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THE UNIVERSITY OF AUCKLAND

INCOURSE TEST 2011

BIOLOGICAL SCIENCES Foundations of Biochemistry

BIOSCI.106SC WEDNESDAY, 24 AUGUST 2011 6.30 - 8.30 P.M.
(Time Allowed: TWO hours)

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PLEASE COMPLETE THE FOLLOWING:

Family Name:

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First Name:

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Signature:

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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, 24 August 2011 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 30718916. 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 30718916
(40 marks) (Recommended time: 40 minutes)

Choose ONE correct answer from the alternatives provided.

Question 1:

The amino acid glycine has a side chain which consists of only a hydrogen atom. This means that glycine: 1. is not incorporated into -helices in proteins. 2. does not have D- and L- optical isomers. 3. is not able to be involved in any tertiary structure interactions. 4. does not form a zwitterion as a free amino acid. The side chain of the amino acid asparagine is means that the side chain will be: 1. basic. 2. able to form hydrogen bonds. 3. able to ionise at low pH. 4. predominantly hydrophobic. . This

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Question 3:

A polypeptide chain consists of a series of amino acid residues joined into a chain by peptide bonds. Which of the following is NOT true? 1. The amino acid sequence carries all the information to determine the tertiary structure of the protein. 2. The sequence of amino acids is called the primary structure of the protein. 3. The C atoms of adjacent amino acid residues are almost always in a trans conguration about each peptide bond. 4. Only one amino group and one carboxyl group will be present in the polypeptide. An -helix is a form of protein secondary structure that has 3.6 residues per turn of helix. The non-integral repeat arises because it: 1. allows the formation of base pairs on the inside of the helix. 2. leads to formation of an amphipathic helix. 3. prevents clashes between neighbouring amino acid side chains. 4. positions the C=O and N-H groups to give favourable linear hydrogen bonds.

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BIOSCI 106

Denaturation of a protein describes the process in which: 1. side chains become modied by enzymes. 2. unnatural amino acids are introduced to a protein structure. 3. a protein loses its biologically active three-dimensional structure. 4. the natural amino acid sequence of a protein is changed. Which of the following is NOT an example of post-translational modication? 1. hydroxylation of proline 2. ionisation of an aspartic acid or glutamic acid side chain 3. glycosylation of an asparagine side chain 4. phosphorylation of serine or threonine residues Some serious neurodegenerative diseases are associated with the formation of amyloid deposits. These result from: 1. the interaction of proteins with toxins. 2. the burial of hydrophobic residues between -helices. 3. mutations which cause the protein molecules to precipitate. 4. protein misfolding which results in -sheet aggregates. The structure of a particular protein is found to consist of three domains. This means that: 1. its polypeptide chain is organised into three separately-folded regions. 2. it is oligomeric. 3. it forms a trimer. 4. it is likely to have three different functions. The formation of coiled-coil brous protein structures depends on: 1. the formation of disulde bonds as in hair or wool. 2. proline residues which disrupt normal -helix formation. 3. the burial of hydrophobic side chains between amphipathic helices. 4. repetition of a three-residue repeat (Gly-X-Y). Drugs directed against the inuenza virus neuraminidase are based on: 1. blocking the ability of the virus to enter cells. 2. blocking the ability of the neuraminidase to cleave sialic acid residues. 3. preventing processing of the viral polyprotein during maturation. 4. disrupting the structure of the neuraminidase protein. The presence of an enzyme will: 1. speed up only the rate of product formation. 2. increase the activation energy of the reaction. 3. lead to the production of more product than would be made in a non-enzymic reaction. 4. produce the equilibrium amount of the product more quickly. CONTINUED

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Question 12:

In a simple enzyme reaction Vmax is the: 1. maximum rate at which the enzyme can work. 2. rate of product formation. 3. rate at which enzyme binds substrate. 4. equilibrium constant for substrate binding to the enzyme. A particular enzyme is only active when composed of both a protein part and a prosthetic group. The complete or active form of the enzyme is known as the: 1. apo protein. 2. pro-protein. 3. pre-protein. 4. holo protein. In the case of competitive inhibition, at a xed concentration of inhibitor, the addition of an excess of substrate will: 1. stop the reaction. 2. remove the inhibitory effect of the inhibitor. 3. prevent the formation of ES. 4. bind to the inhibitor. During an allosteric enzyme reaction, the rate is dependent on substrate concentration in a relationship that is described as: 1. hyperbolic. 2. exponential. 3. sigmoidal. 4. linear. In the Lineweaver-Burk plot the x and y axes are: 1. v/[S] and v. 2. 1/[S] and 1/v. 3. v and [S]. 4. v and v/[S]. For an allosteric enzyme reaction to be fully described it is necessary to evaluate: 1. Km only. 2. Vmax only. 3. Km, Vmax and h. 4. Vmax and Km. In an allosteric enzyme the heterotrophic effect is seen when: 1. an effector modies the activity of the enzyme. 2. a competitive inhibitor binds to the enzyme. 3. substrate binds to the enzyme. 4. an effector binds to the active site.

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Question 19:

The uidity of a biological membrane decreases when: 1. less cholesterol is present in the membrane. 2. less unsaturated (cis) lipids are added. 3. temperature is raised. 4. the average chain length of the lipids is increased. A membrane is found to transport one potassium and one chloride ion simultaneously into the cell. This type of transport is called: 1. symport. 2. biport. 3. uniport. 4. antiport. Which of the following DOES NOT contribute to the signicant energy release when ATP is hydrolysed in a cell? 1. resonance stabilization of the products 2. internal charge repulsion in the unhydrolysed molecule 3. proton release into a buffered system 4. charge repulsion in the products Glycogenolysis is a pathway for: 1. the breakdown of glucose to pyruvate. 2. producing NADPH for cell biosynthesis. 3. the breakdown of glycogen. 4. glycogen synthesis. Which of the following metabolic intermediates exists as a branch point for glycogen synthesis, glycolysis, and the pentose phosphate pathway? 1. fructose-6-phosphate 2. glyceraldehyde-3-phosphate 3. glucose 4. glucose-6-phosphate The conversion of two molecules of glucose to four molecules of pyruvate via glycolysis results in the net formation of: 1. four molecules of ATP 2. two molecules of ATP 3. thirty-eight molecules of ATP 4. two molecules of NADH There are three main points of regulation in glycolysis. In terms of what they have in common, they all involve reactions: 1. before the 6-carbon backbone is split into two 3-carbon compounds. 2. that are coupled to the synthesis of ATP from ADP. 3. where there is a large negative free energy change. 4. where chemical oxidation of the sugar backbone takes place.

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Question 26:

How many CO2 and ATP molecules are formed during two complete turns of the tricarboxylic acid cycle (Krebs cycle)? 1. 2 CO2 and 12 ATP 2. 2 CO2 and 16 ATP 3. 4 CO2 and 2 ATP 4. 2 CO2 and 1 ATP Which of the following is a product of the pentose phosphate pathway? 1. NADH 2. pyruvate 3. ATP 4. xylulose-5-phosphate How many ATP molecules can be ultimately derived from two molecules of acetyl CoA that enter the Krebs cycle? (Assume NADH yields 2.5 ATP and FADH2 yields 1.5 ATP.) 1. 10 2. 38 3. 18 4. 20 Which of the following is NOT produced in any of the steps of glycolysis? 1. ATP 2. ADP 3. NADH 4. NAD+ What type of linkage occurs between the glucose units in the following diagram?

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1. 2. 3. 4. Question 31:

-l,6 -1,4 -l,6 -l,4

When pyruvate is converted to acetyl-CoA: 1. carbon dioxide, NADH, and ATP are formed. 2. NADH and carbon dioxide are formed. 3. NADH and ATP are formed. 4. carbon dioxide and ATP are formed. CONTINUED

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Question 32:

Liver glycogen breakdown is stimulated by: 1. both glucagon and epinephrine. 2. insulin. 3. glucagon. 4. epinephrine. Which of the following is NOT a true statement? 1. Glycogen formation is favoured when intracellular energy status is low. 2. Muscle glycogen is broken down enzymatically to glucose-1phosphate. 3. Glucagon has generally antagonistic actions to those of insulin. 4. Liver glycogen is important in the maintenance of the blood glucose concentration. A principal product of the Krebs cycle is: 1. acetyl-CoA. 2. reduced electron carriers. 3. oxidized electron carriers. 4. ADP. Which of the following is a true distinction between fermentation and cellular respiration? 1. Only respiration oxidizes glucose. 2. Fermentation, but not respiration, is an example of a catabolic pathway. 3. NADH is converted to NAD+ only in fermentation. 4. NADH is oxidized by the electron transport chain only in respiration. In cellular respiration, O2 is used: 1. in fermentation. 2. in the Krebs cycle. 3. as a terminal electron acceptor. 4. in glycolysis. The chemiosmotic generation of ATP is driven by: 1. substrate-level phosphorylation. 2. the addition of protons to ADP and phosphate using enzymes. 3. a difference in hydrogen ion concentration on either side of a membrane. 4. osmotic movement of water into an area of high solute concentration. 5 mL of a riboavin solution contains 0.25 mol. The concentration of the solution is: 1. 0.05 mM 2. 0.05 mmol/mL 3. 0.05 mol 4. 0.05 M CONTINUED

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Question 39:

The pI of a protein: 1. is the pH at which it does not move in an electrical eld. 2. is the pH at which it has no charged groups. 3. alters depending on how much acid or alkali is present. 4. is always 7. Three proteins A, B and C were run on an electrophoresis apparatus using a buffer of pH 8. The pIs of the proteins are as follows: A pI = 5.0 B pI = 7.5 C pI = 11.0 Indicate the expected movement of these proteins. 1. 2. 3. 4. A and C will always move an equal distance in opposite directions from the origin. A and B move towards the +ve electrode. C only will move towards the anode. B will not move at all.

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)

In the space below, draw a structural diagram for a polypeptide chain with the amino acid sequence: Ser-Aly-Ala. [Note: the side chains for these amino acids are: CH2-OH; -H; -CH3 respectively.] In the diagram you should clearly indicate: (i) the terminal amino and carboxyl groups (ii) the peptide bonds (iii) the bonds in the polypeptide chain that allow free rotation. (3 marks)

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41.

cont. (b) Explain, with the aid of a diagram in each case, how hydrophobic interactions between secondary structures play an important role in determining the structures of: (i) myoglobin and (ii) ribonuclease. (i) (4 marks)

(ii)

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

41.

cont. (c) List three factors that can cause a protein to become denatured. In each case, explain why the denaturation occurs. (3 marks) ____________________________________________________________ ____________________________________________________________ ____________________________________________________________ (ii) ____________________________________________________________ ____________________________________________________________ ____________________________________________________________ (iii) ____________________________________________________________ ____________________________________________________________ ____________________________________________________________

(i)

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

Q42 Total 9 For ofcial use

42.

(a)

The polypeptide chain of the protein lactoferrin is found to fold up into four domains. In the space below: (i) dene what is meant by the term domain. (1 mark)

____________________________________________________________ ____________________________________________________________ ____________________________________________________________ ____________________________________________________________

and (ii)

explain with the aid of a diagram how its domain structure helps lactoferrin to bind and release iron. (2 marks)

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42.

cont. (b) Myoglobin (Mb) and hemoglobin (Hb) have extremely similar tertiary structures but very different oxygen binding behaviour. (i) Draw the oxygen binding curves for both proteins in the graph below.

1.0 Degree of Saturation

0 Oxygen pressure

(ii)

Explain, in the box, how the two protein structures cause them to behave so differently.

(3 marks)

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42.

(c)

The diagram below shows a phosphorylcholine molecule bound in the antigen binding site of an antibody. (i) List TWO kinds of non-covalent interaction that help the antibody to recognise the phosphorylcholine molecule.
(1) ____________________________________________________ (2) ____________________________________________________

(ii)

Show on the diagram where these interactions occur.

(3 marks)

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

Q43 Total 10 For ofcial use

43.

An enzyme, Aucklandase, has been found to have maximum activity when its active site contains a positively charged histidine amino acid and a negatively charged glutamic acid amino acid. In the box provided, draw a graph of the most likely dependence of enzyme rate versus pH for this enzyme. On the same graph draw the likely ionisation curves for the two amino acids. Indicate the pH for maximum enzyme activity and the pK values for the two amino acids. (10 marks)

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Q44 Total 5 For ofcial use

44.

(a)

Name TWO common features of membranes. (i) (ii) ________________________________________________________ ________________________________________________________

(b)

Name the THREE modes of membrane transport. (i) (ii) ________________________________________________________ ________________________________________________________

(iii) ________________________________________________________

(5 marks)

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

Q45 Total 15

45.

Fill in the gaps. (a)

For ofcial use

_________________________ and _______________________ are two enzymes other than phosphofructokinase that control the rate of glycolysis. (1 mark)

(b)

(i)

The structure above is the repeating unit of which structural polysaccharide? _____________________________________________.

(ii)

What is the deacetylated form called? _____________________________________________________ (1 mark)

(c)

Name three compounds that inhibit the activity of the pyruvate dehydrogenase complex. (i) (ii) ______________________________ ______________________________ ( mark) ( mark) ( mark)

(iii) ______________________________

(d)

What is one possible effect on the Krebs cycle following inhibition of the pyruvate dehydrogenase complex? ________________________________________________ ( mark) 4 CONTINUED
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45. cont.

(e)

What effects would abundant levels of acetyl CoA have on pyruvate carboxylase? ____________________________________ ( mark)

(f)

List the individual sugars which comprise lactose. ____________________________ and _________________________ (1 mark)

(g)

The diagram below shows part of the glycolytic pathway. In box (i) write the name of the enzyme that catalyses this reaction. In box (ii) write the name of the compound. In box (iii) write the letter of the corresponding compound labeled A, B, C, or D. In box (iv) write the name of the compound. (2 marks)

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

45. cont.

(h)

Read each statement and circle whether TRUE or FALSE. A.

(2 marks)

Insulin decreases the capacity of the liver to synthesize glycogen. False / True

B.

Insulin is secreted in response to high levels of blood glucose. False / True

C.

Glucagon and epinephrine have similar effects on glycogen metabolism. False / True Glucagon inhibits glycogen breakdown in liver. False / True

D.

(i)

What are the two main sites of glycogen storage?

(1 mark)

_______________________ and _________________________

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45.

cont. (j) Below is a schematic of the Krebs cycle. In boxes (i), (iii), and (vii) write the name of the enzymes that catalyse these reactions. (1 marks) In boxes (ii), (iv), (vi), and (viii) write the name of the compounds. (2 marks) In box (v) write the name of the reduced cofactor ( mark)

The name of the enzyme which is also part of the electron transport chain, is: ______________________________________ ( mark)

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

Q46 Total 10 For ofcial use

46.

(a)

The reaction below is catalyzed by the enzyme pyruvate kinase. (i) In what metabolic pathway does this reaction occur? __________________________________ (ii) ( mark)

Write in the left-hand box below the name of a compound that stimulates pyruvate kinase activity (Indicated by the + symbol) ( mark)

(iii) Write in the right hand boxes below the names of two compounds that inhibit pyruvate kinase activity. (1 mark)

(b)

Pyruvate kinase activity is also regulated by covalent modication. In the liver, insulin acts to dephosphorylate pyruvate kinase. In no more than two sentences describe what effect this has on activity and its signicance in terms of how glucose is metabolized in the liver by insulin. Do NOT write outside the box. (2 marks)

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BIOSCI 106

The scheme below shows the regulation of phosphofructokinase by compounds produced through glycolysis, the Krebs cycle, and the electron transport chain/oxidative phosphorylation.

(i)

In the boxes (on the diagram) write the names of the compounds that regulate phosphofructokinase activity. (1 marks) Name one other molecule that has an effect on activity of phosphofructokinase ______________________________________. State whether it activates or inhibits activity. ___________________ (1 mark) CONTINUED 2
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(ii)

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46. (c)

cont. (iii) During the biosynthesis of lipid in the liver, inhibition of phosphofructokinase leads to increased metabolic ux through the pentose phosphate pathway. What metabolite is produced by the pentose phosphate pathway that is important for lipid biosynthesis? ___________________________________________________ ( mark)

(iv) What two intermediates are shared by both glycolysis and the pentose phosphate pathway? ________________________________________________________ ________________________________________________________ ________________________________________________________ (1 mark)

(v)

In no more than TWO sentences describe the following and do NOT write outside the box. What are the effects of high levels of ATP and glucose-6-phosphate on glycogen phosphorylase activity? Under these conditions how does the epinephrine signalling modify this activity? (2 marks)

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