1
TAP Biochemistry 30.1.07
.1
Compare the two reaction coordinate diagrams below and select the answer that
correctly describes their relationship. In each case, the single intermediate is the ES
complex.
(a) The rate limiting stage of the enzyme described in (b) is the catalysis (given by #3)
(b) The activation energy for the catalyzed reaction is #5 in (a) and is #7 in (b)
(c) The activation energy for the uncatalyzed reaction is given by #5 + #6 in (a)
and by #7 + #4 in (b)
(d) The contribution of binding energy is given by #1 in (a) and by #7 in (b)
(e) The ES complex is given by #2 in (a) and #3 in (b)
.2
The following statement is INCORRECT:
(a) Hemoglobin in the adult normally releases about 60% of its bound oxygen in the
peripheral tissues
(b) In the majority of cases, the heme group iron ion in hemoglobin remains in its
bivalent form, Fe2+, after oxygen is released
(c) Myoglobin releases about 50% of its bound oxygen in muscle tissue at partial
oxygen pressure of 20-40 mm Hg
(d) Hemoglobins of different species possess widely different affinities for oxygen
2
.3
A biochemist obtained the following set of data for an enzyme that is known to
follow Michaelis-Menten kinetics
Substrate
concentration
(μM)
1
2
8
50
100
1,000
5,000
Initial
velocity
(μmol/min)
49
96
349
621
676
698
699
Km value for the reaction is approximately:
(a)
(b)
(c)
(d)
(e)
(f)
(g)
2 mM
10 μM
25 μM
6 mM
50 mM
6 μM
Cannot be determined from the given data
.4
In a plot of 1/V against 1/[S] for an enzyme-catalyzed reaction, the presence of a
competitive inhibitor will alter the
(a)
(b)
(c)
(d)
(e)
Curvature of the plot
Intercept on the 1/[S] axis
Intercept on the 1/V axis
PK of the plot
Vmax
3
.5
An enzyme-catalyzed reaction was carried out with the substrate concentration
initially a thousand times greater than the Km for the substrate. After 9 minutes, 1%
of the substrate had been converted to product, and the amount of product formed in
the reaction mixture was 12 μmol. If, in a separate experiment, one-third as much
enzyme and twice as much substrate had been combined, how long would it take for
the same amount (12 μmol) of product to be formed?
(a)
(b)
(c)
(d)
(e)
1.5 min
13.5 min
27 min
3 min
6 min
.6
Aspartate transcarbamoylase (ATCase) is an allosteric enzyme. Succinate is
competitive inhibitor resembling aspartate. Between Succinate and PALA, which is a
more potent inhibitor of ATCase?
(a) Succinate is structurally related to Aspartate and therefore the best inhibitor
(b) PALA is the better inhibitor because it forms a covalent bond with the enzyme
active site.
(c) PALA is a weak inhibitor of the enzyme as it does not undergo the catalytic stage.
(d) PALA fitness to the active site is the highest because it is a transition state analog,
and therefore the best possible inhibitor.
(e) Binding of Succinate to one active site induces a conformational change to the
other sites, enabling their better binding of aspartate. Therefore, Succinate is in
fact an activator and not an inhibitor.
.7
The 5’ → 3’ exonuclease activity of E. coli DNA polymerase I is involved in:
(a)
(b)
(c)
(d)
(e)
Formation of a nick at the DNA replication origin.
Formation of Okazaki fragments.
Proofreading of the replication process
Removal of RNA primers by nick translation.
Sealing of nicks by ligase action
4
.8
The cooperative binding/release of oxygen by hemoglobin and the resulting sigmoid
kinetics is due to:
(a)
(b)
(c)
(d)
(e)
The presence of eight alpha helices in each globin chain
The hydrophobic nature of the heme group
The distance between the distal histidine residue HisE7 and the heme group iron ion.
The hydrophilic nature of the hemoglobin molecule surface
The tetrameric structure of hemoglobin
.9
Aminoacyl-tRNA synthetases (amino acid activating enzymes):
(a)
(b)
(c)
(d)
(e)
“Recognize” specific tRNA molecules and specific amino acids
In conjunction with another enzyme attach the amino acid to the tRNA
Interact directly with free ribosomes.
Occur in multiple forms for each amino acid.
Require GTP to activate the amino acid.
. 10
The number of saturating molecules converted by a single enzyme molecule to
product in given unit of time is referred to as the:
(a)
(b)
(c)
(d)
(e)
Dissociation constant
Half-saturation constant
Maximum velocity
Michaelis-Menten number
Turnover number
5
. 11
A peptide (9 mer) was determined to have the following amino acid composition:
(Lys)2, (Gly)2, (Phe)2, His, Leu, Met. The native peptide was incubated with
1-fluoro-2,4-dinitrobenzene (FDNB) and then hydrolyzed. 2,4-dinitrophenylthiatidine
was identified by HPLC. When the native peptide was exposed to cyanogens
bromide (CNBr), an octapeptide and free glycine were recovered. Incubation of the
native peptide with trypsin gave a pentapeptide, a tripeptide, and free Lys. 2,4Dinotrophenyl-histidine was recovered from the pentapeptide, and 2,4dinitrophenylphenylalanine was recovered from the tripeptide. The native sequence
as determined to be:
(a)
(b)
(c)
(d)
(e)
His-Gly-Phe-Lys-Lys-Gly-Leu-Met-Phe
His-Leu-Gly-Lys-Lys-Phe-Phe-Gly-Met
His-Leu-Phe-Gly-Lys-Lys-Phe-Met-Gly
His-Phe-Leu-Gly-Lys-Lys-Met-Phe-Gly
Met-Leu-Phe-Lys-Phe-Gly-Cly-Lys-His
. 12
Urobilinogen levels will be HIGHER than normal in the following, EXCEPT:
(a)
(b)
(c)
(d)
A Gilbert’s syndrome individual that went on hunger strike
Hemolysis
Liver cirrhosis
A patient who underwent surgery to remove a gallstone that completely
obstructed his biliary tree.
. 13
Protein S will fold into its native conformation only when protein Q is also present in
the solution. However, protein Q can fold into its native conformation without
protein S. Protein Q, therefore, may function as a ______________ for protein S.
(a)
(b)
(c)
(d)
(e)
Ligand
Molecular chaperone
Protein precursor
Structural motif
Supersecondary structural unit
6
. 14
It is reasonable that hemoglobin will display a HIGHER than normal oxygen affinity
under the following condition:
(a) Elevation in the intracellular concentration of 2,3-biphosphoglycerate (2,3-BPG)
in the erythrocytes.
(b) Decrease in the activity of carbonic anhydrase in the blood.
(c) Acidification (decreased pH) of the blood
(d) Elevation in the concentration of CO2 in the blood
. 15
The following statement is INCORRECT:
(a) It is to be expected that a mutation in globin that increases the affinity of
hemoglobin for oxygen will lead to anemia
(b) One of the expected outcomes of (yet to be realized) total eradication of malaria
in Africa is a pronounced decrease in the frequency of the β0 globin allele in the
African population in future generations.
(c) A (hypothetical) drug that elevates the intracellular concentration of K+ ions in
erythrocytes of a sickle cell anemia homozygote should postpone and diminish
cell sickling
(d) A (hypothetical) drug that lowers the intracellular concentration of Ca2+ ions in
erythrocytes of a sickle cell anemia homozygote should postpone and diminish
cell sickling
. 16
The turnover number for an enzyme in known to be 5,000 min-1. From the following
set of data, calculate the total amount of enzyme (μM) present in these experiments.
Substrate
concentration
(μM)
1
2
8
50
100
1,000
(a)
(b)
(c)
(d)
(e)
10 μM
0.1 μM
1 μM
2 μM
Cannot be determined
Initial
velocity
(μmol/min)
49
96
349
621
676
698
7
. 17
The affinity of hemoglobin for oxygen will decrease in all the following cases EXCEPT:
(a) Increase in the concentration of 2,3-biphosphoglycerate (2,3-BPG) in the
erythrocytes.
(b) Elevated concentration of CO2 in the blood
(c) Decreased partial pressure of oxygen in the peripheral tissues
(d) A mutation in beta globin chains that eliminates an electrostatic bond of the
protein chain with 2,3-BPG
. 18
A premature baby that had 12 mg/dl bilirubin in the blood was treated with an
antibiotic that binds to albumin with high affinity, displacing bilirubin from its
“binding-site”. Which of the following statements is most correct regarding the
antibiotic treatment?
(a) The antibiotic will decrease the incidence of Kernicterus.
(b) The antibiotic will increase the rate of direct bilirubin production.
(c) In order to prevent Kernicterus, babies receiving the antibiotic may require
phototherapy treatment as bilirubin levels lower than the usual limit.
(d) The antibiotic will decrease the clearance of direct bilirubin from the circulation.
(e) The incidence of Kernicterus will depend solely on the total bilirubin levels,
which will not be affected by the antibiotic.
. 19
The EARLIEST alpha type globin to appear in the human embryo is:
(a)
(b)
(c)
(d)
(e)
zeta (ζ) globin
epsilon (ε) globin
α1 globin
α2 globin
delta (δ) globin
. 20
High levels of bilirubin in the urine will be typically present in:
(a)
(b)
(c)
(d)
(e)
A patient with sickle cell disease.
An individual that has a mutation in the MRP2 transporter protein.
An individual with Gilbert’s syndrome.
A baby with Criegler-Najjar syndrome.
An individual that has a mutation in the organic acid transporter (OAT) present in
the hepatocyte plasma membrane
8
. 21
The following statement is INCORRECT:
(a) Oxygen (O2) molecule is positioned in oxyhemoglobin between the Fe2+ iron ion
of the heme group and the proximal histidine residue HisF8 in the globin chain.
(b) The secondary structure of globin chains in myoglobin and hemoglobin is
characterized by a series of alpha helices that are separated by random coil
regions and by a complete absence of beta sheet domains.
(c) As a result of the binding of oxygen to the iron ion Fe2+ in the heme group, the
proximal histidine residue, HisF8, rotates by 8 degrees to assume a 90 degree
position relative to the plane of the heme molecule.
(d) The heme pocket in myoglobin or hemoglobin is rich in hydrophobic amino acids.
. 22
Which of the following statements about allosteric control of enzymatic activity is
FALSE?
(a)
(b)
(c)
(d)
(e)
Allosteric effectors give rise to sigmoidal V0 vs. [S] kinetic plots.
Allosteric proteins are generally composed of several subunits.
An effector may either inhibit or activate an enzyme.
Binding of the effector changes the conformation of the enzyme molecule.
Heteroallosteric effectors compete with substrate for binding sites.
. 23
β0 thalassemia is characterized by:
(a)
(b)
(c)
(d)
Accumulation of the abnormal hemoglobin HbH in the erythrocytes
Accumulation of the abnormal hemoglobin Hb Bart in the erythrocytes
Aggregation of free α globin chains in the erythrocytes
A fully compensatory replacement of the missing HbA by HnF in erythrocytes of
the patients
9
. 24
A biochemist is attempting to separate a DNA-binding protein (protein X) from three
other proteins (A, B, and C). The proteins have the following properties:
protein A
protein B
protein C
protein X
pI
(isoelectric
point)
Size
M1
Binds to
DNA?
7.4
3.8
7.9
7.8
2,000
21,500
23,000
22,000
yes
yes
no
yes
What type of protein separation techniques will yield the best result in separating
protein X from protein C, and next from protein B?
(a)
(b)
(c)
(d)
(e)
Isoelectric Focusing and Gel Filtration
Gel Filtration and Affinity Chromatography
Affinity Chromatography and Isoelectric Focusing
Two dimensional gel electrophoresis
Affinity Chromatography and Gel Filtration
. 25
The following statement is INCORRECT:
(a) Indirect bilirubin is converted into lumirubin upon phototherapy.
(b) The activity of the UDP-glucouronosyl transferase enzyme generates more
diglucuronide bilirubin than monoglucuronide bilirubin.
(c) Lumirubin does not directly react with the diazotized sulphanilic acid reagent
used in the Van Der Bergh reaction.
(d) Direct bilirubin undergoes deconjugation and oxidation in the gut, generating
urobilinogen and urobilins.
(e) In Criegler Najjar type II syndrome, most of the bilirubin-glucuronide conjugates
are of the monoglucoronide type
10
. 26
Please mark the one INCORRECT statement in regard to the conformations of
hemoglobin:
(a) The relaxed (“R”) conformation displays higher oxygen affinity than the taut (“T”)
conformation.
(b) Some mutations in the sliding contacts region (i.e., α1β2 globin contacts) may
cause shift of the equilibrium from R to the T conformation of hemoglobin.
(c) Binding of CO2 to hemoglobin shifts the equilibrium from the T to the R
conformation of hemoglobin.
(d) Some mutations in the sliding contacts region (i.e., α1β2 globin contacts) may
cause shift of the equilibrium from T to the R conformation of hemoglobin.
. 27
A (hypothetical) drug causes inactivation of the enzyme methemoglobin reductase. It
is expected that as a result of exposure to this drug, the following ill occur:
(a)
(b)
(c)
(d)
The heme group iron ion will dissociate from hemoglobin
The heme group iron ion will accumulate in its trivalent form Fe+3
Hemoglobin will have an abnormally high affinity for oxygen
CO2 will not be able to form a carbamate moiety HN-COO- at the N-terminus of a
globin chain
(e) Such a drug will not have any effect on the structure or function of hemoglobin
and thus will not have clinically distinguishable side effects
. 28
The levels of the following proteins will decrease during the acute phase reaction
EXCEPT:
(a)
(b)
(c)
(d)
(e)
Albumin
Transthyretin
Transferin
Alpha-fetoprotein
C-reactive protein
11
. 29
It is likely that hemoglobin S fiber formation and cell sickling will be ENHANCED
in a homozygous sickle cell anemia patient under all the following listed conditions
EXCEPT.
(a) Decrease in the erythrocyte volume
(b) Elevation of the intracellular pH in erythrocytes
(c) Increase in the intracellular concentration of 2,3-biphosphoglycerate (2,3-BPG) in
the erythrocytes
(d) The presence of a second mutation in a globin chain of the patient that will cause
a shift of the hemoglobin from the R (relaxed) th the T (taut) conformation
. 30
The DNA in a eukaryotic chromosome is best described as:
(a)
(b)
(c)
(d)
(e)
A single circular double-helical molecule
A single linear double-helical molecule
A single linear single-stranded molecule
Multiple linear double-helical molecules
Multiple linear single-stranded molecules
. 31
RNA polymerase:
(a) Binds tightly to a region of DNA thousands of base pairs away from the DNA to
be transcribed.
(b) Can synthesize RNA chains de novo (without a primer).
(c) Has a subunit called λ (lambda), which acts as a proofreading ribonuclease.
(d) Separates DNA strands throughout a long region of DNA (up to thousands of base
pairs), then copies one of them.
(e) Synthesizes RNA chains in the 3’→5’ direction
. 32
In a mammalian cell, DNA repair systems:
(a)
(b)
(c)
(d)
(e)
Are extraordinarily efficient energetically.
Are generally absent, except in egg and sperm cells.
Can repair deletions, but not mismatches.
Can repair most types of lesions except those caused by UV light.
Normally repair more than 99% of the DNA lesions that occur.
12
. 33
The phosphodiester bonds that link adjacent nucleotides in both RNA and DNA:
(a)
(b)
(c)
(d)
(e)
Always link A↔T and G↔C
Are susceptible to alkaline hydrolysis
Are uncharged at neutral pH
Form between the planar rings of adjacent bases
Join the 3’hydroxyl of one nucleotide to the 3’ hydroxyl of the next.
. 34
The formation of bilirubin from heme involves the following reactions EXCEPT:
(a) Rupture of the α-methylene bridge of the heme molecule by the heme oxygenase
enzyme.
(b) Release of Fe2+ from heme.
(c) Production of CO.
(d) Conjugation of bilirubin with UDP-glucuronic acid.
(e) Formation of the green pigment biliverdin IX-α
. 35
Theoretically, administration of an inhibitor of the heme oxygenase enzyme will be
beneficial in which of the following conditions?
(a)
(b)
(c)
(d)
(e)
Criegler-Najjar syndrome, type 1.
Dubin-Johnson syndrome.
Deficiency in glucose 6-phosphate dehydrogenase enzyme.
Advanced cirrhosis
Complete obstruction of the biliary tree by a tumor at the pancreas head.
. 36
Which one of the following is NOT true of the mRNA for ovalbumin?
(a)
(b)
(c)
(d)
(e)
Exons are used for polypeptide synthesis
Introns are complementary to their adjacent exons and will form hybrids with them.
The mature mRNA is substantially shorter than the corresponding region on the DNA.
The mRNA is originally synthesized in the nucleus, but ends up in the cytoplasm.
The splicing that yields a mature mRNA occurs at very specific sites in the RNA
primary transcript.
13
. 37
The aspartate aminotransferase enzyme (AST) catalyzes:
(a) The transfer of the amino group of glutamate to oxaloacetate, generating aspartate
and alpha-ketoglutarate.
(b) The transfer of the amino group from glutamate to pyruvate, generating aspartate
and alpha-ketoglutarate.
(c) The transfer of the amino group from aspartate to alpha-ketoglutarate, generating
glutamate and pyruvate.
(d) The transfer of the amino group of aspartate to oxaloacetate, generating glutamate
and alpha-ketoglutarate.
(e) The transfer of the amino group from glutamate to alpha-ketoglutarate, generating
aspartate and oxaloacetate.
. 38
Which of the following pairs of bonds within a peptide backbone show free rotation
around both bonds?
(a)
(b)
(c)
(d)
(e)
Cα–C and N–Cα
C–O and N–C
C–O and N–Cα
N–C and Cα–C
N–Cα and N–C
. 39
Which of the following statements about aminoacyl-tRNA synthetases is FALSE?
(a)
(b)
(c)
(d)
(e)
Some of the enzymes have an editing/proofreading capability
The enzyme attaches an amino acid to the 3’ end of a tRNA
The enzyme splits ATP to AMP + PPi
The enzyme will use any tRNA species, but is highly specific for a given amino acid.
There is a different synthetase for every amino acid.
14
. 40
After receiving excessive doses of paracetamol (Tylenol) a child developed jaundice
followed by coma. Biochemical analysis of the revealed a large increase in the
aminotransferase levels (both ALT and AST) as well as the following changes
EXCEPT:
(a)
(b)
(c)
(d)
(e)
Higher levels of ammonia
Lower levels of coagulation factors
Higher levels of indirect bilirubin
Lower levels of prealbumin
Higher levels of urea
. 41
Which one of the following types of eukaryotic regulatory proteins interact with
enhancers?
(a)
(b)
(c)
(d)
(e)
Basal transcription factors
Coactivators
Repressors
TATA-binding proteins
Transactivators
. 42
Which of the following conditions will cause the HIGHEST increase in the blood
citruline concentration
(a)
(b)
(c)
(d)
(e)
A defect in the argininosuccinase enzyme.
A defect in the argininosuccinic acid synthetase enzyme.
A defect in carbamoyl phosphate synthetase enzyme.
A defect in the argininosuccinase enzyme in a patient treated with arginine.
A defect in argininosuccinic acid synthetase enzyme in a patient treated with
arginine.
. 43
Splicing of introns in nuclear mRNA primary transcripts requires:
(a)
(b)
(c)
(d)
(e)
A guanine nucleoside or nucleotide.
Endoribonucleases.
Polynucleotide phosphorylase.
RNA polymerase II.
Small nuclear ribonucleoproteins (snurps).
15
. 44
When a DNA molecule is described as replicating bidirectionally, that means that it
has two:
(a)
(b)
(c)
(d)
(e)
Chains.
Independently replicating segment.
Origins.
Replication forks.
Termination points.
. 45
For amino acids with neutral R groups, at any pH below the pI of the amino acid, the
population of amino acids in solution will have:
(a)
(b)
(c)
(d)
(e)
A net negative charge
A net positive charge
No charged groups
No net charge
Positive and negative charges in equal concentration
. 46
Assuming that the average amino acid residue contributes 110 daltons to the peptide
molecular weight, what will be the nucleotide length of the mRNA encoding a protein
of molecular weight 50,000?
(a)
(b)
(c)
(d)
(e)
133 nucleotides
460 nucleotides
1,365 nucleotides
5,000 nucleotides
A minimum length cannot be determined from the data given.
16
. 47
A 60-year-old male experienced pronounced pain in the thoracic region and the
doctor suspected of myocardial infarction (MI). Which of the following statements is
most CORRECT regarding the case?
(a) The presence of normal levels of cardiac troponin T, creatine kinase (CR) and
creatine kinase-MB (CK-MB) in the blood two hours after the appearance of the
symptoms ill discard the possibility of MI.
(b) Higher levels of alanine aminotransferase (ALT) in the blood will indicate that the
MI occurred several hours ago, as ALT is a “late” marker for MI.
(c) As a means to diagnose MI, analysis of the ratio between CK-MB and total CK is
always preferable over the analysis of the absolute values of each enzyme.
(d) Higher levels of acid phosphatases in the patient’s blood will indicate that he
probably has a bone or liver disease unrelated to the MI.
. 48
A genetic defect in the enzyme ornithine transcarbamoylase will cause all of the
following biochemical changes EXCEPT:
(a)
(b)
(c)
(d)
(e)
Decrease the citrulline levels in the blood.
Increase the levels of carbamoyl phosphate in the hepatocytes
Increase blood ammonia concentration
Alter the intracellular levels of argininosuccinate
Block the urea formation, which can be partially restored by administration of
phenylacetate or benzoate.
. 49
Indirect bilirubin is insoluble in water. This can be best explained by:
(a) The absence of hydrophilic groups in bilirubin
(b) The presence of strong hydrogen bridges within the bilirubin molecule
(intramolecular bonds) that shields the hydrophilic groups that otherwise would
interact with water.
(c) The strong binding of bilirubin to albumin.
(d) The absence of conjugation with glucuronic acid.
(e) The presence of a tetrapyrole ring that confers a hydrophobic character to the
bilirubin molecule.
17
. 50
Which one of the following statements about the elongation phase of protein
synthesis is true?
(a) At least five high-energy phosphoryl groups are expended for each peptide bond
formed.
(b) During elongation, incoming aminoacylated tRNAs are first bound in the P site.
(c) Elongation factor EF-Tu facilitates translocation
(d) Peptidyl transferase catalyses the attack of the carboxyl group of the incoming
amino acid on an ester linkage in the nascent polypeptide.
(e) Peptidyl transferase is a ribozyme.
. 51
A 27-year old male was admitted to the hospital following a car accident. The patient
exhibited very large bruises in the abdominal and thoracic regions. Biochemical
analysis of the serum after the accident will probably reveal the following changes
EXCEPT:
(a)
(b)
(c)
(d)
Higher levels of urobilinogen in the urine.
Lower levels of haptoglobin.
Lower levels of hemopexin.
Lower levels of serum lactate dehydrogenase.
. 52
Small signal molecules that regulate transcription are not known to:
(a)
(b)
(c)
(d)
(e)
Cause activator proteins to bind DNA sites
Cause repressor proteins to bind DNA sites
Directly bind DNA sites
Prevent activator proteins from binding to DNA sites
Release repressor proteins form DNA sites
18
. 53
Michaelis and Menten assumed that the overall reaction for an enzyme catalyzed
reaction could be written as:
k1
E+S
k2
ES
E+P
k-1
Using this reaction, the rate of breakdown of the enzyme-substrate complex can be
described by the expression:
(a)
(b)
(c)
(d)
(e)
k1 ([Et] – [ES]).
k1 ([Et] – [ES])[S].
k2 [ES].
k-1 [ES] + k2 [ES].
k-1 [ES].
19
Question #
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
Answer
(a)
(c)
(f)
(b)
(c)
(d)
(d)
(e)
(a)
(e)
(c)
(a)
(b)
(b)
(a)
(b)
(d)
(c)
(a)
(b)
(a)
(e)
(c)
(c)
(c)
(c)
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
(b)
(d)
(b)
(b)
(b)
(e)
(e)
(d)
(a)
(b)
(a)
(a)
(d)
(e)
(e)
(e)
(e)
(d)
(b)
(c)
(c) or (d)
(e)
(b)
(e)
(d)
(c)
(d)