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BIOSCI 106

THE UNIVERSITY OF AUCKLAND

INCOURSE TEST 2009

BIOLOGICAL SCIENCES Foundations of Biochemistry

BIOSCI.106SC WEDNESDAY, 26 AUGUST 2009 6.30 - 8.30 P.M.
(Time Allowed: TWO hours)

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Student Identication Form

PLEASE COMPLETE THE FOLLOWING:

Family Name:

_______________________________________________

First Name:

_______________________________________________

ID Number:

_______________________________________________

Signature:

_______________________________________________

Submit this page to supervisors at the beginning of the test. (Failure to do this may result in non-assessment of your script!)

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BIOSCI 106

THE UNIVERSITY OF AUCKLAND

BIOLOGICAL SCIENCES Foundations in Biochemistry
In-course Assessment Test Wednesday, 26 August 2009 6.30 - 8.30 p.m.

GENERAL INSTRUCTIONS Roll Slip: Short Answers: Fill this in and pass it to the nearest aisle seat. Print your name and I.D. at the top of EVERY ANSWER PAGE. Record your answers in spaces provided. All questions must be attempted.

Multiple Choice Questions: Use the Teleform Sheet. Use pencils only. Shade the rectangle completely. Do not cross out mistakes. ERASE them completely. Complete family name, rst name, initial and ID Number. Do not complete your stream. Fill spaces from left to right. Your code is 23669790. Check this is correct on your teleform. Failure to enter the version code or other details correctly will mean your MCQ cannot be marked. (Total marks = 100) ALL QUESTIONS MUST BE ATTEMPTED. 40 marks 60 marks

Test Format:

Multiple Choice Questions: Section A: Short Answers: Section B:

Hand in the teleform answer sheet and short answer sheets (Sections B). Retain your multiple choice question pages.

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Section A:
MULTIPLE CHOICE QUESTIONS Test Version Code 23669790
(40 marks) (Recommended time: 40 minutes)

Choose ONE correct answer from the alternatives provided.

Question 1:

The side chain of the amino acid tyrosine is

This means that it: 1. has the properties of an alcohol. 2. can form covalent bonds through its OH group. 3. has both hydrophobic and hydrogen bonding properties. 4. cannot participate in hydrophobic interactions. 5. is strongly acidic. For the polypeptide chain Ser-Pro-Ala-Val-Asp-Gly-Lys-Phe which statement is true? 1. There are two free carboxyl groups. 2. There are no hydrophobic groups. 3. The N-terminal amino acid is phenylalanine. 4. There are no free carboxyl groups. 5. There is one free amino group. An -helix is stabilised by: 1. proline residues, whose side chains add rigidity. 2. hydrogen bonding between stacked base pairs. 3. the separation of hydrophobic and polar residues on different faces. 4. hydrogen bonding between C=O and NH groups from adjacent residues along the polypeptide. 5. hydrogen bonding between C=O and NH groups that are separated by four residues along the polypeptide chain.

Question 2:

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Question 4:

Disulde bonds: 1. are covalent S-S bonds between cysteine residues. 2. are disrupted in acid by the formation of H2S. 3. are formed only at high pH when cysteine side chains are ionised. 4. are the strongest form of non-covalent interaction between amino acids. 5. cause proteins to fold into their biologically active structures. Proteins tend to be denatured at very low or very high pH. This occurs because: 1. hydrolysis of polar side chains occurs. 2. ionic interactions are disrupted. 3. the N- and C-termini repel each other. 4. hydrophobic interactions lose their strength at extremes of pH. 5. peptide bonds are broken and the polypeptide chains are cleaved. The glycine residues in the (Gly-X-Y) n repeat in collagen are necessary because: 1. their small size allows the three chains to pack closely together. 2. they are not optically active. 3. they allow amphipathic helices to form. 4. they are modied in a vitamin C dependent process. 5. they enable hydrogen bonding along the collagen chains. Which of the following is an example of post-translational modication? 1. Protonation of an acidic side chain. 2. Attachment of a sugar to an asparagine side chain. 3. Denaturation of a protein by heating. 4. Conversion of DNA into RNA. 5. Formation of disulde bonds. Oligomeric proteins are proteins in which: 1. the polypeptide chain is divided into several separately folded regions. 2. a number of subunits are held together by weak non-covalent interactions. 3. a number of different biological properties are combined. 4. several different types of polypeptide are combined into one protein. 5. cooperative interactions occur.

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Question 9:

Cooperativity occurs in haemoglobin because: 1. it is able to bind oxygen at the higher oxygen pressure that exists in the lungs. 2. it is tetrameric, with two subunits and two subunits. 3. the binding of oxygen to one subunit increases the oxygen afnity of the other subunits. 4. the eight -helices in each subunit pack together to give a very stable structure. 5. it contains haem groups. The structure of immunoglobulin domains is based on: 1. loop structures that create binding sites for antigen molecules. 2. puckered -sheets with alternating Gly and Ala residues. 3. a series of repeating amino acid sequence motifs. 4. an amphipathic helix packed against a -sheet. 5. two -sheets packed against each other. In an enzyme catalysed reaction the underlying reason for the increased rate is because the enzyme: 1. lowers the activation energy. 2. produces more product. 3. lowers the energy of the product. 4. lowers the energy of the substrate 5. increases the free energy change. In a simple enzyme reaction Km is: 1. the equilibrium constant for substrate binding to the enzyme. 2. the equilibrium constant for product binding to the enzyme. 3. the rate of product formation. 4. the rate at which enzyme binds substrate. 5. the maximum rate at which the enzyme can form product. For an enzyme which is active when composed of both a protein part and a prosthetic group, the protein part is known as the: 1. pre-protein. 2. holo-protein. 3. co-factor. 4. apo-protein. 5. pro-protein.

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For a simple enzyme reaction which shows competitive inhibition, the addition of more substrate to the reaction mixture, at a xed inhibitor concentration will: 1. remove the inhibitory effect of the inhibitor. 2. have no effect. 3. slow down the reaction. 4. leave Vmax unaltered. 5. leave Km unaltered. In an allosteric enzyme reaction, a substance which when added increases the rate of reaction with substrate but is not itself changed by the reaction is called: 1. co-substrate. 2. positive effector. 3. deactivator. 4. negative effector. 5. inhibitor. In the Eadie-Hofstee plot the y and x axes are: 1. 1/v and 1/[S]. 2. [S] vs v 3. v/[S] and v. 4. v and [S]. 5. v and v/[S]. For an enzyme which contains one positively charged amino acid at its active site the initial-rate vs pH prole is usually: 1. bell shaped. 2. exponential. 3. sigmoidal. 4. logarithmic. 5. linear. In an allosteric enzyme the heterotropic effect is seen when: 1. an effector modies the activity of the enzyme. 2. an effector competes with substrate for the active site. 3. an effector binds to the active site. 4. substrate binding changes the interaction between subunits. 5. the subunits of the enzyme do not interact. The uidity of a biological membrane increases when: 1. the average chain length of the lipids is increased. 2. temperature is lowered. 3. proteins are added. 4. more cholesterol is added to the membrane. 5. more unsaturated (cis) lipids are added.

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Question 20:

Which of the following is not correct? In biological systems, membranes normally: 1. have symmetric surfaces. 2. contain proteins. 3. are held together by non-covalent forces. 4. are very uid. 5. are made of a lipid bi-layer. A membrane transporter protein is found to simultaneously transport one potassium ion into and one sodium ion out of the cell. This type of transport is called: 1. uniport. 2. monoport. 3. symport. 4. equiport. 5. antiport. When ATP is hydrolysed in a cell a considerable amount of energy is released. Which of the following does not contribute to this energy change? 1. Internal charge repulsion in the unhydrolysed molecule. 2. Proton release into a buffered system. 3. Resonance stabilization of the products. 4. An increase in temperature. 5. Loss of hydration of ATP. Sucrose is a disaccharide formed from: 1. glucose and glucose 2. galactose and glucose 3. glucose and ribose 4. galactose and galactose 5. fructose and glucose The enzyme that catalyses the metabolism of acetaldehyde to ethanol belongs to a class of enzymes known as: 1. dehydrogenases. 2. kinases. 3. mutases 4. lyases. 5. hydrolases

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Question 25:

Which enzyme catalyses the reaction indicated by the question mark in the diagram above? 1. 2. 3. 4. 5. Glyceraldehyde-3-phosphate dehydrogenase. Phosphoglyceromutase. Triose phosphate isomerase. Pyruvate kinase. Enolase

Question 26:

Which of the following generates free glucose during the enzymatic breakdown of glycogen in skeletal muscle? 1. Phosphoglucomutase 2. Glycogen synthase 3. Amylase 4. Phosphorylase 5. Debranching enzyme When a muscle cell metabolises glucose in the complete absence of molecular oxygen, all of the following substances are produced except: 1. glucose-6-phosphate. 2. lactic acid. 3. acetyl-CoA. 4. ATP. 5. pyruvate. Which of the following is false about the pyruvate dehydrogenase complex? 1. It uses thiamine pyrophosphate as a cofactor. 2. It is located within the mitochondrial matrix. 3. Carbon dioxide is produced as a product. 4. The E2 subunit is called dihydrolipoyl transacetylase. 5. The E1 subunit is called dihydrolipoyl dehydrogenase. Which of the following statements is correct about fructose-2,6bisphosphate? 1. It is produced through the pentose phosphate pathway. 2. Glucagon lowers the levels of fructose-2,6-bisphosphate in liver. 3. It is produced by the enzyme phosphofructokinase. 4. It stimulates the activity of fructose-1,6-bisphosphatase. 5. It inhibits the activity of phosphofructokinase.

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In most tissues, an increase in the following ratio directly causes a decrease in TCA cycle activity: 1. GDP/GTP 2. ADP/ATP 3. NADH/NAD+ 4. NADP+/NADPH 5. FAD/FADH2 Which of the following statements about pyruvate is false? 1. It plays a role in the Cori cycle. 2. Under anaerobic conditions it can be converted to ethanol. 3. Under anaerobic conditions it can be converted to acetyl CoA. 4. Under anaerobic conditions it can be converted to lactate. 5. It can be converted into alanine. Embedded in the inner membrane of the mitochondrion are: 1. the components of the electron transport chain. 2. glycogen molecules. 3. glycolytic enzymes. 4. all the enzymes of the tricarboxylic acid cycle (Krebs cycle). 5. fructose-1,6-bisphosphatase. Which of the following statements concerning the electron transport system is false? 1. Coenzyme Q is a lipid component of the mitochondrial membrane. 2. A proton gradient is produced. 3. There are four major complexes each of which act as proton pumps. 4. All four complexes contain prosthetic groups. 5. The nal electron acceptor is oxygen. Name the enzyme involved in both the TCA cycle and the electron transport chain. 1. Pyruvate kinase 2. Hexokinase 3. Glycogen synthase 4. Succinate dehydrogenase 5. Glycogen phospohrylase Which of the following is not an enzyme in the gluconeogenesis pathway? 1. Aldolase 2. Phosphoglycerate kinase 3. Glucose phosphate isomerase 4. Enolase

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Question 32:

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Question 34:

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Question 36:

Which statement about glycogen phosphorylase is correct? 1. Its activity is not regulated by AMP. 2. Its activity is not regulated by phosphorylation. 3. It is converted to the less active phosphorylase b form by phosphorylase kinase. 4. Its activity is activated by insulin. 5. The active form can be deactivated by the enzyme phosphoprotein phosphatase. Which of the following is not a product of the pentose phosphate pathway? 1. Glyceraldehyde-3-phosphate 2. Ribulose-5-phosphate 3. D-erythrose-4-phosphate 4. D-xylulose-5-phosphate 5. ATP 10 nM is equivalent to: 1. 1 x 10-9 M 2. 1 x 10 4 M 3. 10 pmol/mL 4. 10 mol/L 5. 10 nmol/mL Calculate the amount of haemoglobin in a test tube if 1.5 mL of a 0.4 mg/mL solution of haemoglobin had 2.5 mL of buffer added to it. 1. 0.6 mg/mL 2. 600 g 3. 0.15 mg/mL 4. 0.6 x 10-3 g 5. 150 Two protein samples were run on an electrophoresis foil at pH 7. Both samples moved towards the +ve electrode. One sample moved twice the distance of the other. The following could be concluded from this: 1. They both had a pI below 7. 2. One had twice the number of ve charges than the other one. 3. One had a pI closer to 7 than the other. 4. One had a higher molecular weight than the other one. 5. One of the proteins had been denatured more than the other.

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Question 39:

Question 40:

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FIRST NAME: ________________ FAMILY NAME: ________________________ ID NUMBER: ________________________

SECTION B SHORT ANSWER QUESTION

(60 marks) (Recommended time 60-80 minutes)
Q41 Total 10 For ofcial use

41. (a)

The diagram below shows a portion of a polypeptide chain, in which the -carbon atoms are labelled C1, C2 and C3.

Use this diagram to answer the following questions: (i)

(3 marks)

Which amino acid residue (C1, C2 and C3) would not form optical isomers? Explain why and give its name. __________________________________________________________ __________________________________________________________

(ii)

Which amino acid residue (C1, C2 and C3) would not be able to participate in -helix formation? Explain why and give its name. __________________________________________________________ __________________________________________________________

(iii)

Which amino acid (C1, C2 and C3) has a hydrophobic side chain, and which has a side chain that can form hydrogen bonds? __________________________________________________________ 3 __________________________________________________________
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41.

(b)

In the space below, draw a diagram illustrating a 3-stranded antiparallel -sheet. What kind of interactions stabilise this structure, and what functional groups are involved in forming these interactions? (2 marks)

(c)

Explain what is meant by the term hydrophobic interactions and explain why hydrophobic interactions provide the driving force for the folding of most globular proteins. (2 marks)

(d)

Dene the meaning of the term domain, as applied to protein structure, and describe two ways in which the formation of domains can be important for the function of a protein. (3 marks)

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FIRST NAME: ________________ FAMILY NAME: ________________________ ID NUMBER: ________________________

Q42

42.

(a)

The structure of the protein -keratin is based on a coiled-coil structure. In the space below, draw a diagram For ofcial use that illustrates the main features of a coiled coil, and explain how regular repeats in the amino acid sequence of -keratin lead to the formation of this structure. (3 marks)

Total 10

(b)

The weedkiller glyphosate (the active ingredient of Round-up) has the chemical structure shown below. Identify THREE structural or chemical features of glyphosate that could be recognised by a human antibody and suggest in each case how this recognition might occur. (3 marks)

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42.

(c)

Write short notes to describe how knowledge of the interactions between the inuenza virus neuraminidase protein and sialic acid were used to design an anti-inuenza drug. (4 marks)

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FIRST NAME: ________________ FAMILY NAME: ________________________ ID NUMBER: ________________________

Q43 Total 15 For ofcial use

43.

(a)

In the box above and on the same graph draw the reaction prole for a simple chemical reaction (S Label appropriately. P) and an enzyme catalysed reaction. (11 marks)

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43.

(b)

Give the equations: (i) relating energy change and equilibrium constant and

(4 marks)

(ii) activation energy and rate.

Total 15 marks

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FIRST NAME: ________________ FAMILY NAME: ________________________ ID NUMBER: ________________________

Q44 Total 15 For ofcial use

44

(a)

Draw the Haworth projection (5-membered cyclic form) for the monosaccharide shown below with the anomeric carbon in the beta-position.

(2 marks)

____________________________________________________________ (b) Number the carbon atoms in your drawing above and write the name of the monosaccharide underneath the structure. (1 mark) The following diagram shows four sterioisomers of an aldotetrose. Answer the following questions below by selecting one or two from the following terms: diasterisomer; enantiomer; epimer for each question below.

(c)

(i)

(ii)

(iii)

(iv) (1 mark) (1 mark) (1 mark) 6

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Compounds (i) and (ii): __________________________________ Compounds (i) and (iii): __________________________________ Compounds (ii) and (iv): __________________________________

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44.

(d)

Write the number of the structures shown below in their respective positions in the glycolytic pathway. (2 marks)

(e)

Fill in the spaces: The pancreas releases the hormone ________________________ in response to high blood glucose and the hormone ___________________ in response to low blood glucose. (1 mark)

(f)

The nal step in gluconeogenesis involves the removal of the phosphate group from glucose-6-phosphate by the enzyme, ______________________ Does muscle contain this enzyme? (answer either yes or no) ___________ (1 mark)

(g)

How many molecules of ATP would be produced by the complete oxidation of 2 molecules of glucose via aerobic respiration taking into account the ATP generated by NADH and FADH2 and via GTP in the TCA cycle. Assume 2.5 ATP molecules produced for every NADH molecule (including the ones produced from glycolysis) and 1.5 ATP molecules for every FADH2 produced. Show calculations for partial credit. (1 mark) _____________________________________________________________ _____________________________________________________________ _____________________________________________________________ _____________________________________________________________ 5
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FIRST NAME: ________________ FAMILY NAME: ________________________ ID NUMBER: ________________________

(h)

In the situation on the previous page in (g), how many ATP would be produced if the TCA cycle enzyme, malate dehydrogenase, was completely inactivated? ( i.e. could not produce NADH). Show calculations for partial credit. (1 mark) _____________________________________________________________ _____________________________________________________________ _____________________________________________________________

(i)

In the situation described on the previous page for (g) how many ATP would be produced if complex 1 in the electron transport chain was inactivated by the inhibitor rotenone. Show calculations for partial credit. (1 mark) _____________________________________________________________ _____________________________________________________________ _____________________________________________________________

(j)

Name two enzymes in glycolysis which produce ATP from ADP by substrate level phosphorylation. ___________________ AND ___________________ (1 mark)

(k)

What are the other two other TCA cycle dehydrogenase enzymes in addition to malate dehydrogenase that produce NADH? ___________________ AND ___________________ (1 mark)

Total 15 Marks 4
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FIRST NAME: ________________ FAMILY NAME: ________________________ ID NUMBER: ________________________

Q45 Total 10 For ofcial use

45.

(a)

Name the two pentose phosphate products resulting from the reaction between D-xylulose-5-phosphate (5 carbons) and D-ribose-5-phosphate (5 carbons). ___________________ AND ___________________ (1 mark)

(b)

Name the two pentose phosphate products resulting from the reaction between D-fructose-6-phosphate (6 carbons) and D-erythrose-4-phosphate (4 carbons). ___________________ AND ___________________ (1 mark)

(c)

Name two enzymes that catalyse the reversible reactions described above. ___________________ AND ___________________ (1 mark)

(d)

High levels of acetyl CoA in the mitochondria can divert pyruvate metabolism into gluconeogenesis. Describe how this can occur through the effects of acetyl CoA on the activities of pyruvate dehydrogenase and pyruvate carboxylase. Do not write outside the box. (2 marks)

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45.

(e)

Outline the steps of the gluconeogenesis pathway from pyruvate to phosphoenolpyruvate. Do not write outside the box. (2 marks)

(f)

A deciency in a certain enzyme can lead to hemolytic anemia and loss of red blood cells. In the space below, state what this enzyme is called, the metabolic pathway involved, and how loss of this enzyme activity is linked to loss of red blood cells. Do not write outside the box. (3 marks)

Total 10 Marks

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