Living matter (organics) has cropped up as a subject in several Sections of this Tutorial. Some readers may desire to build up a basic background in Biology. Using the same mini-tutorial approach as was implemented elsewhere in this Tutorial for Geology and Meteorology, and in this Astronomy/Cosmology Section, the writer (NMS) has produced this and the next page. I have relied on one of my most valuable books, Biology, by Peter Raven and George Johnson (McGraw-Hill). In addition, I have drawn heavily on material located on the Internet. Internet tutorial on this subject found by the writer seems to be An Online Biology Book by M.J. Farabee. And here is another Internet site that specifically focuses on paleolife topics: Paleobiology (this site is actually a part of the abovementioned tutorial on Biology, prepared by M.J. Farabee of Estrella Mountain Community College of Avondale, AZ). We also recommend this paperback book: Life Evolving: Molecule, Mind, and Meaning, by Nobel Laureate Christian de Duve, Oxford Press. Two other web sites worth a visit are: (1) a thorough review of almost all aspects of Biology prepared by John Kimball and the more specialized Dolan DNA Learning Center. For a thorough immersion into Earth's early life history, we recommend Andrew Knoll's Life on a Young Planet: The First Three Billion Years of Evolution on Earth, Princeton Univ. Press, Nov. 2003. There is also a helpful Web site that treats developments in the field of Astrobiology (also called Exobiology) hosted by the Astrobiology Branch at Ames Research Center
A proviso:While the main goal of this and the next page is to provide a limited background for the reader on those aspects of Biology that deal with the origin and history of life, the effort will seem sketchy in that many topics that comprise the essence of the subject are treated either cursorily or have of necessity been omitted. The overall treatment of Biology requires considerable time and space (the writer's textbook has more than 900 pages), far more than can be devoted in this Section. But we will examine in some detail the biochemistry of life on this page, a topic of value in reviewing the story of life on Earth on the next page.
The capstone of this Section on Cosmology must surely be a consideration of the most provocative and fascinating Quest in the history of human life: the attempts to determine whether life of any kind - but specifically intelligent life (Pyschozoic is a term created to generalize such a stage of life on exoplanets) - exists elsewhere in the Universe. Philosophically, many on Earth hope that we are unique - thinking beings that are the pinnacle and teleological goal of a Creator's act. Scientifically, most cosmologists, biologists, etc. are coming around to the firm conviction that life does indeed exist elsewhere - throughout the Universe. This is a logical conclusion, since a huge Universe with just one tiny inhabited body on which conscious creatures exist strikes most scientists, and a growing number of philosophers, as extremely unlikely, and, from a practical sense, even a foolish, wasteful action by any Creator (this viewpoint is touched upon again later on this page).
We remind you at the outset of the excellent 2003 book on the subject of life in the Universe, David Grinspoon's Lonely Planets: The Natural Philosophy of Alien Life, cited on page 19-2. A few comments about the history of this idea, extracted from his book, are briefly treated before we begin with the review below:
Grinspoon points out that mankind has been speculating on life beyond the Earth for more than two millenia. The Epicureans of the late period of Greek philosophy before Rome took over that part of the Mediterranean believed that living creatures with intellects lived on one or more of the planets and possibly the stars. Aristotle and Plato, however, argued against multiple worlds. Some early Christian theologians developed ideas that allowed for thinking life within the observed Cosmos (not quite a Universe as we know it today, but a realm that perhaps extended beyond the "spheres" that contained the Moon and Planets; see page 19-2). Similar speculations affected the medieval thinkers. But until Renaissance times, the vast majority held life to be unique to Earth. Copernicus, Kepler, and Galileo gave thought to the possibility of life elsewhere but never did seriously conjecture on the possiblities. Although not well-known to the public and even many scientists, the Italian Giordano Bruno (a Dominican friar fried at the stake by the Church for his radical beliefs) by 1600 had conceptualized a Cosmos filled with multiple Suns and their planets on which life was widespread. At the dawn of the Age of Enlightenment, a treatise advocating a "plurality of worlds" was published in 1686 by Bernard le Bovier de Fontenelle. This work had a strong influence on thinkers of the day. In the first half of the 18th Century several similar and provocative books by European natural theologians followed. The German philosopher Immanuel Kant was much influenced by these writings and came up with a precursor to modern ideas for the formation of the Solar System. He espoused a much wider distribution of life within our Solar System and probably elsewhere. Laplace, who modified Kant's models, also took the view that life was established beyond Earth. The 19th Century saw similar and varied views favoring the "universality" of life. In the early 20th Century, Percival Lowell popularized this notion with his claims that "canals" existed on Mars. As the dawn of the Space Age arrived in the 1950s, many scientists and much of the general public retained the view that life was likely to be found in other parts of our solar System. The first spacecraft to fly by, orbit, and land on Mars tended to dampen this enthusiasm. But flying saucers and movies about ET and Close Encounters have pumped up the hopes of the Common Man that in time life will be found beyond the Earth. From an anthropocentric outlook, the importance in understanding planetary formation mechanisms and history is the assumption (not yet a clearcut fact) that planets possessing certain appropriate conditions are the harbors of life. Life, it is believed by Earth dwellers who can think, may well be the most complex and advanced feature in the Universe, based on the presumption that it has evolved into a state resulting in lifeforms that perceive beyond sensing, analyze through reason, and evaluate most other aspects of known existence. Life, under this viewpoint, is the quintessential achievement in the evolution of the Universe to date. Whether life on Earth stands at the pinnacle, or somewhere below, has yet to be established - statistically, it is most likely that somewhere in the Universe even more highly developed living creatures, with superior intellects, exist today or have in the past. (The ideas just enunciated are closely associated with the modern doctrine called humanism). The expectation that some life exists elsewhere in the Universe will depend on the nature of and conditions for life itself. Life can be defined by properties that are both chemical and functional. Paul Davies, in his excellent book Other Worlds, cites seven essential prerequisites for life to originate, survive, and flourish: 1. There must be an adequate supply of the elements that comprise organic matter - Carbon, Oxygen, Hydrogen, Phosphorus, Sulphur, Calcium, and other elements.
2. There must be little or no risk of contamination by poisonous chemicals (mainly in the atmosphere and oceans), such as ammonia or methane.
3. The climatic temperature must remain within the narrow range of 5 to 40 degrees Centigrade, which is a mere 2% of the temperature range found within the Solar System as a whole.
4. A stable supply of available energy must power living matter; for Earth this is primarily the Sun; internal heat sources, such as the "smokers" vents on the seafloor may also have been involved.
5. Gravity must be strong enough to keep the atmosphere from escaping into space, but it must be weak enough to enable life to move freely within the surficial envIronment.
6. A protective screen must exist to filter out the Sun's harmful Ultraviolet rays, which for Earth is the delicate layer of ozone in the upper atmosphere.
7. A magnetic field must exist in order to prevent cosmic subatomic particles that can damage or kill life from impinging on the Earth.
Missing from the Davies list, but crucial, is the presence of water (whether this is a universal condition or just applies to Earth is not yet established). Water is one of the most versatile and essential substances known on Earth and in and on most planets (both those of the Solar System and around other stars). Water is in essence an Oxygen atom with two embedded protons (from the Hydrogen). Here is a structural representation: In this configuration the H2O acts as a polar molecule, with one end being positively charged and the other negatively charged. In this sense, water acts both as an acid and a base (but with its pH of 7, it is considered neutral). Water can perform many functions, providing itself as a molecule or as a source of H and O ions. Among functions named as terms are its role as a solvent (breaks down the chemical structures of other substances - especially those held together by ionic bonds), hydrolysis (water splits into H+ and OH-, which react with various substances, especially organic molecules), hydration (water incorporated without change into the crystal structure of a substance), and redox (reduction; oxidation) reactions. Water is the most abundant molecule at the Earth's surface. It is known to humans in its three states or phases: solid (ice), liquid (water), and gas (steam). Water makes up about 70% (by weight) of the human body. Judging on what we know conclusively from the one sample available to earthlings - namely, life on Earth itself as the only confirmed example in the Solar System - the essential chemical incredients are Carbon, the crucial element in organic molecules (of which proteins are the fundamental component) of great complexity and variety that are the basis of life, together with Hydrogen, Oxygen (some of which is combined as water which dominates the soft parts of human and many other organisms), Nitrogen, Phosphorus, Calcium (mainly in hard parts) and Sulphur, and to a lesser degree other elements as important functionaries, such as Iron, Magnesium, Chromium, etc. The amazing thing about this assemblage of critical elements is that they all at times in the past resided in stars and much of the Hydrogen itself can be traced back to the first minute of the Big Bang. You and I, as humans, are truly star people - our heritage is cosmic in that our ingredients are either primordial- or stellar-derived. As a quick synopsis on the nature of life, here is a simple list of the "The Characteristics (Properties) of Life", adapted from one put online by the Department of Zoology, Oklahoma State University. *Organized structures: composed of heterogenous chemicals - in units of "cells"
*Metabolism: chemical transformations that either break down molecules to release energy (catabolism) or use energy to build up molecules (anabolism)
*Homeostasis: which maintains internal conditions separated from an outside environment
*Growth and Development: conversion of materials from the envIronment into components of organism
*Regulation: coordination of the organism's internal functions, including transportation of materials needed to function
*Sensitivity: reaction to select stimuli, physiologically and/or behaviorally
*Reproduction: making copies of individuals via the mechanism of genetic transfer: sections of DNA molecules that contain instructions for organization and metabolism
*Evolution: change in characteristics of individuals, resulting from mutation and natural selection - these result in adaptations; Heredity is the outcome.
Thus, the principal functional manifestations of life (based on our studies of this phenomenon on Earth - our only sample so far) are, to reiterate what was listed above: cellular-organization; reproducibility; growth cycle and dependence on nutrition; metabolism (in higher forms) respiration (in some types); (usually) movement of some kind; propensity to evolutionary modification, and, for vegetative types, utilization of photosynthesis. Intelligent life, furthermore, is marked by consciousness, reasoning, abstraction, reliance on memory, communication, and awareness of time and other essentials of existence; free will and "soul" are properties of a more metaphysical nature and harder to prove as realities. This next diagram was taken from the Internet without any indication of its source nor any explanation of its content. It is put here without any comment, treating it as a "talking point" relating to some of the questions that are relevant to the nature and origin of life on Earth. The implications within the diagram should also pertain to life elsewhere in the Universe. Draw your own ideas and conclusions. Life falls into two broad categories: prokaryotic (no cell nucleus) and eukaryotic (nucleus). Life also can be categorized as single celled or multicelled and as autotrophic (obtains nutrients from inorganic sources) or heterotrophic (nutrients obtained by "feeding" on other organic sources). Life is classified by a taxonomic system (first espoused by Linnaeus) of hierarchical catetories - from the highest level (broadest number of constituents) to the lowest (most limited or particular). This ranges through Kingdom; Phylum; Class; Order; Family; Genus; Species; (Subspecies). As an example, consider a honey bee: its species name is mellifera, its genus is Apis, it belongs to te Family Apidae, which is part of the order Hymenoptera, a nenber if the Class Insecta, that falls within the Phylum Arthropoda, in the Kingdom Animalia. Various proposed subdivisions of life at the Kingdom level are used: a common one is the six-kingdom system proposed by Woese: Eubacteria; Archaebacteria (some use Archaea) - both being largely single celled organisms; Protista (eukaryotic; both uni- and multi- cellular), which include algae, foraminifera, radiolaria, and diatoms; (the next three are all eukaryotic and multicellular) Fungi (yeasts; mushrooms); Plantae, with nonvascular plants (mosses et al) and vascular plants (ferns, conifers, angiosperms [flowering plants]); and Animalia,, with 14 phyla, to us the most important of which is Chordata, that includes amphibians, fish, reptiles, birds, and mammals. The evolutionary "Tree of Life" has followed this generalized pattern (alternate schemes have been proposed):
Life is often classified in three broad groupings. Here is such a version of this Tree of Life, with yellow denoting Bacteria, green assigned to Archaea, and blue representing the Eukarya, is (this type of plot of evolutionary trends is known as a cladistic diagram): This is probably a good place on this page to present an overview about cells. For a fuller treatment go to the Wikipedia web site on Cell
Two fundamental cell types exist: Prokaryotic (no nucleus) and Eukaryotic (nucleus). Both single-celled and multi-celled organisms exist among each type. Both types contain DNA and ribosomes. Prokaryotic cells typically are 1 to 10µm in size; Eukaryotic cells can be 100 µm wide; larger cells are known. This figure depicts the two cell types: A Eukaryote cell is much more complex, as suggested by this generalized diagram showing its makeup: Each of these components (most are lumped under the term "organelles") will be concisely defined: The Cell Wall (called Cell Membrane in animals), in bacteria is usually made of peptilogycan and in eukaryotes cellulose or chitin. Its functions are to enclose the cell interior, protect the cell, and aid in transfer of material in and out. The Nucleus, commonly spherical and enclosed by a double membrane, contains the chromosomes (gene assemblages of DNA). The Nucleolus is host to genes for rRNA synthesis. Cytoplasmis the jelly-like matrix that surrounds the nucleus of a cell and is bounded by the cell membrane. It includes the organelles of the cell as well as the sugars, amino acids, and proteins that the cell uses for growth and reproduction. Ribosomes are protein-RNA complexes that are sites of protein synthesis. Vacuoles are open sacs available for digestion or storage of waste products; may contain degraded protein, can become water-filled. Gogli Apparatus consists of stacks of vesicles (openings) in which proteins made in the cell are prepared for export from the cell
Lysosomes are vesicles, derived from Gogli A., containing digestive enzymes that attack defunct organelles and other cell debris. Centrioles are specialized organelles that produce microtubules that influence cell shape, move chromosomes during division, and aid in developing cilia and flagella. Peroxisome use enzymes to remove superfluous electrons and Hydrogen atoms; Hydrogen peroxide is a by-product.
Mitochondria are double-membrane organelles that provide "power" from the cell by oxidative metabolism. Endoplasmic Reticulum serve as networked membranes that aid in making vesibles; also assist in synthesizing proteins and lipids.
Not shown in diagram: Chloroplasts, which control photosynthesis in plants and Chromosomes, which are long DNA threads that host hereditary information. These definitions refer repeatedly to DNA and RNA. These are two nucleic acids which will be discussed in detail further down this page. Understanding how life is organized into cells (through the science of Biology) requires some core knowledge of Organic Chemistry and its subfield Biochemistry. Only the most rudimentary ideas can be covered on the relevant sections of this page. Most of the illustrations were taken from the Online Biology Book, cited above, prepared by M.J. Farabee. He attributes on his site most of the illustrations we will use to Purves et al.; Life: The Science of Biology; Sinauer and Assoc. Publishers and M. Freeman & Company.
Organic substances are combinations of Carbon with other elements (most common are Hydrogen, Oxygen, Nitrogen, Sulphur, and Phosphorus). Bonding with the Carbon is of the covalent type - two atoms share one or more valence electrons. There are literally tens of thousands of organic compounds. But most of these can be grouped in systematic ways. One is the so-called functional group in which there is a basic unit built around carbon that can be combined with other elements or radicals. This diagram gives some examples as an overview (other, more specific diagrams will appear later on this page):
Organic molecules in their simplest form constitute the Hydrocarbons which are built from Carbon atoms (which have 4 electrons in their outer shell and can accept 4 more to complete the shell. This can start from the simplest Hydrocarbon (CH4, methane, and built up in chains or rings, as indicated in the diagrams below: A wide range of more complex organic molecules can develop from adding various molecular functional groups that include N, O, P, S and other elements to open positions in the Carbon shell or to Hydrogens. These are the principal units: These molecular varieties fall into groups such as saturated Hydrocarbons with single H-C bonds (Alkanes), double bonds (Alkenes), and triple bonds (Alyknes); ring structures are represented by Aromatic Hydrocarbons. Isomers are organic molecules with the same chemical formula but different atomic arrangements. Among the derivative organic molecules (Hydrocarbons with parts replaced by functional groups) are Alchohols (--OH functional group), Ether (--O--), Aldehyde (--CHO), Ketone (--CO--), and Carboxylic Acid (--CO3H).
Biochemistry is a vast subfield of the more general Organic Chemistry. While the subject is complex and detailed (see links above), a few general ideas developed around key illustrations taken from M.J. Farabee's site (cited above), and one from Raven/Johnson are introduced here: There are four major groups of organic molecules that also are the fundamental categories in living matter: Lipids; Carbohydrates; Proteins; Nucleic Acids (RNA; DNA). We will describe the first two in limited detail.
Lipids include fats, fatty acids, certain oils, waxes, terpenes, and steroids (one example being cholesterol). They consist of polymers of CH2 and CH3. Glycerol, a typical fatty acid, has the formula: HOCH2CH(OH)CH2OH. Palmitic Acid has this structural arrangement: The molecular structures of some common steroids are depicted below:
The second major group, the Carbohydrates, also known as Saccharides, includes sugars, starches, glycogens, and cellulose. The basic formulaic unit is: CH2O. One important group, the Monosaccharides, includes ribose and deoxyribose, ring structures made up of pentagonal (5 Carbon) sites - these are two fundamental components of RNA and DNA. Example:
Glucose is said to be the most abundant biochemical molecule within terrestrial life: Its formula is C6H12O6. Here are several views of glucose; at the top are two isomers, below is a 3-D stick and ball representation, and at the bottom is a side view: Structures comprised of two joined rings are Dissarcharides (e.g. Sucrose and Lactose). Chains of rings make up Polysaccharides" These include starches (which store food energy in plants), glycogen (energy storage in animals) and cellusose (important cell wall component in plants). A starch molecule and Proteins, the most abundant constituents of organic matter, are built from linked individual amino acids. There are 100s of such acids but only 20 occur in proteins involving human tissue. The basic protein unit consists of a central Carbon, an amino group, a carboxyl group, and a side group, labeled R, that can consist of a variety of functional groups; the general molecule looks like this: Three examples of individual amino acid types are shown below: The 20 amino acids are shown structurally in terms of different side groups in this chart: All 20 are α-amino acids, meaning that the amino group is always bounded to a Carbon atom. Various combinations of the 20 can link (bond) with one another (amino group to carboxyl group) to form polymers. The linkage is termed peptide bonding. Oligopeptides link only a few amino acids; chains of 100s of amino acids (polypeptides) are common: Protein synthesis is a major goal in biochemistry. This is proving difficult because getting the amino acids in the right order is hard, unwanted reactions among side chains is common, and peptidization gives off energy which can decompose the desired end product. Protein structure can be simple chains (primary) or helical or pleated (secondary) or complexly folded (tertiary and quaternary structures). Proteins are the dominant molecular types in cells. Specific proteins (composition and/or structure) can specialize into Enzymes (that promote change and formation of new organic material by catalysis (bring about reactions without themselves being changed), Hormones (perform important physiological functions), Structural proteins (hair, skin, etc.), Transport proteins (carry material across membranes); Antibodies (involved in immune systems), and Muscle proteins (actin and myosin in fibrous forms). Enzymes are particularly important since they are involved in most biochemical reactions and can be very efficient; many enzymes work by attaching to the molecule they affect, which serves as the substrate responsive to their action. The list of important proteins is long and diverse. This table names many that are important: An example of how sequences of amino acids give rise to a specific protein molecule is given by insulin, used by mammals to extract energy from sugars: One of the most important proteins is hemoglobin, the main constituent of a red blood cell found in the circulatory systems of many mammals, including Man. As seen in the illustration below, hemoglobins consist of 4 folded units, 2 α-globin twisted chains and 2 β-globin chains, each harboring a heme (haem) group (blue disk) that contains Iron. The four hemes allow loose bonding of Oxygen to the Iron, which is carried in the blood and released where needed to promote oxidation reactions; this globular molecule also can carry CO2 for removal during lung exhalation: Proteins have many uses in animals. For the human body, these are some of the more common functions: 1) Enzymes - control metabolism; 2) Immuniglobulins - provide antibody defense against foreign cell invaders; 3) Globins - carry O2 and CO2 in blood and muscle; 4) Transporters - controls osmosis; 5) Fibers - affect cartilage, nails, hair; 6) Muscles - control movement of body parts; 7) Albumin - osmosis in the blood; 8) Hormones - affect blood glucose; water retention. The topic of how new proteins are generated is a vital one in general Biology. We must defer an answer to this until you have grasped the basics of how Nucleic Acids function, after which we will return to the protein production topic near the bottom of this page. The fourth group, Nucleic Acids, are of fundamental essence to life in that they contain the biochemical molecules that hold the blueprints for making and copying cells. RNA and DNA are called the information-bearing cells that determine the nature of any given organism, from simple bacteria to humans. DNA is found within all cells, both prokaryotic and eukaryotic. The basic unit is called a Nucleotide, consisting as shown below of a monosaccharide 5-Carbon sugar (pink), one of 5 Nitrogenous bases (purple), and a phosphate group (yellow). The 5-carbon sugar molecule comes in two forms (ribose and dioxyribose). These are nearly identical, the only difference being that OH (hydroxyl)is the radical attached to Carbon-2 in the ribose and O (Oxygen) is attached to Carbon-2 in the dioxyribose molecule. The structure and composition of the five bases (usually identified by their first letters: Adenine; Cytosine; Guanine; Thymine, and Uracil) is given by this diagram; note that they are organized into two group - the single ring Pyrimidines and the double ring Purines. The bases can be part of important organic molecules involved in various life-sustaining processes. For example, Adenine is a component of ATP (Adenosine Triphosphate) (see below) that has several crital functions including metabolism (energy-supplying reactions) and the formation of DNA. Here is the structural formula for ATP: However, the trilogy of the 5-carbon sugar molecule, a phosphate radical, and four of the five Nitrogenous bases organized together makes up the most fundamental organic units in all life forms. The two units are Ribonucleic acid (RNA) and Dioxyribonucleic acid (DNA). These are compared in this diagram:
RNA occurs in single strands in which the sugars are linked by the phosphate (PO4) phosphodiester bond and the bases lie on the other side of the chain. The four bases present are A, C, G, and U. Multiple chains of nucleotides make up the nucleic acid. The main roles of RNA are in its intimate involvement in the production of proteins, and its intermediary action in duplicating DNA during cell division and growth. DNA, arguably the most famous organic molecule of all, consists of two chains (sometimes called "backbones") side by side that are coiled into spiral shapes. This diagram shows the general pattern of their structure:
The bases A, C, G, and T (note that T replaces the U present in RNA) produce a link (the straight lines in the above diagram) between the two chains that tie them together. Only certain pairings are allowed: A - T and G - C. These couple by Hydrogen bonds. Here is a schematic of this arrangement. A DNA molecule is very long (a few meters) but extremely thin (narrow; measured in nanometers). Here is an electron microscope photo of a DNA strand: In 1953 Francis Crick and James Watson discovered through analysis of X-ray crystallography photos (done earlier by Rosalind Franklin and Maurice Wilkins - all four living in England) that the double-chained DNA was composed of two spiraling chains arranged in the famed appellation "Double Helix"; this discovery won Crick Watson, and Wilkins the Nobel Prize in Biology - Franklin unfortunately was dead by then). Here is how it looks as rendered by colored balls representing the sugar, phosphate, and base components: A process called "replication" involves duplicating specific DNA molecules. Rather than a lengthy discussion of this topic here, we refer you to the relevant Wikipedia web site. However, you should look at this next diagram (found commonly on the Internet) to gain a quick overview:
During replication mistakes in reproducing a gene pairing constitute the biochemical explanation for the mutations that Charles Darwin and his compatriot Alfred Wallace cited as the basic cause for natural selection. That is the cornerstone of the Theory of Evolution - this holds that individuals in a species that have the best adapted means for survival in their envIronment(s) will live longer and therefore have the better likelihood of passing their specific gene makeup to offspring in the gene pool ("Survival of the fittest"). These "good" genes thus persist in the population, and enrich it. Occasional mutations over thousands of generations in an organism's reproductive history lead to gradual changes until differences are great enough to warrant designation as new species. More fundamental and long-ranging changes lead to generic, familial, and higher level variants that become new types of animals or plants. The importance of RNA and DNA reside in their roles in making new cells and in determining the nature/function of a cell by imparting correct instructions for that in the process. DNA codes the hereditary information needed to reproduce an organism and also is involved with RNA in producing new protein cells. This subject, at the heart of concepts of genetics (genes, chromosomes, and genomes), is far too voluminous (knowledge-intensive) to cover on this page (see the Biology Tutorial Internet sites for the details). Suffice to say that the RNA and DNA strands may be very long (macromolecules consisting of 1000s of nucleotides). For DNA, the sequence of A-T amd G-C, arranged in groups of 3 (codons), can, at such lengths, encode a huge number of combinations. These lead to differences in a cell's nature (for example, different proteins are produced by RNA groupings that in turn are produced from DNA control), and when they are set in some fixed pattern of the sequenced pairings, a specific gene is determined. A gene is the fundamental unit of a (usually very long) sequence of nucleotides involved in DNA and RNA molecules. A string of varying genes make up a linear or circular chain of DNA and proteins that comprise chromosomes, the organic molecule that determine sex, heredity and the production of proteins. The full complement of various genes in some particular pattern establishes the genome that uniquely specifies a given organism.
A whole Tutorial could be devoted to describing and explaining genes and chromosomes. Worthy as these subjects are, we will divert you to these two Wikipedia sites, the first on genes and the second on chromosomes. Here we will make a few comments using illustrations with brief write-ups.
First, this general diagram which shows a paired set of individual chromosomes, with black and white bands representing genes, each of which contains thousands of DNA strands (one being shown as expanded) each one of which can consist of a base pair CG or AT. The number of pairs of chromosomes differs for different living organisms. The genes contain the basic information that defines the species and characterizes its individual traits. Note the number of genes estimated for the 46 chromosomes of the human species. The human chromosome assemblage is shown in this general diagram; the black and white markings are meant only to convey the idea that various genes of differing makeup are present in each chromosome: In the human gene assemblage there are 46 (23 times 2) chromosomes (long strands of DNA containing all the genetic information [the number varies among species]). Two of these are the sex chromosomes; the remainder are "autosomes" in which each chromosome has its own individual assemblage of genes that controls some aspect of the genetic makeup (other than the sex) of the organism (22 on the haploid strand of a human). The male human has two X chromosomes; the female has a paired X and Y chromosome. Here is a photo of X and Y chromosomes as imaged in an electron microscope: The number of genes varies from one numbered chromosome to the next (left side of the next diagram). The total number of bases is shown on ther right (unfortunately, the numbers have been cropped off, but each horizontal black line is a jump of 50000 from the preceding line [starting at 0 at the bottom and ending at 450000 at the top]); most but not all the bases have a specific sequence (the coding in the DNA that determines the characteristics of the species). Some of the genes are dedicated to producing proteins instead of species traits. It is interesting to realize that many species share some of the same genes. The sequence may vary. In humans, almost 99% of the genes are the same in any two individuals that can be compared but small differences are distinctive (this fact allows DNA analysis to be used in tracking down an individual suspected of a crime). The sequence of bases, which defines the genetic code, is divided into triplets called codons. The standard genetic code for RNA consists of 43 or 64 combinations. This is the resulting Codon Table:
From Farabee/Purves et al - see above citations
From Farabee/Purves et al - see above citations
From Farabee/Purves et al - see above citations
From Farabee/Purves et al - see above citations
From Farabee/Purves et al - see above citations
From Farabee/Purves et al - see above citations
From Farabee/Purves et al - see above citations
From Farabee/Purves et al - see above citations
From Farabee/Purves et al - see above citations
From Farabee/Purves et al - see above citations
From Farabee/Purves et al - see above citations
From Farabee/Purves et al - see above citations
From Farabee/Purves et al - see above citations
From Farabee/Purves et al - see above citations
From Farabee/Purves et al - see above citations
From Farabee/Purves et al - see above citations
From Farabee/Purves et al - see above citations
From Raven and Johnson, Biology, 6th Ed., McGraw-Hill, Inc
From Farabee/Purves et al - see above citations
From Farabee/Purves et al - see above citations
From Farabee/Purves et al - see above citations
Note how it is organized. The first letter in a Codon is taken from the left side. The second letter is selected according to the Column involved, as indicated in the top row. The third letter is chosen from the right side, in the sequence U, C, A, G. Observe that names have been given to different codons.
The same idea applies to this Codon Table set up for DNA. The difference is that U is now replaced by T:
Thus, in a chromosome, the genes consist of various sequential combinations of codons that can number in the thousands
Working out the genomes of individual species and genera has proved a bonanza for reconstructing the patterns of evolution, both within and between species. This cladistic analysis has led to various "trees of life" that present the relationships among the animals or plants being compared. Here is an interesting one found on page 128 in "The Language of God" by Francis S. Collins:
Another important topic that is just too involved to be treated on this review page is Mendelian genetics. Instead, we refer you to this Wikipedia web site. We also have omitted any discussion of cell division and organism reproduction, both sexual and asexual, two important but very involved topics. Again, we steer you to another Wikipedia web site for a general overview, which has links to other relevant terms such as gametes, alleles, mitosis, meiosis. You may also wish to learn these terms: haploid, diploid, genotype and phenotype, zygote, homozygous and heterozygous, blastula and gastrula (most of these can be looked up directly in an Internet Search engine).
Armed with this knowledge of DNA, RNA, and genetics, we are equipped to examine the roles they play in producing or synthesizing new organic molecules. To illustrate this, we will show how the most abundant and versatile molecules - the proteins - are generated. Start with this Overview diagram:
Deceptively simple in this representation, the process is actually complex. In the first step, Transcription (TrScrip), the RNA complement in one strand is synthesized by enzymes into a messenger segment, m-RNA, that is a reversed copy of the original DNA strand, but with T (thymine) replaced by U (uracil).
The m-RNA serves as a template for natural protein synthesis within a ribosome (see cell diagram below. which also contains r-RNA (ribosomal RBA) This ribosome assemblage participates in the manufacture of a protein by Translation) (TrLate) using t-RNA cells (transfer-RNA containing various amino acids that bind to the m-RNA by Hydrogen bonding. The process continues as the polypeptide protein builds until addition of a 'chain termination' group signals the particular protein with its diagnostic codification is completed. The specific protein composition depends on the sequences involved in the synthesis. The production of mRNA occurs within the nucleus; the mRNA migrates into the cytoplasm and seeks out ribosomes where the next step - Translation - takes place.
In the Transcription phase, segments, called Introns, of the first resulting RNA are not used in building the mRNA. Only the Exons are spliced together in sequence. Note that there are Promotor (initiator) and Terminator segments.
There is a key intermediate step in Translation. The cell in which the synthesis occurs contains various amino acids. The mRNA must be matched up and bound with its appropriate amino acid. That amino acid is specified by its codon. An enzyme molecule called aminoacyl-tRNA synthetase plays the critical role by serving as a template for preparing a paired tRNA-amino acid that will then be used in the final phase of protein synthesis. Check this figure:
There are two sites on the molecule that are involved. One is so configured that it can accept (bind) only one specific amino acid. The other site accepts the tRNA. The two are brought together through the action of adenosine triphosphate (ATP) as a catalyst. The pair is then released. The same process takes place with other amino acids, each with their site specific aminoacyl-tRNA synthetase molecule. This diagram shows the steps involved in terms of structural formulae:
The organic chemistry of the process is complicated and will not be further summarized here. Consult this NIH web site for more details.
The final phase of protein synthesis now enters the picture. This involves the interaction within a ribosome that uses the various tRNA-amino acid pairs to form a polypeptide protein molecule. The pairs are added sequentially according to the master template. The process is involved and will not be discussed here in any detail. Perhaps these two figures will help to visualize what happens.
Because of the importance of this topic - protein production - the writer has extracted excerpts from two web sites. The information is bounded by two green lines. Examine these paragraphs if you wish, otherwise skip to the final material below the second green line
Activation of amino acids is carried out by a two step process catalyzed by aminoacyl-tRNA synthetases. Each tRNA, and the amino acid it carries, are recognized by individual aminoacyl-tRNA synthetases. This means there exists at least 20 different aminoacyl-tRNA synthetases, there are actually at least 21 since the initiator met-tRNA of both prokaryotes and eukaryotes is distinct from non-initiator met-tRNAs. Activation of amino acids requires energy in the form of ATP and occurs in a two step reaction catalyzed by the aminoacyl-tRNA synthetases. First the enzyme attaches the amino acid to the a-phosphate of ATP with the concomitant release of pyrophosphate. This is termed an aminoacyl-adenylate intermediate. In the second step the enzyme catalyzes transfer of the amino acid to either the 2'– or 3'–OH of the ribose portion of the 3'-terminal adenosine residue of the tRNA generating the activated aminoacyl-tRNA. Although these reaction are freely reversible, the forward reaction is favored by the coupled hydrolysis of PPi.
Accurate recognition of the correct amino acid as well as the correct tRNA is different for each aminoacyl-tRNA synthetase. Since the different amino acids have different R groups, the enzyme for each amino acid has a different binding pocket for its specific amino acid. It is not the anticodon that determines the tRNA utilized by the synthetases. Although the exact mechanism is not known for all synthetases, it is likely to be a combination of the presence of specific modified bases and the secondary structure of the tRNA that is correctly recognized by the synthetases.
It is absolutely necessary that the discrimination of correct amino acid and correct tRNA be made by a given synthetase prior to release of the aminoacyl-tRNA from the enzyme. Once the product is released there is no further way to proof-read whether a given tRNA is coupled to its corresponding tRNA. Erroneous coupling would lead to the wrong amino acid being incorporated into the polypeptide since the discrimination of amino acid during protein synthesis comes from the recognition of the anticodon of a tRNA by the codon of the mRNA and not by recognition of the amino acid.
Most microorganisms and plants can biosynthesize all 20 standard amino acids, while animals (including humans) must obtain some of the amino acids from their diet. The amino acids that an organism cannot synthesize on its own are referred to as essential amino acids. Key enzymes that synthesize certain amino acids are not present in animals — such as aspartokinase, which catalyzes the first step in the synthesis of lysine, methionine, and threonine from aspartate. If amino acids are present in the environment, microorganisms can conserve energy by taking up the amino acids from their surroundings and downregulating their biosynthetic pathways.
In animals, amino acids are obtained through the consumption of foods containing protein. Ingested proteins are broken down through digestion, which typically involves denaturation of the protein through exposure to acid and hydrolysis by enzymes called proteases. Some ingested amino acids are used for protein biosynthesis, while others are converted to glucose through gluconeogenesis, or fed into the citric acid cycle. This use of protein as a fuel is particularly important under starvation conditions as it allows the body's own proteins to be used to support life, particularly those found in muscle.
Humans can produce 10 of the 20 amino acids. The others must be supplied in the food. Failure to obtain enough of even 1 of the 10 essential amino acids, those that we cannot make, results in degradation of the body's proteins—muscle and so forth—to obtain the one amino acid that is needed. Unlike fat and starch, the human body does not store excess amino acids for later use—the amino acids must be in the food every day. The 10 amino acids that we can produce are alanine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine and tyrosine. Tyrosine is produced from phenylalanine, so if the diet is deficient in phenylalanine, tyrosine will be required as well. The essential amino acids are arginine (required for the young, but not for adults), histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. These amino acids are required in the diet.
Now we shall finish this page with several special topics: Mentioned in passing are viruses. These are strands or segments of nucleic acids encased in a lipid and/or protein coating. They are not living matter although they can reproduce in cells. Although some viruses are beneficial, most disrupt chromosomes, and can insert themselves into DNA or RNA, causing infections. The best known virus today is HIV, which through AIDS destroys the body's ability to overcome disease and cancer. These belong to the class of organic materials known as antigens. In animals, the antigens that threaten their well-being are attacked by antibodies, generated by immune response systems (e.g., lymphocytes)
A brief comment about how living organisms derive energy needed to function, usually through metabolism, which describes several possible chemical reactions. A general way is any process that releases energy when bonds are broken. In plants, photosynthesis is an endothermic reaction involving interaction of sunlight with chloroplasts. In animals, respiration and fermentation release energy when appropriate organic molecules are catabolized (degraded or broken down). About half that energy is stored in a group of molecules, chief of which is ATP (Adenosine TriPhosphate) synthesized naturally from ribose sugar, an adenine base, and phosphate molecules. Here is its structural formula: At the beginning of this page we pointed out that there are three fundamental life forms: Bacteria, Plants, and Animals. Bacteria cells are, as was shown, fairly simple. Plant and animal cells are more complex, as summarized by these diagrams: Plants are very important in that they are the largest source of "food" which provides both the material and the energy needed to create and sustain life. The basic process involves photosynthesis in which the energy sources is (usually) the Sun. Solar photons (hν) energize a reaction between CO2 and H2O to yield glucose and Oxygen, according to this formula: This diagram describes the photosynthesis process: Oxygenic photosynthesis is carried out in two steps, 1) the light reactions which use pigments to capture solar energy and 2) the dark reactions which use the energy from the light reactions to fix atmospherically derived carbon (CO2) into organic carbon (sugars). It should be noted that the final product is not actually glucose as depicted in the equation above,we just don't usually discuss the last step when we talk about photosynthesis. Glucose does result from photosynthesis, but it usually present in polymeric form either as sucrose (a dimer) or starch (a polymer).
The organic molecule Chlorophyll is the essential agent in plant photosynthesis. It consists of a porphyrin ring and a hydrophobic phytol tail, as shown in this structural formula. The process is centered within the chloroplasts. It is interesting to note the structural similarities between chlorophyll and hemoglobin, a molecule found in higher order animals. Hemoglobin is involved in one of the most vital processes in the human body (and in other higher animals) - respiration. Oxygen from the air attaches to hemoglobin carried in the blood and reacts with various molecules to catabolically break them down, releasing energy. Aerobic oxidation is expressed in this formula: Some animals and plants can obtain energy without the use of Oxygen. This is an anaerobic process. Plants and animals interact with each other as sources of life-sustaining food. Plants form the base of the food chain. Next are the herbivores - animals that consume only plants. At the top are the omnivores - animals that eat both plants and other animals. Food chains can also be described in terms of producers and consumers, predators and prey, or trophic levels. The sequence of consumption will vary with the different ecosystems involved. Here is one example:
From Farabee/Purves et al - see above citations
6CO2 + 12 H2O + hv ---> C6H12O6 + 6O2 + 6 H2O
C6H12O6 (aq) + 6 O2 (g) --> 6 CO2 (g) + 6 H2O (l) 
Twenty-first century humankind has a sophisticated food chain system in terms of its infrastructure. Consider this example which starts with a farm (upper left) and shows food production as illustrated by chickens (it could be cows or pigs or crops) as it moves to its final destination - people - through modern food distribution centers.
Now, armed with this general background in Biology/Biochemistry, we will proceed to the next page, which covers the origin and history of life (primarily on Earth) and the tenets of Evolution.
