Biochemistry Test
(1) Late submissions will not be accepted. (2) All answers must be provided in the order they are asked. Answers not provided in sequence will not be marked (3) You will receive zero credit for any given answer if you do not show all your work. (4) Your answer sheet should be neat, clear and legible. (5) Make sure to use pen. Do not use any whiteout. If you need to cross something out do so with a single line through the middle.
1. (a) Show the reaction catalyzed by DNA polymerase that occurs at the end of a DNA chain between the deoxyribose and 5’ phosphates of a deoxyribonucleoside triphosphate. Make sure to include the appropriate chemical structure of the phosphate groups, sugar and base and show the rearrangement of electrons.
(b) What effect would the absence of Mg2+ have on the activity of the polymerase?
(c) DNA polymerases cannot initiate the synthesis of a new DNA chain, instead they elongate a preexisting chain (i.e. they require a primer). However, during DNA replication a completely new daughter DNA chain is synthesized. Explain the process that allows for this.
(d) Describe the two regions found in the DNA polymerase enzyme pocket and provide an example of an error correction by 3’-exonuclease.
2. (a) Gene regulation can occur at many steps in the gene expression pathway. Discuss regulation at the level of transcription initiation, protein stability and protein posttranslational modifications.
(b) Define and discuss differences in positive regulation and negative regulation in gene expression.
(b) Provide two examples of each for both prokaryotes and eukaryotes.
3. Show the pathway from glucose to glycogen; include cofactors and indicate the enzymes involved. Then show the reverse pathway. Discuss structure and function relationship of glycogen branching detail each step of the reaction.
