Biochemistry Analysis Questions for Exams (Solved)
1. Provide a reasonable systematic name for an enzyme that catalyzes the following reaction:
Fructose + ATP ―> Fructose-1 phosphate + ADP
- Fructose: ATP phosphotransferase or
- Fructose: ATP kinase
2. The IUBMB has a developed a set of rules for classifying enzymes based upon the type of the reaction they catalyze. The classification scheme assigns an Enzyme Commission (EC) the number of each enzyme. Answer the following questions regarding EC numbers and the class of the reaction catalyzed:
(a) What name is associated with class 4 enzymes and what type of reaction do they
(b) Oxidoreductases catalyze redox reactions. What class of enzymes are
(c) What types of reactions are catalyzed by ligases?
Ans: (a) Lyases catalyze group eliminations that form double bonds
(b) Class 1
(c) Bond formation coupled to ATP hydrolysis.
3. There are many mechanisms that enzymes utilize to enhance reaction rates. Explain how the following mechanisms enhance reaction rates:
(a) Covalent catalysis
(b) Proximity effects
Ans: (a) Covalent catalysis enhances reaction rates by breaking down an overall reaction into at least two elementary reaction steps. In particular, the Ea (activation energy) for each of the elementary steps is smaller than the Ea (activation energy) associated with the single step reaction. The mechanism is referred to as covalent catalysis as a covalent enzyme: substrate intermediate is formed and broken during the overall reaction. (b) Proximity effects enhance reaction rates by forcing the reacting groups to be near one another in space. This increases the rate at which the reacting groups encounter one another and increases the rate of product forming reactions.
4. List four characteristics that define a metabolic pathway.
Ans: Metabolic pathways are (1) irreversible, (2) have a committed step, (3) are regulated and (4) catabolic and anabolic pathways differ
5. Identify two amino acids that commonly act as nucleophiles in enzyme-catalyzed reactions.
Ans: Serine, threonine, and cysteine are nucleophilic in their ionized form, while histidine and lysine are nucleophiles in their neutral-charged form.
6. What is the difference between an
a. isomerization reaction and
b. a rearrangement?
Ans: Isomerization reactions inevitably involve the movement of an H atom without changing the carbon backbone while rearrangements involve changes to the carbon backbone.
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 a Schiff’s base. Draw a structure of :
a. a Schiff’s base carbanion
b. the resonance stabilized Schiff’s base in the ene-amine form
Ans: a. Schiff’s base carbanion b. Schiff’s base -enamine form
8. How can metabolic inhibitors be used to determine the sequence of reactions in a metabolic pathway?
Ans: Metabolic inhibitors specifically block a metabolic pathway and result in the accumulation of metabolic pathway intermediates. By identifying the metabolic pathway intermediate(s) that accumulate, one can identify the step in a metabolic pathway that has been inhibited. The use of several metabolic inhibitors that act at different points in the pathway (together with ‘chemical intuition’) is sufficient to propose and verify the sequence of reactions associated with a metabolic pathway.
9. Isotopes of C, N, S, P and H have been extensively used to investigate metabolic pathways. Why?
Ans: The greatest difficulty in metabolism research is identifying the intermediates of a metabolic pathway. A large number of related compounds in an organism make the identification of metabolic intermediates difficult. Further, many metabolic intermediates are only present at very low levels making them difficult to detect. The use of isotopes (especially radioisotopes) can overcome this problem as they can be readily detected at very low concentrations and serve to ‘tag’ or ‘label’ each of the metabolic intermediates of a pathway.
10.The standard transformed free energy change for the following bimolecular reaction:
Glucose + ATP —-> Glucose-6-phosphate + ADP
is -16.7 kJ/mol. Consequently, this reaction is spontaneous under standard conditions. Under what conditions would this reaction NOT be spontaneous at 298K?
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 reaction
0 > -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 no longer be spontaneous. (Note, at exactly 837.1 fold excess of products to reactants the reaction will be at equilibrium)