Living systems can be organized into the following levels or categories, starting with the simplest units and proceeding to the largest and most complex levels of organization:
Subatomic particles (electrons, protons and neutrons) form atoms (hydrogen, helium, oxygen, iron, etc.) which form molecules (water, glucose, cellulose, etc.) which form complex macromolecules (glycoproteins, DNA, RNA, etc.) which form subcellular units called organelles (nucleus, mitochondrion, chloroplast, etc.) which form cells which form tissues (muscle, nerve, adipose, epithelial, etc.) which form organs (brain, heart, liver, root, leaf, etc.) which form an individual organism. All of the elements are listed in a periodic table by their atomic number or number of protons. In a neutral atom the number of protons is equal to the number of electrons. To calculate the number of neutrons for each element see the following link to a periodic table.
Individual oganisms form species populations (ant, human, deer, ponderosa pine, duckweed, etc.) which are further organized into complex communities composed of many species populations (chaparral, coastal sage scrub, yellow pine forest, redwood forest, etc.). These communities interact with physical environmental factors (soil, terrain, water, atmosphere, climate, etc.) to form complex ecosystems (ocean, coral reef, prarie, tundra, tropical rain forest, etc.). These ecosystems are often named after the plant communities they are associated with (chaparral, coastal sage scrub, creosote bush scrub, Douglas fir forest, etc.).
There are many different kinds of atoms from the 103 elements. Ninety-two of these elements occur naturally on the planet Earth. Six of these elements (carbon, hydrogen, nitrogen, oxygen, phosphorus & sulfur) comprise about 98% of the body weight of most living organisms. Two or more atoms joined together by chemical bonds form molecules of chemical compounds such as water (H2O), glucose (C6H12O6) and sucrose (C12H22O11).
The four major elements of living systems are carbon (C), hydrogen (H), oxygen (O) and nitrogen (N).
The four major compounds of living systems are carbohydrates, lipids, proteins and nucleic acids. Molecules of these compounds are composed mostly of atoms from the four major elements, plus some additional elements, such as phosphorus (P), sulfur (S), iron (Fe), magnesium (Mg), sodium (Na), chlorine (Cl), potassium (K), iodine (I) and calcium (Ca).
The following is a brief outline of the major chemical compounds of living systems; please refer to your recommended textbook for more information, illustrations and structural formulas.
I. Carbohydrates: Compounds containing carbon (C), hydrogen (H) and oxygen (O); the H and O atoms typically occur in a 2:1 ratio.
II. Lipids: A large group of chemicals that are generally insoluble in polar solutions such as water, but soluble in nonpolar solvents such as alcohol. Note: Some of the chemical groups included in this outline, such as terpene steroids and carotenoids, are classified as lipids in general biology textbooks.
Blood Triglycerides and Cholesterol
Cholesterol is a complex lipid and vital precursor of sex hormones, vitamin D and bile salts. It is produced by the body, although some dietary cholesterol comes from animal products. Cholesterol is carried to sites in the body by low-density lipoprotein molecules (LDLs). High-density lipoproteins (HDLs) remove cholesterol from these sites and deliver it to the liver for breakdown. Excessive levels of cholesterol in the blood can lead to fatty deposition in blood vessels (arteries) called plaque. For example, damage to a blood vessel wall (by injury or strain) causes cells underlying the internal wall to divide. White blood cells (macrophages) accumulate in the area to ingest particles of damaged cells. LDLs carrying cholesterol gather in the area to provide materials for repairing the wall. While waiting to be used, the cholesterol molecules can become oxidized, causing them to be engulfed by macrophages. After engulfing several oxidized molecules, the macrophages die and become deposited as fatty "foam cells" in the area of the wall being repaired. A buildup of these fatty deposits mixed with fibrous muscle cells is called plaque, which can narrow the diameter of an artery and seriously impede the blood flow. This can be life threatening if the blood vessel happens to be a coronary artery that supplies the heart muscle with oxygen-rich hemoglobin. Even without injury, plaque can form in arteries if cholesterol levels in the blood are high enough, particularly if they become oxidized and are engulfed by roving macrophages. The condition or disease in which blood vessels become clogged with plaque is called atherosclerosis.
Any substance that lowers the LDLs and increases the HDLs tends to reduce the probability of plaque formation and a heart attack. Lowering the intake of saturated animal fats can reduce the total cholesterol level but does not alter the ratio of lipoproteins. Saturated fatty oils in tropical palms and hydrogenated oils in margarines can increase the amount of LDLs in the blood. At this time, the best type of fatty acids for a healthy balance of LDLs and HDLs are the monounsaturated fatty acids found in olive oil (Olea europea) and canola oil (Brassica napus).
III. Proteins: This is a huge group of macromolecules produced by plants and animals. Structural protein include collagen of fibrous connective tissue and skin, which constitutes about one third of the total protein of mammals, and keratin of nails, horn, hair, wool, claws, beaks, scales and feathers. Proteins are composed of long chains (polypeptides) of subunits called amino acids, with an average of about 400 or 500 amino acid molecules per protein. For example, the human red blood pigment hemoglobin contains 584 amino acids. Amino acids of living systems are the L-form optical isomer, in contrast to the D-form for sugars. There are 20 different amino acids in human protein, although many additional amino acids occur in nature. Eight of the 20 amino acids are called "essential" because they must come from a protein diet. The remaining 12 are called "nonessential" because they can be synthesized by cells. All the amino acids must be present to synthesize protein, if one or more are missing, the organism will eventually die from protein deficiency. Essential amino acids are to proteins as vowels are to words. If one or more vowels are missing, then words canot be spelled correctly and sentences become meaningless. For example, the short sentence "the man and boy are sad" is meaningless without vowels. If you take away the vowels, the sentence becomes "th mn nd b re sd" Although plants can synthesize all of their amino acids, the herbicide Roundup® blocks the synthesis of certain aromatic amino acids, thus gradually killing the plant.
The eight essential amino acids in human protein are: tryptophan, phenylalanine, lysine, threonine, valine, methionine, leucine, and isoleucine. The twelve nonessential amino acids in human protein are glycine, alanine, serine, cystine (cysteine), aspartic acid (aspartate), asparagine, glutamic acid (glutamate), glutamine, arginine, histidine, tyrosine, and proline. The essential amino acid lysine is deficient in grains, but is present in adequate levels in legumes. Likewise, the essential amino acid methionine is deficient in legumes, but is present in adequate levels in grains. If either of these two essential amino acids is missing from your diet, you may suffer from protein deficiency. Some general biology textbooks state that a vegetarian diet should include legumes, such as beans and peas from the legume family (Fabaceae), and grains, such as wheat and rice from the grass family (Poaceae). The problem with this statement is that the diet of preagricultural humans, evolving as it did from primate ancestors, consisted primarily of fruits, nuts, wild legumes, edible roots and tubers, and some meat. Not until about 10,000 years ago did cereal grains and legume crops become an important component of the human diet. This subject is summarized by G. Wadley & A. Martin (1993) in an article entiltled "The Origins of Agriculture--A Biological Perspective and a New Hypothesis," Australian Biologist 6: 96-105.
The salts of glutamic acid (called glutamates), plus the nucleotides guanosine monophoshate (GMP) and inosine monophsphate (IMP), are natural flavor enhancers in our diet. In fact, the savory flavor of glutamates in food was termed "umami" by Japanese Professor Kikunae Ideda of Tokyo Imperial University in 1908. Only the L-glutamate enantiomer has the flavor-enhancing properties. According to some authors, umami is one of the five basic tastes in addition to sweet, sour, bitter and salty. Umami is spelled umami in all major languages, including English, Spanish, French, German, etc. The sensation of umami is due to the detection of the carboxylate anion of glutamate by specialized receptor cells present on the tongue of humans and other animals. Described by some authors as "meaty," umomi explains the flavor of some delicious mushrooms. Glutamates are commonly added to food in the form of MSG (monosodium glutamate), and not just in Chinese restaurants. The deleterious side effects of excess MSG in the diet have been well-documented, including allergies, asthma, brain damage and high blood pressure. Glutamates are also involved in many important biochemical reactions, including the lowering of toxic ammonia in the blood and its excretion in the kidneys. In fact, glutamates play a major role in mammalian nitrogen metabolism, serving as both a nitrogen donor and nitrogen acceptor. Details of these reactions are beyond the scope of this outline.
In the book Jurassic Park by Michael Crichton (1990), the dinosaurs on Isla Nublar (off the coast of Costa Rica) were genetically engineered to be "lysine dependent." All the dinosaurs received a mutant gene that produced a faulty enzyme in protein metabolism. As a result, they could not manufacture the amino acid lysine. Unless they received a rich dietary supplement of lysine they would die within days. This was a protective measure to prevent the dinosaurs from surviving in the real world. In the last chapter, some unknown animals were eating certain crops on the Costa Rica mainland. It turned out that the crops were agama beans and soy beans, two species of legumes rich in lysine. The book ended on this note, making you wonder if certain dinosaurs (perhaps velociraptors) had escaped and reached the mainland.
Amino acids are to proteins as letters are to words. An unabridged dictionary reveals the astonishing number of words that can be created with a 26 letter English alphabet, with most words less than 20 letters. Although human protein is constructed from a "20 letter" alphabet, the average protein "word" is made from hundreds of amino acid "letters," resulting in astronomical possibilities for different proteins. Some of the vital proteins in human systems are (1) Structural Proteins which comprise the body and its organs and tissues; (2) Enzymes which serve as vital catalysts in biochemical reactions; (3) Hormones such as the vital compound insulin that regulates the blood sugar level; and (4) Antibodies which serve to protect the body from renegade viruses and bacterial invasions. Proteins come in four main structural forms: (1) Primary: A straight chain of amino acids; (2) Secondary: A helical coil of amino acids stabilized by hydrogen bonds; (3) Tertiary: Folding and looping of a coiled polypeptide stabilized by hydrogen bonds; and (4) Quaternary: Four tertiary proteins joined together (e.g. hemoglobin). A molecule of hemoglobin is composed of four polypeptides, each with 146 amino acids, a grand total of 584. Heat or weak acid solutions can destroy the hydrogen bonding causing the tertiary proteins to uncoil, a condition termed denaturation. This is why vinegar (acetic acid) can actually "cook" an egg white (albumen) without heat. Proteins in raw fish called seviche (ceviche) are denatured by citric acid when the fish are marinated in lime or lemon juice. Hemotoxic proteins at the site of a rattlesnake bite can also be denatured by an electrical discharge from a device similar to a stun gun.
Enzymes: Enzymes are large protein molecules that catalyze specific biochemical reactions. A phenomenon known as bioluminescence, where living organisms glow in the dark, requires a specific enzyme catalyst. The emission of light by an organism or population of organisms involves the oxidation of luciferin in the presence of ATP and the enzyme luciferase. If luciferase or ATP is lacking, the reaction will not occur. Examples of bioluminesence include dinoflagellates causing "red tide," lightning "bugs" (beetles), glow worms (beetle larvae), comb jellies (phylum Ctenophora), the deep sea angler fish, and a remarkable fungus called the jack-o-lantern mushroom.
The complex folding of tertiary proteins produces their characteristic three-dimensional structure with unique shapes and grooves analogous to a key that fits into a lock. In fact, the "Lock & Key Theory of Enzyme Specificity" is a plausible model that explains how a specific enzyme only fits into a certain substrate molecule because of the unique shape of its active site. This temporary joining of the enzyme molecule affects the chemical structure of the substrate, weakening certain bonds within the molecule so that it breaks down (hydrolyzes). It is devastating to a living system if vital proteins, such as enzymes and antibodies, are not synthesized or are blocked by a genetic disease, invasive virus or poison. For example the AIDS (HIV) virus attacks the immune system that produces T-cells and antibodies, thus rendering the body helpless against infections by other viruses, bacteria and cancer cells. Some poison molecules, such as certain plant alkaloids, can attach to the active site of vital enzymes, thus blocking the action of these enzymes.
The order and position of amino acids in a protein molecule is critical for the vital function of the molecule. The red bood pigment hemoglobin is a quaternary protein composed of two alpha polypeptides and two beta polypeptides. The substitution of valine for glutamic acid (glutamate) in the beta polypeptide changes the oxygen-carrying potential of this vital blood cell pigment, and is the biochemical explanation for the genetic disease called sickle-cell anemia. At position number six on the beta polypeptides, the amino acid glutamic acid is replaced by valine. This structural change in the protein results in a distortion of the blood cell from a normal biconcave disk to a sickle shape. The exact number and order of amino acids in protein molecules are determined by the DNA base sequence in genes, and genetic mutations are essentially "misspelled " genes.
For the sake of simplicity, let B stand for the gene that produces the normal beta polypeptide and B' stand for the mutant allele that produces the abnormal (mutant) form of the beta polypeptide. Normal homozygous people inherit two normal genes (BB) and have normal beta polypeptides in their hemoglobin molecule. Homozygous people suffering from sickle-cell anemia inherit two mutant genes (B'B') and have abnormal (mutant) beta polypeptides. Some people have the intermediate sickle-cell trait and are heterozygous BB'. These people have normal and abnormal beta polypeptides. Although their blood cells appear normal, they may become distorted under lower oxygen conditions, such as high elevation roads or in airplanes; therefore gene B is not completely dominant over gene B'. Some references (including your recommended text) refer to this condition as incomplete dominance.
Prions: Renegade Proteins That Cause Mad Cow Disease. Prions (pronounced PREE-ons) are disease-causing protein particles. They may be a mutated form of a brain protein with an abnormal (improper) tertiary structure. Prion diseases are referred to as spongiform encephalopathies because of the post mortem appearance of the brain with large vacuoles in the cortex and cerebellum. A number of diseases of animals may be caused by prions, including Scrapie (sheep), TME (Transmissible Mink Encephalopathy), CWN (Chronic Wasting Disease in muledeer and elk), and BSE (Bovine Spongiform Encephalopathy in cows). The latter condition is better known as Mad Cow Disease. There are also several human diseases attributed to prions including CJD (Creutzfeldt-Jacob Disease), FFI (Fatal Familial Insomnia), Kuru, and Alpers Syndrome.
Prions are thought by some researchers to be proteins with an abnormal tertiary structure. Exactly what causes this 3-dimensional protein to be folded improperly has been a topic of great speculation. Some earlier hypotheses stated that it was due to an incorrect amino acid sequence, but this may not be the case. The prion protein may interact with normal protein molecules, forcing them to fold abnormally. Over time, the improperly folded proteins increase in concentration and may destroy brain tissue. Prions reproduce without DNA or RNA. They replicate by interacting with other proteins in a chain reaction, thereby causing subsequent proteins to also fold improperly. The precise mechanism by which they multiply is unknown at this time, but they appear to work like a enzyme that catalyzes its own multiplication. Prions may be inherited, possibly by a recessive gene that shows up in homozygous recessive individuals. Or, they may be transmitted by eating infected brain tissue that has been ground up in animal feed or in hamburger and sausage. Muscle tissue contains nerve tissue and blood vessels; however, preliminary tests indicate that prions are confined to the brain and spinal cord of livestock. The bottom line here is that prions are renegade proteins that multiply and destroy the brains of livestock and people. They are not a bacterium or virus, and they are practically impossible to kill by conventional methods. In a sense they are "immortal molecules" that truly represent a serious threat to mammalian life forms.
Glycoproteins (protein plus carbohydrate) are complex polypeptides (amino acid chains) plus polysaccharide chains. They include a number of large molecules in living systems, including membrane proteins that provide cell recognition. Patrolling white blood cells called T-cells can recognize "self" versus "alien" cells by these special membrane proteins. Glycoproteins also include blood cell antigens and antibodies. They are also involved in pollen grain recognition on the receptive stigmas of the same or different species.
Immunotoxins are conjugated proteins consisting of monoclonal antibodies (made from another animal) with an attached protein toxin called a lectin. For example, the deadly lectin from the castor bean (called ricin) is joined to special antibodies against a specific type of cancer. Like armed, molecular missiles, the antibodies carry the deadly ricin directly to the tumor, thus killing the tumor cells without affecting other mitotic cells in the patient. See the following references for more information about lectins and the anti-tumor uses of castor beans.
One of the deadliest seeds on Earth is the castor bean (Ricinus communis). The seeds contain ricin, a very toxic protein compound known as a lectin. According to the Merck Index: An Encyclopedia of Chemicals, Drugs, and Biologicals(1997), a dose of ricin weighing only 70 micrograms or two millionths of an ounce (roughly equivalent to the weight of a single grain of table salt from a salt shaker) is sufficient to kill a 150 pound (68 kg) person. In striking contrast with its use in medicine to prolong human life, there are also reports of ricin being used in covert assassination attempts and as a potential toxin for biological warfare.
In 1978, a Bulgarian dissident, Georgi Markov, was assasinated in London after being pricked by a ricin-tipped umbrella. Ricin causes a slow and painful death through blood poisoning and a breakdown of the circulatory system. There is no known antidote for ricin poisoning. Even before the tragic terrorist plane crashes into the Trade Center Twin Towers in New York, some airports hand-inspected umbrellas packed in carry-on luggage. Following the Gulf War, UN investigator teams (UNSCOM) discovered that Iraq was purifying ricin for possible use in biological warfare, along with anthrax (Bacillus anthracis), botulism toxin (Clostridium botulinum), gas gangrene (C. perfringens), and aflatoxin (Aspergillus parasiticus). From: Facts on File News Services (23 January and 13 February 1998).
According to The Washington Post Online (16 November 2001), Osama bin Ladens's Al-Qaeda network also had working plans for making ricin. Instructions for preparing the poison were found in the cellar of an abandoned house once used as a terrorist training center. According to the article, the ricin may be ingested, injected and inhaled. The article also states that the laxative effect of castor oil is due to ricin, but this is doubtful. Castor oil is derived from the seeds of the castor bean. It contains 87 percent ricinoleic acid, a fatty acid with many industrial uses, along with small amounts of several other fatty acids including oleic (7%), linoleic (3%), palmitic (2%) and stearic (1%). The deadly protein ricin is not a component of purified castor oil.
Although they are not proteins, some respiratory pigments called porphyrins, such as the heme component of the red blood cell pigment hemoglobin, are associated with polypeptides. Porphyrins contain a complex nitrogenous ring with a metallic atom (iron, magnesium or copper) in the center. Porphyrins are included here because of their similarity to the heme component of the protein hemoglobin. Chlorophylls a & b are certainly the most common and conspicuous pigments in our visible world. They are magnesium porphyrins with the following empirical formulas:
Hemoglobin (C3032H4816O872N780S8Fe4), the vital red blood cell pigment, contains four iron porphyrins. Some invertebrates with green blood have copper porphyrins. Porphyrins also include the iron-containing cytochrome pigments located on the inner membranes (cristae) of mitochondria in plants and animals. Cytochrome pigments also occur on the inner membranes of bacteria. They are involved in oxidative phosphorylation (electron transport system) and ATP production. Leghemoglobin is a porphyrin within the cells of symbiotic nitrogen-fixing bacteria living in the root nodules of legumes. Nitrogen fixation, the conversion of atmospheric nitrogen into ammonia, requires the enzyme nitrogenase which is inhibited by free oxygen. To maintain a low level of free oxygen in these bacterial cells, the oxygen is bound to leghemoglobin where it is readily available for cellular respiration, but not at a level that is damaging to the nitrogenase. In N-fixing cyanobacteria such as Anabaena azollae living symbiotically within leaf cavities of the water fern Azolla, the site of N-fixation occurs in non-photosynthetic cells called heterocysts. Heterocysts have a much lower level of oxygen compared to photosynthetic, oxygen-producing cells with thylakoid membranes.
Phycobiliproteins are complex photoreceptor pigments found in cyanobacteria (Division Cyanobacteria) and red algae (Division Rhodophyta). They are composed of water-soluble phycobilin pigments and protein. The phycobilin component is similar to porphyrins but without the metallic atom. Phycobilins include the blue-green pigment phycocyanin and the red pigment phycoerythrin. The latter phycobilin is a photoreceptor pigment associated with chlorophyll, enabling red algae to be photosynthetically efficient in deep water where blue light predominates. The red light waves that activate green chlorophyll pigments do not penetrate the deeper water of the photic zone; hence, green algae cannot survive at this depth. Phytochromes are phycobilin-protein pigments involved in floral induction. They are activated by the length of day (hours of darkness). The cocklebur is a classic example of a short-day plant (i.e. it only flowers when the nights are long). At least one leaf of a cocklebur plant needs 15 hours of darkness to undergo various complex biochemical reactions leading to the release of a hypothetical flower stimulant called "florigen." The protein leaf pigment called "phytochrome" controls the release of florigen from the leaves. One form of this pigment (P-660) is formed during the hours of darkness and is essential for the release of florigen. The phytochrome P-660 pigment is very sensitive to specific wavelengths of light, and a flash of light during the 15 hours of darkness can instantaneously convert it into another form called P-730 which inhibits the release of florigen, thus blocking the flowering process. Cocklebur plants can bloom in the tropics where the days are short and the nights are long, thus greatly increasing its range and potential for seed production. In North America, cockleburs typically bloom during the fall months when the days are shorter and the nights longer. They will not bloom during the long days of summer or near a street light.
IV. Nucleic Acids: This class of compounds includes the genetic material DNA (deoxyribonucleic acid), largest of the biomolecules, and RNA (ribonucleic acid), a smaller nucleic acid made from a section of DNA called a gene. Two main types of RNA are made in the nucleus of a cell, including messenger RNA (M-RNA) and transfer RNA (T-RNA). A third type called ribosomal RNA is made in the nucleolus of the nucleus. All three types of RNA are involved in protein synthesis. M-RNA molecules are made from sections of DNA in the nucleus, a process called transcription. The M-RNA strands are essentially complementary copies from one side of the DNA ladder after it has separated or "unzipped."
Completed M-RNA molecules then leave the nucleus and travel to organelles in the cytoplasm called ribosomes (made of ribosomal RNA). Smaller T-RNA molecules attach to specific amino acids in the cytoplasm and bring them to the ribosomes where they join with precise base triplets called codons along the M-RNA strand, a process called translation. A complementary base triplet on each T-RNA called the anticodon joins with the codon of M-RNA (e.g. the anticodon AUG joins with the codon UAC). Different T-RNA molecules carry different amino acids, depending on their anticodons. Since there are 64 different codons (4X4X4) and only 20 different amino acids (in human protein), some codons of M-RNA stand for the same amino acid. [E.g. the codons UUA, UUG, CUU, CUC, CUA and CUG all stand for the amino acid leucine.] As each amino acid is linked to the growing polypeptide, a molecule of water is released, a chemical reaction called dehydration synthesis. The completed polypeptides become vital proteins, such as enzymes, antibodies or structural proteins of muscles, blood vessels and other tissues. This remarkable process is essentially the same in all animals as well as in plants.
DNA is the master molecule that carries all of the inherited characteristics (genes) of an individual in the form of chromosomes. Each individual (such as a human) receives one haploid set of 23 chromosomes from their father's sperm and one haploid set of 23 chromosomes from their mother's egg. The two sets come together at conception when the diploid zygote (fertilized egg) is formed. Each eukaryotic chromosome (the chromosomes of algae, fungi, plants and animals) carries thousands of genes, about 100,000 functional genes per cell. A chromosome is analogous to a high capacity storage disk (DVD disk), while genes are analogous to files on this storage disk. If a chromosome could be completely unraveled it would reveal a long, ladder-shaped DNA molecule that is coiled into helical spirals. At intervals along this double helix, the DNA ladder is wrapped around small beads of protein called nucleosomes. There are also extrachromosomal genes in the form of bacteria-like (prokaryotic) plasmids within cytoplasmic organelles called mitochondria and chloroplasts. Photosynthetic chloroplasts are found only in plant cells, while mitochondria are present in both plant and animal cells. Indeed, some biologists believe these intracellular organelles evolved from bacteria-like ancestors. It has been generally thought that all mitochondrial and chloroplast DNA was passed on solely through the egg cells of animals and plants, although this theory has been challenged in a recent article in Science Vol. 286 (24 Dec. 1999).
The spiral, ladder-like (double helix) structure of DNA was discovered by James Watson and Francis Crick in 1953. Using data from x-ray diffraction, Rosalind Franklin was also close to this discovery, but Watson and Crick got their research published first. For their discovery that truly revolutionized the science of biology, Watson and Crick received the Nobel Prize in 1962. Basically, the uprights or rails of the ladder are composed of alternating 5-carbon sugars (deoxyribose) and phosphates, while the rungs of the ladder are composed of nitrogenous base pairs. Four bases occur in DNA, larger purine bases (adenine and quanine), and smaller pyrimidine bases (cytosine and thymine). DNA (and RNA) are composed of subunits called nucleotides, each nucleotide consisting of a phosphate, a sugar and a base. DNA is recycled into nucleotides which are used to synthesize more DNA in the nucleus of the cell. In the DNA ladder, adenine always pairs with thymine, and guanine always pairs with cytosine. Depending on their sequence and left vs. right configurations in the DNA ladder, every base pair has four different arrangements: A-T, T-A, C-G and G-C. The total number of different possible arrangements in a DNA molecule with a million base pairs is equal to 4 raised to the one millionth power, or a number with more than 600,000 digits. This astronomical number far exceeds the number of electrons in some models of the visible universe. Herein lies the tremendous variability factor of DNA, and the computer-like chemical coding of all the genetic characteristics of a complete plant or animal. The amount of genetic information stored in the DNA within one human nucleus is enormous. In terms of printed information (using a 26 letter English alphabet), this represents about 500 volumes of Encyclopedia Britannica. All this is stored in a microscopic nucleus 5 micrometers in diameter (smaller than a human red blood cell). Imagine a computer using the storage potential of DNA. RNA is similar to DNA except it is single-stranded in M-RNA , has the 5-carbon sugar ribose instead of deoxyribose, and the pyrimidine base uracil instead of thymine.
ATP: Energy Currency Of The Cell
Can you locate all the atoms of carbon, hydrogen, nitrogen, oxygen and phosphorus?
The structure of adenosine monophosphate, an RNA nucleotide containing the purine base adenine, is very similar to ATP (adenosine triphosphate), except that ATP has three phosphates (PO4) instead of one. ATP is synthesized in all living cells by the addition of a phosphate to ADP (adenosine diphosphate). ATP is the vital energy molecule of all living systems which is absolutely necessary for key biochemical reactions within the cells. The terminal (3rd) phosphate of ATP is transferred to other molecules in the cell, thereby making them more reactive. For example, the monosaccharide glucose is very stable at ordinary body temperatures and would require a great amount of heat (such as from a flame) to break it down into carbon dioxide and water. After receiving a phosphate from ATP (a process called phosphorylation), glucose becomes glucose-phosphate and can be enzymatically broken down within seconds.
Most of the ATP in eukaryotic cells of animals is made inside cellular organelles called mitochondria from the oxidation of glucose, a process called cellular respiration. Glucose combines with oxygen (oxidation), forming carbon dioxide, water and 38 molecules of ATP. During the oxidation process, electrons from glucose are shuttled through an iron-containing cytochrome enzyme system on the inner mitochondrial membranes (called cristae). The actual synthesis of ATP from the coupling of ADP (adenosine diphosphate) with phosphate is very complicated and involves a mechanism called chemiosmosis. The electron flow generates a higher concentration (charge) of positively-charged hydrogen (H+) ions (or protons) on one side of the membrane. When one side of the membrane is sufficiently "charged," these protons recross the membrane through special channels (pores) containing the enzyme ATP synthetase, as molecules of ATP are produced.
Light Reactions Of Photosynthesis
In addition to mitochondrial ATP synthesis, plants can also make ATP by a similar process during the light reactions of photosynthesis within their chloroplasts. Electrons flow through a cytochrome transport system on thylakoid membranes in a region of the chloroplast called the grana; except that the electrons come from excited (light activated) chlorophyll molecules rather than the break down of glucose. This is an especially vital source of ATP for plants because ATP is also needed for them to synthesize glucose in the first place. Without a photosynthetic source of ATP, plants would be using up their ATP to make glucose, and then using up glucose to make ATP, a "catch-22" situation.
A transparent-green solution of chlorophyll is made by grinding up spinach or grass leaves in acetone (in a mortar and pestle), and then filtering it through cheesecloth and course filter paper. If a bright beam of light is directed at this chlorophyll solution, a deep red glow is emitted from the test tube. The chlorophyll electrons become excited by the light energy, but have no cytochrome transport system to flow along because the chloroplast thylakoid membranes have been dissolved away. Therefore, the chlorophyll electrons give up their excited energy state by releasing energy in the form of a reddish glow. This phenomenon is known as fluorescence, and is essentially the same principle as a neon light. In a neon light, the electrons of neon gas become excited and then release their energy of activation as a white glow inside the glass tube. In an intact chloroplast with thylakoid membranes, ATP is generated by an electron flow along the cytochrome transport system. Since the electrons are being transported to other "carrier" molecules, their energy is used to generate ATP and no reddish glow is emitted. Leaves generally appear green because wavelengths of light from the red and blue regions of the visible spectrum are necessary to excite the chloroplast electrons, and unused green light is reflected. Thus, we perceive trees, shrubs and grasses as green. During the fall months when chlorophyll production ceases in deciduous trees and shrubs, the leaves turn golden yellow or red due to the presence of other pigments, such as yellow and orange carotenoids and bright red anthocyanins.
Another important ingredient for photosynthesis is also produced during the light reactions. During these light-dependent reactions of photosynthesis, a chemical called NADP picks up two hydrogen atoms from water molecules forming NADPH2, a powerful reducing agent that is used to convert carbon dioxide into glucose during the dark reactions of photosynthesis (also called the Calvin Cycle). When the two atoms of hydrogen join with NADP, oxygen is liberated, and this is the source of oxygen gas in our atmosphere. ATP and NADPH2from the light reactions are used in the dark reactions of photosynthesis that take place in the stroma region of the chloroplast.
Similar electron transport systems occur in the membranes of prokaryotic bacteria. Methanogenic bacteria live in marshes, swamps and your gastrointestinal tract. In fact, they are responsible for some intestinal gas, particularly the combustible component of flatulence. They produce methane gas anaerobically (without oxygen) by removing the electrons from hydrogen gas. The electrons and H+ ions from hydrogen gas are used to reduce carbon dioxide to methane. In the reaction, the H+ ions combine with the oxygen from carbon dioxide to form water. During this process, the electrons are shuttled through an anaerobic electron transport system within the bacterial membrane which results in the phosphorylation of ADP (adenosine diphosphate) to form ATP (adenosine triphosphate). This process is much less efficient than aerobic respiration, so only two molecules of ATP (rather than 38) are formed. Desert varnish bacteria make their ATP in a similar fashion, only the electrons are coming from the aerobic oxidation of iron and manganese. A thin coating of iron or manganese oxide is deposited on the surfaces of desert boulders and rocky slopes. During the oxidation process, the electrons are shuttled through an iron-containing cytochrome enzyme system on the inner bacterial membrane. One has only to gaze at the spectacular panoramas of varnish-coated, granitic boulders throughout desert areas of the American southwest to appreciate the magnitude of this bacterial ATP production. The mechanism of ATP synthesis in prokaryotic bacteria is remarkably similar to eukaryotic cells. In addition, the circular DNA molecules of these bacteria are similar to the DNA molecules within some organelles of eukaryotic cells. In fact, some biologists believe that mitochondria (and chloroplasts) within eukaryotic animal and plant cells may have originated from ancient symbiotic bacteria that were once captured by other cells in the distant geologic past. This fascinating idea is called the "Endosymbiont Theory" (or "Endosymbiont Hypothesis" for those who are more skeptical).
Trace amounts of DNA can be amplified (cloned) into millions of copies using the PCR technique (Polymerase Chain Reaction) discovered by Kary Mullis of UCSD. This technique provides investigators with sufficient DNA to use in sequencing gels in which the banding patterns represent different base pair sequences. DNA sequencing is widely used in modern research, including crime scene investigations to determine genetic "fingerprints" (e.g. the O.J. Simpson Trial). [And remember the DNA evidence on Monica Lewinski's dress that almost led to the removal of President Clinton from office!] DNA is also used in phylogenetic studies (cladistics) to show evolutionary trends and relationships among plant and animal species. Depending on the level of study, certain types of genes are preferred. For larger taxonomic groups at the plant family level, chloroplast DNA is particularly useful. For phylogenetic studies at the species level, mitochondrial DNA and small subunit ribosomal DNA is commonly used. Researchers can compare their results with others and download gene sequences from the GenBank Data Base at the National Center For Biotechnology Information. Please consult your textbook for more information and illustrations of this remarkable class of compounds which truly are the chemicals of life.
V. Terpenes: An enormous group of plant hydrocarbons formed by the polymerization of 5-carbon isoprene (C5H8) subunits. Terpenes are one of the largest and most varied group of plant chemicals. They may contain carbon chains and rings in different structural forms called isomers. They may also be reduced and oxidized into a vast array of compounds, including alcohols, ketones, acids and fragrant aldehydes. There are five main types of terpenes, including 10-carbon monoterpenes (2 isoprenes), 15-carbon sesquiterpenes (3 isoprenes), 20-carbon diterpenes (4 isoprenes), 30-carbon triterpenes (6 isoprenes) and 40 carbon tetraterpenes (8 isoprenes). Terpene chemicals present in the resinous foliage and fallen leaves of chaparral shrubs inhibit germination of nearby wildflower seeds, a phenomenon known as allelopathy. This explains the abundance of wildflowers in recently cleared chaparral that has not burned. It has also been shown that the burned remains of shrubs greatly stimulate the germination of certain seeds. The developing wildflowers thrive in the ash and often grow much more vigorously than in soil without ash. There are also allelopathic phenolic compounds.
Some terpenes are poisonous and can cause painful rashes. Excellent examples of these terpenes can be found in the milky sap of some members of the euphorbia family (Euphorbiaceae). The commonly cultivated Milkbush or aveloz (Euphobia tirucalli) contains several highly unsaturated diterpene esters in its milky latex. These caustic terpenes are structurally similar to phorbol, a potent carcinogen listed among organic compounds in the Merck Index. The infamous manchineel tree (Hippomane mancinella) of the Caribbean region and coastal Central America contains two potent diterpene compounds with carbon atoms arranged in rings, including the tetracyclic (4-ring) mancinellin and the tricyclic (3-ring) huratoxin. Contact with these terpenes can cause inflammation and a painful, blistering rash. One of the earliest written accounts of the manchineel tree appeared in memoirs of Columbus' second voyage to the West Indies in 1493. On November 3 a landing party went ashore on the island of Marie Galante. The fleet physician, Dr. Chanca, writes: "There were wild fruits of various kinds, some of which our men, not very prudently, tasted; and upon only touching them with their tongues, their countenances became inflamed, and such great heat and pain followed, that they seemed to be mad, and were obliged to resort to refrigerants to cure themselves."
One of the most poisonous terpenes is cicutoxin, the toxic component in the sap of water hemlock (Cicuta douglasii). Water hemlock is a member of the carrot family (Apiacaeae). Like some members of this family, such as carrots and parsnip, this widespread perennial has large taproots and umbrellalike clusters of small white flowers. Cicutoxin is an unsaturated aliphatic alcohol that acts directly on the central nervous system. [Aliphatic compounds have carbon atoms in straight chains rather than the benzene rings of aromatic compounds.] In sufficient doses cicutoxin causes paralysis and death from respiratory failure. Water hemlock is not to be confused with the true hemlocks, coniferous trees of the pine family (Pinaceae) belonging to the genus Tsuga. The "hemlock" given to Socrates in 399 B.C. was undoubtedly an alkaloid mixture from the roots of poison hemlock (Conium maculatum), another member of the carrot family.
One of the most famous poisonous terpenes may have affected the creativity of Vincent van Gogh. The terpenoid compound thujone is composed of several volatile monoterpenes found in the resins of several species of cone-bearing species in the cypress family (Cupressaceae). The resins of conifers (especially the monoterpenes) are the primary defensive mechanism against the ravaging effects of bark beetles. Thujone is also found in the sap of wormwood (Artemisia absinthium), a European shrub related to our North American sagebrushes. Wormwood oil derived from A. absinthium was the principal flavoring of absinthe liqueur, an alcoholic beverage that was taken regularly by van Gogh. Ingested repeatedly, absinthe can cause dramatic personality changes and may have affected van Gogh's creativity and fondness for the color yellow. See the link below for more information
For further details log on website :
http://waynesword.palomar.edu/chemid1.htm
Subatomic particles (electrons, protons and neutrons) form atoms (hydrogen, helium, oxygen, iron, etc.) which form molecules (water, glucose, cellulose, etc.) which form complex macromolecules (glycoproteins, DNA, RNA, etc.) which form subcellular units called organelles (nucleus, mitochondrion, chloroplast, etc.) which form cells which form tissues (muscle, nerve, adipose, epithelial, etc.) which form organs (brain, heart, liver, root, leaf, etc.) which form an individual organism. All of the elements are listed in a periodic table by their atomic number or number of protons. In a neutral atom the number of protons is equal to the number of electrons. To calculate the number of neutrons for each element see the following link to a periodic table.
Individual oganisms form species populations (ant, human, deer, ponderosa pine, duckweed, etc.) which are further organized into complex communities composed of many species populations (chaparral, coastal sage scrub, yellow pine forest, redwood forest, etc.). These communities interact with physical environmental factors (soil, terrain, water, atmosphere, climate, etc.) to form complex ecosystems (ocean, coral reef, prarie, tundra, tropical rain forest, etc.). These ecosystems are often named after the plant communities they are associated with (chaparral, coastal sage scrub, creosote bush scrub, Douglas fir forest, etc.).
There are many different kinds of atoms from the 103 elements. Ninety-two of these elements occur naturally on the planet Earth. Six of these elements (carbon, hydrogen, nitrogen, oxygen, phosphorus & sulfur) comprise about 98% of the body weight of most living organisms. Two or more atoms joined together by chemical bonds form molecules of chemical compounds such as water (H2O), glucose (C6H12O6) and sucrose (C12H22O11).
The four major elements of living systems are carbon (C), hydrogen (H), oxygen (O) and nitrogen (N).
The four major compounds of living systems are carbohydrates, lipids, proteins and nucleic acids. Molecules of these compounds are composed mostly of atoms from the four major elements, plus some additional elements, such as phosphorus (P), sulfur (S), iron (Fe), magnesium (Mg), sodium (Na), chlorine (Cl), potassium (K), iodine (I) and calcium (Ca).
The following is a brief outline of the major chemical compounds of living systems; please refer to your recommended textbook for more information, illustrations and structural formulas.
I. Carbohydrates: Compounds containing carbon (C), hydrogen (H) and oxygen (O); the H and O atoms typically occur in a 2:1 ratio.
A. Sugars: Relatively small carbohydrate molecules composed of one or two sugar subunits (monomers).
|
5. True Gums: Complex polysaccharides composed of sugars other than glucose (primarily arabinose, fucose, galactose, mannose, rhamnose and xylose). Many different species of plants in a variety of families produce sticky saps composed of gums. These chemicals presumably seal off wounds and help to protect the plant from bacterial and fungal infections. The resinous pitch of conifers, such as pines (Pinus), also retards the boring larvae of bark beetles, but this is a terpene compound and not a gum. True carbohydrate gums are an entirely different class of chemicals from pine pitch (raw turpentine), gum mastic, gum guaiac and the chicle gum used in chewing gums. The latter chemicals are terpene derivatives which will be discussed later in this outline. Eucalyptus gums (gum kino) are chemically related to yet another group of plant chemicals called phenolic compounds. True plant gums are polysaccharides composed of many sugar subunits linked together. Unlike chicle gum, true gums are soluble in water. In fact, water-soluble plant gums are commonly used as thickening agents and emulsifiers, such as guar gum and gum tragacanth. Guar gum comes from the powdered seeds of Cyamopsis tetragonolubus, a herbaceous perennial legume from Africa. It is used in ice creams to prevent the formation of ice crystals by absorbing water. Guar gum comes from the powdered seeds of Cyamopsis tetragonolubus, a herbaceous perennial legume from Africa. It is used in ice creams to prevent the formation of ice crystals by absorbing water. Powdered guar gum is also a key ingredient in a process called fracking, which is used to extract natural and shale gas from beneath the earth's surface. Guar gum powder has unique binding, thickening and emulsifying qualities which make it ideal for fracking. Gum tragacanth is considered one of the world's best natural plant gums. It comes from the sap of several species of spiny, shrubby, Middle Eastern locoweeds of the genus Astragalus, including A. gummifer. It was largely imported from the Zagros Mountains of Iran, when the United States was on better diplomatic terms with that nation. Locust bean gum, a thickening agent in ice creams and salad dressings, comes from the ground seeds of the carob tree (Ceratonia siliqua). Another valuable plant gum is gum arabic, obtained from the spiny, shrubby Acacia senegal of northeastern Africa. In addition to its use in foods, hand lotions and soaps, it is used in fine water colors, inks and confections. It also produces the water-soluble adhesive on postage stamps and the "lace curtain" on the sides of your beer glass. Plant gums also provide the soluble fiber in a healthy diet by absorbing water and adding bulk to the large intestine. Several dietary supplements contain the powdered husks of psyllium seeds from Plantago ovata (Plantaginaceae). Insoluble fiber comes from the indigestible cellulose cell walls of fruits and vegetables. Both types of fiber are beneficial in maintaining a healthy colon, particularly in older adults with diverticulosis.
Another polysaccharide gum used as a water soluble thickening agent, binder, and emulsifier in foods and cosmetics is xanthan gum. This natural gum is produced by fermenting corn sugar with the bacteria Xanthomonas campestris. The bacteria produce xanthan as part of their cell walls. Like starch and cellulose, xanthan gum is a long chain polysaccharide composed of many sugar subunits. Xanthan gum has the consistency of corn starch but is undigestible like cellulose. It is used in many food products, including salad dressings and low cholesterol egg substitutes made from egg whites and vegetable gums. 
The ability of polar water molecules to form hydrogen bonds explains water's remarkable "magnetic" properties which are absolutely vital for life on earth. In addition to the swelling and bursting of seed coats prior to germination, cohesive water molecules form continuous chains from the roots to the leaves of trees hundreds of feet above the ground. Without this strong force of attraction between adjacent water molecules, water could never rise in tall stems, and plant life on earth would be limited to low-growing species like mosses and liverworts. Because of its polarity, water is a very stable substance and tends to remain a liquid rather than changing into steam as in other liquids. Frozen water is lighter and floats, thus insulating the deeper water of lakes and ponds from freezing solid. Without this important attribute, aquatic animals living in lakes and ponds in cold climates could never survive the severe winter months. And because of its polarity, water is a universal solvent essential for the myriad of biochemical reactions necessary for life. Alginates, carrageenans and agars are hydrophilic (water-loving) polysaccharides closely related to gums. In fact, they are treated here under the category of carbohydrate gums. Like gums, they absorb water and are used as thickening agents, emulsifiers and to prevent the formation of ice crystals in frozen deserts. They are also referred to as phycocolloids because they all come from algae (phyco) and they form jelly-like, colloidal suspensions in water. Alginates (also called algin) are obtained from species of Laminaria and another macroscopic brown algae called giant bladder kelp (Macrocystis pyrifera) that grows along the coast of southern California. In some fast food restaurants, shakes without the word "milk" were thickened with algin. For this reason they were called shakes rather than milk shakes. Algin colored with various dyes is also the source of the "fruits" in some fruitcakes. [Artificial candied "fruits" are also made from gelatin.] Carrageenans are extracted from a red alga called Irish moss (Chondrus crispus). Agar is another phycocolloid obtained from several red algae genera, including Gelidium and Gracilaria. Chemically, agar is similar to carrageenan, except that it has the superior quality of forming stiff gels in smaller concentrations. Agar gels have a superior capacity for changing into a liquid when heated, and then readily cooling back into a gel. They are unsurpassed for nutrient media used for tissue culture and in bacteriology (microbiology). Note: the animal counterpart to plant gums and phycocolloids is gelatin, a heterogeneous mixture of water-soluble proteins. Gelatin is a thickening agent or hydrogel derived from denatured collagen protein in fibrous animal connective tissue, and is the key ingredient in Jello® desserts. It is not found in nature but is derived chemically from collagen. Its thermoreversibility properties allow gelatin to change from a liquid state to a gel as it cools. Gelatin is obtained by boiling skin, tendons, ligaments and bones with water. Gelatin from cattle bones and hides is used primarily in photographic and pharmaceutical applications, while pork skin is the most significant raw material for edible food-grade gelatin. Some of the uses for gelatin include Gummi Bears, Gummi Worms, soft caramels and other chewy confections. Gelatin also provides the elasticity and chewy consistency of marshmallows. Prior to the use of gelatin in the early 1800s, the precursor of modern-day marshmallows was thickened with the mucilaginous sap from the root of the European marsh mallow (Althaea officinalis), a hollyhock relative in the mallow family (Malvaceae). It should be noted here that Jello® is not recommended with the following fresh or frozen fruits and roots: pineapple (Bromeliaceae: Ananas comosus), papaya (Caricaceae: Carica papaya), figs (Moraceae: Ficus carica), guava (Myrtaceae: Psidium guajava), kiwi (Actinidiaceae: Actinidia chinensis), and ginger root (Zingiberaceae: Zingiber officinale). All of these plants contain proteolytic enzymes which prevent the gelatin from setting (changing into a gel state) as it cools. Some of these protease enzymes have been used medicinally and as meat tenderizers, such as ficin from figs (Ficus), papain from papaya (Carica), and bromelain from pineapples (Ananas). Try adding some pineapple juice to milk. The milk protein begins to coagulate and degrade as it reacts with the bromelain. Pineapple juice will also remove the gelatin-emulsion surface on black & white photographic film. [The emulsion surface contains light sensitive silver halides in a gelatin that is rinsed away during processing. The silver that remains on the film emulsion reveals the negative image from which the photographic print is created.] In French Polynesia, the ficin-rich sap from a native banyan fig is used to kill parasitic worms and to treat worts and skin cancers. Ficin also breaks down the female pollinator wasp inside wasp-pollinated Calimyrna figs grown in California's Central Valley. When you eat one of these delicious figs, you won't find the wasp inside that was responsible for the seed formation and superior nutty flavor. Note: Finger nails, horn, hair, wool, claws, beaks, scales, and feathers are composed of hard keratin. Soft keratin or pseudokeratin includes dead skin epidermal tissue and whalebone. Keratin is a fibrous protein with a high percentage of the amino acid cystine. Unlike other proteins, including collagen of connective tissue, tendons and cartilage, keratin is resistant to hydrolysis by most solvents (including weak acids and bases), and by proteolytic enzymes of the gastrointestinal tract. The stability of keratin is due to numerous primary disulfide (-S-S-) cross-linkages within the molecule and secondary hydrogen bonding between neighboring polypeptide chains. Keratoses are horny, wartlike, keratinized growths on the skin often associated with the precusors of certain skin cancers, such as basal cell carcinomas. |
II. Lipids: A large group of chemicals that are generally insoluble in polar solutions such as water, but soluble in nonpolar solvents such as alcohol. Note: Some of the chemical groups included in this outline, such as terpene steroids and carotenoids, are classified as lipids in general biology textbooks.
Glycerol + Three Fatty Acids = A Fat Molecule (Triglyceride).
Any substance that lowers the LDLs and increases the HDLs tends to reduce the probability of plaque formation and a heart attack. Lowering the intake of saturated animal fats can reduce the total cholesterol level but does not alter the ratio of lipoproteins. Saturated fatty oils in tropical palms and hydrogenated oils in margarines can increase the amount of LDLs in the blood. At this time, the best type of fatty acids for a healthy balance of LDLs and HDLs are the monounsaturated fatty acids found in olive oil (Olea europea) and canola oil (Brassica napus).
Although castor oil is rather malodorous and distasteful, it is the source of several synthetic flower scents and fruit flavors (esters), such as jasmine, apricot, peach, plum, rose, banana and lemon. The chemicals (esters) responsible for these flavors and aromas are obtained from ricinoleic acid, one of the important ingredients of natural castor oil. In fact, ricinoleic acid comprises about 90% of the total triglyceride fatty acids of castor oil. Castor oil is also the primary raw material for the production of sebacic acid, which is the basic ingredient in the production of nylon and other synthetic resins and fibers. Approximately three tons of castor oil are necessary to produce one ton of nylon. Sebacic acid is a 10-carbon dicarboxylic acid with a carboxylic group (C-OOH) at each end of the molecule. It is reacted with 1,6-hexanediamine, a 6-carbon molecule with an amino group (C-NH2) at each end. The free carboxylic and amino ends of these molecules begin bonding together in a chain reaction called condensation polymerization, in which a water molecule is produced at each link. The resulting nylon polymer is called Nylon 6,10 to denote the 6-carbon diamine and 10-carbon sebacic acid. Linoleum, discovered in 1863 by Frederick Walton, is named after the flax plant (Linum) and oil (oleum). Oxidized linseed oil was mixed with ground cork and pigments, pressed onto a burlap or felt backing, and then baked. The tough, elastic, waterproof qualities of oxidized linseed oil gave linoleum its fine quality features.
|
III. Proteins: This is a huge group of macromolecules produced by plants and animals. Structural protein include collagen of fibrous connective tissue and skin, which constitutes about one third of the total protein of mammals, and keratin of nails, horn, hair, wool, claws, beaks, scales and feathers. Proteins are composed of long chains (polypeptides) of subunits called amino acids, with an average of about 400 or 500 amino acid molecules per protein. For example, the human red blood pigment hemoglobin contains 584 amino acids. Amino acids of living systems are the L-form optical isomer, in contrast to the D-form for sugars. There are 20 different amino acids in human protein, although many additional amino acids occur in nature. Eight of the 20 amino acids are called "essential" because they must come from a protein diet. The remaining 12 are called "nonessential" because they can be synthesized by cells. All the amino acids must be present to synthesize protein, if one or more are missing, the organism will eventually die from protein deficiency. Essential amino acids are to proteins as vowels are to words. If one or more vowels are missing, then words canot be spelled correctly and sentences become meaningless. For example, the short sentence "the man and boy are sad" is meaningless without vowels. If you take away the vowels, the sentence becomes "th mn nd b re sd" Although plants can synthesize all of their amino acids, the herbicide Roundup® blocks the synthesis of certain aromatic amino acids, thus gradually killing the plant.
The eight essential amino acids in human protein are: tryptophan, phenylalanine, lysine, threonine, valine, methionine, leucine, and isoleucine. The twelve nonessential amino acids in human protein are glycine, alanine, serine, cystine (cysteine), aspartic acid (aspartate), asparagine, glutamic acid (glutamate), glutamine, arginine, histidine, tyrosine, and proline. The essential amino acid lysine is deficient in grains, but is present in adequate levels in legumes. Likewise, the essential amino acid methionine is deficient in legumes, but is present in adequate levels in grains. If either of these two essential amino acids is missing from your diet, you may suffer from protein deficiency. Some general biology textbooks state that a vegetarian diet should include legumes, such as beans and peas from the legume family (Fabaceae), and grains, such as wheat and rice from the grass family (Poaceae). The problem with this statement is that the diet of preagricultural humans, evolving as it did from primate ancestors, consisted primarily of fruits, nuts, wild legumes, edible roots and tubers, and some meat. Not until about 10,000 years ago did cereal grains and legume crops become an important component of the human diet. This subject is summarized by G. Wadley & A. Martin (1993) in an article entiltled "The Origins of Agriculture--A Biological Perspective and a New Hypothesis," Australian Biologist 6: 96-105.
In the book Jurassic Park by Michael Crichton (1990), the dinosaurs on Isla Nublar (off the coast of Costa Rica) were genetically engineered to be "lysine dependent." All the dinosaurs received a mutant gene that produced a faulty enzyme in protein metabolism. As a result, they could not manufacture the amino acid lysine. Unless they received a rich dietary supplement of lysine they would die within days. This was a protective measure to prevent the dinosaurs from surviving in the real world. In the last chapter, some unknown animals were eating certain crops on the Costa Rica mainland. It turned out that the crops were agama beans and soy beans, two species of legumes rich in lysine. The book ended on this note, making you wonder if certain dinosaurs (perhaps velociraptors) had escaped and reached the mainland.
Amino acids are to proteins as letters are to words. An unabridged dictionary reveals the astonishing number of words that can be created with a 26 letter English alphabet, with most words less than 20 letters. Although human protein is constructed from a "20 letter" alphabet, the average protein "word" is made from hundreds of amino acid "letters," resulting in astronomical possibilities for different proteins. Some of the vital proteins in human systems are (1) Structural Proteins which comprise the body and its organs and tissues; (2) Enzymes which serve as vital catalysts in biochemical reactions; (3) Hormones such as the vital compound insulin that regulates the blood sugar level; and (4) Antibodies which serve to protect the body from renegade viruses and bacterial invasions. Proteins come in four main structural forms: (1) Primary: A straight chain of amino acids; (2) Secondary: A helical coil of amino acids stabilized by hydrogen bonds; (3) Tertiary: Folding and looping of a coiled polypeptide stabilized by hydrogen bonds; and (4) Quaternary: Four tertiary proteins joined together (e.g. hemoglobin). A molecule of hemoglobin is composed of four polypeptides, each with 146 amino acids, a grand total of 584. Heat or weak acid solutions can destroy the hydrogen bonding causing the tertiary proteins to uncoil, a condition termed denaturation. This is why vinegar (acetic acid) can actually "cook" an egg white (albumen) without heat. Proteins in raw fish called seviche (ceviche) are denatured by citric acid when the fish are marinated in lime or lemon juice. Hemotoxic proteins at the site of a rattlesnake bite can also be denatured by an electrical discharge from a device similar to a stun gun.
| Oversimplified diagram of the four main structural forms of protein: (1) Primary: A straight chain of amino acids; (2) Secondary: A helical coil of amino acids stabilized by hydrogen bonds; (3) Tertiary: Folding and looping of a coiled polypeptide stabilized by various types of bonds, including hydrogen bonds and disulfide bridges; and (4) Quaternary: Four tertiary proteins joined together. The various types of chemical bonds between loops and folds in the molecules are shown as short black lines. In the helical protein of hair, hydrogen bonds within individual helices of keratin, and disulfide bridges between adjacent helices, impart strength and elasticity to individual hairs. Water can disrupt the hydrogen bonds, making the hair limp. When the hair dries, new hydrogen bonding allows it to take on the shape of a curler. Permanent wave solutions induce new disulfide bridges between the helices. Genetically determined, natural curly hair also has a different arrangement of disulfide bridges compared with straight hair. |
For the sake of simplicity, let B stand for the gene that produces the normal beta polypeptide and B' stand for the mutant allele that produces the abnormal (mutant) form of the beta polypeptide. Normal homozygous people inherit two normal genes (BB) and have normal beta polypeptides in their hemoglobin molecule. Homozygous people suffering from sickle-cell anemia inherit two mutant genes (B'B') and have abnormal (mutant) beta polypeptides. Some people have the intermediate sickle-cell trait and are heterozygous BB'. These people have normal and abnormal beta polypeptides. Although their blood cells appear normal, they may become distorted under lower oxygen conditions, such as high elevation roads or in airplanes; therefore gene B is not completely dominant over gene B'. Some references (including your recommended text) refer to this condition as incomplete dominance.
Prions: Renegade Proteins That Cause Mad Cow Disease. Prions (pronounced PREE-ons) are disease-causing protein particles. They may be a mutated form of a brain protein with an abnormal (improper) tertiary structure. Prion diseases are referred to as spongiform encephalopathies because of the post mortem appearance of the brain with large vacuoles in the cortex and cerebellum. A number of diseases of animals may be caused by prions, including Scrapie (sheep), TME (Transmissible Mink Encephalopathy), CWN (Chronic Wasting Disease in muledeer and elk), and BSE (Bovine Spongiform Encephalopathy in cows). The latter condition is better known as Mad Cow Disease. There are also several human diseases attributed to prions including CJD (Creutzfeldt-Jacob Disease), FFI (Fatal Familial Insomnia), Kuru, and Alpers Syndrome.
Prions are thought by some researchers to be proteins with an abnormal tertiary structure. Exactly what causes this 3-dimensional protein to be folded improperly has been a topic of great speculation. Some earlier hypotheses stated that it was due to an incorrect amino acid sequence, but this may not be the case. The prion protein may interact with normal protein molecules, forcing them to fold abnormally. Over time, the improperly folded proteins increase in concentration and may destroy brain tissue. Prions reproduce without DNA or RNA. They replicate by interacting with other proteins in a chain reaction, thereby causing subsequent proteins to also fold improperly. The precise mechanism by which they multiply is unknown at this time, but they appear to work like a enzyme that catalyzes its own multiplication. Prions may be inherited, possibly by a recessive gene that shows up in homozygous recessive individuals. Or, they may be transmitted by eating infected brain tissue that has been ground up in animal feed or in hamburger and sausage. Muscle tissue contains nerve tissue and blood vessels; however, preliminary tests indicate that prions are confined to the brain and spinal cord of livestock. The bottom line here is that prions are renegade proteins that multiply and destroy the brains of livestock and people. They are not a bacterium or virus, and they are practically impossible to kill by conventional methods. In a sense they are "immortal molecules" that truly represent a serious threat to mammalian life forms.
Glycoproteins (protein plus carbohydrate) are complex polypeptides (amino acid chains) plus polysaccharide chains. They include a number of large molecules in living systems, including membrane proteins that provide cell recognition. Patrolling white blood cells called T-cells can recognize "self" versus "alien" cells by these special membrane proteins. Glycoproteins also include blood cell antigens and antibodies. They are also involved in pollen grain recognition on the receptive stigmas of the same or different species.
Immunotoxins are conjugated proteins consisting of monoclonal antibodies (made from another animal) with an attached protein toxin called a lectin. For example, the deadly lectin from the castor bean (called ricin) is joined to special antibodies against a specific type of cancer. Like armed, molecular missiles, the antibodies carry the deadly ricin directly to the tumor, thus killing the tumor cells without affecting other mitotic cells in the patient. See the following references for more information about lectins and the anti-tumor uses of castor beans.
The Deadliest Seeds On Earth |
In 1978, a Bulgarian dissident, Georgi Markov, was assasinated in London after being pricked by a ricin-tipped umbrella. Ricin causes a slow and painful death through blood poisoning and a breakdown of the circulatory system. There is no known antidote for ricin poisoning. Even before the tragic terrorist plane crashes into the Trade Center Twin Towers in New York, some airports hand-inspected umbrellas packed in carry-on luggage. Following the Gulf War, UN investigator teams (UNSCOM) discovered that Iraq was purifying ricin for possible use in biological warfare, along with anthrax (Bacillus anthracis), botulism toxin (Clostridium botulinum), gas gangrene (C. perfringens), and aflatoxin (Aspergillus parasiticus). From: Facts on File News Services (23 January and 13 February 1998).
According to The Washington Post Online (16 November 2001), Osama bin Ladens's Al-Qaeda network also had working plans for making ricin. Instructions for preparing the poison were found in the cellar of an abandoned house once used as a terrorist training center. According to the article, the ricin may be ingested, injected and inhaled. The article also states that the laxative effect of castor oil is due to ricin, but this is doubtful. Castor oil is derived from the seeds of the castor bean. It contains 87 percent ricinoleic acid, a fatty acid with many industrial uses, along with small amounts of several other fatty acids including oleic (7%), linoleic (3%), palmitic (2%) and stearic (1%). The deadly protein ricin is not a component of purified castor oil.
Although they are not proteins, some respiratory pigments called porphyrins, such as the heme component of the red blood cell pigment hemoglobin, are associated with polypeptides. Porphyrins contain a complex nitrogenous ring with a metallic atom (iron, magnesium or copper) in the center. Porphyrins are included here because of their similarity to the heme component of the protein hemoglobin. Chlorophylls a & b are certainly the most common and conspicuous pigments in our visible world. They are magnesium porphyrins with the following empirical formulas:
Chlorophyll a: C55H72O5N4Mg Chorophyll b: C55H70O6N4Mg
|
Iron porphyrin (heme) compared with magnesium porphyrin of chlorophyll.
|
IV. Nucleic Acids: This class of compounds includes the genetic material DNA (deoxyribonucleic acid), largest of the biomolecules, and RNA (ribonucleic acid), a smaller nucleic acid made from a section of DNA called a gene. Two main types of RNA are made in the nucleus of a cell, including messenger RNA (M-RNA) and transfer RNA (T-RNA). A third type called ribosomal RNA is made in the nucleolus of the nucleus. All three types of RNA are involved in protein synthesis. M-RNA molecules are made from sections of DNA in the nucleus, a process called transcription. The M-RNA strands are essentially complementary copies from one side of the DNA ladder after it has separated or "unzipped."
Completed M-RNA molecules then leave the nucleus and travel to organelles in the cytoplasm called ribosomes (made of ribosomal RNA). Smaller T-RNA molecules attach to specific amino acids in the cytoplasm and bring them to the ribosomes where they join with precise base triplets called codons along the M-RNA strand, a process called translation. A complementary base triplet on each T-RNA called the anticodon joins with the codon of M-RNA (e.g. the anticodon AUG joins with the codon UAC). Different T-RNA molecules carry different amino acids, depending on their anticodons. Since there are 64 different codons (4X4X4) and only 20 different amino acids (in human protein), some codons of M-RNA stand for the same amino acid. [E.g. the codons UUA, UUG, CUU, CUC, CUA and CUG all stand for the amino acid leucine.] As each amino acid is linked to the growing polypeptide, a molecule of water is released, a chemical reaction called dehydration synthesis. The completed polypeptides become vital proteins, such as enzymes, antibodies or structural proteins of muscles, blood vessels and other tissues. This remarkable process is essentially the same in all animals as well as in plants.
A transparent-green solution of chlorophyll is made by grinding up spinach or grass leaves in acetone (in a mortar and pestle), and then filtering it through cheesecloth and course filter paper. If a bright beam of light is directed at this chlorophyll solution, a deep red glow is emitted from the test tube. The chlorophyll electrons become excited by the light energy, but have no cytochrome transport system to flow along because the chloroplast thylakoid membranes have been dissolved away. Therefore, the chlorophyll electrons give up their excited energy state by releasing energy in the form of a reddish glow. This phenomenon is known as fluorescence, and is essentially the same principle as a neon light. In a neon light, the electrons of neon gas become excited and then release their energy of activation as a white glow inside the glass tube. In an intact chloroplast with thylakoid membranes, ATP is generated by an electron flow along the cytochrome transport system. Since the electrons are being transported to other "carrier" molecules, their energy is used to generate ATP and no reddish glow is emitted. Leaves generally appear green because wavelengths of light from the red and blue regions of the visible spectrum are necessary to excite the chloroplast electrons, and unused green light is reflected. Thus, we perceive trees, shrubs and grasses as green. During the fall months when chlorophyll production ceases in deciduous trees and shrubs, the leaves turn golden yellow or red due to the presence of other pigments, such as yellow and orange carotenoids and bright red anthocyanins.
Another important ingredient for photosynthesis is also produced during the light reactions. During these light-dependent reactions of photosynthesis, a chemical called NADP picks up two hydrogen atoms from water molecules forming NADPH2, a powerful reducing agent that is used to convert carbon dioxide into glucose during the dark reactions of photosynthesis (also called the Calvin Cycle). When the two atoms of hydrogen join with NADP, oxygen is liberated, and this is the source of oxygen gas in our atmosphere. ATP and NADPH2from the light reactions are used in the dark reactions of photosynthesis that take place in the stroma region of the chloroplast.
Archaebacteria: Possible Life Form On Mars? |
V. Terpenes: An enormous group of plant hydrocarbons formed by the polymerization of 5-carbon isoprene (C5H8) subunits. Terpenes are one of the largest and most varied group of plant chemicals. They may contain carbon chains and rings in different structural forms called isomers. They may also be reduced and oxidized into a vast array of compounds, including alcohols, ketones, acids and fragrant aldehydes. There are five main types of terpenes, including 10-carbon monoterpenes (2 isoprenes), 15-carbon sesquiterpenes (3 isoprenes), 20-carbon diterpenes (4 isoprenes), 30-carbon triterpenes (6 isoprenes) and 40 carbon tetraterpenes (8 isoprenes). Terpene chemicals present in the resinous foliage and fallen leaves of chaparral shrubs inhibit germination of nearby wildflower seeds, a phenomenon known as allelopathy. This explains the abundance of wildflowers in recently cleared chaparral that has not burned. It has also been shown that the burned remains of shrubs greatly stimulate the germination of certain seeds. The developing wildflowers thrive in the ash and often grow much more vigorously than in soil without ash. There are also allelopathic phenolic compounds.
One of the most famous poisonous terpenes may have affected the creativity of Vincent van Gogh. The terpenoid compound thujone is composed of several volatile monoterpenes found in the resins of several species of cone-bearing species in the cypress family (Cupressaceae). The resins of conifers (especially the monoterpenes) are the primary defensive mechanism against the ravaging effects of bark beetles. Thujone is also found in the sap of wormwood (Artemisia absinthium), a European shrub related to our North American sagebrushes. Wormwood oil derived from A. absinthium was the principal flavoring of absinthe liqueur, an alcoholic beverage that was taken regularly by van Gogh. Ingested repeatedly, absinthe can cause dramatic personality changes and may have affected van Gogh's creativity and fondness for the color yellow. See the link below for more information
 |  |
|
A. Essential Oils Smaller, monoterpenes and sesquiterpenes that are volatile at room temperature. They occur in leaves, flowers and fruits, often imparting a distinctive odor and flavor. Note: Some essential oils include phenolic compounds and terpene-phenolic derivatives. Phenolic compounds typically contain one or more benzene rings with one or more hydroxyl groups (C-OH) attached to the rings. Essential oils serve several functions in plants, such as repelling fungi and harmful insects, and the sweet fragrances of flowers that attract insect pollinators. The 10-carbon monoterpene limonene is enantiomorphic and occurs in two mirror image forms called stereoisomers. Fragrant D-limonene found in citrus peels is an effective insect repellant and insecticide. Known as "orange oil" it is readily absorbed into wood and is used to exterminate dry wood termites. It is much safer than methyl bromide gas and doesn't require the tenting and evacuation of houses. It is a good solvent for grease and is a common ingredient of orange-scented hand soaps and cleaners. Lemon oil from the rind of lemons is approximately 90 percent D-limonene. In contrast to the citrus scent of D-limonene, the enantiomer L-limonene has a piney, turpentine-like odor. It occurs naturally in essential oils of pine and other conifers, certain herbs (e.g. peppermint and spearmint), and as a minor component of raw turpentine.
Some resins are referred to as gums, but they are chemically very different. True gums are complex polysaccharides composed of many sugar subunits. Although the sap of the mastic tree (P. lentiscus) is called a gum, it is really an oleoresin used in perfumes, chewing gums, pharmaceuticals, dental adhesives, and in high grade varnishes for protecting pictures. Gum mastic is one of the oldest known high grade resins utilized by people, and it is extensively cultivated on the Greek island of Chios. Gum guaiac is another famous resin from a Caribbean tree called lignum vitae (Guaiacum officinale), one of the world's hardest and heaviest woods. A similar species (G. sanctum) is native to the Florida Keys. Both species are members of the caltrop family (Zygophyllaceae) along with North and South American creosote bush and the ubiquitous puncture vine (Tribulus terrestris). The name lignum vitae means "wood of life," owing to the medicinal properties of the heavy, resinous wood. During the days of masted sailing ships, the wood and sweet-smelling resin globs were sought after for treatments and cures for a variety of human ailments, including gout, syphilis and rheumatism. Today the resin is still used for expectorants and as a dye to detect the presence of occult (hidden) blood. Peroxidase enzymes in the blood cells oxidize chemicals in the resin resulting in a characteristic blue-green color change. The raw resin contains about 15 percent vanillin (artificial vanilla), resulting in the sweet aroma. The density and high resin content of the wood make it extremely resistant to friction and abrasion and account for its remarkable self-lubrication properties. In fact, under certain conditions the wood wears better than iron. Because of this, the wood has been highly valued for pulley sheaves, bearings, casters, food-handling machinery, and especially for end grain thrust blocks which once lined the propeller shafts of steamships. During World War I, attempts were made to use other ironwoods such as Tabebuia guayacan from Central America for propeller shaft bearings, but the wood lacked the oily resin of lignum vitae.
 
Ripe tomatoes are particularly rich in the carotenoid lycopene (C40H56). In addition to imparting the bright red color to tomatoes, 40 milligrams of lycopene ingested daily may reduce the risk of atherosclerosis (clogged arteries) and heart disease. Lycopene may also reduce the risk of certain cancers, including cancers of the prostate, lung, bladder, cervix, skin and digestive tract. According to Dr. A.V. Rao (Experimental Biology and Medicine 227 (10): 908-913, 2002), lycopene is an antioxidant that prevents the oxidation of low density lipoproteins (LDLs). High LDL oxidation is associated with increased risk of atherosclerosis and coronary heart disease. According to the Merck Index (1983), one kilogram (2.2 pounds) of fresh tomatoes yields 20 milligrams of lycopene. To obtain 40 milligrams of lycopene, you would need to eat about eight medium-sized tomatoes (or four large tomatoes) every day. Apparently lycopene is absorbed more readily in the processed form, such as tomato paste and juices. Several on-line references recommended drinking two glasses of tomato juice every day. Perhaps it is also wise to eat plenty of tomato soup, stewed tomatoes and tomato sauce on pasta and pizzas. Intact pollen grains have been extracted from sedimentary strata that is millions of years old, and from animal exrement that has passed through a digestive system. The perfectly preserved pollen grains still retain the distinctive grooves and ornamentation in the outer exine layer. The chemical composition of exine is different from the siliceous shells of microscopic diatoms and grass phytoliths found in fossilized dinosaur dung. It also different from the chitinous exoskeletons of arthropods and the calcareous shells of mollusks. The exine layer is composed of a tough biopolymer called sporopollenin. Although it contains only carbon, hydrogen and oxygen, it is different from carbohydrate polymers such as starch and cellulose. In fact, it is one of the most stable organic compounds known. It has been extracted from plant spores using strong acid and alkali solutions that would disintegrate other substances. Although its structure is not completely understood, some scientists describe sporopollenin as "polycarotenoid in character." |
Langenheim, J.H. 2003. Plant Resins (Chemistry, Evolution, Ecology andFor further details log on website :
http://waynesword.palomar.edu/chemid1.htm
No comments:
Post a Comment