Answers BS 106 Tutorial 1: Enzyme catalysis & regulation 1. See the slide of the lecture notes stickase analogy.

The enzyme that binds the substrate loosely is better than enzyme that binds the substrate tightly. Tight binding makes the ES more stable than that for loose binding. This implies lower free energy. Thus higher activation energy is expected to be needed. 2. Rate const K is related to the activation energy G as K = (kT/h)exp(- G /RT). Write the equation twice; one for catalyzed reaction, other for uncatalyzed reaction. Then take the ratio which gives Kcat/Kuncat = exp( G/RT) where G = ( Guncat - Gcat).

Given, Kcat/Kuncat = 10, T = 298. Using, R = 8.31 J K-1 Mol-1 we get G = 5.7 kJ mol-1. (b) The rate enhancement is 10/10-13 = 1014 in this case. Therefore, exp( G/RT) = 1014 So, G = 5.7 kJ mol-1 x 14 = 79.8 kJ Mol-1 3. Specificity arises from the shape, size and the nature of the functional groups of the active site of the enzyme in relation to the shape, size and the nature of the functional groups of the substrate. These factors determine the degree of formation of multiple weak interactions (van der waals, electrostatic, hydrogen bonding, and hydrophobic interactions) between the enzyme and its specific substrate molecule. 4. Although the process of proteolytic cleavage is based on covalent modifications, the process is more elaborate than what happens with the category conventionally defined as covalent modification. More importantly, proteolytic cleavage is an irreversible process, while covalent modification is reversible. That is why these two regulatory processes are put in two different categories. 5. Tyr-Arg-Gly-Met-Asp-Ile-Lys-Gln-Met-Lys-Phe-Ala-Met-Lys 6. (a) Because there are 4 subunits in each enzyme, the possible combinations and their relative proportions are given by the binomial distribution (H + M)4 = 1H4 + 4H3M + 6H2M2 + 4HM3 + 1M4 So, there are 5 possible combinations with relative proportions 1:4:6:4:1 (b) The distribution is possible when H and M are produced in equal molar concentrations. Therefore, if heart cells produce more of H subunits than M subunits, the distribution will be in favour of H-containing subunits; and if skeletal muscle cells produce more of M subunits than H subunits, the distribution will be in favour of M-containing subunits. 7. (a) cofactor, (b) holoenzyme, (c) apoenzyme, (d) coenzyme, (e) prosthetic group. [Zn is also a cofactor for carbonic anhydrase and carboxypeptidase]

8. The statement is consistent with the induced-fit model, because this model implies that the substrate binding initiates to conformational changes in both the substrate and the enzyme leading to the formation of the transition state of the substrate. The lock-and-key model implies that the substrate binding (formation of ES complex) as such is a stable conformation. 9. Pyruvate decarboxylase removes CO2 from pyruvate (MVA, p-461). It is a lyase because a group is removed and a double bond is formed (O==C==O). Pyruvate carboxylase condenses pyruvate with CO2 to make oxaloacetic acitic acid using ATP (MVA, p-507). It is a ligase because (1) it is a condensation reaction, (2) a CC bond is formed, and (3) ATP is required.