CONFIDENTIAL 1 AS/DEC 2014/BIO462

UNIVERSITI TEKNOLOGI MARA

FINAL EXAMINATION

COURSE : BIOCHEMISTRY
COURSE CODE : BIO462
EXAMINATION : DECEMBER 2014
TIME : 2 HOURS

ANSWER SCHEME

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QUESTIO ANSWER MARK

N S
a)
1 Carbonic acid-bicarbonate buffer system 1
b)
CO2 +H2O H+ + HCO3- 1
c)
During hyperventilation, the concentration of CO2 in the lungs 3
and arterial blood falls. This drives the equilibrium to the left,
which requires the consumptions of hydrogen ions, reducing
[H+] and increasing pH.
d)
pH = pKa + log ([base]/[acid]) 2
= pKa + log ([acetate]/ [acetic acid])
= 4.76 + log (0.20/0.60)
= 4.76 + (-0.48)
= 4.28
e)
In all natural (spontaneous) processes, the entropy of the 3
universe increases.
Example;
A hot frying pan. (System: pan. Surroundings: room air.)The
iron atoms in a hot frying pan (system) in a room
(surroundings) are vibrating very rapidly. The pans localized
energy thus becomes dispersed, spread out more widely to
molecules in the room air.

TOTAL 10
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2 a) One of each hydrophilic amino acids 3

b) One of each:
1. increases in temperature 2
2. alterations in pH
3. high concentrations of polar substances (Urea for
example)
4. Nonpolar substances

c) Differences as below:
the alpha helix (-helix) is a right-handed coiled or spiral
conformation, in which every backbone N-H group
donates a hydrogen bond to the backbone C=O group
of the amino acid four residues earlier
Beta sheets consist of beta strands connected laterally 2
by at least two or three backbone hydrogen bonds,
forming a generally twisted, pleated sheet. A beta strand
(also strand) is a stretch of polypeptide chain typically
3 to 10 amino acids long with backbone in an almost 2
fully extended conformation

d) concepts of primary, secondary, tertiary and quaternary

protein structure.
The primary structure refers to amino acid sequence of the
polypeptide chain
1
Secondary structure refers to highly regular local sub-
structures. Two main types of secondary structure are the
alpha helix and the beta strand. These secondary structures
1
are defined by patterns of hydrogen bonds between the
main-chain peptide groups. They have a regular geometry.
Tertiary structure refers to three-dimensional structure of a
single protein molecule.
The alpha-helices and beta-sheets are folded into a
compact globule. The folding is driven by the non-specific 1
hydrophobic interactions (the burial of hydrophobic residues
from water), but the structure is stable only when the parts
of a protein domain are locked into place by specific tertiary 2
interactions, such as salt bridges, hydrogen bonds, and the
tight packing of side chains and disulfide bonds. The
disulfide bonds are extremely rare in cytosolic proteins,
since the cytosol is generally a reducing environment.
Quaternary structure is a larger assembly of several protein
molecules or polypeptide chains, usually called subunits in
this context. The quaternary structure is stabilized by the
same non-covalent interactions and disulfide bonds as the
tertiary structure.
1
TOTAL 15

3 10
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a)
1. L-ornithine
2. carbamoyl phosphate
3. L-citrulline
4. argininosuccinate
5. fumarate
6. L-arginine
7. urea
L-Asp L-aspartate
CPS-1 carbamoyl phosphate synthetase I
OTC Ornithine transcarbamoylase
ASS argininosuccinate synthetase
ASL argininosuccinate lyase
ARG1 arginase 1

b) Urea contains two amino groups. One derived from 2

deamination of glutamate in mitochondria, the other from
deamination of amino also in mitochondria.

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TOTAL 12
4 a) Cofactor 1

b)

c) An enzyme-substrate complex is a combination of the

enzyme and the substrate in which the two are bound
together very closely so that atoms on each are essentially 3
in physical contact with each other. The physical contact
regions involve H-bonding, ionic bonds, hydrophobic
interactions, and occasionally, covalent bonds.

d) The rate of an enzyme-catalyzed reaction is proportional to

the amount of E.S since the formation of product occurs 3
after the formation of such a complex. No product is formed
by the simple collision of E with S. E and S must bind
together before product is formed.

e) Saturation of the enzyme means that the entire E is bound

to S and no free E exists. The enzyme has bound to as 2
much substrate as possible. This situation occurs at high
levels of S.

TOTAL 11
5 a) Because there three irreversible steps in glycolysis which
are bypassed by gluconeogenesis. The first step is the
production of pyruvate and ATP from 4
phosphoenolpyruvate. Second is the production of
fructose-1,6-bisphosphate from fructose-6-phosphate, and
third is production of glucose-6-phosphate from glucose.

b) Gluconeogenesis begins in the mitochondria with the

formation of oxaloacetate by the carboxylation of
12
pyruvate. This reaction also requires one molecule
of ATP, and is catalyzed by pyruvate carboxylase.
Oxaloacetate is reduced to malate using NADH, a step
required for its transportation out of the mitochondria.
Malate is oxidized to oxaloacetate using NAD+ in the
cytosol, where the remaining steps of gluconeogenesis
take place. Oxaloacetate is decarboxylated and then
phosphorylated to form phosphoenolpyruvate using
the enzyme PEPCK. A molecule of GTP is hydrolyzed

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to GDP during this reaction.The next steps in the reaction

are the same as reversed glycolysis.
However, fructose 1,6-
bisphosphataseconverts fructose 1,6-
bisphosphate to fructose 6-phosphate, using one
water molecule and releasing one phosphate (in
glycolysis phosphofructokinase 1 converts F6P to
F1,6BP). This is also the rate-limiting step of
gluconeogenesis. Glucose-6-phosphate is formed
from fructose 6-
phosphate by phosphoglucoisomerase (the reverse
of step 2 in glycolysis). Glucose-6-phosphate can be
used in other metabolic pathways or dephosphorylated to
free glucose. Whereas free glucose can easily diffuse in
and out of the cell, the phosphorylated form (glucose-6-
phosphate) is locked in the cell, a mechanism by which
intracellular glucose levels are controlled by cells. The
final reaction of gluconeogenesis, the formation of
glucose, occurs in the lumen of the endoplasmic
reticulum, where glucose-6-phosphate is hydrolyzed
by glucose-6-phosphatase to produce glucose and
release an inorganic phosphate. Like two steps prior, this
step is not a simple reversal of glycolysis, in which
hexokinase catalyzes the conversion of glucose and
ATP into G6P and ADP. Glucose is shuttled into the
cytoplasm by glucose transporters located in the
endoplasmic reticulum's membrane.

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TOTAL 16
6 a) Fatty acyl CoA synthetase enzyme catalyzing the"priming" 8
reaction in fatty acid metabolism which converts free fatty
acids in the cytosol into fatty acyl-CoA using the energy
available from ATP and PPi hydrolysis. When the energy
charge in the cell is low, the fatty acyl-CoA is used for fatty
acid oxidation inside the mitochondria, however, when the
energy charge is high, the fatty acyl-CoA is used to
synthesize triacylglycerols or membrane lipids. Carnitine
acyltransferase I - catalyzes the commitment step in fatty
acid oxidation which links fatty acyl-CoA molecules to the
hydroxyl group of carnitine. The activity of carnitine
acyltransferase I is inhibited by malonyl CoA, the product of
the acetyl-CoA carboxylase reaction, which signals that
glucose levels are high and fatty acid synthesis is favored.
Acetyl CoA carboxylase - catalyzes the commitment step in
fatty acid synthesis using a biotinmediated reaction
mechanism that carboxylates acetyl CoA to form the C3
compound malonyl CoA. The activity of acetyl CoA
carboxylase is regulated by both reversible phosphorylation
(the active conformation is ephosphorylated) and allosteric
mechanisms (citrate binding stimulates activity, palmitoyl-
CoA inhibits activity).Fatty acid synthase - this large multi-
functional enzyme is responsible for catalyzing a series of
reactions that sequentially adds C2 units to a growing fatty
acid chain covalently attached to the enzyme complex. The
mechanism involves the linking malonyl-CoA to an acyl
carrier protein, followed by a decarboxylation and
condensation reaction that extends the hydrocarbon chain.

b) Fat has qualities that make food taste good. It delivers

flavor from foods, and provides aroma. It also gives a
smooth, creamy texture to many foods like ice cream,
chocolate and peanut butter. Fat also makes foods such as
meat and baked goods moist and tender or brown and 2
crispy. Fat is important for slowing the digestive process so
you are not hungry an hour after eating a meal. Fat also
adds satiety and a sense of fullness after eating a meal.
One role of fat in the diet is to aid in the absorption of fat-
soluble vitamins, which include vitamins A, D, E, and K.

c)
Fatty acid oxidation:
Palmitate + 7 NAD+ + 7 FAD + 8 CoA + 7 H2O + ATP -->
8 acetyl CoA + 7 NADH + 7 FADH2 + AMP + 2 Pi + 7 H+

Fatty acid synthesis: 2

8 Acetyl CoA + 7 ATP + 14 NADPH + 14 H+ -->
palmitate + 8 CoA + 7 ADP + 7 Pi + 14 NADP+ + 6 H2O

d) Cytoplasmic fatty acyl CoA is converted to fatty acyl 2

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carnitine by carnitine acyl transferase (CAT I), an enzyme

of the inner leaflet of the outer mitochondrial membrane.
Fatty acyl carnitine is then trransported by an antiport in
exchange for free carnitine to the inner surface of the inner
mitochondrial membrane. There carnitine acyl transferase 4
II (CAT II) reverses the process, producing fatty acyl CoA
and carnitine. This shuttle mechanism is required only for
longer chain fatty acids. Medium- and short chain fatty
acids are carnitine-independent. They cross the
mitochondrial membranes, and are activated in the
mitochondrion.

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TOTAL 18
7 a) Fluidity of a biological membrane depends on the
composition of the bilayer. If it consist mainly of saturated
fatty acids, then the linear arrangements of these fatty cids
will lead to close packing of the molecules causing the 6
bilayer to be rigid. Similarly, the presence of cholesterol will
also cause dense packing of the molecules and makes the
bilayer more rigid. On the other hand, if unsaturated fatty
acids are abundant, the kinks in the fatty acids will lead to
a less condense packing causing the bilayer membrane to
be more fluid.
b) Adaptations maybe in the form of the composition of the
bilayer. The amount of unsaturated fatty acids is likely to be
very high so as to ensure that the fluidity of the membrane
remains high. The saturated and cholesterol composition is 4
expected to be reduced to avoid membrane rigidity.
TOTAL 10
8

a)
A purine is a heterocyclic aromatic
organic compound containing 4 nitrogen atoms. It contains
two carbon rings, and is made of a pyrimidine ring fused to
an imidazole ring. A pyrimidine is a heterocyclic aromatic
organic compound containing 2 nitrogen atoms. It contains
only one carbon ring.
b) There are three types of RNA molecules namely
messaenger RNA (mRNA), transfer RNA (tRNA), and
ribosomal RNA (rRNA). mRNA is a type of RNA that carries
specific amico acids that will be used to decode the mRNA. 4
mRNA is a typr if RNA molecule that carries codes that is
meant for translation process to form specific protein. rRNA
is a type of RNA molecule that will fold and finally form the
ribosome units needed for the translation process from
DNA to mRNA.

TOTAL 8

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