C483 Final Exam Study Guide

C483 Final Exam Study Guide

The final will be held in Chemistry 122 at 8 AM, Friday, July 28. There will be no excused absences for the final.

Final exam content

A. about 100 points covering topics particular to chapters 17-19. Major topics include: lipoproteins, three stages of fatty acid degradation, b oxidation, ATP accounting of fat catabolism, degradation of unsaturated and odd chain fatty acids, ketone bodies, synthesis of fatty acids, regulation of fatty acid metabolism, cholesterol synthesis and regulation, ammonia fixing pathway, glutamine synthetase, transamination mechanism, essential/nonessential amino acids, carbon sources of nonessential amino acids, role of THF, activated methyl cycle, ketogenic/glucogenic amino acids, entry of carbon backbone into metabolism for the amino acids on the slides, branched amino acid problems like #40, nitrogen cycle from muscle, urea cycle input and outcome and ATP expenditures, role of main amino acids in nitrogen metabolism, compartmentalization of cells, specialization of organs in metabolism, metabolism under well fed/fasting states, major points of pathway regulation, local regulation, covalent modification, insulin/glucagon/epinephrine effects, hexokinase/glucokinase, regulation of phosphorylase, diabetes

B. about 100 point cumulative exam. This exam will cover major themes and integrated concepts for the course, from chapter 1-15 and 17-19.

Final Exam format

It will be about 2/3 multiple choice, short answer, true/false and about 1/3 problems. The questions below will serve as a good review for the major topics of the course. Approximately 1/3 of the questions on the final will come directly from the questions below and the practice final exam. You are encouraged to use them as a study guide. You may work with others in the class to work through these problems. The instructor and AI will not assist you or provide answers.

Questions:

1. Pratt question 13.20, 14.14, 14.40, 14.59, 17.34, 18.41, 18.43, 19.28

2. Given a name, draw chemical structures of: ATP, all amino acids, carbohydrates from chapter 11, all glycolysis intermediates, all citric acid cycle intermediates. Know the 1 and 3 letter abbreviations for amino acids.

3. Explain the logic of these pathway regulations:

A. Phosphofructokinase, not hexokinase, is the main regulation site of glycolysis.

B. SuccinylCoA inhibits the entry of acetyl CoA into the citric acid cycle.

C. NADH inhibits pyruvate dehydrogenase.

D. Citrate inhibits the citric acid cycle and activates acetyl-CoA carboxylase.

E. Insulin leads to activation of glycogen synthase.

4. Describe each cycle/transport system (compounds, compartments, tissues) and explain its purpose:

A. malate/aspartate shuttle

B. citrate transport system

C. Cori cycle

D. glucose/alanine cycle

5. For each of these cofactors, explain its chemical function and give an example of a particular enzyme that would use it: TPP, PLP, biotin, FAD, NADPH. Be ready to draw mechanisms that incorporate these cofactors. (Structures of cofactors will be given.)

6. Drawing figures. In the spaces below, draw an appropriately shaped figure, including necessary axis labels.

A. A titration curve for lysine, with a side chain pKa of 10.5.

B. A DNA melting curve for a poly(AT) sequence and a poly(GC) sequence (indicate which is poly(AT) and which is poly(GC))

C. A plot of initial velocity versus substrate concentration for a Michaelis-Menton enzyme.

D. The same plot as (B), but the enzyme is treated with a competitive inhibitor

E. a pH profile for an enzyme with two key ionized residues: a cysteine with pKa 4.2 and a Histidine with pKa 8.2

F. Saturation curve for myoglobin and hemoglobin (indicate which is which)

7. Integrated metabolism

A. A molecule of glucose that you eat can eventually be transformed into part of a fatty acid that you store. Circle the pathways/cycles below that are part of this overall flow of carbon atoms. Cross out any that are not.

Gluconeogenesis, beta-oxidation, citric acid cycle, glycolysis, urea cycle, fatty acid synthesis

B. Trace the metabolic path of this glucose molecule through the enzymes it encounters along the way to being made into fat. Write all the enzymes in the list below into the proper places in the figure below. If the enzyme is not used, write its name in the “not used” box. If it is used, write the enzyme in the order that the carbon atoms from glucose encounter the enzymes.

Pyruvate dehydrogenase, fumarase, aldolase, lactate dehydrogenase, pyruvate kinase, acetyl CoA carboxylase, fatty acid synthase, hexokinase, carnitine acyltransferase, ATP synthase

B. What is the minimum number of glucose molecules necessary to produce the carbon source for synthesis of a 16-carbon fatty acid through this pathway?

C. How many net glucose can be made from one molecule of a 16-carbon fatty acid?

8. Integrated metabolism

A. A molecule of glutamate that you eat can eventually be transformed into part of a glucose molecule that you store in your liver. Circle the pathways/cycles below that are part of this overall transformation. Cross out any that are not.

Gluconeogenesis, pentose phosphate pathway, glycogen synthesis, glycolysis, citric acid cycle

B. Trace the metabolic path of this glutamate molecule through the intermediates it becomes on the way to being glucose. Draw the structure of glutamate and a-D-glucose in the boxes. Indicate the order of transformation by writing “1”, “2”, etc next to each appropriate structure. Cross out the one molecule not involved in this pathway.

C. The nitrogen atom of glutamate must be removed by oxidative deamination, and is incorporated into a molecule that is excreted. Draw the structure of this molecule.