incourse test 2011

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VERSION 30718916 i BIOSCI 106

THE UNIVERSITY OF AUCKLAND

INCOURSE TEST 2011

BIOLOGICAL SCIENCES

Foundations of BiochemistryBIOSCI.106SC

WEDNESDAY, 24 AUGUST 2011 6.30 - 8.30 P.M.

(Time Allowed: TWO hours)

VERSION 30718916

Student Identification 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!)

CONTINUED


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VERSION 30718916 ii 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: Fill this in and pass it to the nearest aisle seat.

Short Answers: 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, first 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.

Test Format: (Total marks = 100)

ALL QUESTIONS MUST BE ATTEMPTED.

Multiple Choice Questions:

Section A: 40 marks

Short Answers:

Section B: 60 marks

Hand in the teleform answer sheet and short answer sheets (Sections B).

Retain your multiple choice question pages.

CONTINUED


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VERSION 30718916 2 BIOSCI 106

Section A:

MULTIPLE CHOICE QUESTIONS

Test Version Code 30718916(40 marks)

(Recommended time: 40 minutes)

Choose ONE correct answer from the alternatives provided.

CONTINUED

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.

Question 2: The side chain of the amino acid asparagine is . This

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.

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 configuration about each peptide bond.

4. Only one amino group and one carboxyl group will be present in

the polypeptide.

Question 4: 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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CONTINUED

Question 5: Denaturation of a protein describes the process in which:

1. side chains become modified 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.

Question 6: Which of the following is NOT an example of post-translational

modification?

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

Question 7: 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.

Question 8: 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.

Question 9: The formation of coiled-coil fibrous protein structures depends on:

1. the formation of disulfide 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).

Question 10: Drugs directed against the influenza 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.

Question 11: 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 anon-enzymic reaction.

4. produce the equilibrium amount of the product more quickly.


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CONTINUED

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.

Question 13: 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.

Question 14: In the case of competitive inhibition, at a fixed concentration ofinhibitor, 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.

Question 15: 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.

Question 16: 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].

Question 17: 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.

Question 18: In an allosteric enzyme the heterotrophic effect is seen when:

1. an effector modifies 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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CONTINUED

Question 19: The fluidity 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.

Question 20: 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.

Question 21: Which of the following DOES NOT contribute to the significant

energy release when ATP is hydrolysed in a cell?

1. resonance stabilization of the products2. internal charge repulsion in the unhydrolysed molecule

3. proton release into a buffered system

4. charge repulsion in the products

Question 22: 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.

Question 23: 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

Question 24: The conversion oftwo molecules of glucose to four molecules of

pyruvate via glycolysis results in the net formation of:

1. four molecules of ATP2. two molecules of ATP

3. thirty-eight molecules of ATP

4. two molecules of NADH

Question 25: 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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CONTINUED

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 ATP4. 2 CO2

and 1 ATP

Question 27: Which of the following is a product of the pentose phosphate

pathway?

1. NADH

2. pyruvate

3. ATP

4. xylulose-5-phosphate

Question 28: 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

Question 29: Which of the following is NOT produced in any of the steps of

glycolysis?

1. ATP

2. ADP3. NADH

4. NAD+

Question 30: What type of linkage occurs between the glucose units in the

following diagram?

1. -l,6

2. -1,4

3. -l,6

4. -l,4

Question 31: 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.


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CONTINUED

Question 32: Liver glycogen breakdown is stimulated by:

1. both glucagon and epinephrine.

2. insulin.

3. glucagon.

4. epinephrine.

Question 33: 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-1-

phosphate.

3. Glucagon has generally antagonistic actions to those of insulin.

4. Liver glycogen is important in the maintenance of the blood

glucose concentration.

Question 34: A principal product of the Krebs cycle is:1. acetyl-CoA.

2. reduced electron carriers.

3. oxidized electron carriers.

4. ADP.

Question 35: 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.

Question 36: In cellular respiration, O2

is used:

1. in fermentation.

2. in the Krebs cycle.

3. as a terminal electron acceptor.

4. in glycolysis.

Question 37: 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.

Question 38: 5 mL of a riboflavin solution contains 0.25 mol. The concentration of

the solution is:

1. 0.05 mM2. 0.05 mmol/mL

3. 0.05 mol

4. 0.05 M


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CONTINUED

QUESTION/ANSWER SHEETS FOLLOW

Question 39: The pI of a protein:

1. is the pH at which it does not move in an electrical field.

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.

Question 40: 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. A and C will always move an equal distance in opposite

directions from the origin.

2. A and B move towards the +ve electrode.

3. C only will move towards the anode.

4. B will not move at all.


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CONTINUED

THERE ARE NO QUESTIONS ON THIS PAGE.


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SECTION B

SHORT ANSWER QUESTION(60 marks)

(Recommended time 60-80 minutes)

QUESTION/ANSWER SHEET

FIRST NAME: ________________ FAMILY NAME: ________________________

ID NUMBER: ________________________

Q41

Total 10

For official use

CONTINUED

3

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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; -CH

3respectively.] 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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CONTINUED

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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. (4 marks)

(i)

(ii)


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ID NUMBER: ________________________

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CONTINUED

41. cont.

(c) List three factors that can cause a protein to become denatured. In each

case, explain why the denaturation occurs. (3 marks)

(i) ____________________________________________________________

____________________________________________________________

____________________________________________________________

(ii) ____________________________________________________________

____________________________________________________________

____________________________________________________________

(iii) ____________________________________________________________

____________________________________________________________

____________________________________________________________


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CONTINUED



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ID NUMBER: ________________________

CONTINUED

Q42

Total 9

For official use

42. (a) The polypeptide chain of the protein lactoferrin is found to fold up into four

domains. In the space below:

(i) define 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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CONTINUED

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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.

(ii) Explain, in the box, how the two protein structures cause them to

behave so differently.

(3 marks)

1.0

Degree

of

Saturation

0

Oxygen pressure


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CONTINUED



ID NUMBER: ________________________

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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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CONTINUED



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ID NUMBER: ________________________

CONTINUED

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Q43

Total 10

For official 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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CONTINUED


Q44

Total 5

For official use

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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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ID NUMBER: ________________________

45. Fill in the gaps.

(a) _________________________and _______________________are two

enzymes other than phosphofructokinase that control the rate of glycolysis.

(1 mark)

Q45

Total 15

For official use

CONTINUED

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(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) ______________________________ ( mark)

(ii) ______________________________ ( mark)

(iii) ______________________________ ( mark)

(d) What is one possible effect on the Krebs cycle following inhibition of the

pyruvate dehydrogenase complex?

________________________________________________ ( mark)


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(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)

45. cont.

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(h) Read each statement and circle whether TRUE or FALSE. (2 marks)

A. 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

D. Glucagon inhibits glycogen breakdown in liver. False / True

(i) What are the two main sites of glycogen storage? (1 mark)

_______________________ and _________________________



ID NUMBER: ________________________

CONTINUED

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45. cont.


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(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)

45. cont.

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CONTINUED


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46. (a) The reaction below is catalyzed by the enzyme pyruvate kinase.

(i) In what metabolic pathway does this reaction occur?

__________________________________ ( mark)

(ii) 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)



ID NUMBER: ________________________

Q46

Total 10

For official use

CONTINUED

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(b) Pyruvate kinase activity is also regulated by covalent modification. In the

liver, insulin acts to dephosphorylate pyruvate kinase. In no more than two

sentences describe what effect this has on activity and its significance in

terms of how glucose is metabolized in the liver by insulin. Do NOT write

outside the box. (2 marks)


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(c) The scheme below shows the regulation of phosphofructokinase by

compounds produced through glycolysis, the Krebs cycle, and the electron

transport chain/oxidative phosphorylation.

46. cont.

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CONTINUED

(i) In the boxes (on the diagram) write the names of the compounds that

regulate phosphofructokinase activity. (1 marks)

(ii) Name one other molecule that has an effect on activity of

phosphofructokinase ______________________________________.

State whether it activates or inhibits activity. ___________________

(1 mark)


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(iii) During the biosynthesis of lipid in the liver, inhibition of

phosphofructokinase leads to increased metabolic flux 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 doNOT 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)



ID NUMBER: ________________________

46. (c) cont.

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