Exam questions

Question 1

Protein purification and characterization (6p)
You have a mixture of 3 enzymes (1, 2 and 3). A colleague was kind enough to run a 2D gel (see
figure below).
a) What information can you extract from the 2D gel?

You have at your disposal size exclusion columns and ion exchange columns.
b) How do you purify protein 1? Motivate your answer
c) How do you purify protein 2? Motivate your answer
d) How do you purify protein 3? Motivate your answer

Question 2

2. Bioinformatics (3p)
   a) What is the difference between divergent- and convergent evolution?
   b) Alignment tools are utilizing a scoring system. Briefly explain the purpose of the scoring system.
   c) What is a conservative substitution, in the context of sequence alignments?

Question 3

3. Enzyme regulation (4p)
   a) Briefly explain how allosteric regulators (also called effectors or modulators) act to regulate the
   activity of an allosteric enzyme.
   b) Which properties of the phosphate group make it suitable for causing structural change of a protein
   that is being regulated by phosphorylation/dephosphorylation?
   c) Why is zymogen activation not reversible?

Question 4

4. Biomolecules and signal transduction (7p)
   a. D-Glucose is a 6-carbon aldose and can be found in several interconvertible forms in the cell.
   Which ones? Explain their structures and how they differ from each other. (2,5p)
   b. Carbohydrates on the outside of a cell can be used as receptors for a virus. Describe how the
   influenza virus attack a host cell and continue to spread. (1,5p)
   c. Describe the insulin receptor and what happens to the receptor upon insulin binding. (3p)

Question 5

6. Glycolysis and gluconeogenesis (5p)
   6.1. How many ATP and NADH are produced when one glucose molecule is turned into pyruvate
   through glycolysis? (1p)
   6.2. What is the electron carrier used in gluconeogenesis? (1p)
   6.3. What is the most important reaction that is controlled to regulate glycolysis? Explain how this is
   achieved. (1p)
   6.4. Which reaction is catalyzed by the enzyme aldolase in glycolysis? Explain what are the substrate
   and product. (1p)
   6.5. What is the prosthetic group in pyruvate carboxylase? What is the function of this prosthetic
   group? (1p)

Question 6

. Citric acid cycle and oxidative phosphorylation (5p)
7.1. What is the function of pyruvate dehydrogenase complex? Write the overall reaction that is
catalyzed by pyruvate dehydrogenase complex. (1p)
7.2. Citric acid cycle is considered as a metabolic hub, why? (1p)
7.3. When every two-carbon fragment is changed into CO2 through citric acid cycle, how many GTP
(or ATP) are produced? How many NADH and FADH2 are produced? (1p)
7.4. What is proton motive force? Explain how proton motive force is formed. (1p)
7.5. Describe the basic structure of ATP synthase and explain how it generates ATP. (1p)

Question 7

8. Photosynthesis – light reaction (3p)
   8.1. Explain why water-oxidizing complex is able to split water, a very stable molecule, to generate
   oxygen gas. (1p)
   8.2. What is/are the product(s) of cyclic electron flow in photosynthesis? Explain. (1p)
   8.3. What is common between oxidative phosphorylation and photophosphorylation? (1p)

Question 8

9. Calvin cycle and pentose phosphate pathway, cont.
   9.2. For every CO2 molecule to be converted into carbohydrate in Calvin cycle, how many NADPH
   is/are needed? How many ATP is/are needed? Explain. (1p)
   9.3. Calvin cycle and pentose phosphate pathway use similar enzymes in some of their reactions.
   What are these enzymes, and what kind of reactions are catalyzed by these enzymes? (1p)
   9.4. In pentose phosphate pathway, the flow of glucose 6-phosphate depends on the need for three
   molecules. What are these three molecules? (1p)

Question 9

10. Glycogen metabolism (4p)
    a. Glycogen phosphorylase is an important enzyme involved in glycogen degradation. Describe its
    action on glycogen and why additional enzymes are needed for complete glycogen degradation. (2p)
    b. By what mechanism(s) is glycogen phosphorylase regulated? What are the major ways for
    regulation of this enzyme in the liver and the muscle cells respectively? (2p)

Question 10

11. Fatty acid metabolism (4p)
    Describe the initial round of beta oxidation of a 18:1(Δ9)-CoA. What steps are included, in what form
    is energy produced and what are the end products? Names of enzymes or intermediate products are
    not needed.

Question 11

12. Protein turnover and amino acids (4p)
    Write the missing words.
    a. Protein to be degraded are marked with (i) _____ and degraded in the (ii)________. (1p)
    b. Excess nitrogen is transported from muscles to the (i)_______ in the blood in the form of (ii)
    _________, where the nitrogen is converted to (iii) __________ in an energy consuming reaction
    cycle using (iv) _________ per molecule. (2 p)
    c. Nitrogen-fixing mikroorganisms fix atmospheric nitrogen into the form of (i) _______ in an energy
    consuming reaction catalyzed by (ii) _________ (1p)

Question 12

13. Cholesterol biosynthesis (6p)
    How is cholesterol synthesized in the liver cells?