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Chem 454 – Regulatory Mechanisms in BiochemistryReview for Exam I - Spring 2003

Chapter 14 – Metabolism: Basic Concepts and DesignBe able to:

• Classify organisms based on their source of energy.• Describe the energy requirements for living organisms.• Describe relationships between energy and metabolism. (Question 1)• Discuss phosphoryl transfer potentials and their importance in metabolism. (Question 1)• Demonstrate an understanding of free energy, DG, standard free energy, DG° or DG°’, and the

dependence of these terms on the concentrations of products and reactants in a reaction, and on theequilibrium constant, Keq, for a reaction. (Question 4)

• Describe the factors that contribute to a high negative free energy for phosphoryl transfer. (Question 2)• Discuss the relationship between oxidation and metabolism. (Question 1)• Describe the structures of the nucleotides that are used in oxidation/reduction reactions.• Describe some of the activated carriers that we have encountered so far, including ATP, NADH, FADH2,

FMNH2, CoenzymeA, Lipoamide and Biotin. (Question 3)• Describe why the stability of activated carriers is important.• Classify reactions according to reaction type: oxidation/reduction, ligation, group transfer, hydrolytic or

lyase (addition/elimination).• Discuss the different ways in which the rates of metabolic reactions are controlled.

Chapter 15 – Signal-Transduction Pathways: An Introduction to Information MetabolismBe able to:

• Discuss the function of signal transduction pathways.• Describe the relationship between signal molecules, such as hormones, and the signal that reaches the

inside of a cell.• Give some specific examples of primary and secondary messengers. (Question 5)• Discuss the role that protein phosphorylation plays in signal transduction.• Describe the signal transduction pathway for the 7-transmembrane helix receptor/G-protein systems.

(Question 5)• Describe the signal transduction pathway for phosphotidylinositol bisphosphate systems.• Describe the signal transduction pathway systems, which have their receptors dimerize in response to

ligand bonding.• Discuss the roles that calcium ions and the protein calmodulin play in signal transduction.• Describe the link between certain diseases, such as cancer, and signal transduction pathways.• Discuss the concept of amplification as it is applied to signal transduction pathways.

Chapter 16 – Glycolysis and GluconeogeneisBe able to:

• Describe the steps in the glycolytic and gluconeogenic pathways. (Question 2), (Question 3)• Describe the structures of the intermediates in glycolysis and gluconeogenesis. (Question 2)• Discuss the role that oxygen plays in glycolysis and gluconeogenesis.• Discuss the purpose behind investing 2 ATP’s in the glycolytic pathway, when ostensibly, the purpose of

the pathway is to produce ATP.

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• Describe the mechanism of the triosephosphate isomerase reaction. (Question 4)• Describe the mechanism and energetics of the glyceraldehyde 3-phosphate dehydrogenase reaction.

(Question 2)• Describe the mechanism of the phosphoglycerate mutase reaction.• Describe the strategy used to produce phophoenolpyruvate, a molecule having a high negative free

energy for phosphoryl transfer.• Discuss the fates of the pyruvate that is produced by glycolysis.• Describe the protein fold that is often observed in nucleotide binding proteins.• Describe the pathways used for the entry of other sugars, such as galactose and fructose, into the

glycolytic pathway.• Discuss how the flow of material through glycolysis is regulated in response to the needs of the cell,

including both allosteric and covalent modification of phosphofructokinase and hexokinase. (Question 5)• Describe the strategies used to bypass the irreversible steps in glycolysis when carrying out

gluconeogenesis.• Describe the overall stoichiometry of the glycolysis, gluconeogenesis, alcohol fermentation and lactic

acid fermentation.• Describe the cellular location of glycolysis, gluconeogenesis and the citric acid cycle.• Discuss how glycolysis and glycuconeogenesis are reciprocally regulated to minimize substrate cycling.• Discuss some of the benefits of substrate cycling.• Discuss how the liver and muscles cooperate to provide the muscles with energy under anaerobic

conditions.

Chapter 17 – Citric Acid CycleBe able to:

• Describe the primary purpose of the citric acid cycle. (Question 6)• Discuss the various roles played by the citric acid cycle in cellular metabolism (Question 6)• Describe the steps in the citric acid cycle. (Question 3)• Describe the structures of the intermediates in citric acid cycle. (Question 6)• Discuss the role that oxygen plays in the citric acid cycle.• Discuss the roles played by such cofactors as CoenzymeA, NADH, FADH2, Thiamine pyrophosphate

and lipoamide. (Question 3)• Describe the mechanism for the pyruvate dehydrogenase reaction and the structure of pyruvate

dehydrogenase complex.• Discuss the mechanism for the citrate synthase reaction.• Describe the cofactor used in the aconitase reaction.• Compare the a-ketoglutarate dehydrogenase reactions with the pyruvate dehydrogenase reaction.• Describe the strategy used to produce GTP in the succinyl-CoA synthetase reaction. (Question 6)• Describe the overall stoichiometry for the citric acid cycle.• Discuss how the flow of material into the citric acid cycle is controlled by the allosteric and covalent

modification of pyruvate dehydrogenase to meet the needs of the cell.• Describe the points in the citric acid cycle that are under allosteric control and how this control is exerted

to meet the need of the cell.• Compare the outcomes of catabolism under aerobic versus anaerobic conditions.• Describe the glyoxylate cycle and discuss its purpose.