These are exams from other similar but not identical classes, to give some sense of how an exam might be constructed. Please note that in these classes, fewer, longer exams were given. Your exams will be shorter, since we have more of them...BIOCHEMISTRY - sample exam A

Choose 16 of the following questions to answer (6 points each)

1. How many essential amino acids are there? Why might some sources state a slightly higher number than this (hint: to answer this, you should explain what "essential" means.)

2. Identify the four size categories in which monosaccharides are typically found. Monosaccharides can be further classified into two chemically distinct groups: identify (name) and describe these.

3. What is the yield of ATP when each of the following substrates is completely oxidized to CO₂ by a human cell (assuming that glycolysis, citric acid cycle, and oxidative phosphorylation are fully active)?

a. phosphoenolpyruvate b. fructose 1,6-bisphosphate

c. FADH₂ d. NADH formed in citric acid cycle

e. glucose f. NADH formed by glycolysis

4. Why is glucose-6-phosphate converted to fructose-6-phosphate early in glycolysis? What is the end-product of this part (stage I) of glycolysis?

5. Three common disaccharides are sucrose, maltose, and lactose. For each, state a common nutritional source, and the component monosaccharides.

6. Three common homopolysaccharides are glycogen, starch, and cellulose. Fill in the following table:

source monomer form function is this human

(branched/unbranched) food? (yes/no)

starch

cellulose

glycogen

7. Glycolysis can be thought of as being comprised of two stages - ATP consumption and ATP formation. Briefly explain or describe this overview: what happens during stage I? What happens during stage II?

8. How many ATPs would you expect to be generated by complete metabolism of a 14C fatty acid? Show all work to explain your answer.

9. At what cellular location or compartment are fatty acids synthesized? Where are they metabolized?

10. Glucagon and epinephrine are released into the bloodstream in response to low concentrations of glucose. Briefly describe two ways these hormones affect the availability of glucose in the body. How do they differ?

11. Fig.1 describes an important regulatory pathway in glycolysis. Explain the allosteric regulation of phosphofructokinase. Why is this so important? (Do not forget to mention roles of ATP, AMP, citrate, and pH, and how they relate to metabolic rates)

12. Fig.1 describes an important regulatory pathway in glycolysis. Explain the hormonal regulation of phosphofructokinase. Why is this so important? (Do not forget to mention roles of ATP, AMP, citrate, and pH, and how they relate to metabolic rates)

13. Explain how ATP is formed by oxidative phosphorylation and electron transport in mitochondria. Explain how the proton gradient is established in mitochondria and how it is used to generate ATP.

14. Give one example of an o-glycosidic bond and one example of an n-glycosidic bond. How do these differ?

15. Certain muscle wasting diseases are caused by malfunctioning mitochondria. How would such a muscle get energy? Would a person with such a disease have to eat more, less, or the same amount of food in order to do work? Explain.

16. Oxygen is not utilized directly in the citric acid cycle, but this cycle is considered to be part of aerobic metabolism. Explain why oxygen is required for the citric acid cycle reactions to proceed, even though it is not consumed by any of these reactions.

17. Why are ketone bodies formed during starvation or diabetes? The liver lacks CoA transferase, so it cannot use ketone bodies as a source of energy. What happens to them? Why is this more of a problem for the brain than for the heart?

18. a. Indicate on Fig. 2 where the GTP is released.

b. Indicate on Fig. 2 where each of 2 CO₂ are released.

c. Indicate on Fig. 2 where each of 2 NADH are released.

d. Indicate on Fig. 2 where the FADH₂ is released.

e. What is the molecule entering at #1? Where did it come from?

19. Indicate on Fig. 2: the sites of three major regulatory steps, and identify one modulator (and its effect - positive or negative) for each.

20. Indicate on Fig 2: 5 sites at which amino acid metabolism feeds into the TCA cycle. For extra credit: for each pathway, give an example of an amino acid which enters the cycle there.

EXTRA CREDIT: Write you own question and answer it. HINT: this is you opportunity to show what you know. Do not ask yourself a question if you aren't sure of the answer. Ask the question you were sure would be on the exam, so you studied the material, and then somehow it was left off! Your score will depend on the quality of the question as well as the answer - up to a possible maximum of 6 pts.

BIOCHEMISTRY - sample exam B

1. For each of the following, indicate whether it is typical of eukaryotes (E), prokaryotes (P), both (B) or neither (N).

a. DNA as the hereditary material b. nuclear envelope

c. multicellular organisms d. ribosomes

e. membranous organelles f. cell wall

g. <0.2mm diameter h. plasma membrane

2. a. What is a homopolymer? -- a heteropolymer? Explain how they differ and how they are similar.

b. illustrate an example of a homopolymer and a heteropolymer carbohydrate, lipid, and protein, if possible. If this class of molecule does not exist, indicate N/A.

homopolymer heteropolymer

carbohydrate

lipid

protein

3. Identify each of the following amino acids, and indicate whether they would be most likely to be found on the surface or interior of a protein found in an aqueous medium.

4. Draw a titration curve for glutamine. Its pK_as are

5. Define or explain the following terms as they are used to describe protein structure:

a. primary structure

b. secondary structure

c. tertiary structure

d. quarternary structure

6. Draw two heterotetrapeptides linked by a disulfide bond. Use at least three amino acids not shown in question #3. Using the three letter symbols, identify each of the amino acids shown.

7. a. Draw and name a aldohexose in linear and a-pyranose forms

b. Draw and name a ketohexose in linear and ß-furanose forms

c. Draw your sugars in a dimer aldose-ketose a(1-->6)

d. Draw your sugars in a dimer aldose-ketose ß(1-->1)

e. Draw a dimer of your aldose ß(1-->4)

f. Draw a dimer of your aldose a(1-->6)

8. Identify the following structures: several molecular structures e.g. amino acids, sugars, etc. would be given ...

9. Considering lipids, proteins, and carbohydrates: which class of molecule is the most efficient biological energy storage form? Which is the best for very fast mobilization of stored energy? Explain.

10. Some homopolymers of glucose are effective for energy storage while others are effective structural molecules. Explain the chemical difference between the two types of polymer, and how this chemical difference leads to different structure and function.

11. For the following fatty acids pairs, indicate which would increase membrane fluidity.

several pairs of fatty acids would be given for comparison ...

12. a. Draw a sphingolipid b. a phospholipid c. a neutral lipid

d. What is the primary function of each of these categories of lipid. Explain why each structure is suited to its function.

e. carbohydrates are often found modifying lipids. Show where monosaccharide or oligosaccharides would be linked to these lipids (or indicate that such modification is not usual). What is usually the function of such saccharide moieties?

13. Explain the cohesive and adhesive properties of water at the molecular level. Distinguish between these two properties. Give a distinctive example of each.

BIOCHEMISTRY - sample exam C -- TAKEHOME

This is an open notebook, open book exam. The answers MUST BE TYPED - no handwritten work (other than diagrams and drawings) will be read. Answers should be limited to about 1 page double-spaced (or ½ page single-spaced). Explanations should be focused and brief (usually a sentence or two should suffice). Since you have a week to complete this, please take some care that your use of English is coherent. DO NOT CONSULT WITH OTHER STUDENTS. Answer 8 of these questions (12.5 points each)

1. If you read about a molecule called preprolipase (a) where would you expect to find it? (b) what would you expect to be the name of the active form? (c) what would be the function of the active form, and where might it be found? (d) describe what must take place to convert the inactive form to the active form? (e) are these processes likely to be reversible? Explain each portion of this answer.

2. What is cooperative binding? Explain the significance of cooperativity by comparing myoglobin and hemoglobin structurally, and relating the structures to their ability to bind and release oxygen. Why is this important physiologically?

3. Identify and describe the five levels of protein structure. What are the main forces which govern each? What is the significance of these levels of structure? Explain where each of the following might be found in a polypeptide, and its special role or function in protein structure:

a. hydrophobic amino acids

b. hydrophilic amino acids

c. cysteine

d. methionine

e. proline

4. Why is protein generally considered to be the final product of gene expression (rather than, e.g., carbohydrates or lipids)? Where do other biological molecules, like lipids and carbohydrates, come from? Does the genome control their production - and if so, how?

5. Eukaryotic post-transcriptional mRNA processing has several stages.

(a) briefly describe the series of events from transcription to finding cytosolic mature mRNA. A flow labeled diagram showing the products at different stages and naming the processes involved would be sufficient.

(b) Choose at least two of the processes described in (a) to describe and explain their (potential) importance. Possible topics include, but are not restricted to: evolution of functionally related genes (exon shuffling); more than one polypeptide product having sequences in common; mRNA half-life; mechanisms of mRNAs passing through the nuclear envelope.

6. What are the major important features or characteristics required for a useful vector?

(a) expression vector?

(b) cloning vector?

In addition to specific restriction sites, list (at least) 3 other types of DNA sequences or elements which need to be found in a vector in order for it to be used (a) for the expression of a recombinant protein in a eukaryotic cell or (b) for generating many copies of the DNA. Explain why each of these is important.

7. If a human gene is isolated from a cDNA library and also from a genomic DNA library, would you expect the sequences of these isolated DNAs to be the same or different? Explain. Which would you choose to use if your goal was to produce large quantities of the encoded polypeptide? Explain. Which would you choose to use if your goal was to study how this gene is regulated in people? Explain.

8. Gene regulation may occur at any of several reactions. Briefly outline the scheme of gene expression, pointing out the major regulatory steps. Which of these do you think might be likely targets for intervention? Explain your logic. (Note - there are many possible answers here).

9. Describe a specific operon - either the lac operon or the trp operon. Two distinct regulatory mechanisms must be described, and their relationship - how they are integrated with the organism's needs - must be described.