Leslie Ann Labuga BSN 1A

11-11-08

ANATOMY @ PHYSIOLOGY
Assignment: ORGANIC COMPOUND-THE BASIS OF LIFE 1. Differentiate carbohydrates, lipids, and proteins: give their basic structural attribution. Answer; Carbohydrates (from 'hydrates of carbon') or saccharides (Greek , skcharon, meaning "sugar") are the most abundant of the four major classes of biomolecules. They fill numerous roles in living things, such as the storage and transport of energy (starch, glycogen) and structural components (cellulose in plants, chitin in animals). Additionally, carbohydrates and their derivatives play major roles in the working process of the immune system, fertilization, pathogenesis, blood clotting, and development. Chemically, carbohydrates are simple organic compounds that are aldehydes or ketones with many hydroxyl groups added, usually one on each carbon atom that is not part of the aldehyde or ketone functional group. The basic carbohydrate units are called monosaccharides, such as glucose, galactose, and fructose. The general stoichiometric formula of an unmodified monosaccharide is (CH O) , where n is any number of three or greater; however, the use of this word does not follow this exact definition and many molecules with formulae that differ slightly from this are still called carbohydrates, and others that possess formulae agreeing with this general rule are not called carbohydrates (eg formaldehyde).
2 n

Monosaccharides can be linked together into what are called polysaccharides (or oligosaccharides) in almost limitless ways. Many carbohydrates contain one or more modified monosaccharide units that have had one or more groups replaced or removed. For example, deoxyribose, a component of DNA, is a modified version of ribose; chitin is composed of repeating units of N-acetylglucosamine, a nitrogen-containing form of glucose. The names of carbohydrates often end in the suffix -ose. *karbo-hi drat = organic compound compose of carbon, hydrogen, and oxygen includes; starch, sugars, cellulose. Lipids are broadly defined as any fat-soluble (lipophilic), naturally-occurring molecule, such as fats, oils, waxes, cholesterol, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The main biological functions of lipids include energy storage, acting as structural components of cell membranes, and participating as important signaling molecules. Although the term lipid is sometimes used as a synonym for fats, fats are a subgroup of lipids called triglycerides and should not be confused with the term fatty acid. Lipids also encompass molecules such as fatty acids and their derivatives (including tri-, di-, and monoglycerides and phospholipids), as well as other sterol-containing metabolites such as cholesterol.The emulsion test is a crude method for determining the presence or absence of lipids in a given sample. Lipids are a diverse group of compounds that have many key biological functions, such as structural components of cell membranes, energy storage sources and intermediates in signaling pathways. Lipids may be broadly defined as hydrophobic or amphiphilic small molecules that originate entirely or in part from two distinct types of biochemical subunits or "building blocks": ketoacyl and isoprene groups. Using this approach, lipids may be divided into eight categories : fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, saccharolipids and polyketides (derived from condensation of ketoacyl subunits); and sterol lipids and prenol lipids (derived from condensation of isoprene subunits).

*lipid = organic compound form of carbon, hydrogen, and oxygen examples are fats and cholesterol. Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by a gene and encoded in the genetic code. Although this genetic code specifies 20 "standard" amino acids plus selenocysteine and - in certain archaea - pyrrolysine, the residues in a protein are sometimes chemically altered in post-translational modification. This can happen either before the protein is used in the cell, or as part of control mechanisms. Proteins can also work together to achieve a particular function, and they often associate to form stable complexes. Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in every process within cells. Many proteins are enzymes that catalyze biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. Proteins are also necessary in animals' diets, since animals cannot synthesize all the amino acids they need and must obtain essential amino acids from food. Through the process of digestion, animals break down ingested protein into free amino acids that are then used in metabolism. The word protein comes from the Greek word (proteios) "primary". Proteins were first described and named by the Swedish chemist Jns Jakob Berzelius in 1838. However, the central role of proteins in living organisms was not fully appreciated until 1926, when James B. Sumner showed that the enzyme urease was a protein.The first protein to be sequenced was insulin, by Frederick Sanger, who won the Nobel Prize for this achievement in 1958. The first protein structures to be solved included hemoglobin and myoglobin, by Max Perutz and Sir John Cowdery Kendrew, respectively, in 1958.The three-dimensional structures of both proteins were first determined by x-ray diffraction analysis; Perutz and Kendrew shared the 1962 Nobel Prize in Chemistry for these discoveries. *proten = a complex nitrogenous substance; the main building materials of cells. 2. Monosaccharides, disaccharides, and polysaccharides are carbohydrates; distinguish each of them and give example. Answer; Monosaccharides are the simplest carbohydrates in that they cannot be hydrolyzed to smaller carbohydrates. Monosaccharides are classified according to three different characteristics: the placement of its carbonyl group, the number of carbon atoms it contains, and its chiral handedness. If the carbonyl group is an aldehyde, the monosaccharide is an aldose; if the carbonyl group is a ketone, the monosaccharide is a ketose. Monosaccharides with three carbon atoms are called trioses, those with four are called tetroses, five are called pentoses, six are hexoses, and so on. These two systems of classification are often combined. For example, glucose is an aldohexose (a six-carbon aldehyde), ribose is an aldopentose (a five-carbon aldehyde), and fructose is a ketohexose (a six-carbon ketone). Each carbon atom bearing a hydroxyl group (-OH), with the exception of the first and last carbons, are asymmetric, making them stereocenters with two possible configurations each (R or S). Because of this asymmetry, a number of isomers may exist for any given monosaccharide formula. The aldohexose D-glucose, for example, has the formula (CH O) , of which all but two of its six carbons atoms are stereogenic, making D-glucose one of 2 = 16 possible stereoisomers. In the case of glyceraldehyde, an aldotriose, there is one pair of possible stereoisomers, which are enantiomers and epimers. 1,3-dihydroxyacetone, the ketose corresponding to the aldose glyceraldehyde, is a symmetric molecule with no stereocenters). The assignment of D or L is made according to the orientation of the asymmetric carbon furthest from the carbonyl group: in a standard Fischer projection if the hydroxyl group is on the right the molecule is a D sugar, otherwise it is an L sugar. Because D sugars are biologically far more common, the D is often omitted.
4 2 6

*Simple sugar that contain 3 to 7 carbon atoms.

Example: Glucose (main blood sugar), Fructose (found in fruits), Galactose(milk sugar), Deoxyribose( DNA), Ribose(RNA) Disaccharide is a sugar (a carbohydrate) composed of two monosaccharides. Example: Common disaccharides

Disaccharide

Unit 1

Unit 2

Bond

Sucrose (table sugar, cane sugar, saccharose, or beet sugar) glucose

fructose (12)

Lactose (milk sugar)

galactose glucose (14)

Maltose

glucose

glucose (14)

Trehalose

glucose

glucose (11)

Cellobiose

glucose

glucose (14)

Maltose and cellobiose are hydrolysis products of the polysaccharides, starch and cellulose, respectively. Less common disaccharides include:

Disaccharide

Units

Bond

Gentiobiose

two glucose monomers

(16)

Isomaltose

two glucose monomers

(16)

Kojibiose

two glucose monomers

(12)

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Laminaribiose two glucose monomers

(13)

Mannobiose

two mannose monomers

either (12), (13), (14), or (16)

Melibiose

a glucose monomer and a galactose monomer (16)

Nigerose

two glucose monomers

(13)

Rutinose

a rhamnose monomer and a glucose monomer (16)

Xylobiose

two xylopyranose monomers

(14)

Polysaccharides represent an important class of biological polymers. Their function in living organisms is usually either structure or storage related. Starch (a polymer of glucose) is used as a storage polysaccharide in plants, being found in the form of both amylose and the branched amylopectin. In animals, the structurally similar glucose polymer is the more densely branched glycogen, sometimes called 'animal starch'. Glycogen's properties allow it to be metabolized more quickly, which suits the active lives of moving animals. Cellulose and chitin are examples of structural polysaccharides. Cellulose is used in the cell walls of plants and other organisms, and is claimed to be the most abundant organic molecule on earth. It has many uses such as a significant role in the paper and textile industries, and is used as a feedstock for the production of rayon (via the viscose process), cellulose acetate, celluloid, and nitrocellulose. Chitin's structure has a similar structure, but has nitrogen containing side branches, increasing its strength. It is found in arthropod exoskeletons and in the cell walls of some fungi. It also has multiple uses, including surgical threads.Other polysaccharides include callose or laminarin, xylan, mannan, fucoidan, and galactomannan. 3. Define and familiarized yourself with the ff. processes involved in carbohydrate metabolism A. Glycolysis- breakdown of glucose to pyruvic acid. B. Krebs Cycle- eroxic pathways with the mitocondria in which energy is liberated during metabolism of carbohydrates, fats, amino acid, and CO is produced.
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C. Glycogenesis- syntesis of glycogen, pathway converts glucose into glycogen. D. Glycogenolysis- pathway breakdown glycogen into glucose. E. Gluconeogenesis- convertion of non-carbohydrate molecules (amino acid, lactic acid, glycerol) into glucose. 4. What is the importance of glucose in the body? How does the body store and release glucose to and from tissue? Answer: glucose is important in the body because it is the principal sugar in the blood, a monosaccharide. Glucose is a simple monosaccharide sugar and is used as a source of energy in animals and plants. Glucose is one of the smallest units which have the characteristics of this class of carbohydrates. The body digests carbohydrates in foods, transforming them into glucose, which serves as the primary fuel for the brain and muscles. Glucose is also

called blood sugar as it circulates in the blood at a concentration of 65-110 mg/mL of blood. The most common form of this sugar is called dextroglucose, commonly referred to as dextrose. Glucose is a monosaccharide containing six carbon atoms. Chemically joined together, glucose and fructose form sucrose. Starch, cellulose, and glycogen are common glucose polymers (polysaccharides). Glucose is the end product of carbohydrate metabolism and is the chief source of energy for living organisms. The human body converts most dietary carbohydrates into a substance called blood sugar or glucose. In respiration , through a series of enzyme-catalysed reactions, glucose is oxidized to eventually form carbon dioxide and water, yielding energy, mostly in the form of ATP. Glucose is one of the main products of photosynthesis and starts respiration. Blood glucose concentrations are kept within a relatively narrow range by such factors as hepatic and renal uptake and release, glucose removal by peripheral tissues, hormone influences on uptake and release, and intestinal absorption. The normal concentration of glucose in the blood is about 0.1%, but it becomes much higher in persons suffering from diabetes. Insulin is the main hormone that affects glucose blood levels. When glucose levels fall to hypoglycemic levels, cells cannot function normally, and symptoms develop such as nervousness, cool skin, headache, confusion, convulsions or coma.Glucose is found in the sap of plants, and is found in the human bloodstream , where it is referred to as "blood sugar". The only endogenous sources of glucose are the liver and kidneys which convert glucose-6-phosphate to glucose. Glucose is usually manufactured by hydrolysis of cornstarch with steam and dilute acid. Liquid glucose is known as corn syrup in the USA. The corn syrup thus obtained contains also some dextrins and maltose. When glucose is mixed with maple syrup, it is called pancake syrup. Industrially glucose is used in the manufacture of candy, chewing gum, jams, jellies, table syrups, and other foods, and for many other purposes. Glucose is most commonly used in confectionery to give elasticity to caramel or sugar piece and to help prevent crystallization. It can also be added to chocolate to produce a modeling paste. Glucose's role in metabolism Carbohydrates are the human body's key source of energy. Glucose is absorbed into the bloodstream through the intestinal wall. Only the monosaccharides glucose, fructose and galactose are absorbed in humans. Breakdown of carbohydrates yields mono- and disaccharides, most of which is glucose. Oxidation of glucose is known as glycolysis. Glucose is oxidized to either lactate or pyruvate. Two different pathways are involved in the metabolism of glucose: one anaerobic and one aerobic . The anaerobic process occurs in the cytoplasm and is only moderately efficient. The aerobic cycle takes place in the mitochondria and is results in the greatest release of energy. Under aerobic conditions, the dominant product in most tissues is pyruvate and the pathway is known as aerobic glycolysis. Through glycolysis, glucose is directly involved in the production of ATP, the cell's energy carrier. The NADH generated during glycolysis is used to fuel mitochondrial ATP synthesis via oxidative phosphorylation, producing either two or three equivalents of ATP depending upon whether the glycerol phosphate shuttle or the malate-aspartate shuttle is used to transport the electrons from cytoplasmic NADH into the mitochondria. Glucose is a major source of energy for most cells of the body. Some of glucose goes directly to fuel brain cells, while the rest makes its way to the liver and muscles, where it is stored as glycogen, and to fat cells, where it is stored as fat. Glycogen is the body's auxiliary energy source, tapped and converted back into glucose when it needs more energy. Although stored fat can also serve as a backup source of energy, it is never directly converted into glucose. The fructose and galactose are taken up by the liver, where they are converted into glucose. Glucose in the bloodstream diffuses into the cytoplasm and is locked there by phosphorylation. A glucose molecule is then rearranged slightly to fructose and phosphorylated again to fructose diphosphate. Glucose is vital to brain function. The brain requires that glucose concentrations in the blood remain within a certain range in order to function normally. Glucose metabolism is disturbed in depression, manic-depression, anorexia, and bulimia. In addition, Alzheimers patients, for instance, register much lower glucose levels than those with other forms of brain malfunction that resulted from stroke or other vascular disease.

5. Describe the different lipids in the body a. Fats - consist of a wide group of compounds that are generally soluble in organic solvents and largely insoluble in water. Chemically, fats are generally triesters of glycerol and fatty acids. Fats may be either solid or liquid at normal room temperature, depending on their structure and composition. Although the words "oils", "fats", and "lipids" are all used to refer to fats, "oils" is usually used to refer to fats that are liquids at normal room temperature, while "fats" is usually used to refer to fats that are solids at normal room temperature. "Lipids" is used to refer to both liquid and solid fats, along with other related substances. The word "oil" is used for any substance that does not mix with water and has a greasy feel, such as petroleum (or crude oil) and heating oil, regardless of its chemical structure.
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Fats form a category of lipid, distinguished from other lipids by their chemical structure and physical properties. This category of molecules is important for many forms of life, serving both structural and metabolic functions. They are an important part of the diet of most heterotrophs (including humans). Fats or lipids are broken down in the body by enzymes called lipases produced in the pancreas. Examples of edible animal fats are lard (pig fat), fish oil, and butter or ghee. They are obtained from fats in the milk, meat and under the skin of the animal. Examples of edible plant fats are peanut, soya bean, sunflower, sesame, coconut, olive, and vegetable oils. Margarine and vegetable shortening, which can be derived from the above oils, are used mainly for baking. B. Phospholipids major lipid component of cell membrane. C. Steroids are basically flat molecules form of four interlocking rings, thus their structure differs quite a bit from that of fats.like fats it is made largely of hydrogen and carbon atoms and are fat soluble. D.Prostaglandins - prostaglandin is any member of a group of lipid compounds that are derived enzymatically from fatty acids and have important functions in the animal body. Every prostaglandin contains 20 carbon atoms, including a 5-carbon ring. They are mediators and have a variety of strong physiological effects; although they are technically hormones, they are rarely classified as such. The prostaglandins together with the thromboxanes and prostacyclins form the prostanoid class of fatty acid derivatives; the prostanoid class is a subclass of eicosanoids. 6. What is the difference between the saturated and unsaturated fatty acid; what is their clinical significance? Answer: A saturated fatty acid is one in which all the carbons along the chain have two hydrogen molecules bonded to them, with the exception of the last carbon which has three hydrogen molecules attached (this is called the omega carbon), have no double bonds and are very rigid and hard, found in high amounts in things like butter, coconut oil, palm kernel oil and beef fat. Unsaturated fatty acid the formation of a double bond between two carbon molecules. Omega-6 vs. Omega-3 Over the past 100 years a dramatic change in our diet has occurred. We have invented an industry of prepared foods made in factories and shipped to consumers via supermarkets. With this invention, shelf-life became a premium. EFAs, on the other hand, kill shelf-life because they have a tendency to go rancid when exposed to heat, light and oxygen. At the same time, large commercial oil manufacturers began producing the refined vegetable oils we are now so familiar with. Currently, 4 oils (soybean, cottonseed, corn, and canola) account for 96% of the vegetable oil use in the U.S. The w6:w3 ratio of these combined oils is between 12:1 and 25:1. An estimate of the w6:w3 ratio in our diet 100 years ago is between 3:1 and 5:1. This dramatic shift toward w6 oil consumption, coupled with the alteration of the fats via hydrogenation and oxidation is thought to be one of the leading factors in the rise of chronic illnesses, especially cardiovascular diseases over the past century. Modern agricultural practices have a dramatic effect on the EFA ratios of animal products. For example, a free-range chicken egg has a w6:w3 ratio of 1.3, while a corn fed USDA chicken egg has a w6:w3 of 19.4 (1). To regain a balanced w6:w3 ratio in our diet is almost impossible without

supplementing our diets with high levels of w-3 containing oils such as flaxseed oil or concentrated fish oil supplements. Recommended levels of linoleic acid (omega-6 EFA) are 6-9 grams per day (3-5% of total calories) and alpha-linolenic acid (omega-3 EFA) are 4-6 grams per day (2-3% of total calories). Of course, therapeutic levels may exceed these several-fold with almost no toxicity known for these substances. Therapeutic use of Omega-3 fatty acids Therapeutic uses of the omega-3 essential fatty acid linolenic acid, and its derivatives EPA and DHA (usually from fish oil) have become more prevalent in the past several decades. Omega 3 fatty acids have been used therapeutically for cardiovascular diseases, hypertension, inflammatory and autoimmune disorders, cancer, diabetes and several lipid disorder/deficiency syndromes. Omega 3 and Cardiovascular Effects Recent interest in omega-3 fatty acids stems from the fatty acid profile and low rate of coronary heart disease discovered among Greenland Eskimos. While having a diet high in total fat, they consumed a high proportion of marine fats (seal, whale, and fish). These fats contain high amounts of the long chain, highly-unsaturated, omega-3 fatty acids (EPA and DHA), originally made by plankton and consumed by these marine animals. A current review has concluded that omega-3 fatty acids prevent heart disease through the following actions: Prevention of arrhythmias (ventricular tachycardia and fibrillation) formation of and competition against various prostaglandins and leukotrienes anti-inflammatory properties (partly by prostaglandin effect) antithrombotic effect hypolipidemic effect on triglycerides and VLDLs inhibition of atherosclerosis. We will briefly summarize some of the more important aspects of these activities. Induced cardiac arrhthymias, in both animal and cell culture studies, were halted by the administration of EPA and DHA. The mechanism seems to be related to the PUFAs ability to stabilize the membrane excitability of heart cells that leads to arrhthymia. While these experiments cannot be reproduced in humans (ethically), a population case- controlled study showed that increased intake of long-chain omega-3 fatty acids from seafood is associated with a reduced risk of primary cardiac arrests .Additionally, patients advised to eat fatty fish after recovering from a myocardial infarction had a 29% reduction in mortality in the following 2 years than those not advised to do so. A similar secondary prevention trial was also done using increased levels of the essential fatty acid linolenic acid (18:3w3) (7). 302 patients were randomly selected and placed on an LNA-rich diet after a first myocardial infarction, another 303 patients were placed on a normal post-infarct prudent diet. After two years, the group receiving the LNA- rich diet had 70% fewer fatal and nonfatal myocardial infarctions as well as a 70% reduction in overall mortality. The use of flaxseed oil and fish oil should be considered to reduce the risk of primary cardiac arrest and certainly as a post infarct secondary prevention. A recent review discusses the aspects of using long-chain omega-3 fatty acids from fish oil as prevention for therosclerosis. The mechanism of action includes modification of lipid profile (lower triglycerides, lower cholesterol concentration, increased HDL), moderate reduction in blood pressure, a shift in eicosanoid patterns (increased vasodilation, decreased platelet aggregation) and a decrease in platelet-derived growth factor (thought to play a role in atherosclerosis). The data, while promising in the prevention of atherosclerosis, is less conclusive for reversing already formed plaques. Perhaps the most conclusive therapeutic result using fish oils is the reduction of serum triglycerides. Studies have shown that the consumption of fish oil reduces cholesterol levels moderately and tryglycerides significantly. 7. Where would you classify cholesterol? Answer: Cholesterol is classified as a lipid, the most abundant steroid in animal tissues located in cell membranes and use for synthesis of steroid hormones and biles salts. 8. Enumerate some example of steroids, which are hormones? Answer: Steroid hormones

Sex steroids are a subset of sex hormones that produce sex differences or support reproduction. They include androgens, estrogens, and progestagens. Corticosteroids include glucocorticoids and mineralocorticoids. Glucocorticoids regulate many aspects of metabolism and immune function, whereas mineralocorticoids help maintain blood volume and control renal excretion of electrolytes. Anabolic steroids are a class of steroids that interact with androgen receptors to increase muscle and bone synthesis. There are natural and synthetic anabolic steroids. In popular language the word "steroids" usually refers to anabolic steroids. Cholesterol which modulates the fluidity of cell membranes and is the principle constituent of the plaques implicated in atherosclerosis. 9. Amino acids are the building blocks of proteins, familiarize yourself with them.

Amino Acid Abbrev.

Remarks

Alanine

Very abundant, very versatile. More stiff than glycine, but small enough to pose only small A Ala steric limits for the protein conformation. It behaves fairly neutrally, can be located in both hydrophilic regions on the protein outside and the hydrophobic areas inside.

Cysteine

The sulfur atom binds readily to heavy metal ions. Under oxidizing conditions, two cysteines can join together in a disulfide bond to form the amino acid cystine. When cystines are part of a protein, insulin for example, this stabilises tertiary structure and makes the protein more C Cys resistant to denaturation; disulfide bridges are therefore common in proteins that have to function in harsh environments including digestive enzymes (e.g., pepsin and chymotrypsin) and structural proteins (e.g., keratin). Disulfides are also found in peptides too small to hold a stable shape on their own (eg. insulin).

Behaves similarly to glutamic acid. Carries a hydrophilic acidic group with strong negative charge. Usually is located on the outer surface of the protein, making it water-soluble. Binds Aspartic acid D Asp to positively-charged molecules and ions, often used in enzymes to fix the metal ion. When located inside of the protein, aspartate and glutamate are usually paired with arginine and lysine.

Glutamic acid E Glu Behaves similar to aspartic acid. Has longer, slightly more flexible side chain.

Phenylalanine F

Essential for humans. Phenylalanine, tyrosine, and tryptophan contain large rigid aromatic group on the side chain. These are the biggest amino acids. Like isoleucine, leucine and Phe valine, these are hydrophobic and tend to orient towards the interior of the folded protein molecule.

Glycine

Because of the two hydrogen atoms at the carbon, glycine is not optically active. It is the smallest amino acid, rotates easily, adds flexibility to the protein chain. It is able to fit into the G Gly tightest spaces, e.g., the triple helix of collagen. As too much flexibility is usually not desired, as a structural component it is less common than alanine.

Histidine

In even slightly acidic conditions protonation of the nitrogen occurs, changing the properties of histidine and the polypeptide as a whole. It is used by many proteins as a regulatory H His mechanism, changing the conformation and behavior of the polypeptide in acidic regions such as the late endosome or lysosome, enforcing conformation change in enzymes. However only a few histidines are needed for this, so it is comparatively scarce.

Isoleucine

Ile

Essential for humans. Isoleucine, leucine and valine have large aliphatic hydrophobic side chains. Their molecules are rigid, and their mutual hydrophobic interactions are important for the correct folding of proteins, as these chains tend to be located inside of the protein molecule.

Lysine

Essential for humans. Behaves similarly to arginine. Contains a long flexible side-chain with a positively-charged end. The flexibility of the chain makes lysine and arginine suitable for binding to molecules with many negative charges on their surfaces. E.g., DNA-binding K Lys proteins have their active regions rich with arginine and lysine. The strong charge makes these two amino acids prone to be located on the outer hydrophilic surfaces of the proteins; when they are found inside, they are usually paired with a corresponding negatively-charged amino acid, e.g., aspartate or glutamate.

Leucine

L Leu Essential for humans. Behaves similar to isoleucine and valine. See isoleucine.

Essential for humans. Always the first amino acid to be incorporated into a protein; sometimes removed after translation. Like cysteine, contains sulfur, but with a methyl group Methionine M Met instead of hydrogen. This methyl group can be activated, and is used in many reactions where a new carbon atom is being added to another molecule.

Asparagine

N Asn Similar to aspartic acid. Asn contains an amide group where Asp has a carboxyl.

Proline

Contains an unusual ring to the N-end amine group, which forces the CO-NH amide sequence into a fixed conformation. Can disrupt protein folding structures like helix or P Pro sheet, forcing the desired kink in the protein chain. Common in collagen, where it often undergoes a posttranslational modification to hydroxyproline. Uncommon elsewhere.

Glutamine

Q Gln

Similar to glutamic acid. Gln contains an amide group where Glu has a carboxyl. Used in proteins and as a storage for ammonia.

Arginine

R Arg Functionally similar to lysine.

Serine

Serine and threonine have a short group ended with a hydroxyl group. Its hydrogen is easy to Ser remove, so serine and threonine often act as hydrogen donors in enzymes. Both are very hydrophilic, therefore the outer regions of soluble proteins tend to be rich with them.

Threonine

T Thr Essential for humans. Behaves similarly to serine.

Valine

V Val Essential for humans. Behaves similarly to isoleucine and leucine. See isoleucine.

Tryptophan W Trp

Essential for humans. Behaves similarly to phenylalanine and tyrosine (see phenylalanine). Precursor of serotonin. Naturaly fluorescent.

Tyrosine

Behaves similarly to phenylalanine and tryptophan (see phenylalanine). Precursor of melanin, Y Tyr epinephrine, and thyroid hormones. Naturaly fluorescent, although fluorescence is usually quenched by energy transfer to tryptophans.

10. Enumerate the important function of proteins in the body. Functional Group Roles in the body

Antibodies highly specialize proteins that recognize, bind with, and inactivate immunoglobulins ) bacteria,toxins,and some viruses, function in the imumune response which helps protect the body from invading foreign substances. Hormones Help to regulate growth and developmnet. Examples include *growth hormones- an anabolic hormonenecessary for optimal growth. *Insulin- helps regualate blood sugar levels *Nerve growth factor- guides the growth of nuerons in the development of the nervous system. Transport proteins hemogloben transport oxygen in the blood; other transport organism in the blood carry iron, cholesterol, or other substance. Catalysts (enzymes) essential to virtually every biochemical reaction in the body, increase the rates of chemical reactions by at lest a million fold, in their absence (or destruction ) biochamecal reaction cease.

11. What are a dipeptide, tripeptide, and polypeptide; define a peptide bond. Answer: Dipeptide is a molecule consisting of two amino acids joined by a single peptide bond tripeptide is a peptide consisting of three amino acids joined by peptide bonds. Examples of tripeptides are: Glutathione (-glutamyl-cysteinyl-glycine) is an antioxidant, protecting cells from toxins such as free radicals. Thyrotropin-releasing hormone (TRH, thyroliberin or protirelin) (L-pyroglutamyl-L-histidinyl-L-prolinamide) is a peptide hormone that stimulates the release of thyroid-stimulating hormone and prolactin by the anterior pituitary. Melanostatin (prolyl-leucyl-glycinamide) is a peptide hormone produced in the hypothalamus that inhibits the release of melanocyte-stimulating hormone (MSH). Ophthalmic acid (L--glutamyl-L--aminobutyryl-glycine) is an analogue of glutathione isolated from crystalline lens. Norophthalmic acid (y-glutamyl-alanyl-glycine) is an analogue of glutathione (L-cysteine replaced by Lalanine) isolated from crystalline lens. Eisenin (pGlu-Gln-Ala-OH) is a peptide with immunological activity isolated from the Japanese marine alga Eisenia bicyclis.

Proteins are polypeptide molecules (or consist of multiple polypeptide subunits). The distinction is that peptides are short and polypeptides/proteins are long. There are several different conventions to determine these, all of which have caveats and nuances.

A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, thereby releasing a molecule of water (H O). This is a dehydration synthesis reaction (also known as a condensation reaction), and usually occurs between amino acids. The resulting CONH bond is called a peptide bond, and the resulting molecule is an amide. The four-atom functional group C(=O)NH- is called an amide group or (in the context of proteins) a peptide group. Polypeptides and proteins are chains of amino acids held together by peptide bonds, as is the backbone of PNA. Polyamides, such as nylons and aramids, are synthetic molecules (polymers) that possess peptide bonds.
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A peptide bond can be broken by amide hydrolysis (the adding of water). The peptide bonds in proteins are metastable, meaning that in the presence of water they will break spontaneously, releasing about 10 kJ/mol of free energy, but this process is extremely slow. In living organisms, the process is facilitated by enzymes. Living organisms also employ enzymes to form peptide bonds; this process requires free energy. The wavelength of absorbance for a peptide bond is 190-230nm.

12. What are the different levels of proteinstructure, primary, secondary, tertiary, and quaternary Answer: Most proteins fold into unique 3-dimensional structures. The shape into which a protein naturally folds is known as its native state. Although many proteins can fold unassisted, simply through the chemical properties of their amino acids, others require the aid of molecular chaperones to fold into their native states. Biochemists often refer to four distinct aspects of a protein's structure:

Primary structure: the amino acid sequence Secondary structure: regularly repeating local structures stabilized by hydrogen bonds. The most common
examples are the alpha helix and beta sheet. Because secondary structures are local, many regions of different secondary structure can be present in the same protein molecule. Tertiary structure: the overall shape of a single protein molecule; the spatial relationship of the secondary structures to one another. Tertiary structure is generally stabilized by nonlocal interactions, most commonly the formation of a hydrophobic core, but also through salt bridges, hydrogen bonds, disulfide bonds, and even post-translational modifications. The term "tertiary structure" is often used as synonymous with the term fold. Quaternary structure: the shape or structure that results from the interaction of more than one protein molecule, usually called protein subunits in this context, which function as part of the larger assembly or protein complex.
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13. What are the enzymes and what are there role in the human body? Answer: Enzymes are biomolecules that catalyze (i.e. increase the rates of) chemical reactions. Almost all enzymes are proteins. In enzymatic reactions, the molecules at the beginning of the process are called substrates, and the enzyme converts them into different molecules, the products. Almost all processes in a biological cell need enzymes to occur at significant rates. Since enzymes are selective for their substrates and speed up only a few reactions from among many possibilities, the set of enzymes made in a cell determines which metabolic pathways occur in that cell. Like all catalysts, enzymes work by lowering the activation energy (E or G ) for a reaction, thus dramatically increasing the rate of the reaction. Most enzyme reaction rates are millions of times faster than those of comparable un-catalyzed reactions. As with all catalysts, enzymes are not consumed by the reactions they catalyze, nor do they alter the equilibrium of these reactions. However, enzymes do differ from most other catalysts by being much more specific. Enzymes are known to catalyze about 4,000 biochemical reactions. A few RNA molecules called ribozymes catalyze reactions, with an important example being some parts of the ribosome. Synthetic molecules called artificial enzymes also display enzyme-like catalysis.
a

14. What are the factors that could affect their activity?

Answer: Enzyme activity can be affected by other molecules. Inhibitors are molecules that decrease enzyme activity; activators are molecules that increase activity. Many drugs and poisons are enzyme inhibitors. Activity is also affected by temperature, chemical environment (e.g. pH), and the concentration of substrate. Some enzymes are used commercially, for example, in the synthesis of antibiotics. In addition, some household products use enzymes to speed up biochemical reactions (e.g., enzymes in biological washing powders break down protein or fat stains on clothes; enzymes in meat tenderizers break down proteins, making the meat easier to chew).

15. What are nucleic acids, what are their functions? Answer: Nucleic acids are organic substances. Nucleic acid molecules are long chains that generally occur in combination with proteins. The two chief types are DNA (deoxyribonucleic acid), the main constituent of genes, and RNA (ribonucleic acid), which is involved in protein synthesis and transmission of DNA's genetic information. The two classes of nucleic acids have backbones that are shaped like helical strands. Their molecular weights are in the millions. To the backbones are connected a great number of smaller molecules (side groups) of four different types. Each nucleic acid chain is composed of subunits called nucleotides, each containing a sugar, a phosphate group, and one of four bases: adenine (symbolized A), guanine (G), cytosine (C), and thymine (T). RNA contains the sugar ribose instead of the deoxyribose of DNA and the base uracil (U) instead of thymine. The sequence of these molecules on the strand determines the code of the particular nucleic acid. This code, in turn, signals the cell how to reproduce either a duplicate of itself or the proteins it requires for survival. Function The functions of nucleic acids are the storage, expression and replication of biological information. DNA carries the genetic information in its sequence of bases and this must be transmitted from one generation to the next. During reproduction there must be accurate copying of the base sequence of the DNA so that each of the two new daughter cells receives a copy of the origional parental genome. The specific sequences of nucleotides determine the cell's genetic information: each three-nucleotide DNA sequence specifies one particular amino acid. The long sequences of DNA nucleotides thus correspond to the sequences of amino acids in the cell's proteins. In order to be expressed as protein, the genetic information is carried to the protein-synthesizing machinery of the cell, usually in the cell cytoplasm. Forms of RNA mediate this process. DNA not only provides information but also acts as a blueprint for its own exact replication: The cell replicates its DNA by making a complementary copy of its exact nucleotide sequence: T for every A, C for every G, G for every C, A for every T. Although the triplet nucleotide code seems to be universal, the actual sequences of the nucleotides vary according to the species and individual. Points to remember: DNA and RNA are the two main types of nucleic acid DNA is used to pass on heriditary information and RNA is used to aid in the production of proteins the four bases for DNA are adenine, guanine, cytosine, and thymine

16. What are the different nucleic acid , differentiate DNA and RNA? Answer: genetic information needed for life and the inheritance of characters is encoded in biomolecules known as nucleic acids. There are two forms of nucleic acid - DNA or deoxyribonucleic acid and RNA or ribonucleic acid, both of these forms are the basis of all life and occur in all living cells. In chemical structure, these two molecules are linear and without branching; they are made essentially as polymers of discrete subunits termed the nucleotides - this is the language in which all life on earth is written, encoded and passed on from one generation to the next. Bacteria - called

prokaryotes - along with all the higher organisms collectively called the eukaryotes use DNA as their primary carrier of genetic information and RNA as an information messenger. This DNA is a part of the nucleus of all eukaryotes as well as the nucleiod of prokaryotes - prokaryotes include the bacteria, while the eukaryotes form the fungi, higher plants and animals. While RNA serves as the genetic information carrier in some viruses and is used as the sole molecule of heredity in these viruses. RNA is used only as a messenger in higher forms of true life excluding the viruses, in these forms, the RNA molecules are written using the DNA as the template. The RNA encoded information is than translated into protein, via bio-synthetic mechanism in the cytoplasm of the cell. Thus, DNA carries all information, which is then transcribed into RNA and then translated into protein - which then performs necessary vital actions in the living cell. This is called the central dogma of molecular biology. The basic components of the nucleic acids, the nucleotides are structurally formed from three major units. Every single nucleotide will consist of one five-carbon pentose sugar - ribose in RNA, and deoxy-ribose in DNA; One flat, heterocyclic, nitrogen rich organic base and lastly one phosphate group - this last unit of the nucleic acid polymer is responsible for the acidic nature of the nucleic acid as it is very negative in charge. These components of the nucleic acids are linked together covalently through a glycosidic bond formed between the sugar unit and the nitrogenous base. The addition of the phosphate group also covalently connected to the sugar unit completes the basic component of the nucleic acid polymer. RNA is made from monomers of the sugar -D-ribose and the sugar along with the nitrogenous base and inorganic phosphate is called a ribonucleotide - without the phosphate, its a nucleoside. DNA is made of monomers formed by the pentose sugar deoxy-ribose, along with a nitrogenous base and inorganic phosphate to make a deoxyribonucleotide. The DNA monomers are differentiated from the RNA monomers by the absence of an oxygen at the number two carbon in the sugars and are called a 2-deoxy--D-ribose sugars. The nitrogenous bases can be classed into two basic types of organic bases. Pyrimidines are single-ringed structures while the purines are double ringed-structures. There are three types of pyrimidines and two types of purines used in the construction of nucleic acids - all of them are not used in both RNA and DNA, which is the reason for the difference between the nucleic acids. The bases adenine and guanine are the purines found in both RNA and DNA. While the pyrimidines come in three types, cytosine, thymine, and uracil - the last replaces thymine in RNA and is not found in DNA. While the pyrimidine and thymine are found primarily in DNA, uracil is seen only in RNA. A purine always pair with a pyrimidine and vice versa in a nucleic acid. Along each polynucleotide strand forming DNA or RNA, all the nucleotides adjacent to each other are joined by covalent bonds called phosphodiester bonds formed between the number three carbon of one nucleotide and the number five carbon of the nearest nucleotide. In this way the monomers are interlinked to form a nucleic acid polymer holding all the genetic information necessary for life. Genetic information is stored along the nucleic acid chain because all the bases in the nucleotides form hydrogen bonds with each other in a specific way - this ensures what is called base pairing. Base pairing is the key behind the code formed from four bases. For example, adenine will always combine with thymine in DNA with the formation of two hydrogen bonds, while guanine will always base pair with cytosine via three hydrogen bonds. Since the hydrogen formation occurs between two different strands of linear DNA, it results in the formation of a DNA double helix formed by two complementary DNA strands holding genetic information. Similarly, adenine can also form hydrogen bonds with uracil in DNA-RNA hybrid chains as well as in RNA to RNA complexes. In both DNA and RNA, the base guanine will always form three hydrogen bonds with cytosine. In other words, guanine always pairs with cytosine in DNA as well as RNA, while adenine pair with thymine in DNA but with uracil in RNA. Viable DNA is found in the uniform shape of a double helix in chromosomes, each complementary chain is wound around the other complement in a spiral like a staircase. All nucleic acid chains do not exist in the form of double strands as the RNA molecules that are synthesized from DNA templates are always in the form of single strands - some viruses which use RNA as a genetic information carrier have double stranded RNA. In the body, a single stranded RNA chain is sometimes folded back onto itself so as to form complementary base pairs along the length of the chain to produce unique secondary structures necessary for some biochemical reactions. Along a DNA double helix, each of the two complementary strands forming the helix are found in opposite directions to each other, they are said to be anti-parallel in orientation, which means one chain is starts from the 5' phosphate end, while the other chain starts from the 3' hydroxyl end. In a DNA double helix, the winding of the two chains results in a turn along the helix at every ten base pairs, this has been measured to be about 3.4 nm - nanometers in

length. Base pairings occur along the center of the molecule resulting in stacking of the bases along the chain. As the bases repel water, they form a hydrophobic core at the center and the double helix as a result is approximately two nm across. RNA serve as information messengers for the DNA. The code on the DNA chain is copied onto an RNA chain and this information is translated into a protein, which then affects the desired outcome in the cell. In higher organisms, RNA comes in three basic types according to the function it performs inside the cell. The tRNA or transfer RNAs transfer one amino acid at a time during the formation of a protein. The mRNA or messenger RNAs carry the information written in the DNA to the ribosomes for translation into protein. The rRNA or ribosomal RNAs aid in the formation of proteins on ribosomes - which are the protein manufacturing centers in all cells. All the different classes of RNA are important for the body. In terms of size, the transfer RNAs or tRNAs are the smallest of the lot, being approximately about seventy five to eighty nucleotides long - their main action is the formation of a protein polymer and each tRNA positions single amino acids on the ribosome during the polymerization reaction to form distinct polypeptide chains - which in turn form proteins. The tRNAs also contain additional and unusual bases along with the normal complement of adenine, guanine, cytosine and uracil in their chains - this is in keeping with their specialized nature and function. The linear mRNAs differ according to the information they transcribe from the genetic code in the DNA template. As the genetic code that will specify the unique amino acid sequence for specific proteins resides in the DNA sequence, it follows that the complementary ribonucleotide sequences forming the mRNA will be long or short depending on the length and composition of the template DNA - therefore, mRNA chains are highly variable in length and composition. On the other hand, ribosomal or rRNAs are integral to the structure of the ribosomes - protein building sites in cells. There are also different types of rRNAs, there are four main types of rRNAs in eukaryotes while three main classes of rRNAs are found in the prokaryotes - namely the bacteria and archea.

17. Give the components of nucleotides, what is nitrogenous base, a sugar moiety? Answer: Nucleotides are the building blocks that form DNA and RNA. A nucleotide consists of three parts: nitrogen base + 5-carbon sugar + phosphate. If the phosphate is missing and the molecule consists of the nitrogen base and 5carbon sugar, it is a nucleoside. The linkage between nitrogen base and 5-carbon sugar is a glycosidic bond. Nitrogenous bases are organic compounds that owe their basic properties to the lone pair of electrons of a nitrogen atom. Typical nitrogenous bases are ammonia (NH ), triethylamine, pyridine, and the nucleobases adenine, guanine, thymine, cytosine, and uracil. Nitrogenous bases can be classified under two groups: purines (A and G) and pyrimidines (C, T, and U). These bases make up a crucial part of both deoxyribonucleotides and ribonucleotides, and the interactions between Adenine/Thymine and Guanine/Cytosine are the basis for the universal genetic code. Uracil replaces Thymine in RNA. For the structure and list of purines see this link: http://upload.wikimedia.org/wikipedia/en/5/5d/Purines.png For the structure and list of pyrimidines see this link: Chemical structure of thymine Chemical structure of uracil Chemical structure of cytosine Thymine Uracil Cytosine
3

Sugar moiety : One to 4 sugars are found to be present in most cardiac glycosides attached to the 3b-OH group. The sugars most commonly used include L-rhamnose, D-glucose, D-digitoxose, D-digitalose, D-digginose, D-sarmentose, L-vallarose, and D-fructose. These sugars predominantly exist in the cardiac glycosides in the b-conformation. The

presence of acetyl group on the sugar affects the lipophilic character and the kinetics of the entire glycoside. Because the order of sugars appears to have little to do with biological activity Nature has synthesized a repertoire of numerous cardiac glycosides with differing sugar skeleton but relatively few aglycone structures. Structure - Activity Relationships The sugar moiety appears to be important only for the partitioning and kinetics of action. (see section on pharmacokinetics of cardiac glycosides) It possesses no biological activity. For example, elimination of the aglycone moiety eliminates the activity of alleviating symptoms associated with cardiac failure. The "backbone" U shape of the steroid nucleus appears to be very important. Structures with C/D trans fusion are inactive. Conversion to A/B trans system leads to a marked drop in activity. Thus although not mandatory A/B cis fusion is important. The 14b-OH groups is now believed to be dispensible. A skeleton without 14b-OH group but retaining the C/D cis ring fusion was found to retain activity. Lactones alone, when not attached to the steroid skeleton, are not active. Thus the activity rests in the steroid skeleton. The unsaturated 17-lactone plays an important role in receptor binding. Saturation of the lactone ring dramatically reduced the biological activity. The lactone ring is not absolutely required. For example, using a,b-unsaturated nitrile (C=C-CN group) the lactone could be replaced with little or no loss in biological activity.

18. What is a gene, a chromosome? Answer: A gene is the basic unit of heredity in a living organism. The field of genetics predates modern molecular biology, but it is now known that all living things depend on DNA to pass on their traits to offspring. Loosely speaking, a gene is a segment of genomic information that, taken as a whole, specifies a trait. The colloquial usage of the term gene often refers to the scientific concept of an allele. The notion of a gene has evolved with the science of genetics, which began when Gregor Mendel noticed that biological variations were only inherited from parent organisms as specific, discrete traits. For example, if one parent has blue eyes and the other has brown eyes, there is a 3/4 chance that the child will have brown eyes. The biological entity responsible for defining eye color was termed a "gene", but the biological basis for inheritance remained unknown until the discovery of the genetic code in mid 1950s, when genes were determined to be encoded by DNA. All organisms have many genes corresponding to many different biological traits, some of which are immediately visible, such as eye color or number of limbs, and some of which are not, such as blood type or increased risk for certain diseases, or the thousands of basic biochemical processes which comprise life. In cells, a gene is a portion of an organism's DNA which contains both "coding" sequences that determine what the gene does, and "non-coding" sequences that determine when the gene is active (expressed.) When a gene is active, the coding and non-coding sequences are copied in a process called transcription, producing an RNA copy of the gene's information. This piece of RNA can then direct the synthesis of proteins via the genetic code. In other cases, the RNA is used directly, for example as part of the ribosome. The RNA may undergo special post-transcriptional processing steps required to convert it into a mature, functional form. These molecules resulting from gene expression, whether RNA or protein, are known as gene products, and are responsible for the development and functioning of all living things.

More technically, a gene is a locatable region of genomic sequence, corresponding to a unit of inheritance, and is associated with regulatory regions, transcribed regions and/or other functional sequence regions. The physical development and phenotype of organisms can be thought of as a product of genes interacting with each other and with the environment. A concise definition of a gene, taking into account complex patterns of regulation and transcription, genic conservation and non-coding RNA genes, has been proposed by Gerstein et al: "A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products".

A chromosome is an organized structure of DNA and protein that is found in cells. A chromosome is a single piece of DNA that contains many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions. The word chromosome comes from the Greek (chroma, color) and (soma, body) due to their property of being stained very strongly by some dyes. Chromosomes vary extensively between different organisms. The DNA molecule may be circular or linear, and can contain anything from 10,000 to 100,000,000 nucleotides in length. Typically eukaryotic cells (cells with nuclei) have large linear chromosomes and prokaryotic cells (cells without defined nuclei) have smaller circular chromosomes, although there are many exceptions to this rule. Furthermore, cells may contain more than one type of chromosome; for example, mitochondria in most eukaryotes and chloroplasts in plants have their own small chromosomes. In eukaryotes, nuclear chromosomes are packaged by proteins into a condensed structure called chromatin. This allows the very long DNA molecules to fit into the cell nucleus. The structure of chromosomes and chromatin varies through the cell cycle. Chromosomes may exist as either duplicated or unduplicatedunduplicated chromosomes are single linear strands, whereas duplicated chromosomes (copied during synthesis phase) contain two copies joined by a centromere. Compaction of the duplicated chromosomes during mitosis and meiosis results in the classic four-arm structure (pictured to the right). "Chromosome" is a rather loosely defined term. In prokaryotes, a small circular DNA molecule may be called either a plasmid or a small chromosome. These small circular genomes are also found in mitochondria and chloroplasts, reflecting their bacterial origins. The simplest chromosomes are found in viruses: these DNA or RNA molecules are short linear or circular chromosomes that often lack any structural proteins.