebrates that is protected by the thoracic wall (rib cage and associated skin, muscle, and fascia).

The thoracic diaphragm, or simply the diaphragm, [from Ancient Greek for “partition”] is a sheet of internal skeletal muscle[2] in humans and other mammals that extends across the bottom of the thoracic cavity. The diaphragm separates the thoracic cavity, containing the heart and lungs, from the abdominal cavity and performs an important function in respiration: as the diaphragm contracts, the volume of the thoracic cavity increases, creating a negative pressure there, which draws air into the lungs.

Intercostal muscles are many different groups of muscles that run between the ribs, and help form and move the chest wall. The intercostal muscles are mainly involved in the mechanical aspect of breathing by helping expand and shrink the size of the chest cavity.

A fascia (from Latin: "band") is a band or sheet of connective tissue, primarily collagen, beneath the skin that attaches to, stabilizes, encloses, and separates muscles and other internal organs.

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The body cavities.

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Intercostal muscles highlighted in dark red.

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Internal oblique muscle, left [side abs]

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Respiratory system in a bird.

MES Note: A sinus is a sac or cavity in any organ or tissue, or an abnormal cavity or passage caused by the destruction of tissue.

Paranasal sinuses are a group of four paired air-filled spaces that surround the nasal cavity [in humans]. There is no consensus regarding the physiological functions of the paranasal sinuses. The most likely include: decrease in the relative mass of the anterior sections of the skull, increased voice resonance, etc. One known function of the paranasal sinuses is the production of nitric oxide [colorless gas, NO], which also functions as a facilitator of oxygen uptake. Paranasal sinuses occur in many other animals, including most mammals, birds, non-avian dinosaurs, and crocodilians. The bones occupied by sinuses are quite variable in these other species.

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Paranasal sinuses seen in a frontal view

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Figure: The avian air sacs.

Source: The lungs of birds do not inflate and deflate but rather retain a constant volume. Also, the lungs are unidirectionally ventilated rather than having a tidal, bidirectional flow, as in other vertebrates with lungs.

Birds lack a diaphragm, and therefore use their intercostal and abdominal muscles to expand and contract their entire thoraco-abdominal cavities, thus rhythmically changing the volumes of all their air sacs in unison (illustration below).

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Inhalation–exhalation cycle in birds.

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The cross-current respiratory gas exchanger in the lungs of birds. Air is forced from the air sacs unidirectionally (from right to left in the diagram) through the parabronchi. The pulmonary capillaries surround the parabronchi in the manner shown (blood flowing from below the parabronchus to above it in the diagram).[57][59] Blood or air with a high oxygen content is shown in red; oxygen-poor air or blood is shown in various shades of purple-blue.

Avian lungs do not have alveoli as mammalian lungs do. Instead they contain millions of narrow passages known as parabronchi, connecting the dorsobronchi to the ventrobronchi at either ends of the lungs. Air flows anteriorly (caudal to cranial) through the parallel parabronchi. These parabronchi have honeycombed walls. The cells of the honeycomb are dead-end air vesicles, called atria, which project radially from the parabronchi. The atria are the site of gas exchange by simple diffusion.[60] The blood flow around the parabronchi (and their atria), forms a cross-current gas exchanger (see diagram above).

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Figure: Schematic diagram of a parabronchus showing its various component parts and the geometric relationships between the air flow and the blood flow. (Maina 2002 c)

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Figure: A Mercury Barometer [measures air pressure]

Circulation

Further information: Circulatory system

A circulatory system usually consists of a muscular pump such as a heart, a fluid (blood), and system of blood vessels that deliver it.[198][199] Its principal function is to transport blood and other substances to and from cells and tissues. There are two types of circulatory systems: open and closed. In open circulatory systems, blood exits blood vessels as it circulates throughout the body whereas in closed circulatory system, blood is contained within the blood vessels as it circulates. Open circulatory systems can be observed in invertebrate animals such as arthropods (e.g., insects, spiders, and lobsters) whereas closed circulatory systems can be found in vertebrate animals such as fishes, amphibians, and mammals. Circulation in animals occur between two types of tissues: systemic tissues and breathing (or pulmonary) organs.[198] Systemic tissues are all the tissues and organs that make up an animal's body other than its breathing organs. Systemic tissues take up oxygen but adds carbon dioxide to the blood whereas a breathing organs takes [sic] up carbon dioxide but add oxygen to the blood.[200] In birds and mammals, the systemic and pulmonary systems are connected in series.

MES Note: Medical terms related to the lung often begin with pulmo-, from the Latin pulmonarius (of the lungs).

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Figure: Solar Panels In Series Vs Parallel

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Circulatory systems in arthropods, fish, reptiles, and birds/mammals.

MES Note: Hemolymph, or haemolymph, is a fluid, analogous to the blood in vertebrates, that circulates in the interior of the arthropod (invertebrate) body, remaining in direct contact with the animal's tissues. It is composed of a fluid plasma in which hemolymph cells called hemocytes are suspended. In addition to hemocytes, the plasma also contains many chemicals. It is the major tissue type of the open circulatory system characteristic of arthropods (e.g. arachnids [spiders, etc.], crustaceans [lobsters, etc.] and insects).[1][2] In addition, some non-arthropods such as molluscs [snails, etc.] possess a hemolymphatic circulatory system.
Oxygen-transport systems were long thought unnecessary in insects, but ancestral and functional hemocyanin has been found in the hemolymph.

Hemocyanins (also spelled haemocyanins and abbreviated Hc) are proteins that transport oxygen throughout the bodies of some invertebrate animals.

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The systemic circulation and capillary networks shown and also as separate from the pulmonary circulation

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A simplified illustration of a capillary network

In the circulatory system, blood is important because it is the means by which oxygen, carbon dioxide, nutrients, hormones, agents of immune system, heat, wastes, and other commodities are transported.[198] In annelids [worm phylum] such as earthworms and leeches, blood is propelled by peristaltic waves of contractions of the heart muscles that make up the blood vessels.

Other animals such as crustaceans (e.g., crayfish and lobsters), have more than one heart to propel blood throughout their bodies. Vertebrate hearts are multichambered and are able to pump blood when their ventricles contract at each cardiac cycle, which propels blood through the blood vessels.[198] Although vertebrate hearts are myogenic [rhythmic beating due to inherent properties of cardiac muscle rather than specific stimuli], their rate of contraction (or heart rate) can be modulated by neural input from the body's autonomic nervous system [regulates unconscious bodily functions].

MES Note: The [human] heart has four chambers, two upper atria, the receiving chambers, and two lower ventricles, the discharging chambers.

“Cardiac” means “of or pertains to the heart” and is from the Latin “Cardiacus”.

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Computer-generated animation of a beating human heart

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The heart, showing valves, arteries and veins. The white arrows show the normal direction of blood flow.

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With the atria and major vessels removed, all four valves are clearly visible.[7]

The cardiac cycle is the performance of the human heart from the beginning of one heartbeat to the beginning of the next. It consists of two periods: one during which the heart muscle relaxes and refills with blood, called diastole, following a period of robust contraction and pumping of blood, dubbed systole. After emptying, the heart immediately relaxes and expands to receive another influx of blood returning from the lungs and other systems of the body, before again contracting to pump blood to the lungs and those systems.

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MRI video of a teen's heart beating.

Heart rate is the speed of the heartbeat [cardiac cycle] measured by the number of contractions (beats) of the heart per minute (bpm). The heart rate can vary according to the body's physical needs, including the need to absorb oxygen and excrete carbon dioxide, but is also modulated by a myriad of factors including but not limited to genetics, physical fitness, stress or psychological status, diet, drugs, hormonal status, environment, and disease/illness as well as the interaction between and among these factors.[1] It is usually equal or close to the pulse [physically feeling the heart beat from arteries] measured at any peripheral point.

The American Heart Association states the normal resting adult human heart rate is 60–100 bpm.

Muscle and movement

Further information: Muscular system and Muscle contraction

In vertebrates, the muscular system consists of skeletal, smooth and cardiac muscles. It permits movement of the body, maintains posture and circulates blood throughout the body.[201] Together with the skeletal system, it forms the musculoskeletal system, which is responsible for the movement of vertebrate animals.[202]

MES Note: Skeletal muscles (commonly referred to as muscles) are organs of the vertebrate muscular system that are mostly attached by tendons to bones of the skeleton.[1][2] The muscle cells of skeletal muscles are much longer than in the other types of muscle tissue, and are often known as muscle fibers.[3] The muscle tissue of a skeletal muscle is striated – having a striped appearance due to the arrangement of the sarcomeres [smallest repeating striated muscle tissue]. Skeletal muscles are voluntary muscles under the control of the somatic nervous system.

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Skeletal muscle

A sarcomere (Greek σάρξ sarx "flesh", μέρος meros "part") is the smallest functional [and repeating] unit of striated muscle tissue.[1]

The somatic nervous system (SNS), or voluntary nervous system is the part of the peripheral nervous system associated with the voluntary control of body movements via skeletal muscles.

Smooth muscle is an involuntary non-striated muscle, so-called because it has no sarcomeres and therefore no striations.

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Smooth muscle shown in the tunica media [layers] in the walls of arteries and veins

Cardiac muscle (also called heart muscle or myocardium) is one of three types of vertebrate muscle tissue, with the other two being skeletal muscle and smooth muscle. It is involuntary, striated muscle that constitutes the main tissue of the wall of the heart. The cardiac muscle (myocardium) forms a thick middle layer between the outer layer of the heart wall (the pericardium) and the inner layer (the endocardium), with blood supplied via the coronary circulation.

Coronary circulation is the circulation of blood in the blood vessels that supply the heart muscle (myocardium). Coronary arteries supply oxygenated blood to the heart muscle. Cardiac veins then drain away the blood after it has been deoxygenated. Because the rest of the body, and most especially the brain, needs a steady supply of oxygenated blood that is free of all but the slightest interruptions, the heart is required to function continuously. Therefore its circulation is of major importance not only to its own tissues but to the entire body and even the level of consciousness of the brain from moment to moment. Interruptions of coronary circulation quickly cause heart attacks (myocardial infarctions), in which the heart muscle is damaged by oxygen starvation.

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Coronary arteries labeled in red text and other landmarks in blue text.

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Figure

Skeletal muscle contractions are neurogenic [as opposed to the heart being myogenic] as they require synaptic input from motor neurons. A single motor neuron is able to innervate [distribute to / stimulate] multiple muscle fibers, thereby causing the fibers to contract at the same time. Once innervated, the protein filaments within each skeletal muscle fiber slide past each other to produce a contraction, which is explained by the sliding filament theory. The contraction produced can be described as a twitch, summation, or tetanus [muscle spasm], depending on the frequency of action potentials. Unlike skeletal muscles, contractions of smooth and cardiac muscles are myogenic as they are initiated by the smooth or heart muscle cells themselves instead of a motor neuron. Nevertheless, the strength of their contractions can be modulated by input from the autonomic nervous system. The mechanisms of contraction are similar in all three muscle tissues.

MES Note: A motor neuron (or motoneuron or efferent neuron[1]) is a neuron whose cell body is located in the motor cortex, brainstem or the spinal cord, and whose axon (fiber) projects to the spinal cord or outside of the spinal cord to directly or indirectly control effector organs, mainly muscles and glands.

The motor cortex is the region of the brain involved in the planning, control, and execution of voluntary movements.

Muscle Contraction 3D Video: https://youtu.be/GrHsiHazpsw

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Figure: The Sliding Filament Theory [Note: the right image should have the myosin connection further to right end]

In physiology, an action potential (AP) occurs when the membrane potential of a specific cell location rapidly rises and falls:[1] this depolarization then causes adjacent locations to similarly depolarize. Action potentials occur in several types of animal cells, called excitable cells, which include neurons, muscle cells, endocrine cells and in some plant cells.

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As an action potential (nerve impulse) travels down an axon [long, slender, conducting projection of the nerve cell] there is a change in polarity across the membrane of the axon.

An axon or nerve fiber, is a long, slender projection of a nerve cell, or neuron, in vertebrates, that typically conducts electrical impulses known as action potentials away from the nerve cell body.

In biology, depolarization (British English: Depolarisation) is a change within a cell, during which the cell undergoes a shift in electric charge distribution, resulting in less negative charge inside the cell compared to the outside. Depolarization is essential to the function of many cells, communication between cells, and the overall physiology of an organism.

Most cells in higher organisms maintain an internal environment that is negatively charged relative to the cell's exterior. This difference in charge is called the cell's membrane potential. In the process of depolarization, the negative internal charge of the cell temporarily becomes more positive (less negative). This shift from a negative to a more positive membrane potential occurs during several processes, including an action potential. During an action potential, the depolarization is so large that the potential difference across the cell membrane briefly reverses polarity, with the inside of the cell becoming positively charged.

The change in charge typically occurs due to an influx of sodium ions into a cell, although it can be mediated by an influx of any kind of cation or efflux of any kind of anion.

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Action potential in a neuron, showing depolarization, in which the cell's internal charge becomes less negative (more positive), and repolarization, where the internal charge returns to a more negative value.

Hyperpolarization is a change in a cell's membrane potential that makes it more negative. It is the opposite of a depolarization. It inhibits action potentials by increasing the stimulus required to move the membrane potential to the action potential threshold.

In invertebrates such as earthworms and leeches, circular and longitudinal muscles cells form the body wall of these animals and are responsible for their movement.[203] In an earthworm that is moving through a soil, for example, contractions of circular and longitudinal muscles occur reciprocally [together] while the coelomic fluid serves as a hydroskeleton by maintaining turgidity of the earthworm.[204]

MES Note: The coelom (or celom[1]) is the main body cavity in most animals[2] and is positioned inside the body to surround and contain the digestive tract and other organs.

The fluid inside the coelom is known as coelomic fluid.

A hydrostatic skeleton, or hydroskeleton, is a flexible skeleton supported by fluid pressure.

Turgidity is the state of being swollen or turgid, especially due to high fluid content.

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Cross-section of an oligochaete worm. The worm's body cavity surrounds the central typhlosole.

A typhlosole is an internal fold of the intestine or intestine inner wall.

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Many animals with a wormlike cylindrical body have a hydrostatic skeleton with a flexible skin and a water-filled body cavity (coelom or pseudocoelom). They move by peristalsis, using opposed circular and longitudinal muscles, which act on the hydrostatic skeleton to change the body's shape.

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A simplified image showing earthworm movement via peristalsis

Other animals such as mollusks [snails, octopus, etc.], and nematodes [type of worm], possess obliquely [inclined] striated [banded] muscles, which contain bands of thick and thin filaments that are arranged helically rather than transversely [laterally], like in vertebrate skeletal or cardiac muscles.[205] Advanced insects such as wasps, flies, bees, and beetles possess asynchronous muscles that constitute the flight muscles in these animals.[205] These flight muscles are often called fibrillar muscles because they contain myofibrils that are thick and conspicuous [easily noticed].[206]

MES Note: Asynchronous muscles are muscles in which there is no one-to-one relationship between electrical stimulation and mechanical contraction. These muscles are found in 75% of flying insects and have convergently evolved 7-10 times.[1] Unlike their synchronous counterparts that contract once per neural signal, mechanical oscillations trigger force production in asynchronous muscles. Typically, the rate of mechanical contraction is an order of magnitude greater than electrical signals.[1] Although they achieve greater force output and higher efficiency at high frequencies, they have limited applications because of their dependence on mechanical stretch.

A myofibril (also known as a muscle fibril or sarcostyle)[1] is a basic rod-like organelle of a muscle cell.

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Skeletal muscle, with myofibrils labeled at upper right.

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Figure: Muscle fibers: coordinating morphogenesis in a crowded space. Two examples of different mitochondria-myofibril architectures. Left: Adult Drosophila [a species of flies] fibrillar flight muscles contain round individual myofibrils (red) isolated from each other by large ellipsoid shaped mitochondria (green). Nuclei (blue) are located between the myofibril bundles. Note that myofibrils are squeezing mitochondria into their elongated shapes. Right: Mammalian skeletal muscle contain bundles of vertically aligned cross-striated myofibrils with mitochondria concentrated in groups squeezed in between. These mitochondria form long thin extensions along the sarcomeric I-bands that build networks. In both muscle types the crowded cellular environment generates mechanical pressure that positions the nuclei at the periphery of myofibril bundles adopting an elongated shape.

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Figure: ‘The muscle dimension problem’: structure and dimensions of muscles in fly versus human.

  • Top: Schematic representation of Drosophila and human muscles in a series of magnifications. Each muscle fiber contains hundreds of myofibrils that span the entire length of the myofiber. Sarcomeres are several orders of magnitude shorter but must be assembled perfectly into a myofibril to connect both muscle-tendon attachments at the fiber ends. In fly and human, sarcomeres are similar in length (3.2 μm in flight muscles and 3.0 to 3.4 μm in relaxed human muscles) and many sarcomeric proteins are well conserved.
  • Bottom: Schematic of the sarcomere. Polar actin filaments (also called thin filaments) are anchored at the Z-disc (Z, green) by α-actinin. Thick filaments comprised of myosin bundles are centred at the M-line (M, blue) and interact with actin with their myosin heads. Titin, a connecting filament, is anchored at the Z-disc and spans through the I-band all the way to the M-line.

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Asynchronous muscles power flight in most insects. a: Wings b: Wing joint c: Dorsoventral muscles power upstrokes d: Dorsolongitudinal muscles power downstrokes.

MES Note:

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Nervous system

Further information: Nervous system and Neuroscience

The nervous system is a network of cells that processes sensory information and generates behaviors. At the cellular level, the nervous system is defined by the presence of neurons, which are specialized cells that receive, process, and transmit information. They can send signals that travel along their thin fibers called axons, which can be transmitted directly to a neighboring cell through electrical synapses or cause chemicals called neurotransmitters to be released at chemical synapses. A cell that receives a synaptic signal from a neuron may be excited, inhibited, or otherwise modulated. The connections between neurons can form neural pathways, neural circuits, and larger networks that generate an organism's perception of the world and determine its behavior. Along with neurons, the nervous system contains other specialized cells called glia or glial cells, which provide structural and metabolic support.

MES Note: An electrical synapse is a mechanical and electrically conductive link between two neighboring neurons that is formed at a narrow gap between the pre- and postsynaptic neurons known as a gap junction. At gap junctions, such cells approach within about 3.8 nm of each other,[1] a much shorter distance than the 20- to 40-nanometer distance that separates cells at [sic] chemical synapse.[2] In many[specify] animals, electrical synapse-based systems co-exist with chemical synapses. Compared to chemical synapses, electrical synapses conduct nerve impulses faster, but, unlike chemical synapses, they lack gain—the signal in the postsynaptic neuron is the same or smaller than that of the originating neuron.

A connexon, also known as a connexin hemichannel, is an assembly of six proteins called connexins that form the pore for a gap junction between the cytoplasm of two adjacent cells. This channel allows for bidirectional flow of ions and signaling molecules.

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Diagram of a gap junction

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In a neuron, synaptic vesicles (or neurotransmitter vesicles) store various neurotransmitters that are released at the synapse.

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Mouse pyramidal neurons (green) and GABAergic neurons (red).[207]

MES Note: Pyramidal cells, or pyramidal neurons, are a type of multipolar neuron found in areas of the brain.

A multipolar neuron is a type of neuron that possesses a single axon and many dendrites (and dendritic branches), allowing for the integration of a great deal of information from other neurons.

Dendrites (from Greek δένδρον déndron, "tree"), also dendrons, are branched protoplasmic [refers to living part within a cell membrane] extensions of a nerve cell that propagate the electrochemical stimulation received from other neural cells to the cell body, or soma [body of the neuron], of the neuron from which the dendrites project.

gamma-Aminobutyric acid, or γ-aminobutyric acid, or GABA, is the chief inhibitory neurotransmitter in the developmentally mature mammalian central nervous system. Its principal role is reducing neuronal excitability throughout the nervous system.

Neurons that produce GABA as their output are called GABAergic neurons, and have chiefly inhibitory action at receptors in the adult vertebrate.

Nervous systems are found in most multicellular animals, but vary greatly in complexity.[208] In vertebrates, the nervous system consists of the central nervous system (CNS), which includes the brain and spinal cord, and the peripheral nervous system (PNS), which consists of nerves that connect the CNS to every other part of the body. Nerves that transmit signals from the CNS are called motor nerves or efferent nerves [“exit” nerves], while those nerves that transmit information from the body to the CNS are called sensory nerves or afferent nerves [“arrive” nerves]. Spinal nerves are mixed nerves that serve both functions. The PNS is divided into three separate subsystems, the somatic, autonomic, and enteric nervous systems. Somatic nerves mediate voluntary movement. The autonomic nervous system is further subdivided into the sympathetic and the parasympathetic nervous systems. The sympathetic nervous system is activated in cases of emergencies to mobilize energy, while the parasympathetic nervous system is activated when organisms are in a relaxed state. The enteric nervous system functions to control the gastrointestinal system. Both autonomic and enteric nervous systems function involuntarily. Nerves that exit directly from the brain are called cranial nerves while those exiting from the spinal cord are called spinal nerves.

MES Note:

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Figure 1: Relationship between the ENS and components of the peripheral nervous system.

A dorsal root ganglion (or spinal ganglion; also known as a posterior root ganglion[1]) is a cluster of neurons (a ganglion) in a dorsal root of a spinal nerve.

Dorsal and ventral “roots” emerge from the spinal cord and combine to form a spinal nerve.

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The cranial nerve ganglia are ganglia of certain cranial nerves.

Many animals have sense organs that can detect their environment. These sense organs contain sensory receptors, which are sensory neurons that convert stimuli into electrical signals.[209] Mechanoreceptors, for example, which can be found in skin, muscle, and hearing organs, generate action potentials in response to changes in pressures.[209][210] Photoreceptor cells such as rods and cones, which are part of the vertebrate retina, can respond to specific wavelengths of light.[209][210] Chemoreceptors detect chemicals in the mouth (taste) or in the air (smell).[210]

MES Note: Rod cells are photoreceptor cells in the retina of the eye that can function in lower light better than the other type of visual photoreceptor, cone cells.

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Figure: Light moves through the eye and is absorbed by rods and cones at the back of the eye.

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Fovea (Latin for "pit"; plural foveae) is a term in anatomy. It refers to a pit or depression in a structure.

The fovea centralis is a small, central pit composed of closely packed cones in the eye.

The fovea is responsible for sharp central vision (also called foveal vision), which is necessary in humans for activities for which visual detail is of primary importance, such as reading and driving.

The retina (from Latin: rete "net") is the innermost, light-sensitive layer of tissue of the eye of most vertebrates and some molluscs. The optics of the eye create a focused two-dimensional image of the visual world on the retina, which translates that image into electrical neural impulses to the brain to create visual perception. The retina serves a function analogous to that of the film or image sensor in a camera.

Hormonal control

Further information: Hormone, Endocrine system, and Endocrinology

Hormones are signaling molecules transported in the blood to distant organs to regulate their function.[211][212] Hormones are secreted by internal glands that are part of an animal's endocrine system. In vertebrates, the hypothalamus is the neural control center for all endocrine systems.

MES Note: The hypothalamus (from Ancient Greek ὑπό, "under", and θάλαμος, "chamber") is a portion of the brain that contains a number of small nuclei with a variety of functions. One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland.

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Location of the human hypothalamus

The endocrine system is a messenger system comprising feedback loops of the hormones released by internal glands of an organism directly into the circulatory system, regulating distant target organs.

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Main glands of the endocrine system

The pineal gland, conarium, or epiphysis cerebri, is a small endocrine gland in the brain of most vertebrates. The pineal gland produces melatonin, a hormone which modulates sleep patterns in both circadian and seasonal cycles. The shape of the gland resembles a pine cone, which gives it its name.

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Figure

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Figure

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The ventricular system is a set of four interconnected cavities known as cerebral ventricles in the brain.

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Rotating 3D rendering of the four ventricles and connections.

  • Blue - Lateral ventricles
  • Cyan - Interventricular foramina (Monro)
  • Yellow - Third ventricle
  • Red - Cerebral aqueduct (Sylvius)
  • Purple - fourth ventricle
  • Green - continuous with the central canal

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Figure

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Figure: The Egyptian Eye of Horus (or Third Eye) resembles the cross section of a brain

A circadian rhythm or circadian cycle, is a natural, internal process that regulates the sleep–wake cycle and repeats roughly every 24 hours. It can refer to any process that originates within an organism (i.e., endogenous) and responds to the environment (entrained by the environment). These 24-hour rhythms are driven by a circadian clock, and they have been widely observed in plants, animals, fungi and cyanobacteria.[2]
The term circadian comes from the Latin circa, meaning "around" (or "approximately"), and diēm, meaning "day". Processes with 24-hour cycles are more generally called diurnal rhythms; diurnal rhythms should not be called circadian rhythms unless they can be confirmed as endogenous, and not environmental.[3]

Entrainment occurs when rhythmic physiological or behavioral events match their period to that of an environmental oscillation. It is ultimately the interaction between circadian rhythms and the environment. A central example is the entrainment of circadian rhythms to the daily light–dark cycle, which ultimately is determined by the Earth's rotation. Entrainment helps organisms maintain an adaptive phase relationship with the environment as well as prevent drifting of a free running rhythm.

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Features of the human circadian biological clock

A season is a division of the year[1] based on changes in weather, ecology, and the number of daylight hours in a given region.

The pituitary gland, or hypophysis, is an endocrine gland, about the size of a pea and weighing 0.5 grams (0.018 oz) in humans. Hormones secreted from the pituitary gland help to control growth, blood pressure, energy management, all functions of the sex organs, thyroid glands and metabolism as well as some aspects of pregnancy, childbirth, breastfeeding, water/salt concentration at the kidneys, temperature regulation and pain relief.

The thyroid, or thyroid gland, is an endocrine gland in vertebrates. In humans it is in the neck and consists of two connected lobes. The thyroid gland secretes three hormones: the two thyroid hormones – triiodothyronine (T3) and thyroxine (T4) – and a peptide hormone, calcitonin. The thyroid hormones influence the metabolic rate and protein synthesis, and in children, growth and development. Calcitonin plays a role in calcium homeostasis.

Parathyroid glands are small endocrine glands in the neck of humans and other tetrapods. Humans usually have four parathyroid glands, located on the back of the thyroid gland in variable locations. The parathyroid gland produces and secretes parathyroid hormone in response to a low blood calcium, which plays a key role in regulating the amount of calcium in the blood and within the bones.

The adrenal glands (also known as suprarenal glands) are endocrine glands that produce a variety of hormones including adrenaline and the steroids aldosterone and cortisol. They are found above the kidneys.

Adrenaline, also known as epinephrine, is a hormone and medication[7][8] which is involved in regulating visceral functions (e.g., respiration). It plays an important role in the fight-or-flight response by increasing blood flow to muscles, output of the heart by acting on the SA node,[10] pupil dilation response [pupils widening] and [regulating] blood sugar level.

Viscera (singular viscus) refers to the internal organs of the abdominal, thoracic, and pelvic cavities.

The pelvic cavity is a body cavity that is bounded by the bones of the pelvis.

The pelvis (plural pelves or pelvises) is the lower part of the trunk,[1] between the abdomen and the thighs (sometimes also called pelvic region), together with its embedded skeleton[2] (sometimes also called bony pelvis, or pelvic skeleton).

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Male type pelvis

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Female type pelvis

The fight-or-flight-or-freeze or the fight-flight response (also called hyperarousal or the acute stress response) is a physiological reaction that occurs in response to a perceived harmful event, attack, or threat to survival.[1] It was first described by Walter Bradford Cannon.[a][2] His theory states that animals react to threats with a general discharge of the sympathetic nervous system, preparing the animal for fighting or fleeing.

Cardiac output (CO), also known as heart output, is a term used in cardiac physiology that describes the volume of blood being pumped by the heart, by the left and right ventricle, per unit time.

The sinoatrial node (also known as the sinuatrial node, SA node or sinus node) is a group of cells known as pacemaker cells, located in the wall of the right atrium of the heart.[1] These cells have the ability to spontaneously produce an electrical impulse (action potential), that travels through the electrical conduction system of the heart causing it to contract.

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Dilation and constriction of the pupil

Aldosterone is essential for sodium conservation in the kidney, salivary glands, sweat glands, and colon.[3] It plays a central role in the homeostatic regulation of blood pressure, plasma sodium (Na+), and potassium (K+) levels.

Cortisol is released with a diurnal cycle and its release is increased in response to stress and low blood-glucose concentration. It functions to increase blood sugar through gluconeogenesis, to suppress the immune system, and to aid in the metabolism of fat, protein, and carbohydrates.[3] It also decreases bone formation.

Gluconeogenesis (GNG) is a metabolic pathway that results in the generation of glucose from certain non-carbohydrate carbon substrates.

The ovary is an organ found in the female reproductive system that produces an ovum [egg cell]. It is also an endocrine gland because of the various hormones that it secretes. The ovaries secrete hormones that play a role in the menstrual cycle and fertility.

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The ovaries form part of the female reproductive system, and attach to the fallopian tubes

Testicle or testis (plural testes) is the male reproductive gland or gonad in all animals, including humans. It is homologous to the female ovary. The functions of the testes are to produce both sperm and androgens, primarily testosterone.

A gonad, sex gland, or reproductive gland[1] is a mixed gland that produces the gametes and sex hormones of an organism. Female reproductive cells are egg cells, and male reproductive cells are sperm.[2] The male gonad, the testicle, produces sperm in the form of spermatozoa. The female gonad, the ovary, produces egg cells.

Sex hormones, also known as sex steroids, gonadocorticoids and gonadal steroids, are steroid hormones that interact with vertebrate steroid hormone receptors.

An androgen (from Greek andr-, the stem of the word meaning "man") is any natural or synthetic steroid hormone that regulates the development and maintenance of male characteristics in vertebrates by binding to androgen receptors.

Testosterone is the primary sex hormone and anabolic steroid in males.[3] In humans, testosterone plays a key role in the development of male reproductive tissues such as testes and prostate, as well as promoting secondary sexual characteristics such as increased muscle and bone mass, and the growth of body hair.[4] In addition, testosterone in both sexes is involved in health and well-being, including moods, behaviour, and in the prevention of osteoporosis.[5][6] Insufficient levels of testosterone in men may lead to abnormalities including frailty and bone loss. In men, testosterone is mainly produced in the testes. In women’s bodies, testosterone is produced in the ovaries, adrenal glands, fat cells, and skin cells.

Anabolic steroids increase protein within cells, especially in skeletal muscles, and also have varying degrees of virilizing [masculinization] effects, including induction of the development and maintenance of masculine secondary sexual characteristics such as the growth of facial and body hair.

Osteoporosis is a systemic skeletal disorder characterized by low bone mass, micro-architectural deterioration of bone tissue leading to bone fragility, and consequent increase in fracture risk. It is the most common reason for a broken bone among the elderly.[3]

The prostate is both an accessory gland [accessory = additional] of the male reproductive system and a muscle-driven mechanical switch between urination and ejaculation. The prostate glands produce and contain fluid that forms part of semen, the substance that is emitted during ejaculation as part of the male sexual response.

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The urinary bladder, or simply bladder, is a hollow muscular organ in humans and other vertebrates that stores urine from the kidneys before disposal by urination.

In humans specifically, the major endocrine glands are the thyroid gland and the adrenal glands. Many other organs that are part of other body systems have secondary endocrine functions, including bone, kidneys, liver, heart and gonads. For example, kidneys secrete the endocrine hormone erythropoietin [stimulates red blood cell production in the bone marrow]. Hormones can be amino acid complexes, steroids, eicosanoids [type of oxidized fatty acids], leukotrienes [type of oxidized fatty acids], or prostaglandins [psychologically active lipid compounds, subclass of eicosanoids]. [213] The endocrine system can be contrasted to both exocrine glands, which secrete hormones to the outside of the body, and paracrine signaling between cells over a relatively short distance. Endocrine glands have no ducts [opening or channel], are vascular, and commonly have intracellular vacuoles or granules that store their hormones. In contrast, exocrine glands, such as salivary glands, sweat glands, and glands within the gastrointestinal tract, tend to be much less vascular and have ducts or a hollow lumen.

MES Note: Bone as an Endocrine organ – bone controls phosphate metabolism by releasing fibroblast growth factor 23 (FGF-23) [a protein], which acts on kidneys to reduce phosphate reabsorption. Bone cells also release a hormone called osteocalcin, which contributes to the regulation of blood sugar (glucose) and fat deposition. Osteocalcin increases both the insulin secretion and sensitivity, in addition to boosting the number of insulin-producing cells and reducing stores of fat.[51]

Source: The liver is responsible for secreting at least four important hormones or hormone precursors: insulin-like growth factor (somatomedin), angiotensinogen, thrombopoetin, and hepcidin. Insulin-like growth factor-1 is the immediate stimulus for growth in the body, especially of the bones. Angiotensinogen is the precursor to angiotensin, mentioned earlier [in the source], which increases blood pressure. Thrombopoetin stimulates the production of the blood’s platelets. Hepcidins block the release of iron from cells in the body, helping to regulate iron homeostasis in our body fluids.

Platelets, also called thrombocytes (from Greek θρόμβος, "clot" and κύτος, "cell"), are a component of blood whose function (along with the coagulation factors) is to react to bleeding from blood vessel injury by clumping, thereby initiating a blood clot. Platelets have no cell nucleus; they are fragments of cytoplasm that are derived from the megakaryocytes[2] [platelet producing cells] of the bone marrow or lung,[3] which then enter the circulation.

Coagulation, also known as clotting, is the process by which blood changes from a liquid to a gel, forming a blood clot.

A thrombus, colloquially called a blood clot, is the final product of the blood coagulation step in hemostasis.

Hemostasis or haemostasis is a process to prevent and stop bleeding, meaning to keep blood within a damaged blood vessel (the opposite of hemostasis is hemorrhage [blood loss]).

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Blood clot diagram (Thrombus)

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Table

Source: When the body experiences an increase in blood volume or pressure, the cells of the heart’s atrial wall stretch. In response, specialized cells in the wall of the atria produce and secrete the peptide hormone atrial natriuretic peptide (ANP). ANP signals the kidneys to reduce sodium reabsorption, thereby decreasing the amount of water reabsorbed from the urine filtrate and reducing blood volume. Other actions of ANP include inhibition of vasodilation and the inhibition of renin secretion and of the renin-angiotensin-aldosterone system (RAAS). Therefore, ANP aids in decreasing blood pressure, blood volume, and blood sodium levels.

Source: Urine is the nitrogenous liquid form of waste that is excreted from the body with the help of kidneys through the process of urination. Filtrate is the liquid that is formed in the kidneys while urine formation is taking place.

Vasodilation is the widening of blood vessels.[1] It results from relaxation of smooth muscle cells within the vessel walls, in particular in the large veins, large arteries, and smaller arterioles. The process is the opposite of vasoconstriction, which is the narrowing of blood vessels.

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3D Medical animation still showing normal blood vessel (L) vs. vasodilation (R)

An arteriole is a small-diameter blood vessel in the microcirculation that extends and branches out from an artery and leads to capillaries.[1] Arterioles have muscular walls (usually only one to two layers of smooth muscle cells) and are the primary site of vascular resistance. The greatest change in blood pressure and velocity of blood flow occurs at the transition of arterioles to capillaries.

Vascular resistance is the resistance that must be overcome to push blood through the circulatory system and create flow.

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Types of blood vessels, including an arteriole and artery, as well as capillaries.

The renin–angiotensin system (RAS), or renin–angiotensin–aldosterone system (RAAS), is a hormone system that regulates blood pressure and fluid and electrolyte balance, as well as systemic vascular resistance.

An electrolyte is a medium containing ions that is electrically conducting through the movement of ions, but not conducting electrons.

Animal reproduction

Further information: Sexual reproduction § Animals, and Asexual reproduction § Examples in animals

Animals can reproduce in one of two ways: asexual and sexual. Nearly all animals engage in some form of sexual reproduction.[214] They produce haploid gametes by meiosis [reductional division]. The smaller, motile [ability to move independently] gametes are spermatozoa and the larger, non-motile gametes are ova.[215] These fuse to form zygotes,[216] which develop via mitosis [equational division] into a hollow sphere, called a blastula. In sponges, blastula larvae swim to a new location, attach to the seabed [bottom of the ocean], and develop into a new sponge.[217] In most other groups, the blastula undergoes more complicated rearrangement.[218] It first invaginates to form a gastrula with a digestive chamber and two separate germ layers, an external ectoderm and an internal endoderm.[219] In most cases, a third germ layer, the mesoderm, also develops between them.[220] These germ layers then differentiate to form tissues and organs.[221]

MES Note: Invagination consists of the folding of an area of the exterior sheet of cells towards the inside of the blastula. In each organism, the complexity will be different depending on the number of cells.

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Mechanism of Invagination

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Sexual reproduction in dragonflies.

Some animals are capable of asexual reproduction [no fusion of gametes or change in the number of chromosomes], which often results in a genetic clone of the parent. This may take place through fragmentation; budding, such as in Hydra and other cnidarians; or parthenogenesis, where fertile eggs are produced without mating, such as in aphids [small sap-sucking insects].[222][223]

MES Note: Fragmentation in multicellular or colonial organisms is a form of asexual reproduction or cloning, where an organism is split into fragments. Each of these fragments develop into mature, fully grown individuals that are clones of the original organism.

Hydra is a genus of small, fresh-water organisms of the phylum Cnidaria and class Hydrozoa. They are native to the temperate [wide range of temperatures, more distinct seasons] and tropical [high temperature and rainfall] regions.[2][3] Biologists are especially interested in Hydra because of their regenerative ability – they do not appear to die of old age, or to age at all.

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Hydra species

Source: Ever resilient, Hydra can survive dismemberment by regenerating lost sections of their bodies. Chop a Hydra into segments, and each segment will become a new Hydra. Blend one up, and you’re left with a soup of cells. If you ball up those cells using a centrifuge, they reorganize, eventually forming a new Hydra.

Cnidaria is a phylum under kingdom Animalia containing over 11,000 species[6] of aquatic animals found both in freshwater and marine environments, predominantly the latter. Their distinguishing feature is cnidocytes, specialized cells that they use mainly for capturing prey.

A cnidocyte (also known as a cnidoblast or nematocyte) is an explosive cell containing one giant secretory organelle called a cnidocyst (also known as a cnida (plural cnidae) or nematocyst) that can deliver a sting to other organisms.

Animal development

Further information: Developmental biology and Embryology

Animal development begins with the formation of a zygote that results from the fusion of a sperm and egg during fertilization.[224] The zygote undergoes a rapid multiple rounds of mitotic cell period of cell divisions called cleavage, which forms a ball of similar cells called a blastula. Gastrulation occurs, whereby morphogenetic [development of form] movements convert the cell mass into a [sic] three germ layers that comprise the ectoderm, mesoderm and endoderm.

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Cleavage in zebrafish embryo.

MES Note:

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An adult female zebrafish

The end of gastrulation signals the beginning of organogenesis, whereby the three germ layers form the internal organs of the organism.[225] The cells of each of the three germ layers undergo differentiation, a process where less-specialized cells become more-specialized through the expression of a specific set of genes. Cellular differentiation is influenced by extracellular signals such as growth factors [substances that stimulate cell proliferation] that are exchanged to adjacent cells, which is called juxtracrine signaling, or to neighboring cells over short distances, which is called paracrine signaling.[226][227] Intracellular signals consist of a cell signaling itself (autocrine signaling), also play a role in organ formation. These signaling pathways allows for cell rearrangement and ensures that organs form at specific sites within the organism.[225][228]

MES Note: Organogenesis is the phase of embryonic development that starts at the end of gastrulation and continues until birth. During organogenesis, the three germ layers formed from gastrulation (the ectoderm, endoderm, and mesoderm) form the internal organs of the organism.

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The endoderm of vertebrates produces tissue within the lungs, thyroid, and pancreas.

The mesoderm aids in the production of cardiac muscle, skeletal muscle, smooth muscle, tissues within the kidneys, and red blood cells.

The ectoderm produces tissues within the epidermis [outermost layer of skin] and aids in the formation of neurons within the brain, and melanocytes [melanin, pigment producing cells].

Melanin (from Greek: μέλας melas, "black, dark") is a broad term for a group of natural pigments found in most organisms.

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Cross-section of human skin

Immune system

Further information: Immune system and Immunology

The immune system is a network of biological processes that detects and responds to a wide variety of pathogens. Many species have two major subsystems of the immune system. The innate immune system provides a preconfigured response to broad groups of situations and stimuli. The adaptive immune system provides a tailored response to each stimulus by learning to recognize molecules it has previously encountered. Both use molecules and cells to perform their functions.

Nearly all organisms have some kind of immune system. Bacteria have a rudimentary [basic] immune system in the form of enzymes that protect against virus infections. Other basic immune mechanisms evolved in ancient plants and animals and remain in their modern descendants. These mechanisms include phagocytosis, antimicrobial peptides called defensins, and the complement system.

MES Note: Phagocytosis (from Ancient Greek φαγεῖν (phagein) 'to eat', and κύτος, (kytos) 'cell') is the process by which a cell uses its plasma membrane to engulf a large particle (≥ 0.5 μm), giving rise to an internal compartment called the phagosome. It is one type of endocytosis [process of bringing substances into the cell]. A cell that performs phagocytosis is called a phagocyte.

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Overview of phagocytosis

Antimicrobial peptides (AMPs), also called host defence peptides (HDPs) are part of the innate immune response found among all classes of life. They have been demonstrated to kill bacteria, enveloped viruses, fungi and even transformed or cancerous cells.

The complement system, also known as complement cascade, is a part of the immune system that enhances (complements) the ability of antibodies and phagocytic cells to clear microbes and damaged cells from an organism, promote inflammation, and attack the pathogen's cell membrane. It is part of the innate immune system,[1] which is not adaptable and does not change during an individual's lifetime. The complement system can, however, be recruited and brought into action by antibodies generated by the adaptive immune system. The complement system consists of a number of small proteins that are synthesized by the liver, and circulate in the blood as inactive precursors. When stimulated by one of several triggers, proteases in the system cleave specific proteins to release cytokines and initiate an amplifying cascade of further cleavages. The end result of this complement activation or complement fixation cascade is stimulation of phagocytes to clear foreign and damaged material, inflammation to attract additional phagocytes, and activation of the cell-killing membrane attack complex. About 50 proteins and protein fragments make up the complement system, including serum proteins, and cell membrane receptors. They account for about 10% of the globulin fraction of blood serum.[2]

A protein precursor, also called a pro-protein or pro-peptide, is an inactive protein (or peptide) that can be turned into an active form by post-translational modification, such as breaking off a piece of the molecule or adding on another molecule. The name of the precursor for a protein is often prefixed by pro-. Examples include proinsulin and proopiomelanocortin, which are both prohormones.

A protease (also called a peptidase or proteinase) is an enzyme that catalyzes (increases reaction rate or "speeds up") proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the formation of new protein products. They do this by cleaving the peptide bonds within proteins by hydrolysis, a reaction where water breaks bonds. Proteases are involved in many biological functions, including digestion of ingested proteins, protein catabolism (breakdown of old proteins),[2][3] and cell signaling.

Cytokines are a broad and loose category of small proteins important in cell signaling. Cytokines are peptides and cannot cross the lipid bilayer of cells to enter the cytoplasm. Cytokines have been shown to be involved in autocrine, paracrine and endocrine signaling as immunomodulating agents. Their definite distinction from hormones is still part of ongoing research.

Immunomodulation is modulation (regulatory adjustment) of the immune system. It has natural and human-induced forms.

The membrane attack complex (MAC) or terminal complement complex (TCC) is a complex of proteins typically formed on the surface of pathogen cell membranes as a result of the activation of the host's complement system, and as such is an effector of the immune system.

An effector molecule is usually a small molecule that selectively binds to a protein and regulates its biological activity. In this manner, effector molecules act as ligands that can increase or decrease enzyme activity, gene expression, or cell signaling. Effector molecules can also directly regulate the activity of some mRNA molecules (riboswitches). In some cases, proteins can be considered to function as effector molecules, especially in cellular signal transduction cascades. The term effector is used in other fields of biology. For instance, the effector end of a neuron is the terminus where an axon makes contact with the muscle or organ that it stimulates or suppresses.

The globulins are a family of globular proteins that have higher molecular weights than albumins and are insoluble in pure water but dissolve in dilute salt solutions.

Albumin is a family of globular proteins, the most common of which are the serum albumins. All the proteins of the albumin family are water-soluble, moderately soluble in concentrated salt solutions, and experience heat denaturation.

Denaturation is a process in which proteins or nucleic acids lose the quaternary structure, tertiary structure, and secondary structure which is present in their native state, by application of some external stress or compound such as a strong acid or base, a concentrated inorganic salt, an organic solvent (e.g., alcohol or chloroform), agitation and radiation or heat.

Inflammation (from Latin: inflammatio) is part of the complex biological response of body tissues to harmful stimuli, such as pathogens, damaged cells, or irritants,[1] and is a protective response involving immune cells, blood vessels, and molecular mediators. The function of inflammation is to eliminate the initial cause of cell injury, clear out necrotic cells and tissues damaged from the original insult and the inflammatory process, and initiate tissue repair.

Irritation, in biology and physiology, is a state of inflammation or painful reaction to allergy or cell-lining damage. A stimulus or agent which induces the state of irritation is an irritant. Irritants are typically thought of as chemical agents (for example phenol and capsaicin) but mechanical, thermal (heat), and radiative stimuli (for example ultraviolet light or ionising radiations) can also be irritants. Irritation also has non-clinical usages referring to bothersome physical or psychological pain or discomfort.

Allergies, also known as allergic diseases, are a number of conditions caused by hypersensitivity of the immune system to typically harmless substances in the environment.

Ionizing radiation (or ionising radiation), including nuclear radiation, consists of subatomic particles or electromagnetic waves that have sufficient energy to ionize atoms or molecules by detaching electrons from them.[1] The particles generally travel at a speed that is 99% of the that of light, and the electromagnetic waves are on the high-energy portion of the electromagnetic spectrum.

Necrosis (from Ancient Greek νέκρωσις nékrōsis 'death') is a form of cell injury which results in the premature death of cells in living tissue by autolysis.[1] Necrosis is caused by factors external to the cell or tissue, such as infection, or trauma which result in the unregulated digestion of cell components. In contrast, apoptosis is a naturally occurring programmed and targeted cause of cellular death. While apoptosis often provides beneficial effects to the organism, necrosis is almost always detrimental and can be fatal.

Autolysis, more commonly known as self-digestion, refers to the destruction of a cell through the action of its own enzymes. It may also refer to the digestion of an enzyme by another molecule of the same enzyme.

Jawed vertebrates, including humans, have even more sophisticated defense mechanisms, including the ability to adapt to recognize pathogens more efficiently. Adaptive (or acquired) immunity creates an immunological memory leading to an enhanced response to subsequent encounters with that same pathogen. This process of acquired immunity is the basis of vaccination.

MES Note: Gnathostomata /ˌnæθoʊˈstɒmətə/ are the jawed vertebrates. The term derives from Greek: γνάθος (gnathos) "jaw" + στόμα (stoma) "mouth". Gnathostome diversity comprises roughly 60,000 species, which accounts for 99% of all living vertebrates.

Immunological memory is the ability of the immune system to quickly and specifically recognize an antigen that the body has previously encountered and initiate a corresponding immune response. Generally these are secondary, tertiary and other subsequent immune responses to the same antigen. Immunological memory is responsible for the adaptive component of the immune system, special T and B cells — the so-called memory T and B cells. Immunological memory is the basis of vaccination.[1][2] Emerging resource shows support for the innate immune system's participation in immune memory responses in invertebrates as well as vertebrates.

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The time course of an immune response. Due to the formation of immunological memory, reinfection at later time points leads to a rapid increase in antibody production and effector T cell activity. These later infections can be mild or even unapparent [not apparent or inapparent].

White blood cells (WBCs), also called leukocytes or leucocytes, are the cells of the immune system [also called immune cells] that are involved in protecting the body against both infectious disease and foreign invaders. All white blood cells are produced and derived from multipotent cells in the bone marrow known as hematopoietic stem cells. Leukocytes are found throughout the body, including the blood and lymphatic system.[1]

Hematopoietic stem cells (HSCs) are the stem cells that give rise to other blood cells. This process is called haematopoiesis.

Multipotency describes progenitor cells which have the gene activation potential to differentiate into discrete cell types.

Bone marrow is a semi-solid tissue found within the spongy (also known as cancellous) portions of bones.[2] In birds and mammals, bone marrow is the primary site of new blood cell production (or haematopoiesis). The composition of marrow is dynamic, as the mixture of cellular and non-cellular components (connective tissue) shifts with age and in response to systemic factors. In humans, marrow is colloquially characterized as "red" or "yellow" depending on the prevalence of hematopoietic cells [blood cells] vs fat cells.

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Structure of a long bone

A lymphocyte is a type of white blood cell in the immune system of jawed vertebrates.[1] Lymphocytes include natural killer cells (which function in cell-mediated, cytotoxic innate immunity), T cells (for cell-mediated, cytotoxic adaptive immunity), and B cells (for humoral, antibody-driven adaptive immunity).[2][3] They are the main type of cell found in lymph, which prompted the name "lymphocyte".[4] Lymphocytes make up between 18% and 42% of circulating white blood cells.

Cytotoxicity is the quality of being toxic to cells.

Cell-mediated immunity is an immune response that does not involve antibodies. Rather, cell-mediated immunity is the activation of phagocytes, antigen-specific cytotoxic T-lymphocytes, and the release of various cytokines in response to an antigen.

Natural killer cells, also known as NK cells or large granular lymphocytes (LGL), are a type of cytotoxic lymphocyte critical to the innate immune system and represent 5–20% of all circulating lymphocytes in humans.

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Human natural killer cell, colorized scanning electron micrograph

A T cell is a type of lymphocyte. T cells are one of the [most] important white blood cells of the immune system and play a central role in the adaptive immune response. T cells can be distinguished from other lymphocytes by the presence of a T-cell receptor (TCR) on their cell surface. T cells are born from hematopoietic stem cells,[1] found in the bone marrow. Developing T cells then migrate to the thymus gland to develop (or mature). T cells derive their name from the thymus.[2] After migration to the thymus, the precursor cells mature into several distinct types of T cells. T cell differentiation also continues after they have left the thymus. Groups of specific, differentiated T cell subtypes have a variety of important functions in controlling and shaping the immune response.

The T-cell receptor (TCR) is a protein complex found on the surface of T cells, or T lymphocytes,[1] that is responsible for recognizing fragments of antigen as peptides bound to major histocompatibility complex (MHC) molecules [cell surface proteins essential for the adaptive immune system]. The binding between TCR and antigen peptides is of relatively low affinity [attractive force] and is degenerate: that is, many TCRs recognize the same antigen peptide and many antigen peptides are recognized by the same TCR.

Within biological systems, degeneracy occurs when structurally dissimilar components/modules/pathways can perform similar functions (i.e. are effectively interchangeable) under certain conditions, but perform distinct functions in other conditions.[1][2] Degeneracy is thus a relational property that requires comparing the behavior of two or more components. In particular, if degeneracy is present in a pair of components, then there will exist conditions where the pair will appear functionally redundant but other conditions where they will appear functionally distinct. T cells that successfully develop react appropriately with MHC immune receptors of the body (called positive selection) and not against proteins of the body (called negative selection).

The thymus is a specialized primary lymphoid organ of the immune system. Within the thymus, thymus cell lymphocytes or T cells mature. The thymus is located in the upper front part of the chest and in front of the heart. The thymus is made up of immature T cells called thymocytes, as well as lining cells called epithelial cells which help the thymocytes develop.

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Thymus

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Scanning electron micrograph of a human T cell

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Scanning electron micrograph of a red blood cell (left), a platelet (center), and a T lymphocyte (right); colorized

B cells, also known as B lymphocytes, are a type of white blood cell of the lymphocyte subtype.[1] They function in the humoral immunity component of the adaptive immune system.[1] B cells produce antibody molecules; however, these antibodies are not secreted. Rather, they are inserted into the plasma membrane where they serve as a part of B-cell receptors.[2] When a naïve or memory B cell is activated by an antigen, it proliferates and differentiates into an antibody-secreting effector cell, known as a plasmablast or plasma cell.[2] Additionally, B cells present antigens (they are also classified as professional antigen-presenting cells (APCs)) and secrete cytokines.[1] In mammals, B cells mature in the bone marrow, which is at the core of most bones. In birds, B cells mature in the bursa of Fabricius, a lymphoid organ where they were first discovered by Chang and Glick,[3] which is why the 'B' stands for bursa and not bone marrow as commonly believed.

Humoral immunity is the aspect of immunity that is mediated by macromolecules found in extracellular fluids such as secreted antibodies, complement proteins [part of complement system], and certain antimicrobial peptides.

B cells, unlike the other two classes of lymphocytes, T cells and natural killer cells, express B cell receptors (BCRs) on their cell membrane.[1] BCRs allow the B cell to bind to a foreign antigen, against which it will initiate an antibody response.[1]

The B cell receptor (BCR) is a transmembrane protein on the surface of a B cell. Through biochemical signaling and by physically acquiring antigens from the immune synapses, the BCR controls the activation of the B cell.[2] B cells are able to gather and grab antigens by engaging biochemical modules for receptor clustering, cell spreading, generation of pulling forces, and receptor transport, which eventually culminates in endocytosis and antigen presentation.

Source: Antigen presentation: Process by which an antigen is presented to lymphocytes in a form they can recognize; antigen presenting cells may ingest or digest the antigen and present the fragments to the cell surface for recognition by the lymphocytes.

Antigen presentation is a vital immune process that is essential for T cell immune response triggering. Because T cells recognize only fragmented antigens displayed on cell surfaces, antigen processing must occur before the antigen fragment is transported to the surface of the cell, a process known as presentation, where it can be recognized by a T-cell receptor. If there has been an infection with viruses or bacteria, the cell will present an endogenous or exogenous peptide fragment derived from the antigen by MHC molecules. B-cell receptors on the surface of B cells bind to intact native and undigested antigens of a structural nature, rather than to a linear sequence of a peptide which has been digested into small fragments and presented by MHC molecules [such as in the case of T cells].

An immunological synapse (or immune synapse) is the interface between an antigen-presenting cell or target cell and a lymphocyte such as a T/B cell or Natural Killer cell. The interface was originally named after the neuronal synapse, with which it shares the main structural pattern.[1] An immunological synapse consists of molecules involved in T cell activation, which compose typical patterns—activation clusters. Immunological synapses are the subject of much ongoing research.

An antigen-presenting cell (APC) or accessory cell is a cell that displays antigen bound by major histocompatibility complex (MHC) proteins on its surface; this process is known as antigen presentation. T cells may recognize these complexes using their T cell receptors (TCRs). APCs process antigens and present them to T-cells.

Antigen processing, or the cytosolic pathway, is an immunological process that prepares antigens for presentation to special cells of the immune system called T lymphocytes. It is considered to be a stage of antigen presentation pathways.

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Transmission electron micrograph of a human B cell

In birds, the bursa of Fabricius (Latin: Bursa cloacalis or Bursa fabricii) is the site of hematopoiesis. It is a specialized organ that, as first demonstrated by Bruce Glick and later by Max Dale Cooper and Robert Good, is necessary for B cell (part of the immune system) development in birds. Mammals generally do not have an equivalent organ; the bone marrow is often the site of both hematopoiesis and B cell development. The bursa is present in the cloaca of birds and is named after Hieronymus Fabricius [20 May 1533 to 21 May 1619], who described it [in lecture notes found and published] in 1621.

A cloaca (plural cloacae) is the posterior [backside] orifice [opening] that serves as the only opening for the digestive, reproductive, and urinary tracts (if present) of many vertebrate animals.

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Figure

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Diagram showing the development of different blood cells from hematopoietic stem cells to mature cells.

A naive B cell is a B cell that has not been exposed to an antigen. Once exposed to an antigen, the naive B cell either becomes a memory B cell or a plasma cell that secretes antibodies specific to the antigen that was originally bound. Plasma cells do not last long in the circulation, this is in contrast to memory cells that last for very long periods of time. Memory cells do not secrete antibody until activated by their specific antigen.

A memory B cell (MBC) is a type of B lymphocyte that forms part of the adaptive immune system. Memory B cells circulate in the blood stream in a quiescent [inactive] state, sometimes for decades.[1] Their function is to memorize the characteristics of the antigen that activated their parent B cell during initial infection such that if the memory B cell later encounters the same antigen, it triggers an accelerated and robust secondary immune response.[2][3] Memory B cells have B cell receptors (BCRs) on their cell membrane, identical to the one on their parent cell, that allow them to recognize antigen and mount a specific antibody response. Differentiation of memory B cells into plasma cells is far faster than differentiation by naïve B cells, which allows memory B cells to produce a more efficient secondary immune response.

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B lymphocytes are the cells of the immune system that make antibodies to invade pathogens like viruses. They form memory cells that remember the same pathogen for faster antibody production in future infections.

Memory T cells are a subset of T lymphocytes that might have some of the same functions as memory B cells. Their lineage is unclear. Primary function of memory cells is augmented immune response after reactivation of those cells by reintroduction of relevant pathogen into the body.

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Processes in the primary immune response

MES Note: Macrophages (abbreviated as Mφ, MΦ or MP) (Greek: large eaters, from Greek μακρός (makrós) = large, φαγεῖν (phagein) = to eat) are a type of white blood cell of the immune system that engulfs and digests anything that does not have, on its surface, proteins that are specific to healthy body cells, including cancer cells, microbes, cellular debris, foreign substances, etc.[2][3] The process is called phagocytosis, which acts to defend the host against infection and injury.

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A macrophage stretching its "arms" (filopodia)[1] to engulf two particles, possibly pathogens, in a mouse

Animal behavior

Further information: Ethology

Behaviors play a central a role [sic] in animals' interaction with each other and with their environment.[229] They are able to use their muscles to approach one another, vocalize, seek shelter, and migrate. An animal's nervous system activates and coordinates its behaviors. Fixed action patterns, for instance, are genetically determined and stereotyped behaviors that occur without learning.[229][230] These behaviors are under the control of the nervous system and can be quite elaborate.[229] Examples include the pecking of kelp gull [type of seagull or seabird] chicks at the red dot on their mother's beak.

MES Note: Behavior (American English) or behaviour is the range of actions and mannerisms made by individuals, organisms, systems or artificial entities in within some environment.

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Kelp gull (Larus dominicanus)

Source: In the mid-20th Century, Dutch scientist Niko Tinbergen [15 April 1907 to 21 December 1988] studied nesting Herring Gulls. He noticed that newly hatched gull chicks were fed by their parents only after they pecked at the adults' bills. Tinbergen devised experiments that varied the shape and coloration of the adult's bill. It became clear that the red spot on the adult gull's bill was a crucial visual cue in a chick's demands to be fed, and thus its survival. Tinbergen also made the case that the chick's attraction to the red spot on the bill was instinctive. This conclusion came at a time when there was furious debate among experts about whether such behavior was learned or innate. Tinbergen's gull research helped lay the groundwork for the science of animal behavior, and in 1973 earned him a Nobel Prize. And it all started with that little red spot.

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Other behaviors that have emerged as a result of natural selection include foraging [searching for wild food resources], mating, and altruism [benefiting another individual at one’s expense].[231] In addition to evolved behavior, animals have evolved the ability to learn by modifying their behaviors as a result of early [and late] individual experiences.[229]

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Brood parasites, such as the cuckoo [being fed by a reed warbler], provide a supernormal [beyond the norm] stimulus to the parenting species.

MES Note: Brood parasites are organisms that rely on others to raise their young.

Some [cuckoo] species are brood parasites, laying their eggs in the nests of other species and giving rise to the metaphor cuckoo's egg, but the majority of species raise their own young.

Ecology

Ecosystems

Further information: Ecology and Ecosystem

Ecology is the study of the distribution and abundance of living organisms, the interaction between them and their environment.[232] The community of living (biotic) organisms in conjunction [union, combination] with the nonliving (abiotic) components (e.g., water, light, radiation, temperature, humidity [water vapor/gas concentration in air], atmosphere, acidity, and soil) of their environment is called an ecosystem.[233][234][235] These biotic and abiotic components are linked together through nutrient cycles and energy flows.[236] Energy from the sun enters the system through photosynthesis and is incorporated into plant tissue. By feeding on plants and on one another, animals play an important role in the movement of matter [substances with mass and volume] and energy through the system. They also influence the quantity of plant and microbial biomass [mass of living organisms] present. By breaking down dead organic matter, decomposers release carbon back to the atmosphere and facilitate nutrient cycling by converting nutrients stored in dead biomass back to a form that can be readily used by plants and other microbes.[237]

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Terrestrial biomes [collection of flora (plants) and fauna (animals)] are shaped by temperature and precipitation.

MES Note:

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Tundra in Greenland

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Boreal forest in Russia

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Figure: Temperate grassland

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Cold desert in North India

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Woodland in Illinois, USA.

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Shrubland in Texas, USA

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Temperate seasonal forest in Slovakia

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Temperate rainforest in Gwaii Haanas, Canada

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Figure: Subtropical desert in Arizona, USA.

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Tropical seasonal forest in Northern Thailand

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Savanna in Northern Australia

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Tropical rainforest [Amazon rainforest] in Colombia

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An area of the Amazon rainforest in Brazil.

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Map of the Amazon rainforest ecoregions as delineated by the WWF [World Wildlife Foundation] in white[1] and the Amazon drainage basin in blue.

A drainage basin is any area of land where precipitation collects and drains off into a common outlet, such as into a river, bay, or other body of water.

A bay is a recessed, coastal body of water that directly connects to a larger main body of water, such as an ocean, a lake, or even another bay.

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Top-down illustration of a drainage basin.

The Earth's physical environment is shaped by solar energy and topography [forms and features of land surfaces].[235] The amount of solar energy input varies in space and time due to the spherical shape of the Earth and its axial tilt.

MES Note: Solar energy is radiant light and heat from the Sun.

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The axis of Earth remains oriented in the same direction with reference to the background stars regardless of where it is in its orbit. Northern hemisphere summer occurs at the right side of this diagram, where the north pole (red) is directed toward the Sun, winter at the left.

Variation in solar energy input drives weather and climate patterns. Weather is the day-to-day temperature and precipitation activity, whereas climate is the long-term average of weather, typically averaged over a period of 30 years.[238][239] Variation in topography also produces environmental heterogeneity [variation, non-uniformity]. On the windward [upwind] side of a mountain, for example, air rises and cools, with water changing from gaseous to liquid or solid form, resulting in precipitation such as rain or snow.[235] As a result, wet environments allow for lush [thriving] vegetation to grow. In contrast, conditions tend to be dry on the leeward [downwind] side of a mountain due to the lack of precipitation as air descends and warms, and moisture remains as water vapor in the atmosphere. Temperature and precipitation are the main factors that shape terrestrial biomes.

MES Note: Precipitation is any product of the condensation of atmospheric water vapor that falls under gravitational pull from clouds.

Condensation is the change of the state of matter from the gas phase into the liquid phase, and is the reverse of vaporization.

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Example image showing definitions of windward (upwind) and leeward (downwind)

A biome is a large collection of flora and fauna occupying a major habitat.

Flora is all the plant life present in a particular region or time.

Fauna is all of the animal life present in a particular region or time.

Populations

Further information: Population and Population ecology

A population is the number of organisms of the same species that occupy an area and reproduce from generation to generation.[240][241][242][243][244] Its abundance can be measured using population density, which is the number of individuals per unit area (e.g., land or tree) or volume (e.g., sea or air).[240] Given that it is usually impractical to count every individual within a large population to determine its size, population size can be estimated by multiplying population density by the area or volume. Population growth during short-term intervals can be determined using the population growth rate equation, which takes into consideration birth, death, and immigration rates. In the longer term, the exponential growth of a population tends to slow down as it reaches its carrying capacity, which can be modeled using the logistic equation.[241]

MES Note: The "population growth rate" is the rate at which the number of individuals in a population increases in a given time period, expressed as a fraction of the initial population. Specifically, population growth rate refers to the change in population over a unit time period, often expressed as a percentage of the number of individuals in the population at the beginning of that period. This can be written as the formula, valid for a sufficiently small time interval:

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A positive growth rate indicates that the population is increasing, while a negative growth rate indicates that the population is decreasing. A growth ratio of zero indicates that there were the same number of individuals at the beginning and end of the period.

Exponential growth is a process that increases quantity over time. It occurs when the instantaneous rate of change of a quantity with respect to time is proportional to the quantity itself.

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The graph illustrates how exponential growth (green) surpasses both linear (red) and cubic (blue) growth.

See my earlier video on the logistic equation.

https://peakd.com/mathematics/@mes/differential-equations-population-growth-logistic-equation

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Figure:

  • dP/dt is the population growth rate
  • P is the population size
  • k is a proportionality / relative growth rate coefficient
  • K is the carrying capacity

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Reaching carrying capacity through a logistic growth curve [natality = birth rate]

The carrying capacity of an environment is the maximum population size of a species that can be sustained by that specific environment, given the food, habitat, water, and other resources that are available.[245] The carrying capacity of a population can be affected by changing environmental conditions such as changes in the availability [of] resources and the cost of maintaining them. In human populations, new technologies such as the Green revolution have helped increase the Earth’s carrying capacity for humans over time, which has stymied [hindered/blocked] the attempted predictions of impending [or upcoming] population decline, the famous of which was by Thomas Malthus in the 18th century.[240]

MES Note: The Green Revolution, or the Third Agricultural Revolution, is the set of research technology transfer initiatives occurring between 1950 and the late 1960s, that increased agricultural production in parts of the world, beginning most markedly in the late 1960s.[1] The initiatives resulted in the adoption of new technologies, including high-yielding varieties (HYVs) of cereals, especially dwarf wheat and rice.

Wheat is a grass widely cultivated for its seed, a cereal grain which is a worldwide staple food.

Rice is the seed of the grass species Oryza sativa (Asian rice) or less commonly Oryza glaberrima (African rice).

A staple food, food staple, or simply a staple, is a food that is eaten often and in such quantities that it constitutes a dominant portion of a standard diet for a given person or group of people, supplying a large fraction of energy needs and generally forming a significant proportion of the intake of other nutrients as well.

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After World War II, newly implemented agricultural technologies, including pesticides and fertilizers as well as new breeds of high yield crops, greatly increased food production in certain regions of the Global South.

Pesticides are substances that are meant to control pests.

A pest is any animal or plant harmful to humans or human concerns.

The concept of Global North and Global South (or North–South divide) is used to describe a grouping of countries along socio-economic and political characteristics. The Global South is a term often used to identify lower-income countries on one side of the so-called global North–South divide, the other side being the countries of the Global North (often equated with developed countries).[1] As such the term does not inherently refer to a geographical south; for example, most of the Global South is actually within the Northern Hemisphere.

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World map showing a traditional definition of the North–South divide (red countries in this map are grouped as "Global South", blue countries as "Global North")

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Figure

The Northern and Southern Hemispheres [from Greek for “half of a sphere] refer to the Earth being divided into two parts about the Equator in line with the rotation of the Earth.

In geographical coordinates, the prime meridian is defined as the starting meridian or line of longitude; the lateral lines are called latitudes.

High-yielding varieties (HYVs) of agricultural crops are usually characterized by a combination of the following traits in contrast to the conventional varieties:

  • Higher crop yield per area (hectare)
  • Dwarfness
  • Improved response to fertilizers
  • High reliance on irrigation and fertilizers - see intensive farming
  • Early maturation
  • Resistive to many diseases
  • Higher quality and quantity of crops can be produced.

Dwarfing is a process in which a breed of animals or cultivar of plants is changed to become significantly smaller than standard members of their species. Dwarfing genes are widely used in creating more productive food plants, such as grains. One condition that results in loss of grain crops is called 'lodging', where heavy ears of almost ripe grain bend the stalk until the grain touches the ground, becomes wet, and spoils. During the Green Revolution, research that identified wheat reduced-height genes (Rht)[11] and a rice semidwarf gene (sd1)[12] resulted in crops that yielded significantly more harvestable grain.

An ear is the grain-bearing tip part of the stem of a cereal plant, such as wheat or maize.

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Unripe ears of barley, wheat, and rye

A cultivar is a type of plant that people have bred for desired traits, which are reproduced in each new generation by a method such as grafting, tissue culture or carefully controlled seed production. Most cultivars arise from purposeful human manipulation, but some originate from wild plants that have distinctive characteristics.

Grafting or graftage[1] is a horticultural technique whereby tissues of plants are joined so as to continue their growth together.

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Cherry tree, consolidated "V" graft

Communities

Further information: Community (ecology)

A community is a group of populations of two or more different species occupying the same geographical area at the same time. A biological interaction is the effect that a pair of organisms living together in a community have on each other. They can be either of the same species (intraspecific interactions), or of different species (interspecific interactions). These effects may be short-term, like pollination and predation [predator vs prey interaction], or long-term; both often strongly influence the evolution of the species involved. A long-term interaction is called a symbiosis. Symbioses range from mutualism, beneficial to both partners, to competition, harmful to both partners.[247]

MES Note:

“Intra-“ is from Latin for “within”.

“Inter-“ is from Latin for “between”.

Every species participates as a consumer, resource, or both in consumer–resource interactions, which form the core of food chains or food webs.[248] There are different trophic levels [position, “trophic” derived from Greek for “food”] within any food web, with the lowest level being the primary producers (or autotrophs) such as plants and algae that convert energy and inorganic material into organic compounds, which can then be used by the rest of the community.[54][249][250] At the next level are the heterotrophs, which are the species that obtain energy by breaking apart organic compounds from other organisms.[248] Heterotrophs that consume plants are primary consumers (or herbivores) whereas heterotrophs that consume herbivores are secondary consumers (or carnivores). And those that eat secondary consumers are tertiary consumers and so on. Omnivorous heterotrophs are able to consume at multiple levels. Finally, there are decomposers [and detritivores or detrivores] that feed on the waste products or dead bodies of organisms.[248]

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A (a) trophic pyramid and a (b) simplified food web. The trophic pyramid represents the biomass at each level.[246]

MES Note: The word trophic derives from the Greek τροφή (trophē) referring to food or nourishment.

On average, the total amount of energy incorporated into the biomass of a trophic level per unit of time is about one-tenth of the energy of the trophic level that it consumes. Waste and dead material used by decomposers as well as heat lost from metabolism make up the other ninety percent of energy that is not consumed by the next trophic level.[251]

MES Note: In other words, each trophic level above captures 10% of the energy of the one below.

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A pyramid of energy represents how much energy, initially from the sun, is retained or stored in the form of new biomass at each trophic level in an ecosystem. Typically, about 10% of the energy is transferred from one trophic level to the next, thus preventing a large number of trophic levels. Energy pyramids are necessarily upright in healthy ecosystems, that is, there must always be more energy available at a given level of the pyramid to support the energy and biomass requirement of the next trophic level.

Biosphere

Further information: Biosphere and Climate change

In the global ecosystem (or biosphere), matter exist as different interacting compartments, which can be biotic or abiotic as well as accessible or inaccessible, depending on their forms and locations.[253] For example, matter from terrestrial autotrophs are both biotic and accessible to other living organisms whereas the matter in rocks and minerals are abiotic and inaccessible to living organisms. A biogeochemical cycle is a pathway by which specific elements of matter are turned over or moved through the biotic (biosphere) and the abiotic (lithosphere, atmosphere, and hydrosphere) compartments of Earth. There are biogeochemical cycles for nitrogen, carbon, and water. In some cycles there are reservoirs where a substance remains or is sequestered [separated] for a long period of time.

MES Note: The biosphere (from Greek βίος bíos "life" and σφαῖρα sphaira "sphere"), also known as the ecosphere (from Greek οἶκος oîkos "environment" and σφαῖρα), is the worldwide sum of all ecosystems.

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Fast carbon cycle showing the movement of carbon between land, atmosphere, and oceans in billions of tons per year. Yellow numbers are natural fluxes, red are human contributions, white are stored carbon. Effects of the slow carbon cycle, such as volcanic and tectonic activity, are not included.[252]

MES Note: There is a fast and a slow carbon cycle. The fast cycle operates in the biosphere and the slow cycle operates in rocks. The fast or biological cycle can complete within years, moving carbon from atmosphere to biosphere, then back to the atmosphere. The slow or geological cycle can take millions of years to complete, moving carbon through the Earth's crust between rocks, soil, ocean and atmosphere.

Calculation Check: Out – In = (60 + 60 + 9 + 90) - (120 + 3 + 90 + 2) = 4 GtC/y to the atmosphere.

Climate change includes both global warming driven by human-induced emissions of greenhouse gases and the resulting large-scale shifts in weather patterns.

MES Note: A greenhouse gas (GHG or GhG) is a gas that absorbs and emits radiant energy within the thermal infrared range, causing the greenhouse effect. The primary greenhouse gases in Earth's atmosphere are water vapor (H2O), carbon dioxide (CO2), methane (CH4), nitrous oxide (N2O), and ozone (O3). Without greenhouse gases, the average temperature of Earth's surface would be about −18 °C (0 °F),[2] rather than the present average of 15 °C (59 °F).

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The greenhouse effect of solar radiation on the Earth's surface caused by emission of greenhouse gases.

The greenhouse effect is the process by which radiation from a planet's atmosphere warms the planet's surface to a temperature above what it would be without this atmosphere.[1][2] Radiatively [not to be confused with radioactively] active gases (i.e., greenhouse gases) in a planet's atmosphere radiate energy in all directions. Part of this radiation is directed towards the surface, thus warming it.[3] The intensity of downward radiation – that is, the strength of the greenhouse effect – depends on the amount of greenhouse gases that the atmosphere contains. The temperature rises until the intensity of upward radiation from the surface, thus cooling it, balances the downward flow of energy.

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Greenhouse gases allow sunlight to pass through the atmosphere, but then absorb and reflect the infrared radiation (heat) the planet emits

Thermal radiation is electromagnetic radiation generated by the thermal motion [chaotic/random motion] of particles in matter. Thermal radiation is generated when heat from the movement of charges in the material (electrons and protons in common forms of matter) is converted to electromagnetic radiation.

The thermal infrared range, also known as the medium infrared range, is defined as having wavelengths between 3 to 8 μm (micrometers, 1-millionth of a meter), and is the typical wavelengths emitted at normal atmospheric temperatures.

“Infra” is Latin for “below”; below the visible red range. [less energy, smaller frequency, larger wavelength]

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Figure

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Atmospheric absorption and scattering at different wavelengths of electromagnetic waves. The largest absorption band of carbon dioxide is not far from the maximum in the thermal emission from ground, and it partly closes the window of transparency of water; hence its major effect.

The Spectral Intensity is a measure of energy density per wavelength emitted, and the curves always have the same basic shape for thermal radiation at any temperature.

5525 K (Kelvin) = 5251.85°C = 9485.33°F
210 to 310 K = -63.15 to 36.85°C = -81.67 to 98.33°F

Rayleigh scattering is the phenomena of scattering of light particles mainly by the molecules of gas (sometimes also by solid and liquid). Shorter (blue) wavelengths are scattered more strongly than longer (red) wavelengths. This results in the indirect blue light coming from all regions of the sky.

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Figure

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Observed global average temperature change since the pre-industrial era. The main driver for increased global temperatures in the industrial era is human activity, with natural forces adding relatively minor variability.

Though there have been previous periods of climatic change, since the mid-20th century humans have had an unprecedented impact on Earth's climate system and caused change on a global scale.[254] The largest driver of warming is the emission of greenhouse gases, of which more than 90% are carbon dioxide [CO2] and methane [CH4].[255] Fossil fuel burning (coal, oil, and natural gas) for energy consumption is the main source of these emissions, with additional contributions from agriculture, deforestation, and manufacturing.[256]

MES Note: A fuel is any material that can be made to react with other substances so that it releases energy as thermal energy or to be used for work.

A fossil fuel is a fuel formed by natural processes, such as anaerobic decomposition [decomposition without oxygen] of buried dead organisms, containing organic molecules originating in ancient photosynthesis[1] that release energy in combustion.[2] Such organisms and their resulting fossil fuels typically have an age of millions of years, and sometimes more than 650 million years.[3] Fossil fuels contain high percentages of carbon and include petroleum, coal, and natural gas.[4]

Petroleum, also known as crude oil and oil, is a naturally occurring, yellowish-black liquid found in geological formations beneath the Earth's surface. It is commonly refined into various types of fuels.

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A sample of petroleum.

Coal is a combustible black or brownish-black sedimentary rock, formed as rock strata [layers] called coal seams. Coal is mostly carbon with variable amounts of other elements, chiefly hydrogen, sulfur, oxygen, and nitrogen.[1] Coal is formed when dead plant matter decays into peat and is converted into coal by the heat and pressure of deep burial over millions of years.

Peat also known as turf is an accumulation of partially decayed vegetation or organic matter.

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A lump of peat

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Bituminous coal [black coal]

Natural gas (also called fossil gas; sometimes just gas) is a naturally occurring hydrocarbon gas mixture consisting of methane and commonly including varying amounts of other higher alkanes, and sometimes a small percentage of carbon dioxide, nitrogen, hydrogen sulfide [H2S], or helium.[2] Natural gas is colorless and odorless, and explosive, so a sulfur-smell (similar to rotten eggs) is added for early detection of leaks.

Sedimentary rocks are types of rock that are formed by the accumulation or deposition of mineral or organic particles at the Earth's surface, followed by cementation.

Cementation involves ions carried in groundwater chemically precipitating to form new crystalline material between sedimentary grains. The new pore-filling minerals forms "bridges" between original sediment grains, thereby binding them together.

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Coal, oil, and natural gas remain the primary global energy sources even as renewables [energy sources that can be replenished on a human timescale] have begun rapidly increasing.

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Biofuel is fuel that is produced through contemporary processes from biomass, rather than by the very slow geological processes involved in the formation of fossil fuels, such as oil. Since biomass technically can be used as a fuel directly (e.g. wood logs), some people use the terms biomass and biofuel interchangeably.

Temperature rise is accelerated or tempered [made less intense] by climate feedbacks, such as loss of sunlight-reflecting snow and ice cover, increased water vapor (a greenhouse gas itself), and changes to land and ocean carbon sinks.

MES Note: Feedback in general is the process in which changing one quantity changes a second quantity, and the change in the second quantity in turn changes the first. Positive (or reinforcing) feedback amplifies the change in the first quantity while negative (or balancing) feedback reduces it.

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The primary causes[1] and the wide-ranging effects[2][3] of global warming and resulting climate change. Some effects constitute feedback mechanisms that intensify climate change.

Coral bleaching is the process when corals become white due to various stressors, such as changes in temperature, light, or nutrients.[1][2] Bleaching occurs when coral polyps [a type of cnidarians] expel the algae (zooxanthellae) that live inside their tissue, causing the coral to turn white.[1] The zooxanthellae are photosynthetic, and as the water temperature rises, they begin to produce reactive oxygen species.[2] This is toxic to the coral, so the coral expels the zooxanthellae.[2] Since the zooxanthellae produce the majority of coral pigmentation,[2] the coral tissue becomes transparent, revealing the coral skeleton made of calcium carbonate [CaCO3].[2] Most bleached corals appear bright white, but some are pastel [pale] blue, yellow, or pink due to proteins in the coral.[2]

Reactive oxygen species (ROS) are highly reactive chemicals formed from O2.

Permafrost is ground that continuously remains below 0 °C (32 °F) for two or more years, located on land or under the ocean.

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The percentage of diffusely reflected sunlight relative to various surface conditions

Diffuse reflection is the reflection of light or other waves or particles from a surface such that a ray incident on the surface is scattered at many angles rather than at just one angle as in the case of specular reflection.

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Diffuse and specular reflection from a glossy [shiny] surface.

Cumulus stratus (or stratocumulus) and stratus are types of clouds.

The list of cloud types groups the main genera as high (cirrus, cirro-), middle (alto-), multi-level (nimbostratus, cumulus, cumulonimbus), and low (stratus, strato-) according to the altitude level or levels at which each cloud is normally found.

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Tropospheric cloud classification by altitude of occurrence.

The troposphere is the first and lowest layer of the atmosphere of the Earth, and contains 75% of the total mass of the planetary atmosphere, 99% of the total mass of water vapour and aerosols, and is where most weather phenomena occur.

An aerosol is a suspension of fine solid particles or liquid droplets in air or another gas.

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Figure [radiosonde = instrument for weather data collection and transmission]

A carbon sink is any reservoir, natural or otherwise, that accumulates and stores some carbon-containing chemical compound for an indefinite period and thereby lowers the concentration of carbon dioxide (CO2) from the atmosphere.[1]

Globally, the two most important carbon sinks are vegetation and the ocean.

Vegetation is an assemblage of plant species and the ground cover they provide.

The ocean (also the sea or the world ocean) is the body of salt water which covers approximately 71% of the surface of the Earth and contains 97% of Earth's water.

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World map of the five-ocean model with approximate boundaries

Conservation

Further information: Conservation biology

Conservation biology is the study of the conservation of Earth's biodiversity with the aim of protecting species, their habitats, and ecosystems from excessive rates of extinction and the erosion of biotic interactions.[257][258][259] It is concerned with factors that influence the maintenance, loss, and restoration of biodiversity and the science of sustaining evolutionary processes that engender [cause to exist] genetic, population, species, and ecosystem diversity.[260][261][262][263] The concern stems from estimates suggesting that up to 50% of all species on the planet will disappear within the next 50 years,[264] which has contributed to poverty, starvation, and will reset the course of evolution on this planet.[265][266] Biodiversity affects the functioning of ecosystems, which provide a variety of services upon which people depend.

MES Note: Extinction is the termination of a kind of organism or of a group of kinds (taxon), usually a species.

Ecosystem services are the many and varied benefits to humans provided by the natural environment and from healthy ecosystems.

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Efforts are made to preserve the natural characteristics of Hopetoun Falls, Australia, without affecting visitors' access.

Conservation biologists research and educate on the trends of biodiversity loss, species extinctions, and the negative effect these are having on our capabilities to sustain the well-being of human society. Organizations and citizens are responding to the current biodiversity crisis through conservation action plans that direct research, monitoring, and education programs that engage concerns at local through global scales.[267][260][261][262]

MES Note: The Holocene extinction, otherwise referred to as the sixth mass extinction or Anthropocene extinction, is an ongoing extinction event of species during the present Holocene epoch (with the more recent time sometimes called Anthropocene) as a result of human activity. The current rate of extinction of species is estimated at 100 to 1,000 times higher than natural background extinction rates.

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Figure: Cumulative vertebrate species recorded as extinct or extinct in the wild by the IUCN (2012). Graphs show the percentage of the number of species evaluated among mammals (5513; 100% of those described), birds (10,425; 100%), reptiles (4414; 44%), amphibians (6414; 88%), fishes (12,457; 38%), and all vertebrates combined (39,223; 59%). Dashed black curve represents the number of extinctions expected under a constant standard background rate of 2 E/MSY [E/MSY = extinction per million species per year]. (A) Highly conservative estimate. (B) Conservative estimate.

Context on Above Figure: To estimate modern extinction rates, we compiled data on the total number of described species and the number of extinct and possibly extinct vertebrate species from the 2014 IUCN Red List (17). The IUCN’s list is considered the authoritative, albeit likely conservative, assessment of the conservation status of plant and animal species. About 1.8 million species have been described since 1758 (when the current nomenclature system was developed), of which 1.3 million are animals (3, 17). Of these animal species, about 39,223 (of the currently counted 66,178) vertebrate species have been formally assessed and reported in the 2014 IUCN Red List (17). In the IUCN sample, mammals, birds, and amphibians have had between 88 and 100% of their known species evaluated, whereas only 44% of reptiles and 38% of fish species have been assessed (Table 1). We focus our comparisons on vertebrates because they are the group for which the most reliable data exist, both fossil and modern.

Background extinction rate, also known as the normal extinction rate, refers to the standard rate of extinction in Earth's geological and biological history before humans became a primary contributor to extinctions. This is primarily the pre-human extinction rates during periods in between major extinction events.

The International Union for Conservation of Nature (IUCN; officially International Union for Conservation of Nature and Natural Resources[2]) is an international organization working in the field of nature conservation and sustainable use of natural resources.

Summary

MES Inline Commentary

  • [bold text in square brackets]: Inline sentence commentary.
  • Bold: Sometimes bolded by me for emphasis but sometimes they are as referenced.
  • …: Indicates transition of sentences / paragraphs between referenced text.
  • Figure: or Source: References a figure outside of Wikipedia.
  • [sic]: Indicates quote is copied as is, which includes any errors or spelling mistakes.
    • From Latin “sic erat scriptum” meaning “thus was it written”.

Note on Wikipedia

  • Wikipedia provides and upholds in real time a mainstream narrative of all topics.
  • Publishing on Wikipedia requires referencing major news companies or Scientific Journals.
  • Wikipedia is not a place for new information or debate about existing narratives.
  • For actual truth, it requires personally analyzing each claim with complete disregard for all existing “authorities”.

Overview of Biology

  • While preparing a video on COVID-19 and masks, the background biology information became too extensive for that video.
  • I decided to do a separate overview of biology video to use as reference for all future videos involving biology and other similar topics.
  • Similarly, I had done extensive work on mathematics during school and overall self-learning before I had published any math videos.

Biology

  • The Wikipedia page on “Biology” is very extensive on its own so I have gone over it for the most part while I include further information and clarifications where needed.

Definition

  • Biology is the scientific study of life.
  • All living organisms are made up of cells that process hereditary information encoded in genes, which can be transmitted to future generations.
    • General biological breakdown: Information → genes → cells → life
  • Evolution is used to explain the unity and diversity of life.
  • All living organisms require energy to move, grow, reproduce, and regulate their own internal environment.
  • Biology involves multiple levels of organization:

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  • Life on Earth emerged before 3.7 billion years ago and is remarkably diverse.
  • Basic classifications of the various forms of life.
    • Prokaryotic organisms: Cells without a nucleus, such as Archaea and Bacteria.
    • Eukaryotic organisms: Cells with a nucleus, such as protists, fungi, plants, and animals.
  • The various living organisms have specialized roles in the cycling of nutrients and energy in an ecosystem, which is all the organisms and the physical environment with which they interact.

Etymology (origin/history of words)

  • “Biology” derives from the Ancient Greek words bíos and -λογία (romanized as bios and logía) meaning “life” and “branch of study”. (Romanized = conversion of writing to Roman or Latin script)
    • Latin form first used in 1736 by Carl Linnaeus (23 May 1707 to 10 January 1778).
    • Latin form used again in 1766 by Michael Christoph Hanov (12 December 1695 to 22 September 1773).
    • German form used in a 1771 translation of Linnaeus’ work.
    • German form used again in 1797 by Theodor Georg August Roose (12 February 1771 to 21 March 1803)
    • German form used again in 1800 by Karl Friedrich Burdach (12 June 1776 to 16 July 1847) but in a more restricted sense as the specific study of human beings.
    • The term came into modern usage in 1802 by Gottfried Reinhold Treviranus (4 February 1776 to 16 February 1837) which defined biology as the study of all life.
  • Historically, another term for “biology” was “lifelore” (life + learning) but is rarely used today.

History

  • Science and medicine can be traced to ancient Egypt and Mesopotamia (modern day Iraq, Syria, Iran) from around 3000 to 1200 BCE.
    • Contributions from this time frame shaped Greek natural philosophy.
    • Natural philosophy refers to the philosophical study of nature prior to the development of modern science.
    • The Scientific Revolution, starting from the 15th century, marked the emergence of modern science.
    • The formalization of the scientific method is the key characteristic of the Scientific Revolution, which revised many previously upheld believes of nature.
    • The scientific method is an ongoing process of predictions, experiments or observations, data analysis, and repetition.

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  • Ancient Greek philosophers such as Aristotle (384 to 322 BCE) contributed extensively to biological knowledge.
  • Medieval Islamic scholars who wrote on biology included al-Jahiz (781 to 869), Al Dinawari (828-896), Rhaze (865-925).
  • Biology began to grow with Anton van Leeuwenhoek’s (24 October 1632 to 26 August 1723) dramatic improvement of the microscope, which led to the discovery of small organisms such as bacteria.
  • Jan Swammerdam (12 February 1637 to 17 February 1680) helped to develop the basic techniques for microscopic dissection and staining.
    • Dissection involves cutting up the body of an animal or plant to study its anatomical structure.
    • Staining is a technique used to enhance contrast in samples.
  • In the early 19th century, biologists pointed to the central importance of the cell.
  • In 1838, Matthias Jakob Schledien (5 April 1804 to 23 June 1881) and Theodor Schwann (7 December 1810 to 11 January 1882) promoted the now universal ideas:
    • (1) The basic unit of organisms is the cell.
      • Some biologists consider non-cellular entities such as viruses as living organisms, thus disagree with the first tenet [principal assumption].
    • (2) Individual cells have all the characteristics of life.
    • Note that they rejected the now accepted idea that (3) All cells come from the division of other cells.
  • By the 1860s, Robert Remak (26 July 1815 to 29 August 1865) and Rudolf Ludwig Carl Virchow (13 October 1821 to 5 September 1902) worked to make the above three tenets accepted by most biologists in what is now called “cell theory”.
  • Taxonomy (science of naming, classifying, defining organisms based on shared characteristics) was the focus of Carl Linnaeus and others.
  • Georges-Louis Leclerc, Comte de Buffon (7 September 1707 to 16 April 1788) suggested the possibility of common descent and was opposed to evolution but nonetheless his work has influenced evolutionary theories.
    • Common descent is the concept when one species is the ancestor of 2+ species.
    • The term “Comte” is the French version for “Count” is a historical title of nobility in some European countries.
    • Comte derives from the Latin comes and comitem, which means “companion”.
    • The land owned by a count is called a county.
  • Jean-Baptiste Lamarck (1 August 1744 to 18 December 1829) was the first to present a coherent theory of evolution:
    • He postulated that evolution was the result of environmental stress on properties of animals.
    • The more frequent and rigorous an organ was used the more complex and efficient it would become, thus adapting the animal to its environment.
    • The acquired traits could be passed on to the offspring who would further develop and perfect them.
    • MES Occult Note: Note the religious / occult theme of Jean-Baptiste or John the Baptist preceding the coming of Christ, in this case Charles Darwin.
  • Charles Darwin (12 February 1809 to 19 April 1882) forged a more successful evolutionary theory based on natural selection.
    • Natural selection is the differential survival and reproduction of individuals due to differences in their phenotype, which is the set of characteristics or traits of an organism.
    • Alfred Russel Wallace (8 January 1823 to 7 November 1913) independently reached similar conclusions.
    • Darwin’s theory of evolution by natural selection spread quickly and became a central axiom of the rapidly developing science of biology.
    • In 1842, Darwin wrote the first draft of “On the Origin of Species” and published on 24 November 1859.
  • In 1865, Gregor Mendel (20 July 1822 to 6 January 1884) presented his paper on plant hybridization which outlined the principles of biological inheritance and served as the basis for modern genetics.
  • In the early 20th century, Darwin’s theory of evolution through natural selection was reconciled with the classical genetics of Mendel in what is termed the modern synthesis.
    • Classical genetics refers to the branch of genetics based solely on visible results of reproductive acts.
  • In the 1940s and 1950s, Alfred Hershey (4 December 1908 to 22 May 1997) and Martha Chase (30 November 1927 to 8 August 2003) performed experiments that pointed to DNA as the component of chromosomes that held trait-carrying units, and which would become known as genes.
  • In 1953 James Watson (6 April 1928 to present) and Francis Crick (8 June 1916 to 28 July 2004) discovered the double-helix structure of DNA.
  • Biology transitioned to molecular genetics with focus on new kinds of organisms such viruses and bacteria.
  • The genetic code was cracked by Har Gobind Khorana (9 January 1922 to 9 November 2011), Robert Holley (1922 to 1993), and Marshall Warren Nirenberg (1927 to 2010) after DNA was understood to contain codons.
    • The genetic code is the set of rules used by living cells to translate information encoded within genetic material (codons) into proteins.
    • Codons are DNA or mRNA sequences of nucleotide triplets that contain genetic code.
    • Nucleotides are molecules that make up DNA and RNA.
    • Genetic material refers to DNA and RNA in general, both of which are biopolymers and classed as nucleic acids.
    • A genome is all the genetic material of an organism.
  • The Human Genome Project (HGP) was launched in 1990 to map the general human genome and was essentially completed in 2003 with further analysis still being published.
    • The human genome is a complete set of nucleic acid sequences encoded as DNA within 23 chromosome pairs in cell nuclei (nuclear genome) and in a small DNA molecule found within individual mitochondria (mitochondrial genome).
    • There are over 3 billion base pairs in the human genome.
    • The HGP was a globalized effort to incorporate accumulated knowledge of biology into a functional and molecular definition of the human body as well as the bodies of other organisms.
    • It remains the world’s largest collaborative biological project.

Chemical Basis

Atoms and Molecules

  • All living organisms are made up of matter and all matter is made up of elements.
    • Matter is any substance that has mass and takes up space by having volume.
    • In everyday usage, matter includes atoms and anything made up of them; and does not include massless particles such as photons or waves such as light.
  • Oxygen (O), carbon (C), hydrogen (H), and Nitrogen (N) are the 4 elements that account for 96% of all living organisms.
    • Calcium (Ca), phosphorus (P), sulfur (S), sodium (Na), chlorine (Cl) account for the remaining 3.7%
    • MES Occult Note: The most common isotope of carbon is Carbon-12 which has 6 protons, 6 neutrons, and 6 electrons, which raises interesting questions about:
      • The number 666.
      • The Biblical “Mark of the Beast”.
      • Carbon-based life.
        • Carbon is a primary component of all life on Earth.
        • Carbon represents about 45-50% of all dry biomass.
        • Carbon Tax and Carbon Tax Credits are to be implemented worldwide soon to lower the world’s carbon output.
      • World population is supposedly an issue.
      • Let’s ask Bugs Bunny what he thinks…

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  • Different elements can combine to form compounds such as water, which is fundamental to life.
  • Life on Earth began from water and remained there for about 3 billion years prior to migrating to land.
  • Matter can exist in different states such as solid, liquid, or gas.
  • The smallest unit of an element which still has all the properties of that substance is an atom, which is composed of a nucleus and one or more electrons bound to the nucleus.
    • The nucleus is made of one or more protons and a number of neutrons.
  • Individual atoms can be held together by chemical bonds to form molecules and ionic compounds.
  • Chemical bonds include:
    • Ionic bonding
    • Covalent bonding
    • Hydrogen bonds
  • Ionic bonding involves the electrostatic attraction between oppositely charged ions, or between atoms with sharply different electronegativities.
    • Electrostatic attraction or repulsion is the experimentally determined force between electrically charged particles.
    • Electric charge is a physical property of matter that causes it to experience a force when placed in an electromagnetic field.
      • Electric charge can be positive or negative, commonly carried by protons and electrons respectively.
      • Like charges repel each other.
      • Unlike charges attract each other.
      • An object with an absence of net charge is referred to as neutral.

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  • An electromagnetic field (EMF) is produced by accelerating electric charges.
    • The EMF propagates at the speed of light; in fact, can be identified as light.
    • An EMF is a combination of an electric and magnetic field.
    • Electric field (EF):
      • Produced by stationary electric charges.
      • A physical field that surrounds electrically charged particles and exerts force on all other charged particles in the field, either attracting or repelling them.
      • Sometimes referred to as E-field.

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  • Magnetic field (MF):
    • Produced by moving charges (called currents).
    • A moving charge in a magnetic field experiences a force perpendicular to its own velocity and to the magnetic field.
    • Types of magnetic fields:
      • H field refers to the MF from external currents.
      • M field refers to the intrinsic MF of the materials in the field.
      • B field refers to the total MF that includes the H and M fields.

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  • Force created by the electric field is much stronger than the force created by the magnetic field.
  • MES True Science Note: The exact nature of electric charges and electromagnetism is unknown (publicly) as exemplified by the circular reasoning fallacy in their definitions.
    • “An electric charge is a property of matter that causes it to experience a force when placed in an electromagnetic field, which itself is produced by electric charges”.
    • What is a field? A field of what?
    • A good starting point, however, is to view charges as physical interactions of an aether and the resulting electromagnetic field as the propagation of the resulting disturbances of the aether, like the wakes behind a moving boat (except the boat itself can be seen as a void in the aether itself).

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Source: https://youtu.be/HywoX6UFOe8

  • Electronegativity is the tendency of an atom to attract shared electrons to itself when forming a chemical bond.
    • Electropositivity is the opposite of electronegativity: It is the tendency of an atom to donate valence (outer) electrons.

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The very high electronegativity of fluorine causes uneven distribution of electrons when covalently bond with hydrogen, thus giving it a slightly negative charge. Hydrogen has a very low electronegativity and obtains a slightly positive charge.

  • An ion is an atom or molecule with a net electrical charge.
    • Cation
      • Positively charged ion with fewer electrons than protons.
    • Anion
      • Negatively charged ion with more electrons than protons.
  • Covalent bonding involves the sharing of electron pairs between atoms.
    • Electron pairs consist of two electrons that occupy the same molecular orbital but have opposite spins.
      • A molecular orbital is a mathematical function describing the location and wave-like behavior of an electron in a molecule.
        • This function can calculate chemical and physical properties such as the probability of finding an electron in any specific region.

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The red and blue regions indicate the + or – sign of the mathematical orbital function. The left column shows the ground or low energy state. The right column shows the virtual or excited state.

  • Spin is the intrinsic angular momentum of elementary particles, composite particles, and atomic nuclei.
    • Spin is analogous to classical rotation but has peculiar properties such as elementary particles cannot be made to spin faster or slower even though the direction of spin can be changed.
  • A hydrogen bond is primarily an electrostatic force of attraction between a hydrogen (H) atom that is covalently bound to a more electronegative atom or group such as Oxygen and another electronegative atom bearing a long pair of electrons, deemed the hydrogen bond acceptor.
    • A lone pair refers to valence or outer shell electrons that are not paired in chemical bonds.
    • An example is in water (H2O) which is made up of two hydrogen atoms covalently bound to an oxygen atom with two lone pair of electrons.
      • The hydrogen atoms can form hydrogen bonds with a lone pair of electrons of oxygen atoms of other water molecules.
      • Likewise, the two lone pairs of electrons of the oxygen atom can form hydrogen bonds with the hydrogen atoms of other water molecules.
        • Note that hydrogen is made up of a proton (positive charge), zero or some neutrons (no charge), and zero or some electrons (negative charge).
          • The most common isotope of hydrogen has 1 proton and 0 neutrons, termed “protium” but rarely used.
            • Isotopes refer to atoms with the same number of protons but different number of neutrons.
        • The more water molecules present, such as in liquid water, the more hydrogen bonds that can be formed.
      • Asymmetric distribution of electrons in chemical bonds can result in a net atomic charge that has a “partial charge” value when measured in elementary charge units (charge of a proton or electron).
  • Partial charges are denoted with the Greek letter Delta, namely 𝛿- or 𝛿+.

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  • A metal is material that when prepared, polished, or fractured, shows a shiny appearance and conducts electricity and heat relativity well.
  • A nonmetal is a material that lacks a predominance of metallic properties, and range from colorless gases to shiny and high melting point solids.
  • A metalloid is a type of chemical element which has a preponderance of properties in between those of metals and nonmetals, or a mixture of them.
    • There is no standard definition of a metalloid yet the term remains in common use.
  • Electromagnetic radiation (EMR) consists of waves of the electromagnetic field propagating through space and carrying electromagnetic radiant energy.
    • Light or visible light is electromagnetic radiation within the portion of the electromagnetic spectrum that is perceived by the human eye.
    • Visible light is usually 400-700 nanometers (nm, 1 billionth of a meter).
    • The term “light” may refer more broadly to electromagnetic radiation of any wavelength, whether visible or not.
    • The speed of light or EMR in a vacuum is 299 792 458 m/s.
      • This is an exact value because of a 1983 international agreement:
        • A meter is defined as the length of the path travelled by light in a vacuum during a time interval of 1/299,792,458 second.
        • Note the circular reasoning, once again.
      • Approximately 300,000 km/s or 186,000 mi/s.
    • EMR is propagated by massless particles called photons.
      • The photons represent the quanta of EMF and can be analyzed as both waves and particles.
      • A quantum (plural quanta) is the minimum amount of any physical entity involved in an interaction.

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  • Fractal Woman (YouTuber) light quantization:

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  • Polarization is a property of transverse waves that specifies the geometrical orientation of the oscillations.
    • In a transverse wave, the direction of the oscillation is perpendicular (at 90 degrees) to the direction of motion of the wave.

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  • EMR can exhibit polarization.

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  • In contrast, longitudinal waves displace particles always in the direction of propagation, thus don’t exhibit polarization.

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  • Types of polarization can be converted into other types, such as circular to linear polarization in a rubber thread.

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Organic Compounds

  • Organic compounds are generally any chemical compound that contain a carbon-hydrogen bond.
  • With the exception of water, nearly all molecules that make up living organisms contain carbon (C).
  • Carbon can form long, strong, and stable interconnecting covalent bonds between carbon atoms, called a carbon-carbon bond.
  • Hydrocarbons are the simplest form of an organic molecule and consist entirely of hydrogen and carbon.
    • Hydrocarbons form a large family of organic compounds.
    • Hydrogen atoms are bonded to a chain of carbon atoms.

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Glucose, C6H12O6

  • A hydrocarbon backbone can be substituted by other atoms.
    • The backbone chain is the longest series of covalently bonded atoms in a polymer.
  • When Carbon is combined with other elements such as oxygen (O), hydrogen (H), phosphorus (P), and sulfur (S), it can form many important biological compounds such as sugars, fats, amino acids, and nucleotides.

Carbohydrates / Saccharides

  • Carbohydrates are biomolecules that contain carbon (C), hydrogen (H), and Oxygen (O), usually with a H-O atom ratio of 2:1 (as in water).
    • General empirical formula of Cm(H2O)n
      • m and n may or may not be different.
      • The empirical formula of a chemical compound is the simplest positive integer ratio of atoms present in a compound.
      • Not all carbohydrates conform to this general formula.
      • Not all chemicals that conform to this definition are classified as carbohydrates.
  • Carbohydrate is a synonym (means the same or similar) of saccharide.
    • The word saccharide comes from the Greek word for “sugar”.
    • Many carbohydrates end in “-ose”, which was originally taken from the Ancient Greek word for “wine”.
  • Carbohydrates / saccharides are classified by the degree of polymerization, which is the number of monomeric units in a macromolecule, and divided into 3 principal groups:
    • Sugars (1 to 2 degrees)
      • Monosaccharide has 1 degree.
      • Disaccharides has 2 degrees.
    • Oligosaccharides (3 to 9 degrees)
    • Polysaccharides (>9 degrees)

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Acids and Bases

  • An acid is a molecule or ion capable of either:
    • Donating a proton, known as Brønsted-Lowry acid.
      • In aqueous solutions, proton donors form the hydronium ion H3O+ and are known as Arrhenius acids.
    • Forming a covalent bond with an electron pair, known as a Lewis acid.
  • An aqueous solution is a solution in which the solvent is water.
    • The solvent is a substance that dissolves the solute.
  • The word “acid” is derived from the Latin word for “sour”.
  • A base has 3 commonly used definitions, all of which react with acids.
    • Arrhenius base: Gives OH- (hydroxide ions) in water.
    • Brønsted-Lowry bases: Accepts protons.
    • Lewis bases: Donates electron pair.
  • Acids and bases are seen as chemical opposites because acids increase H3O+ in water while bases reduce it.
  • MES Memory Tip:
    • Acids become more negative.
    • Bases become more positive.

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  • Acid-base reaction theories:
    • Arrhenius theory: Acids dissociate in aqueous solution to give H+ while bases dissociate in aqueous solution to give OH-.
      • This was the first modern definition of acids and bases.
      • It was devised by Svante Arrhenius in 1984 which led to him receiving a Nobel Prize in Chemistry in 1903.
      • In the model, the symbol H+ is interpreted as shorthand for H3O+ because it is now known that a bare proton does not exist as a free species in aqueous solution.

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  • Brønsted–Lowry theory: Acid and base form their conjugate base and acid, respectively, via a proton transfer.
    • Also called the Proton Theory of Acids and Bases.
    • Proposed independently in 1923 by Johannes Nicolaus Brønsted (22 February 1879 to 17 December 1947) and Thomas Martin Lowry (26 October 1874 to 2 November 1936).
    • It is a generalization of the Arrhenius theory.

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  • Lewis theory: An acid accepts an electron pair, and a base donates an electron pair to complete a stable group of one of its own atoms.
    • It was proposed by Gilbert Newton Lewis (23 October 1875 to 23 March 1946) in 1923.
    • It is a generalization of the Brønsted-Lowry theory.

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  • Conjugates In the Brønsted-Lowry theory:
    • A conjugate base is an acid with a hydrogen ion (proton) removed from it.
    • A conjugate acid is a base with a hydrogen added to it.
    • Equilibrium expressions:
      • Acid + Base ⇌ Conjugate Base + Conjugate Acid
      • HA + B ⇌ A- + HB+

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  • Chemical equilibrium is the state in which the reactants and products are produced at the same rate so there is no net changes in either of their concentrations nor any observable change in the properties of the system.
  • The pH is a scale used to specify the acidity or basicity of an aqueous solution.
    • pH refers to the “potential (or power) of hydrogen”.
    • The pH scale is a base-10 logarithmic scale that inversely indicates the concentration of hydrogen ions in the solution.
      • pH = -log ([H3O+])
      • [H3O+] = 10-pH
        • [H3O+] = 1/10pH
        • 10pH = 1/[H3O+]
      • The higher the pH the more exponentially [H3O+] decreases.
    • Acidic solutions have higher H+ ions and lower pH values.
      • At 25°C, solutions with a pH less than 7 are acidic.
    • Basic solutions have lower H+ ions and higher pH values.
      • At 25°C, solutions with a pH more than 7 are basic.
  • Acid strength is the tendency of an acid, HA, to dissociate into a proton, H+, and an anion, A-, in a solvent, S (most commonly water).
    • Strong acid: Dissociation is effectively complete (except in its most concentrated solutions).
      • HA + S → SH+ + A-
    • Weak acid: Partial dissociation, remaining undissociated acid and dissociated products are in equilibrium.
      • HA + S ⇌ SH+ + A-
    • Acid strength is solvent-dependent.

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Important Chemistry Terms

  • A moiety is part of a molecule that is identified as part of other molecules as well.
  • A substituent is 1 or a group of atoms that replaces 1+ hydrogen atoms on the parent chain of a hydrocarbon, therefore becoming a moiety of the new molecule.
    • The parent chain is the longest unbranched chain.
  • The terms substituent, functional group, side chain, and pendant group are used almost interchangeably to describe branches from the parent structure.
  • A functional group is a substituent or mo