LESSON NOTES
Subject: Biological Science
Teacher: Helen Boon
Date: Wednesday 11th May 2005
CHEMICALS IN CELLS
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.
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A. Sugars: Relatively small carbohydrate molecules composed of one or two sugar subunits (monomers).
B. Polysaccharides: Complex carbohydrates composed of many 6-carbon sugar subunits (monomers) joined together by dehydration synthesis. Depending on the polysaccharide, the sugar subunits may consist of complex chains of glucose molecules or other 6-carbon monosaccharides.
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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.
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A. Fats & Oils: Plant oils are typically composed of triglyceride molecules (technically called esters) composed of a 3-carbon alcohol (glycerol) plus three 18-carbon (or 16-carbon) fatty acids. Fatty acids are long, linear hydrocarbon chains containing 12 to 24 carbon atoms. One end of the molecule contains a carboxylic acid group (COOH) from which chemists count the number of carbon atoms. The other end is the methyl or omega end from which nutritionists and biochemists count the position of the first bond. The location of the first double bond determines whether the fatty acid is an omega-6 or an omega-3 fatty acid. Unlike the saturated fatty acids of animal fats which are solid at room temperature, plant fatty acids are typically unsaturated and liquid at room temperature, with one or more double bonds between the carbon atoms (mono-unsaturated and polyunsaturated). [Note: The palm fatty acid palmitin is saturated and contains 16 rather than 18 carbon atoms.] Examples of unsaturated plant oils include safflower, soybean, sunflower, corn, sesame, cottonseed and canola. The degree of unsaturation is measured by allowing iodine to combine with a standard amount of a particular oil. Iodine ions are incorporated into the oil's fatty acid chains at positions where there were double bonds. Of the examples of unsaturated plant oils listed earlier in this paragraph, safflower oil has the highest iodine value of 140-150. Linseed oil, a polyunsaturated drying oil used in the paint industry, has an iodine value of 165-204. In order for unsaturated oils (such as the corn and soybean oils in margarines) to be solid at room temperature, they must be hydrogenated under heat and pressure, a process that some natural food enthusiasts find deplorable. The following table shows the structure of a typical plant fat molecule (triglyceride) composed of glycerol plus 3 fatty acids. Since it contains unsaturated fatty acids, it is liquid at room temperature and is often referred to as an oil. The fatty acids may be saturated (with all single bonds), mono-unsaturated (with one double bond) or polyunsaturated (with 2 or more double bonds): There is evidence that a diet high in saturated animal and palm fats may be correlated with high levels of blood cholesterol and fatty deposition in the blood vessels, a serious condition known as atherosclerosis. [Omega-3 fatty acids prevalent in fish oils may actually help to reduce levels of LDLs in the blood and lower the risk of atherosclerosis.] Diets rich in polyunsaturated oils have be correlated with an increased risk of certain cancers because of highly reactive carbon fragments from the breakdown of fatty acids. These carbon fragments have unpaired electrons and are powerful oxidizing agents known as free radicals. In oil base paints, unsaturated oils, such as castor and linseed oils, allow the paint to oxidize readily in the air, forming a dry, elastic, waterproof coating. A typical fat molecule has an empirical formula of C57H110O6. Notice that the ratio of H and O atoms is not 2:1 as in carbohydrates.
When polyunsaturated vegetable oils are partially hydrogenated to improve their texture, trans fatty acids are produced. Trans fatty acids tend to raise the level of low density lipoproteins (bad LDLs) and lower the level of high density lipoproteins (good HDLs). These changes in blood lipids (cholesterol levels) may increase the risk of heart disease (atherosclerosis) in some people. Dieticians generally recommend the use of mono-unsaturated, unhydrogenated oils such as canola or olive oil whenever possible, and the avoidance of trans fatty acids found in french fries, donuts, chips, cookies and crackers. Omega-3 and Omega-6 Fatty Acids In the above illustration, the first double bond is located on carbon #6, counting backwards from right to left. [The first carbon is at the end opposite the carboxylic or COOH group.] Therefore, this is an omega-6 fatty acid. Unsaturated fatty acids found in plant oils and seeds are typically omega-6 fatty acids. In omega-3 fatty acids, the first double bond in on carbon #3, counting back from right to left on the above illustration. Omega-3 fatty acids are prevalent in fish oils and flax seeds (Linum usitatissimum).
Some of the most important seed oils used for food are olive oil (Olea europea), mustard oil (Brassica spp., incl. B. nigra), canola oil (B. napus), corn oil (Zea mays), soybean oil (Glycine max), peanut oil (Arachis hypogea), cottonseed oil (Gossypium species), safflower oil (Carthamus tinctorius), sunflower oil (Helianthus annuus) and sesame oil (Sesamum indicum). With the exception of olives, all of these oils are extracted entirely from the seeds. Olive oil is expressed from the seed and the fruit wall or pericarp. Oils used for food and industrial purposes include coconut oil (Cocos nucifera), palm oil from the African oil palm (Elaeis guineensis), castor oil (Ricinus communis), tung oil (Aleurites fordii), candlenut or kukui-nut oil (A. moluccana) and linseed oil (Linum usitatissimum). 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. B. Waxes: Complex lipids composed of a long-chain alcohol (longer than glycerol) plus many fatty acids (more than 3 as in fats & oils). Waxes tend to be solid at room temperature and provide a durable, protective covering for plants and animals. Examples of waxes include the cuticle of leaves (waxy covering over leaf surface); waxy coating on fruits (e.g. apples); beeswax (hexagonal cells of honeycomb); lanolin (waxy layer secreted onto wool of sheep); and, of course, ear wax.
C. Phospholipids: Important lipids found in the cell membranes of plants and animals. Their structure is similar to that of a fat molecule, except that a polar (hydrophilic) phosphate group (PO4) replaces the third fatty acid. Because of their unique bipolar structure, phospholipids form a double lipid layer (bilayer) in cell membranes (sandwiched between two layers of protein) that is permeable to water molecules. This "sandwich structure" provides the vital interface between the interior and exterior of cells that is permeable to water molecules. D. Steroids: A complex group of compounds with the same backbone structure of four fused carbon rings (see hyperlink at end of this paragraph). In botany textbooks they are referred to as terpene derivatives, and perhaps are better treated under the terpene category. [In fact, use the terpene category for plant steroids on Botany 115 Exam #2.] Steroids include vital animal compounds, including cholesterol, cortisone, and the sex hormones estrogen, progesterone and testosterone. Vitamin D and bile salts used for fat digestion are synthesized from cholesterol. Steroids are also common in plants, including diosgenin in the tubers of certain yams of the genus Dioscorea. In fact, diosgenin is used as the steroid precursor for synthetic sex hormones used in birth control pills. Steroidal glycosides (molecules containing a steroid plus sugar) are toxic to some vertebrates, including people. They are synthesized by many flowering plants, including milkweeds of the genus Asclepias. They are taken up by the larvae of monarch butterflies who feed extensively on milkweeds. When the caterpillars metamorphose into butterflies, the stored glycosides make them toxic to birds who learn to avoid these brightly colored insects.
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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.
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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. |
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.
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 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
According to The Washington Post Online (16 November 2001), Osama bin Ladens's al-Qaida 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:
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Chlorophyll a: C55H72O5N4Mg Chorophyll b: C55H70O6N4Mg |
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. 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.
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."
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 like a high capacity storage disk (DVD disk), while genes are like 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 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.
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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.
What
is the surface area: volume ratio?i. Nucleus
ii. Cytoplasm
iii. Flagellum
iv. Plasma Membrane
v. Vacuole
vi. Microvilli
vii. Mitochondria
viii. Cell wall
ix. Ribosomes
x. Nucleolus
xi. Endoplasmic Reticulum
xii. Chloroplast
xiii. Golgi Complex
xiv. Lysosomes
10. For each of the organelles listed above describe what it looks like and what it does in cells.
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E.G. NUCLEUS
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Directs cell processes by signaling the production of various proteins. Involved in cell reproduction – contains the genes |
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