1. FIRST BIOCHEMISTRY EXAM Tuesday 25/10/2016 10-11 40 MCQs. Location : 102, 105, 106, 301, 302 FIRST BIOCHEMISTRY EXAM Tuesday 25/10/2016 10-11 40 MCQs. Location : 102, 105, 106, 301, 302

2. The Behavior of Proteins: Enzymes, Mechanisms, and Control The Behavior of Proteins: Enzymes, Mechanisms, and Control

3. General theory of enzyme action, by Leonor Michaelis and Maud Menten in 1913. Leonor Michaelis, German 1875–1949 Maud Menten, Canadian 1879–1960

4. Learning Objectives 1. What Is the Michaelis–Menten Approach to Enzyme Kinetics? 2. How Do Enzymatic Reactions Respond to Inhibitors? 3. Does the Michaelis–Menten Model Describe the Behavior of Allosteric Enzymes ? 4. What Are the Models for the Behavior of Allosteric Enzymes? 5. What is Lineweaver –Burk plot ? 5. How Does Phosphorylation of Specific Residues Regulate Enzyme Activity? 6. What Are Zymogens, and How Do They Control Enzyme Activity? 7. What Are Coenzymes and Cofactors ? 8. What Are Isoenzymes & what is their clinical application.

5. They postulated that the enzyme first combines reversibly with its substrate to form an enzyme-substrate complex in a relatively fast reversible step: The ES complex then breaks down in a slower second step to yield the free enzyme and the reaction product P:

7. Michaelis-Menten Model 2 V max [S] V = K M + [S] Michaelis-Menten equation

8. Michaelis-Menten Model – When [S]= K M, the equation reduces to 2

9. Michaelis-Menten Model – It is difficult to determine V max experimentally – The equation for a hyperbola (E saturation curve) – Can be transformed into the equation for a straight line by taking the reciprocal of each side

10. The physiological consequence of K M is illustrated by the sensitivity of some individuals to ethanol. Such persons exhibit facial flushing and rapid heart rate (tachycardia) after ingesting even small amounts of alcohol. In the liver, alcohol dehydrogenase converts ethanol into acetaldehyde

11. Normally, the acetaldehyde, which is the cause of the symptoms when present at high concentrations, is processed to acetate by acetaldehyde dehydrogenase.

12. Most people have two forms of the acetaldehyde dehydrogenase, a low K M mitochondrial form and a high K M cytosolic form. In susceptible persons, the mitochondrial enzyme is less active due to the substitution of a single amino acid, and acetaldehyde is processed only by the cytosolic enzyme. Because this enzyme has a high K M, less acetaldehyde is converted into acetate; excess acetaldehyde escapes into the blood and accounts for the physiological effects.

13. Lineweaver-Burk Plot – which has the form y = mx + b, and is the formula for a straight line (linearization) – a plot of 1/V versus 1/[S] will give a straight line with slope of K M /V max and y intercept of 1/V max – such a plot is known as a Lineweaver-Burk double reciprocal plot

14. Lineweaver-Burk Plot – K M is the dissociation constant for ES; the greater the value of K M, the less tightly S is bound (less affinity) to E The units K M are units of [S] that is M or mM

15. Turnover number Turnover number (k cat ): is the moles of S converted to P per mole of E per second. – Unit of k cat is mol S * mol E -1 * s -1 – The higher K cat value the higher the reactivity of the E

16. Turnover Numbers and K M Values for some typical enzymes Enzyme Function CatalaseConversion of H 2 O 2 to H 2 O + O 2 4 x 10 7 25 Carbonic anhydrase Hydration of CO 2 1 x 10 6 12 Acetylcholin- esterase Regeneration of acetylcholine 1.4 x 10 4 9.5 x 10 -2 ChymotrypsinProteolytic enzyme1.9.x 10 2 6.6 x 10 LysozymeHydrolysis of bacterial cell wall polysaccharides 0.5 6 x 10 -3 K M (mmolliter ) Turnover numbr [(mol S)(mol E) s ]

17. Enzyme Inhibition Reversible inhibitor: Reversible inhibitor: a substance that binds to an enzyme to inhibit it, but can be released – competitive inhibitor: – competitive inhibitor: binds to the active (catalytic) site and blocks access to it by substrate – noncompetitive inhibitor: – noncompetitive inhibitor: binds to a site other than the active site; inhibits the enzyme by changing its conformation Irreversible inhibitor: Irreversible inhibitor: a substance that causes inhibition that cannot be reversed – usually involves formation or breaking of covalent bonds to or on the enzyme – Cyanides, Penicillin, Heavy metals, Nerve gas

18. competitive inhibitor A competitive inhibitor diminishes the rate of catalysis by reducing the proportion of enzyme molecules bound to a substrate. At any given inhibitor concentration, competitive inhibition can be relieved by increasing the substrate concentration. Under these conditions, the substrate "outcompetes" the inhibitor for the active site.

19. Methotrexate is a structural analog of tetrahydrofolate, a coenzyme for the enzyme dihydrofolate reductase, which plays a role in the biosynthesis of purines and pyrimidines. It binds to dihydrofolate reductase 1000-fold more tightly than the natural substrate and inhibits nucleotide base synthesis. It is used to treat cancer.

20. The cofactor tetrahydrofolate and its structural analog methotrexate. Regions with structural differences are shown in red.

21. noncompetitive inhibitor In noncompetitive inhibition, which also is reversible, the inhibitor and substrate can bind simultaneously to an enzyme molecule at different binding sites. A noncompetitive inhibitor acts by decreasing the turnover number rather than by diminishing the proportion of enzyme molecules that are bound to substrate. Noncompetitive inhibition, in contrast with competitive inhibition, cannot be overcome by increasing the substrate concentration.

22. Competitive Vs noncompetitive Inhibition

23. Competitive Inhibition Illustrated on a Double-Reciprocal Plot. A double-reciprocal plot of enzyme kinetics in the presence ( I ) and absence ( I ) of a competitive inhibitor illustrates that the inhibitor has no effect on V max but increases K M.

24. Noncompetitive Inhibition Illustrated on a Double-Reciprocal Plot. A double-reciprocal plot of enzyme kinetics in the presence ( I ) and absence ( I ) of a noncompetitive inhibitor shows that K M is unaltered and V max is decreased.

25. Irreversible inhibitor Penicillin acts by covalently modifying the enzyme transpeptidase, thereby preventing the synthesis of bacterial cell walls and thus killing the bacteria. Aspirin acts by covalently modifying the enzyme cyclooxygenase, reducing the synthesis of inflammatory signals.

26. Structure of Penicillin Formation of a Penicilloyl-Enzyme Complex.

27. Chymotrypsin Inhibition Treatment with organofluorophosphates such as diisopropylphosphofluoridate (DIPF) was found to inactivate the enzyme irreversibly. Despite the fact that the enzyme possesses 28 serine residues, only one, serine 195, was modified, resulting in a total loss of enzyme activity. This chemical modification reaction suggested that this unusually reactive serine residue plays a central role in the catalytic mechanism of chymotrypsin.

28. An Unusually Reactive Serine in Chymotrypsin. Chymotrypsin is inactivated by treatment with diisopropylphosphofluoridate (DIPF), which reacts only with serine 195 among 28 possible serine residues

29. Enzyme regulation Enzyme activity can be regulated by several ways: 1.Covalent modification (Phosphorylation) The side chain -OH groups of Ser, Thr, and Tyr can form phosphate esters phosphorylation by ATP can convert an inactive precursor into an active enzyme  Protein kinases phosphorylate enzymes  Protein phosphatases remove phosphate groups

30. Enzyme regulation Covalent modification (Phosphorylation)

31. 2.Noncovalent modification (Allosteric regulation) Using allosteric effectors (activator and allosteric inhibitor ) 3.Control amount of enzyme: enzyme synthesis: gene regulation enzyme degradation

32. 4.Zymogen : an inactive precursor of an enzyme; cleavage of one or more covalent bonds transforms it into the active enzyme – Involved in blood clotting and digestion – Example chymotrypsinogen  Chymotrypsinogen – synthesized and stored in the pancreas – a single polypeptide chain of 245 amino acid residues cross linked by five disulfide (-S-S-) bonds – enzyme trypsin cleaves it to give chymotrypsin

33. Secretion of Zymogens by an Acinar Cell of the Pancreas

34. Proteolytic Activation of Chymotrypsinogen. The three chains of α- chymotrypsin are linked by two interchain disulfide bonds

35. Zymogen Activation by Proteolytic Cleavage Active enzymes are shown in yellow

36. Blood-Clotting Cascade

37. Many Enzymes Require Cofactors for Activity

38. COENZYMES…… Cofactors

39. Enzyme cofactors MetalEnzyme Zn2+Carbonic anhydrase Zn2+Carboxypeptidase Mg2+Hexokinase Ni2+Urease SeGlutathione peroxidase Mn2+Superoxide dismutase Cu2Cytochrome oxidase

40. ISOENZYMES Isozymes or isoenzymes, are enzymes that differ in amino acid sequence yet catalyze the same reaction. Usually, these enzymes display different kinetic parameters, such as K M, or different regulatory properties. They are encoded by different genetic loci, which usually arise through gene duplication and divergence.

41. ISOENZYMES The existence of isozymes permits the fine-tuning of metabolism to meet the particular needs of a given tissue or developmental stage. Consider the example of lactate dehydrogenase (LDH), an enzyme that functions in anaerobic glucose metabolism and glucose synthesis. Human beings have two isozymic polypeptide chains for this enzyme: the H isozyme highly expressed in heart and the M isozyme found in skeletal muscle. The amino acid sequences are 75% identical.

42. The functional enzyme is tetrameric, and many different combinations of the two subunits are possible. The H4 isozyme, found in the heart, has a higher affinity for substrates than does the M4 isozyme. The two isozymes also differ in that high levels of pyruvate allosterically inhibit the H4 but not the M4 isozyme. The other combinations, such as H3M, have intermediate properties depending on the ratio of the two kinds of chains.

43. ISOENZYMES……… LDH

45. END Chapter 7