Faculty of Science & Technology

EXAMINATION PAPER

2019/2020 (April)

BIO1400

Metabolic Biochemistry

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Module leader: Dr Dirk Wildeboer

Time allowed: at home exam, available to submit for 24 h

guide time to complete exam: 2 h

Total number of questions: Thirty multiple-choice questions in Section 1

Seven short-answer questions in Section 2

Instructions to candidates: Answer ALL multiple-choice questions (MCQ). Indicate

the one correct option by highlighting it.

Answer ALL short-answer questions (SAQ).

Write your answers into this examination paper file

directly below each question.

Use the mark values to guide you on the amount to

write, you should not exceed one page for a 10-mark
question.

To allow for anonymous marking do not include your

name in the file or filename.

It is suggested to convert the file to pdf before

submitting through Turnitin.

Total number of pages: 16 (including the cover sheet)

Student ID Number: …………………………………………………………………

Marks Score: Total MCQ (out of 30):

Total SAQ (out of 70):
Total marks (out of 100):
This paper carries a weighting of 60 % of the overall assessment for the module.

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Section 1. Multiple-Choice Questions (1 mark each)

1. Select one correct statement

a) Anabolism is degradative metabolic pathway involving the breakdown of
macromolecules
b) Catabolism is a biosynthetic process involving the building up of macromolecules
c) Catabolism is an exergonic process
d) The overall change in Gibb’s free energy is less than zero for anabolic reactions.

2. Currencies of energy produced during the ten steps of glycolysis are:

a) Acetyl CoA and NADH
b) ATP and NADH
c) Acetyl CoA and ATP
d) pyruvate and ATP

3. The structural components of FAD are.

a) Adenine, ribose, phosphate and riboflavin
b) Cytosine, phosphate, pantothenic acid
c) Guanine, ribose, phosphate,
d) Thymine, phosphate, niacin

4. Niacin is the vitamin component of:

a) Acetyl Coenzyme A
b) ATP
c) FAD
d) NAD+

5. Components of acetyl coenzyme A include

a) Vitamin B5, adenine and cytosine
b) Thiamine, ribose and thymine
c) Pantothenic acid, adenine and ribose
d) Flavin, phosphate and uracil

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6. Select one correct equation relating to thermodynamics.
a) TH = G + S
b) G = H - TS
c) S = H - TG
d) H = G - TS

7. Glycogenolysis is:
a) biosynthetic and endergonic
b) degradative and exergonic
c) degradative and endergonic
d) biosynthetic and exergonic

8. Impaired glycogen utilisation is caused by genetic defects in glucose-6-phosphatase

enzymes in liver tissues. The condition is classified as _______________________.
a) Glycogen storage disease type I (von Gierke disease)
b) Glycogen storage disease type II (Pompe’s disease)
c) Glycogen storage disease type III (Cori’s disease)
d) Glycogen storage disease type IV (Andersen’s disease)

9. Which of the below is NOT a correct example for a lipid?

a) Diacyl glycerophosphatidylserine
b) Cholesterol
c) Lipase
d) Triacylglyceride

10. The catabolism of fats, especially unsaturated (omega-6), produces an important energy
source for the brain. What are these metabolites called?
a) Alkene bodies
b) Alcohol bodies
c) Aldehyde bodies
d) Ketone bodies

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11. Which of these statements on fatty acids is correct?
a) Animal fats contain only saturated fatty acids.
b) Plant fats contain only unsaturated fatty acids.
c) Humans can’t metabolise unsaturated fats.
d) Mammals can only introduce double bonds up to carbon 9 in the chain.

12. The figure below shows the absorption spectrum for chlorophyll a (solid line) and the rate
of photosynthesis in a plant (dashed line) over a range of wavelengths. Why are they
different?

a) Bright sunlight destroys photosynthetic pigments

b) Green and yellow wavelengths inhibit the absorption of red and blue wavelengths
c) Other pigments absorb light in addition to chlorophyll a
d) Oxygen given off during photosynthesis interferes with the absorption of light

13. What wavelength of light in the figure shown in question 12 is most effective at driving
photosynthesis?
a) 420nm
b) 450nm
c) 560nm
d) 680nm

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14. Di-sulfide bonds are a covalent link joining the side chains of which amino acid?
a) Arginine
b) Cysteine
c) Methionine
d) Tyrosine

15. Which of the following amino acids would most likely to be present within the
transmembrane domain of a protein due to its hydrophobic side chain?
a) Aspartate
b) Cysteine
c) Histidine
d) Isoleucine

16. Which of the following amino acids plays an important role as proton acceptor and donor
in the active site of enzymes?
a) Histidine
b) Proline
c) Serine
d) Tryptophan

17. Which of the following processes is NOT part of the biosynthesis of collagen?
a) Transcription
b) Hydroxylation of some proline residues
c) Addition of oligosaccharides to certain amino acid functional groups
d) Folding into anti-parallel beta-sheets

18. Fill in the missing amino acid: The hydroxylation of ___ is important for the stability of
collagen fibres.
a) alanine
b) glycine
c) proline
d) valine

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19. From some proteins, part of the polypeptide chain is removed by proteolytic enzymes to
generate the final mature and biologically active protein. Which of the below is NOT a correct
example for this process?
a) Removal of the active site of an enzyme to regulate metabolism
b) Activation of digestive enzymes in the gut by removal of an inhibitory domain
c) Removal of signal peptide once the protein has reached its cellular destination
d) Activation of blood coagulation by a cascade of enzyme activations

20. Which of the following is part of the nitrogen fixation process in diazotrophic bacteria?
a) MoFe cofactor
b) Sulfatase complex
c) Haber process
d) Pyridoxal Phosphate (PLP)

21. What is the role of ubiquitin in protein degradation?

a) To protect the protein from degradation
b) To facilitate unfolding of the tertiary structure
c) To selectively tag proteins for degradation
d) To bind the active site within the proteasome

22. Which of the following is an example of a proteolytic enzyme?

a) Degradase
b) Trypsin
c) Pepsinogen
d) Amylase

23. Which of the following can be used as carbon skeletons in the anabolism of new amino
acids?
a) Pyruvate
b) Oxaloacetate
c) α-ketoglutarate
d) All of the above

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24. In amino acid degradation, what process specifically converts excess nitrogen for
excretion?
a) Beta oxidation
b) Protease reactions
c) TCA / Krebs cycle
d) Urea cycle

25. In what order would the following compounds elute from a size exclusion
chromatography? Molecular weights – Vitamin B12 – 1.4 kDa, Haemoglobin – 64 kDa,
Alcohol dehydrogenase 82 kDa.
a) Alcohol dehydrogenase, Haemoglobin, Vitamin B12
b) Haemoglobin, Vitamin B12, Alcohol dehydrogenase
c) Vitamin B12, Haemoglobin, Alcohol dehydrogenase
d) Haemoglobin, Alcohol dehydrogenase, Vitamin B12,

26. What amino acid sequence would be produced from the mRNA strand below
representing the amino-terminal region of a peptide?

mRNA sequence: 5’ C A U G C A G U C U U A G A G 3’
a) His – Ala – Val – Leu – Glu
b) Val – Arg – Gln – Asn – Leu
c) Met – Gln – Ser
d) Tyr – Val – Arg – Ile - Leu

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27. Which of the following best describes non-essential amino acids?
a) Amino acids that must be obtained from the diet
b) Amino acids that are produced from nitrogen fixing bacteria
c) Amino acids that can be synthesised from select metabolic intermediates
d) Amino acids that are not needed and get degraded

28. The structure below represents a molecule of

a) β-D-fructose-6-phosphate
b) α-D-glucose-6-phosphate
c) Deoxyribose-6-phosphate
d) β-D-glucose-1-phosphate

29. The structure below represents a molecule of

a) Palmitic acid
b) Vitamin A
c) Cholesterol
d) Sphingomyelin

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30. What is the correct amino acid sequence for the peptide represented by the structure
below?

a) Lys-His-Ile
b) Gly-Asp-Pro-Val
c) Leu-Pro-Gln
d) Val-Pro-Arg

Section 2. Short Answer Questions (10 marks each – answer all 7 questions as
detailed as you can.

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Question 1: Metabolism (10 marks)

Fully describe the three steps in glycolysis in which a currency of energy is produced. Name
reactants, cofactors and products of the reactions and identify the currency of energy
produced [4, 3, 3 marks for the respective steps]

The final stage in glycolysis is the generation of ATP from the phosphorylated three-carbon
metabolites of glucose. Phosphoglycerate kinase catalyses the transfer of the phosphoryl group from
the acyl phosphate of 1,3-bisphosphoglycerate to ADP. ATP and 3-phosphoglycerate are the
products.

The formation of ATP in this manner is referred to as substrate-level phosphorylation because the

phosphate donor, 1,3-BPG, is a substrate with high phosphoryl-transfer potential.

Thus, the outcomes of the reactions catalysed by glyceraldehyde 3-phosphate dehydrogenase and
phosphoglycerate kinase are:

In this step, glyceraldehyde 3-phosphate, an aldehyde, is oxidized to 3-phosphoglycerate, a

carboxylic acid.

Then, NAD+ is concomitantly reduced to NADH.

And finally, ATP is formed from Pi and ADP at the expense of carbon oxidation energy.

Because of the actions of aldolase and triose phosphate isomerase, two molecules of glyceraldehyde
3-phosphate were formed and hence two molecules of ATP were generated. These ATP molecules
make up for the two molecules of ATP consumed in the first stage of glycolysis.

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Question 2 – Translation (10 marks)

Diphtheria is an infectious disease caused by a toxin. This is able to covalently modify

elongation factor 2 (eEF2).

a) Provide a general overview of the normal, eukaryotic translation process and explain
how this would be impacted by the diphtheria toxin. [7 marks]
In the first stage which is initiation, the ribosome gets together with the mRNA and the first tRNA so
translation can begin.

in the next stage, which is elongation, amino acids are brought to the ribosome by tRNAs and linked
together to form a chain.

in the last stage, which is termination, the finished polypeptide is released to go and do its job in the
cell.

Diphtheria toxin blocks protein synthesis in eukaryotes by inhibiting translocation.

b) Tetracycline is an antibiotic that treats bacterial infections such as chlamydia. It’s

mechanism of action is to bind the 30S ribosome subunit. Explain how this may
impact eukaryotic and prokaryotic translation differently. [3 marks]

Antibiotics are chemicals that kill prokaryotic cells but do not harm eukaryotic cells. They are
natural chemicals produced by fungi and bacteria that help to control their bacterial
competitors. For instance, tetracycline stops protein synthesis in prokaryotic cells by binding
to their unusual ribosomes. tetracycline does not stop protein synthesis in eukaryotic cells
because it does not bind to eukaryotic ribosomes.

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Question 3 – Proteins (10 marks)

Summarise the general structural elements of proteins. [6 marks]

The end products of the decoding process are proteins. They start with the information in the
cellular DNA. Proteins compose structural and motor elements in the cell, and they serve as the
catalysts for every biochemical reaction that occurs in living things. This array of functions derives
from a startlingly simple code that specifies a hugely diverse set of structures.

Each gene in cellular DNA contains the code for a unique protein structure. Not only are these
proteins assembled with different amino acid sequences, but they also are held together by different
bonds and folded into a variety of three-dimensional structures. The folded shape, or conformation,
depends directly on the linear amino acid sequence of the protein.

In reference to any one of the following examples explain how protein structure relates to
biological function: [4 marks]

- collagen
- haemoglobin
- myosin
- trypsin

because of the haemoglobin’s unique shape which is globular and made of four subunits of proteins
surrounding an iron group. It transports both oxygen and carbon dioxide

Haemoglobin undergoes changes to its shape to help make it more efficient in its function of

carrying oxygen.

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Question 4 - Lipids (10 marks)

The metabolism of dietary fats can be roughly divided into the following steps:

- emulsification of ingested fats

- degradation and uptake
- transport
- uptake by cells and storage or catabolic release of energy

Give as much detail about the biochemical processes involved as you can. [10 marks]

Lipid metabolism begins in the intestine where ingested triglycerides are broken down into
smaller chain fatty acids and subsequently into monoglyceride molecules by pancreatic
lipases, enzymes that break down fats after they are emulsified by bile salts. When food
reaches the small intestine in the form of chyme, a digestive hormone
called cholecystokinin (CCK) is released by intestinal cells in the intestinal mucosa. CCK
stimulates the release of pancreatic lipase from the pancreas and stimulates the contraction
of the gallbladder to release stored bile salts into the intestine. CCK also travels to the brain,
where it can act as a hunger suppressant.

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Question 5: Photosynthesis (10 marks)

a) The diagram above shows the light-dependent reactions of photosynthesis. Explain

how a proton gradient is established across the thylakoid membrane in the
chloroplast. Specify on which side of the thylakoid membrane protons accumulate.
[4 marks]
Each of respiratory enzyme complexes couples the energy released by electron transfer
across it to an uptake of protons from water in the mitochondrial matrix, accompanied by the
release of protons on the other side of the membrane into the intramembrane space. As
result, the energetically favourable flow of electrons along the electron transport chain
pumps protons across the membrane out of the matrix.

b) The chloroplasts in a plant cell have a mutation that causes hydrogen ions (protons)
to diffuse directly through the phospholipid bilayer of the thylakoid membrane.
Explain how and why this diffusion will affect the following: [6 marks]
i. Synthesis of NADPH
ii. Synthesis of ATP
iii. Calvin cycle

The thylakoid membrane is not able to generate an electrochemical gradient needed to produce ATP
via chemiosmosis.

The plant cells will not be able to produce ATP, as they will not be able to generate the
electrochemical gradient across the thylakoid membrane.

The Calvin cycle needs more ATP than NADPH, and the extra ATP is generated by cyclic
photophosphorylation without generating an excess of NADPH.

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https://www.pdsd.org/cms/lib6/PA01000989/Centricity/Domain/240/Proctor%20Booklet%20-
%202.5%20C-%20Photosynthesis%20Quiz%201462117199656.pdf

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Question 6 – Amino acid metabolism (10 marks)

Amino acids are not stored like carbohydrates or fats. Discuss the fates of excess amino
acids in the body. Include details on any processes involved. [10 marks]

When proteins are digested from the diet, it results in excess amino acids. However, they need to be
excreted safely. In the liver these amino acids are deaminated to form ammonia.

Since ammonia is a toxic and so it’s converted into urea for safe excretion.

In the stomach and small intestine, the digestion of proteins is broken down by protease enzymes

into amino acids.

When massive amounts of protein are eaten, the excess amino acids produced from digesting
proteins are transported to the liver from the small intestine. The liver controls the amino acid
concentration in the body, as excess amino acids which need to be excreted. The body is
unable to store proteins or amino acids. In the liver ammonia is formed by the deamination of
amino acids. Since it is toxic and can’t be allowed to accumulate in the body. It is then
converted to urea. Urea and water are released from the liver cells into the bloodstream and
transported to the kidneys where the blood is filtered, and the urea is passed out of the body
in the urine.

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Question 7 – Laboratory practicals (10 marks)

In the laboratory practical in this module you extracted and characterised a carbohydrate,
lipids and protein from different tissues. For any two of those summarise the main steps,
explain the main principles of the extraction and characterisation and how they relate to
specific properties of the molecules. [10 marks]

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