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Biochemistry Analysis Questions for Exams (Solved)

1. Provide a reasonable systematic name for an enzyme that catalyzes the followingreaction: fructose + ATP > fructose-1 phosphate + ADP

2. The IUBMB has a developed a set of rules for classifying enzymes based upon the type ofreaction they catalyze. The classification scheme assigns an Enzyme Commission (EC)number to each enzyme. Answer the following questions regarding EC numbers and the classof reaction catalyzed:(a) What name is associated with class 4 enzymes and what type of reaction do theycatalyze?(b) Oxidoreductases catalyze redox reactions. What class of enzymes areoxidoreductases?(c) What types of reactions are catalyzed by ligases?

3. There are many mechanisms that enzymes utilize to enhance reaction rates. Explain howthe following mechanisms enhance reaction rates:(a) Covalent catalysis(b) Proximity effects

4. List four characteristics that define a metabolic pathway.5. Identify two amino acids that commonly act as nucleophiles in enzyme catalyzed

reactions.6. What is the difference between an (1) isomerization reaction and (2) a rearrangement?7. Enzyme catalyzed reactions that make or break C-C bonds typically involve carbanion

intermediates. One means of stabilizing a carbanion intermediate involves the formation of aSchiffs base. Draw a strcuture of :(a) a Schiffs base carbanion(b) the resonance stabilized Schiffs base in the ene-amine form

8. How can metabolic inhibitors be used to determine the sequence of reactions in ametabolic pathway?

9. Isotopes of C, N, S, P and H have been extensively used to investigate metabolicpathways. Why?

10. The standard transformed free energy change for the following bimolecular reaction: Glucose + ATP -> Glucose-6-phosphate + ADPis -16.7 kJ/mol. Consequently, this reaction is spontaneous under standard conditions. Underwhat conditions would this reaction NOT be spontaneous at 298K?

Solutions:

1. Fructose:ATP phosphotransferase or Fructose:ATP kinase2. (a) Lyases catalyze group eliminations that form double bonds

(b) Class 1(c) Bond formation coupled to ATP hydrolysis.

3. (a) Covalent catalysis enhances reaction rates by breaking down an overall reaction into at least twoelementary reaction steps. In particular, the E a (activation energy) for each of elementary steps is smallerthan the Ea (activation energy) associated with the single step reaction. The mechanism is referred to ascovalent catalysis as a covalent enzyme:substrate intermediate is formed and broken during the overallreaction.(b) Proximity effects enhance reaction rates by forcing the reacting groups to be near to one another inspace. This increases the rate at which the reacting groups encounter one another and increases the rateof product forming reactions.

4. Metabolic pathways are (1) irreversible, (2) have a committed step, (3) are regulated and(4) catabolic and anabolic pathways differ.

5. Serine, threonine and cysteine are nucleophilic in their ionized form, while histidine and lysine arenucleophiles in their neutral-charged form.

6. Isomerization reactions inevitably involve the movement of an H atom without changing the carbonbackbone while rearrangements involve changes to the carbon backbone.

7. (a) Schiffs base carbanion (b) Schiffs base -eneamine form8. Metabolic inhibitors specifically block a metabolic pathway and result in the accumulation of metabolic

pathway intermediates. By identifying the metabolic pathway intermediate(s) thataccumulate, one can identify the step in a metabolic pathway that has been inhibited. The use of severalmetabolic inhibitors that act at different points in the pathway (together with chemical intuition) is sufficientto propose and verify the sequence of reactions associated with a metabolic pathway.

9. Greatest difficulty in metabolism research is identifying the intermediates of a metabolic pathway. Thelarge number of related compounds in an organism make the identification of metabolic intermediatesdifficult. Further, many metabolic intermediate are only present at very low levels making them difficult todetect. The use of isotopes (especially radioisotopes) can overcome this problem as they can be readilydetected at very low concentrations and serve to tag or label each of the metabolic intermediates of apathway.

10. Reactions are only spontaneous when the G < 0.Given our equation for calculating G':G = G + RT ln ([Products]/[Reactants])0 > G + RT ln ([Products]/[Reactants]) for a spontaneous reaction0 > -16.7 kJ mol -1 + 8.31 J mol-1 K-1 298 K ln ([Products]/[Reactants])16.7 kJ mol-1 / 2.48 kJ mol-1> ln ([Products]/[Reactants])6.73 > ln ([Products]/[Reactants])e6.73 > ([Products]/[Reactants])837.1 > ([Products]/[Reactants])When the ratio of Products to Reactants is greater than or equal to 837.1, the reaction will nolonger be spontaneous. (Note, at exactly 837.1 fold excess of products to reactants thereaction will be at equilibrium)

Biochemistry Analysis Questions for Exams (Solved)