Problem Set 3.


1. Fatty acid biosynthesis and phospholipid biosynthesis.

A. What are the roles of the following enzymes in fatty acid biosynthesis: acetylCoA carboxylase, acetyl transacylase, malonyl transacylase, acyl-malonyl ACP condensing enzyme, enoylACP reductase?

B. Starting from two molecules of acetyl CoA, two molecules of ACP, and one HCO3- ion diagram the reactions to the end of the first elongation cycle.

C. During the acyl-malonyl condensation reaction, no ATP is hydrolyzed. However the reaction requires energy. What supplies this energy? How is the reaction indirectly fueled by ATP hydrolysis?

D. What are the two regulated enzymes in phospholipid biosynthesis, what reactions do they catalyze and how are they regulated.

E. Dihydroxyacetone phosphate is generated during glycolysis. It can then be used for both catabolic reactions, if isomerized, and anabolic reactions, if reduced. What is the product of each of those reactions?

2. Peptidoglycan and its biosynthesis.

A. Diagram peptidoglycan, identify each component and the type of bond found between each component.

B. Peptidoglycan is a large molecule made up or repeating subunits. What is the repeating subunit? What mechanisms do cells employed to ensure the integrity and fidelity of its synthesis?

C. The formation of the crosslinks, which occur outside the cell, requires energy. Although the transpeptidase enzyme that forms the crosslinks does not hydrolyze ATP, ATP hydrolysis indirectly fuels this reaction. Explain.

3. Protein synthesis.

A. Using structural formulae, diagram an amino-acyl tRNA transferase reaction.

B. What are the roles of IF1, IF2, and IF3 in ribosome assembly?

C. How does the mechanism of ribosome assembly ensure that correct reading frame is recognized during translation?

D. What role does molecular mimicry play in the functions of EF-G and release factors?

E. Although N-formyl methionine and methionine share a common codon, why is methionine never found at the beginning of a polypeptide and N-formyl methionine only found at the beginning of the polypeptide.

F. On a molecular level, how do stop codons terminate protein synthesis and lead to the release of the newly synthesized amino acid?

G. Diagram the addition of an amino acid to a growing polypeptide chain, as it would occur on the ribosome. Use E, A and P sites.