University of Florida PHA Biology Discussion Questions

I’m working on a biology multi-part question and need an explanation and answer to help me learn.

1. With respect to thermodynamics, why can biosynthetic pathways not be simply considered the reverse of corresponding catabolic pathways?
2. Compare the net equations of glycolysis and gluconeogenesis and explain why the synthesis of glucose is so costly.
3. Why is the biosynthesis of glucose so important in mammals?
4. List the following:

1. Most common precursors for glucose biosynthesis
2. Organs which use glucose as their primary energy source
3. Organs or tissues where gluconeogenesis takes place

1. Explain in detail how both glycolysis and gluconeogenesis can be irreversible cellular processes.
2. What drives the conversion of fructose 1, 6- bisphosphate to fructose 6 -phosphate?
3. Describe the role of malate transport in gluconeogenesis.
4. How does fatty acid oxidation contribute to gluconeogenesis? Under what conditions do amino acids get converted to glucose?
5. What are the effects of G6P, F1,6-BP, F2,6-BP on glycolysis and gluconeogenesis?
6. What are the effects of cAMP, AMP, ATP, citrate and acetyl-CoA on glycolysis and gluconeogenesis?
7. How many ATP equivalents are required to synthesize a glucose from two pyruvate in order to bypass the irreversible steps in glycolysis?
8. Why are sugar nucleotides suitable for biosynthetic reactions?
9. How does F2,6-BP control the conversion of F6P to F1,6-BP or the reverse?
10. In the final stages of gluconeogenesis, glucose-6-phosphatase converts glucose-6-phosphate to free glucose and inorganic phosphate. Where does this occur?
11. Read the article below. This study addresses the synthesis of a trisaccharide that humans do not metabolize. Why are studies such as this and others which examine bacterial systems for enzymatic activity on carbohydrates ultimately beneficial to addressing human health concerns?
    Perrin V, Fenet B, Prally J, Lecroix F, and Ta CD. (2000) Carbohydrate Research, 325 (3): 202-210.
12. Hepatocytes are an important model for in vitro study of metabolism. Read the article below and describe how the supplementation of cell culture media with amino acids and hormones affected the activity of hepatocytes and the occurrence of futile cycles. Chan C, Berthiaume F, Lee K, and Yarmush M. (2003) Metabolic Engineering, 5 (1): 1-15.
13. Solubilization of dietary lipids, achieved by mixing bile salts and degrading them with pancreatic lipases, is required for transport across the intestine where the free fatty acid and the lysophospholipid can then be resynthesized into triacylglycerols in the intestinal mucosal cells. Why is this necessary?
14. Describe how and why the above differs from the transport of fatty acids into the mitochondria?
15. Fatty acid oxidation occurs in the mitochondrial matrix. In review, where did the oxidative catabolism of glucose take place?
16. How are triacylglycerols functionally sequestered within adipose cells prior to a hormonal signal which causes them to be released into the bloodstream?
17. Explain in detail how different types of lipids are transported in blood to AND from adipose tissue.
18. What is the energetic cost of fatty acyl-CoA formation and where does this fatty acid activation take place?
19. Explain the roles of the two pools of coenzyme A and the processes utilized to keep these pools separate.
20. What types of reactions make up the 4 basic steps of β-oxidation?
21. Describe the enzyme complexes that receive electrons form the reduced electron carriers.
22. How many molecules of ATP are generated by the reoxidation of each type of electron carrier?
23. Compare saturated and unsaturated fatty acid oxidation with respect to the amount of ATP formed.
24. Explain how odd-chain fatty acid oxidation differs from even chain fatty acid oxidation beginning with the 5 carbon fatty acyl-CoA encountered in the last pass through the β-oxidation sequence?
25. Where in the cell are Ketone bodies made, from which metabolite are they made, and how and where are ketone bodies used?
26. Outline the oxidation steps that occur in omega ( ω ) oxidation.
27. We have touched on saturated/unsaturated and even-/odd-numbered chain fatty acids, but dietary consumption also includes branched chain fatty acids. Locate and read the following article, and answer the questions below: Mukherji M, Schofield CJ, Wierzbicki AS, Jansen GA, Wanders RJA, and Lloyd M. (2003). Progress in Lipid Research, 42 (5): 359-376.
    1. In which organelle not previously mentioned in this assignment does metabolism of some branched-chain fatty acids occur?
    2. According to your text and this paper, what is the primary pathway for oxidation of long chain fatty acids in this
       organelle?
    3. What name is given the oxidative pathway for branched-chain fatty acids?
    4. What, in general terms, is an oxygenase?
    5. In the proposed mechanism for 2-hydroxyphytanoyl-CoA lyase, what two products result from the attack of TPP on thioester?