MIC328_ProblemSet1

Problem Set 1

1. Using structural formulae, draw the steps that convert glucose to glucose 6-phosphate and fructose 6-phosphate to fructose 1,6 biphosphate. Remember that each of these steps in glycolysis is really the summation of two reactions. What enzymes catalyze these reactions?

2. Fructose 1,6 biphsophate is cleaved during glycolysis yielding two 3 carbon molecules. What are the names of these two three carbon molecules and the enzyme that catalyses the reaction? Which of the two products is directly on the glycolytic pathway? What must occur to for the other product to re-enter glycolysis.

3. Using structural formulae diagram the reactions catalyzed by the following enzymes:

    A. Glyceraldehyde 3-phosphate dehydrogenase.
    B. Phosphoglycerate kinase.
    C. Phosphoglycerate mutase.
    D. Enolase.
    E. Pyruvate kinase.

4. High levels of ATP in the cell lead to elevated levels glucose 6-phosphate.
    A. What enzyme is inhibited by high levels of ATP?
    B. Why does glucose 6-phosphate accumulate, as opposed to fructose 6-phosphate?
    C. Why is ATP the inhibitor?
    D. What enzyme is inhibited by glucose 6-phosphate and what reaction does it catalyzed?
    E. Why did this regulation evolve?
    F. What is meant by a reaction being the committed step of a pathway? How does this relate to the deltaG of reaction? Why is the hexokinase reaction not the committed step of glycolysis?

5. In two steps of glycolysis, ATP is synthesized by a substrate level phosphorylation. What must be true about the phosphate bond in the glycolytic intermediate for this to occur. Using structural formulae diagram these two steps. Remember that each of these steps in glycolysis is really the summation of two reactions.

6. Most bacteria utilize the pentosephosphate and glycolytic pathways concurrently. What are the primary advantages to the cell of the pentose phosphate pathway.

7. The pentose phosphate pathway converts glucose to the 5-carbon sugar ribulose by oxidizing glucose.

A. Using structural formulae draw these reactions.

B. What important co-enzyme is re-generated by these reactions, and for what will the cell utilize it?
C. After the oxidative stage of the pentosephosphate pathways, what is the fate of excess 5-carbon sugars?

8. Using structural formulae, diagram the reactions that will convert glucose to glyceraldehyde 3-phosphate and pyruvate, without going through a fructose intermediate. What is the name of this pathway? How many ATPs will ultimately be generated by converting both products to two molecules of pyruvate?

9. The ability to make partial diploid bacterial cells for the lac operon was crucial in determining the roles of the individual trans and cis-acting elements.

A. Define cis and trans acting elements? What constitutes a cis or trans acting factor?
B. For the following examples determine whether the transcription of the LacZ, the gene which encodes beta-galactosidase is inducible, noninducible, or constitutive. Determine whether the bacteria would survive on lactose as the sole carbon source.

Nomenclature:
    o⁺   wild type operator.
    o^c   an operator that cannot bind the repressor.
    i⁺   wild-type repressor.
    i^-    repressor that cannot bind the operator.
    i^d   repressor that cannot bind lactose.
    z⁺ wild-type beta-galactosidase protein.
    z^-    beta-galactosidase protein with no enzymatic activity.

Haploid cells

i⁺o^cz^-                i^do^cz⁺            i^-o⁺z-            i^do⁺z⁺

Partial diploid cells

i^do⁺z⁺/i⁺o^cz^-             i^-o⁺z⁺/i⁺o⁺z^-        i^do^cz⁺/i^-o⁺z^-        i⁺o⁺z-/i^-o⁺z⁺

10. Describe the relative level of lac operon transcription (high, low, none) and the level of cAMP (high, low) that would be found in cells under the following conditions.

Carbon source	lac operon transcription	cAMP levels
glucose
maltose
lactose
glucose and lactose
glucose and maltose
lactose and maltose

11. Transcription of the lac operon is under both negative and positive control. Explain.

12. How is the level of cAMP in the cell regulated by the glucose levels.

13. Fatty acids are often used as carbon sources for the generation of the energy. Two carbon units are removed from fatty acids by "oxidize-hydrolyze-oxidize." Remove a two carbon unit from a fatty acid (do not forget the "SCoA steps." How many ATP's can be produced by the complete catabolism of this two carbon unit?

14. Per carbons oxidized to CO2, what molecule is a more efficient energy storage molecule, glucose or a fatty acid? Explain.

15. What enzyme converts oxaloacetate and acetyl-CoA to citrate? Draw the reaction.

16. Two enzymes in the TCA carry out two step reactions. Each reaction goes through an intermediate. What are the names of these two enzymes? Using structural formulae draw the reactions.

17. What types of reactions do dehydrogenases catalyze? What types of co-enzymes do they usually require? What four reactions in the TCA utilize dehydrogenases. Using structural formulae diagram these reactions.

18. How is the conversion of succinate to oxaloacetate similar to the oxidation of fatty acids?

19. The reaction catalyzed by succinyl CoA ligase generates succinate and GTP. This process is the summation of two reactions. Using structural formulae, diagram those reactions. What can be said about the deltaG of hydrolysis of the SCoA bond?

20. What critical difference between the TCA and glyoxalate cycles allow some bacteria to grow with two carbon molecules, such as acetate, that can be converted to acetylCoA? Hint: remember the carbon source must be the carbon source for both catabolism and anabolism?

21. What reactions do the TCA and glyoxalate cycles have in common? What two reactions are unique to the glyoxalate cycle. Using structural formula diagram these reactions.

22. Describe the individual functions of the F0F1 complex? Describe the reactions that occur at the O, L, and T sights of the F1 subunit,

23. Under both aerobic and anaerobic conditions, the cell must regenerate its supply NAD+. How is this done under aerobic conditions? Anaerobic conditions?

24. Under anaerobic conditions, what are the two most common fates of the molecule pyruvate in microorganisms. Using structural formulae draw the reactions in these two pathways?

25. What are the four types of anaerobic respirators?