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Unformatted text preview: CHAPTER 13 HUMAN BIOCHEMISTRY (IB OPTION B) SUMMARY The energy value of a food can be calculated by carrying out a calorimetric experiment involving combustion of a known mass of the foodstuff and then applying the formula ΔH = m × c × ΔT. Proteins Proteins comprise long chains of 2-amino-acids joined to each other through peptide (-NH-CO-) linkages. 2-amino acids have the general formula, where the side-chain (Q) varies between amino acids. Because of their ability to hydrogen bond amino acids are water soluble. They have both acid and base groups so in neutral solution these groups exchange a hydrogen ion so the amino acid exists as a “zwitterion” (+H3N-CH(Q)-CO-O-). This has two opposite charges so is electronically neutral, but if the solution becomes more acidic the carboxylate group becomes protonated (+H3N-CH(Q)-CO-OH) so it becomes positively charged; similarly in alkaline solution the amino group will lose a hydrogen ion (H2N-CH(Q)-CO-O-) so it becomes negatively charged. The exact pH at which this occurs varies from acid to acid and the pH at which there is no net charge is known as the “isoelectronic point” of the acid. Because of these acid-base reactions, solutions of amino acids act as buffers, that is they keep a fairly constant pH when small amount of strong acid or alkali are added. Amino acids can join together to form proteins and polyeptide, (similar to proteins but shorter). The reaction is a condensation reaction. Note that there are two possible products depending on the order of the amino acids. If there were 3 different amino acids there would be 6 possible combinations. The structure of proteins is vital to their correct functioning. There are four levels of structure: • Primary structure – the order of the amino acids in the protein chain • Secondary structure – the initial folding of the structure into hydrogen bonded α-helix or β-pleated sheet conformations. • Tertiary structure – the folding of the secondary structure, generally dictated by the hydrophobic/hydrophilic nature of the side chain and S-S bridges. • Quaternary structure – the grouping together of a number of protein chains to give the protein The amino acids present in a protein can be deduced by hydrolysing the protein (enzymes or 6M HCl) and then carrying out chromatography (perhaps two-dimensional) and electrophoresis (at different pHs) to identify the amino acids present. Usually this is done by comparison with the behaviour of known samples under identical conditions. Proteins play many roles in living organisms: • Structural – collagen • Enzymes – for example amylases which break down starch. • Hormones – insulin • Immunoproteins – forming antibodies • Transport – for example haemoglobin in carrying oxygen • Energy – in starvation conditions protein can be used for energy rather than carbohydrates or fats © IBID Press 2007 1 CHAPTER 13 HUMAN BIOCHEMISTRY (IB OPTION B) SUMMARY Carbohydrates The major function of carbohydrates in humans is as an energy source, though they can also store energy and act as precursors for biologically active molecules, such as nucleic acids. The simplest carbohydrates are the monosaccharides, which have the formula (CH2O)n and contain, in the case of reducing sugars (like glucose) a aldehyde group, and in the case of nonreducing sugars (like fructose) a ketone group. Those that have five (pentoses, like ribose) or six (hexoses, like glucose and fructose) carbon atoms can form a ring structure that results from a hydroxyl group further down the chain bonding to the carbon of the carbonyl group. Two forms (α- and β-) are possible depending on which side of the carbonyl group the oxygen of the hydroxide joins on (see text). Monosaccharides in their ring form, can join together by condensation reactions to form disaccharides (containing two sugars; like lactose, maltose and sucrose) and polysaccharides (containing many sugars; like starch, glycogen and cellulose). Starch and cellulose are both formed from glucose. Starch, which has two forms, one comprising relatively short straight chains (amylose) and a second (amylopectin) which has a much higher molar mass and branched chains, has α-linkages between the glucose rings whereas cellulose has β-linkages. Humans, like most mammals, cannot digest cellulose, nevertheless this and other indigestible plant matter (known as dietary fibre) is a vital component of our diet because it prevents many problems of the digestive system, such as diverticulosis and Crohn’s disease. Lipids There are three types of lipids found in the human body; triglycerides (such as fats and oils), phospholipids (like lecithin) and steroids (for example cholesterol). The major functions of lipids in the include: • energy storage • insulation and protection of organs • acting as precursors of steroid hormones • forming structural components of cell membrane • omega-3 poly-unsaturated fatty acids reduce the risk of heart disease • poly-unsaturated fats may lower levels of LDL cholesterol. Lipids are the most concentrated type of energy storage because, unlike carbohydrates, they contain no oxygen hence they can undergo greater oxidation. Lipids, if eaten to excess, have negative health effects through causing obesity and increasing the risk of cardiovascular disease (especially saturated fats and trans-fatty acids), though a few (especially polyunsaturated and omega-3 ones) have beneficial effects. Cholesterol occurs in two different forms in the human body; HDL (high-density lipoprotein) which has only about 50% cholesterol and hence removes cholesterol from the walls of blood vessels, has a positive effect on cardiovascular health, and LDL (low-density lipoprotein) which contains over 70% cholesterol and deposits cholesterol on the walls of blood vessels, narrowing them and having a negative effect on cardiovascular health, Triglycerides are esters of glycerol and long chain fatty acids. The chains of the fatty acids can be either saturated (no double bonds), mono-unsaturated (one double bond) or poly-unsaturated (more than one double bond). This reaction is reversed when triglycerides are digested, a reaction which is catalysed by the enzyme lipase © IBID Press 2007 2 CHAPTER 13 HUMAN BIOCHEMISTRY (IB OPTION B) SUMMARY The number of double bonds can be found by reacting the triglyceride with iodine (which adds to the double bonds). The “iodine number” is the number of grams of iodine that adds to 100 g of the triglyceride; the greater the iodine number, the more unsaturated, as the number of moles of iodine molecules reacting with one mole of the triglyceride will equal the number of C=C bonds present. Essential fatty acids are those that the body cannot synthesise and therefore are essential components of our diet. Two important examples are linoleic acid (an omega-6 fatty acid) and linolenic (an omega-3 fatty acid). Both contain 18-carbon atoms, but linoleic acid contains two C=C double bonds with the first 6 carbon atoms away from the end (omega) carbon of the chain, whereas linolenic acid contains three C=C double bonds with the closest 3 carbon atoms away from the end carbon. Omega-3 acids are particularly important in brain development. Nutrients The food we eat can be divided into macronutrients (needed in relatively large quantities – proteins, carbohydrates, fats and mineral salts) and micronutrients (necessary but only in small quantities – vitamins, essential oils and many trace elements such as Fe, Cu, Co, Zn etc.). Shortage of particular nutrients can lead to specific diseases: • protein—marasmus and kwashiorkor • iron—anemia • iodine—goitre • retinol (vitamin A)—xerophthalmia (night blindness) • niacin (vitamin B3)—pellagra • thiamin (vitamin B1)—beriberi • ascorbic acid (vitamin C)—scurvy • calciferol (vitamin D)—rickets. Action that can be taken to combat such deficiency diseases include: • providing food rations that are composed of fresh and vitamin- and mineral-rich foods • adding nutrients missing in commonly consumed foods • genetic modification of food • providing nutritional supplements • providing selenium supplements to people eating foods grown in selenium-poor soil. Some vitamins are fat soluble (A, D, E & K) and others water soluble (notably B & C). This is because of their molecular structure; the water soluble ones have a number of hydroxyl groups allowing them to hydrogen bond to water. Hormones, such as (ADH, aldosterone, estrogen, progesterone, testosterone, insulin, adrenaline and thyroxine) are chemical messengers secreted directly into the blood by endocrine glands. Many hormones are steroids and have a similar carbon structure to cholesterol, but with different functional groups attached to it. © IBID Press 2007 3 CHAPTER 13 HUMAN BIOCHEMISTRY (IB OPTION B) SUMMARY The oral contraceptive is based on hormones such as estrogen and progesterone, which mimic changes that occur normally in pregnancy to prevent ovulation. Anabolic steroids are related to testosterone and can lead to an increase in muscle bulk, hence many athletes are tempted to use these illegally in spite of many negative side effects, such as aggressive behaviour, impotence and increased risk of cardiovascular problems. Enzymes Enzymes are biological catalysts that are involved in almost all biochemical processes. They are generally proteins and compared to inorganic catalysts they are: • far more effective • much more specific • easily “denatured” (made ineffective) by changes of temperature, pH etc Denaturing occurs because the shape of the protein has been altered by changes in the tertiary, and sometimes the secondary, structure of the protein. Such changes can be brought about by heating the enzyme (causing hydrogen-bonds to break), altering the pH (and hence the charges on acidic and basic side chains), or adding heavy metal ions (which form complex ions with groups on the protein). Catalysts provide an active site that the substrate bonds to (lock and key model). Whilst bonded the substrate is changed and then released free up the enzyme to bond to more substrate molecules. The shape of the active site is very specific to the substrate, so that reactions of even very closely related molecules are unaffected. For example urease will catalyse the hydrolysis of urea, but not other amides, At low substrate concentrations the reaction rate is proportional to [substrate] because the formation of the enzyme-substrate complex is rate determining, but at high substrate concentration the rate will tend to a limiting value, independent of [substrate] because the change occurring to the substrate become rate determining. Vmax 1 -- v K slope = -- m --------Vmax 1V -- max 2 1 -----------V max Km [Substrate] –1 -----Km 1 ------[ S] If the rate constant for formation of the enzyme-substrate complex is k1, the rate constant for it splitting up to reform the enzyme and substrate is k2 and the rate at which it is converted to the products is k3, then it can be shown that the maximum rate (Vmax) is related to the substrate concentration, [S], by the Michaelis-Menten equation: © IBID Press 2007 4 CHAPTER 13 HUMAN BIOCHEMISTRY (IB OPTION B) SUMMARY where the Michaelis constant, Km = Km is equal to the substrate concentration required to give a rate equal to half the maximum rate and it will vary with temperature and pH, but not concentration. The equation above can be rearranged to give a linear function: 1 Rate From which the Michaelis constant and the maximum rate (Vmax) may be found by plotting 1 /Rate against 1/[S] (see plot above). Enzyme activity can be inhibited (made less effective). There are two types of inhibition, competitive and non-competitive. In competitive inhibition the inhibitor can bond to the active site and hence competes with the substrate, so that the a larger concentration of substrate is required to reach the maximum rate (Vmax), which is however unchanged. A non-competitive inhibitor will bond to some other part of the enzyme with the effect of reducing its activity. In this case the maximum rate (Vmax) is reduced. Nucleic Acids Nucleic acids are polymers made up of nucleotides, joined by a covalent bond between the phosphate of one nucleotide and the sugar of the next. A nucleotide contains a phosphate group, a pentose sugar and a side chain of one of five organic nitrogenous bases {adenine (A), cytosine (C), guanine (G), thymine (T) and uracil (U)} attached to the sugar of the phosphatesugar backbone. DNA (deoxyribonucleic acid) differs from RNA (ribonucleic acid) in three important ways: • DNA contains deoxyribose, containing one less –OH group than the ribose found in RNA • DNA has the base thymine, whereas RNA has uracil, the other bases are found in both • DNA exists as a double strand, joined by the bases, whereas RNA has a single strand DNA comprises two strands of the deoxyribose-phosphate backbone joined by hydrogen bonds between the bases attached to the backbone. Because of their shapes each base can only effectively hydrogen bond to one of the other bases, hence thymine will always bond to adenine and guanine to cytosine, known as complementary base pairs. This means that one strand is a “negative image” of the other. When DNA replicates the two strands untwist and bond on to the complementary nucleotides. That means that where there is a cytosine on the chain, a guanine will attach itself. These new nucleotides then polymerise so that the final result are two double helices, identical to the originals. © IBID Press 2007 5 CHAPTER 13 HUMAN BIOCHEMISTRY (IB OPTION B) SUMMARY The order of the bases on the DNA, present in the nucleus of all cells, acts as a code to provide the instructions about how to construct a new organism. For example to synthesise a particular protein the code on the DNA is transcribed in forming a molecule of messenger RNA (mRNA) with the complementary code. This code is then translated during protein synthesis to give the correct protein primary structure. A particular group of three bases corresponds to a particular amino-acid (the triplet code, or codon). For example the triplet G-C-U corresponds to alanine. Because DNA contains the instructions for making a particular organism and all human beings are unique, each of us has slightly different DNA. This means that the DNA from samples of cells can be identified as belonging to a particular individual and it will be closely related to the DNA of blood relatives. This has many uses, for example in forensics and in establishing paternity. Respiration Cellular respiration, which entails the exothermic oxidation of glucose, normally takes place under either aerobic conditions, though it can also occur under anaerobic conditions. In both glucose is initially converted into the pyruvate ion, in the presence of nicotinamide adenine dinucleotide (NAD+), which is reduced in the first stage and then oxidised in the second: C6H12O6 + 2 NAD+ → 2 C3H3O3– + 2 NADH + 4 H+ + energy In the presence of oxygen (aerobic respiration), this changes to carbon dioxide and water. 2CH3COCOO– + 2NADH + 4H+ + 6O2 → 6CO2 + 6H2O + 2NAD+ In anaerobic respiration, the pyruvate is converted to lactate in human beings (though in yeast it is converted to ethanol and carbon dioxide): CH3COCOO– + NADH + H+ → CH3CHOHCOO– + NAD+ + energy The presence of lactic acid in muscle cells, resulting from oxygen depletion is responsible for the pain resulting from muscle fatigue. Metal ions play a vital role in the oxygen transport process. Firstly iron is a component of haemoglobin. Oxygen molecules bond on to the iron atom and are then transported away from the lungs to cells that have in sufficient of oxygen, in which the low pH, caused by the presence of lactic acid (the product of anaerobic oxidation) causes changes which result in the release of the oxygen. Secondly copper is a vital component of the cytochromes, which are essential enzymes in the processes through which glucose is oxidised. (N.B. Shading indicates AHL material.) © IBID Press 2007 6 ...
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