Biochemistry Questions

Dr T.B.Nyambo
Department of Biochemistry
School of Medicine
MUCHS

Each of the following statements is followed by five suggested

answers or completions. On the answer sheet, mark the one which is best in
each case.

1. All of the following statements are true concerning DNA synthesis

EXCEPT:
A.An RNA-DNA hybrid occurs at one stage.
B.DNA is replicated by several DNA polymerases, one of which
can synthesize DNA in a 3' to 5' direction and another of
which synthesizes DNA in a 5' to 3' direction.
C.The primer for DNA synthesis is RNA.
D.DNA synthesis is discontinuous on the lagging strand in
the sense that small fragments of DNA are made first and
09then sealed together into long strands.
E.DNA synthesis is semi-conservative which means that
daughter cells contain one complete parental DNA strand
and one complete new DNA strand.

2.An anticodon is
A.the part of a DNA molecule which codes for chain
termination.
B.a 3-nucleotide sequence of a mRNA molecule.
C.a specific part of a tRNA molecule.
D.a nucleotide triplet of a rRNA molecule.
E.the portion of a ribosomal subunit which interacts with
aminoacyl-tRNA synthetase.

3.Investigations concerning gene expression in eukaryotic cells

reveal that
A.all segments of chromosomal DNA are either transcribed or
serve as regulatory genes.
B.the process of protein synthesis occurs within the nucleus
in close proximity to the structural genes; consequently,
the mRNA may be translated as it is being transcribed.
C.the initial transcription products of structural genes are
usually very large RNA molecules. Before these RNA
molecules become functional mRNA molecules, they are
usually shortened and a poly-A segment is added to the 3'
end.
D.the evolutionary changes which brought about the existence
of eukaryotic cells necessitated dramatic changes in the
translational process (as developed in prokaryotic cells).
E.DNA synthesis occurs early in the G1 phase of the cell-cycle.

4.During the process of amino acid activation

A.the carboxyl group is activated with the formation of a
mixed anhydride between the carboxyl group and the phosphate of 5'-AMP.
B.the amino group is activated with the formation of a mixed
anhydride between the amino group and the phosphate of 5'-AMP.
C.the energy is derived from GTP.
D.the reaction is catalyzed by a peptidyl transferase.
E.the same tRNA is used for all the amino acids but there is
a different specific activating enzyme for each amino acid.

5.Which of the following statements regarding translation is

INCORRECT?
A.The first amino acid introduced into the protein is MET.
B.mRNA codes for the amino acid sequence during protein
synthesis.
C.tRNA serves to decode the genetic code located in the mRNA
through interactions between the anticodon of the tRNA and
the codons in the mRNA.
D.the mRNA is translated in the 5' to 3' direction.
E.Proteins are synthesized in the carboxyl to amino
direction.

6.With respect to transcription, which statement is false?

A.Eukaryotic cells have 3 RNA polymerases each of which
specializes in the synthesis of a particular class of RNA.
B.Prokaryotic cells contain an RNA polymerase which requires
sigma factor for proper initiation.
C.Transcription is the synthesis, in the 3' to 5' direction,
of RNA from a primer.
D.RNA is produced from one strand of the DNA and is produced
in a direction anti-parallel to this DNA strand.
E.The information for the synthesis of RNA comes from the
DNA and is specified by base pairing.

7.Repressor proteins have specific sites that bind to

A.promoters.
B.ribosomes.
C.operators.
D.mRNA.
E.TATA boxes.

8.All of the following statements concerning histones are true

EXCEPT that they
A.are rich in arginine and lysine.
B.are proteins of relatively low molecular weight.
C.exhibit known interspecies homologies in their amino acid
sequences.
D.are noncovalently attached to DNA in stoichiometric
amounts.
E.exhibit a wide variety of non-homologous molecular
structure.

9.Each of the following components participates DIRECTLY in the

cellular formation of protein from amino acids supplied in the form of
aminoacyl transfer RNA EXCEPT which one?
A.GTP
B.Magnesium ion
C.Ribosomes
D.Messenger RNA
E.ATP

10.Eukaryotic genes coding for proteins usually contain introns.

Production of a eukaryotic protein in bacteria (proinsulin for example)
doesn't necessarily pose a problem because
A.the bacteria possess the necessary enzymes to correctly
process the primary transcript containing intervening
sequences.
B.reverse transcriptase can be used to synthesize a cDNA
from the mRNA. This unfragmented DNA can then be cloned.
C.the protein synthetic machinery of the bacteria will only
translate the exon portions of the resulting RNA.
D.the translation of intron regions usually doesn't alter
the activity of the protein.

11.Regarding the process of replication in E. coli, which of the

following statement is INCORRECT?
A.DNA replication is a semiconservative process.
B.There is a unique site at which replication is initiated.
C.DNA replication is unidirectional.
D.The mechanism of replication is such that there is a
leading strand and a lagging strand at each replicating
fork.
E.DNA synthesis occurs in the 5' to 3' direction.
12.Which of the following statements about RNA is correct?
A.The kind of RNA which in the free form has the greatest
percentage of specific, tertiary structure is mRNA.
B.rRNA binds with phospholipids to form ribosomal subunits.
C.tRNA molecules are relatively small, generally containing
less than 100 nucleotides.
D.Like DNA, RNA is animal cells is often found in
double-stranded, duplex structures.
E.RNA, in contrast to DNA, is found only in the cytoplasm of
cells.

13.Which of the following protein factors are required for the

addition of an amino acid residue to a growing polypeptide chain during
protein biosynthesis in E. coli?
A.IF-1, IF-2 and IF-3
B.Factor G
C.Factor R
D.Factors Tu and Ts
E.Factor L

14.The degree of homology between DNA from two organisms can most
accurately be determined by
A.base composition.
B.comparing melting curves.
C.density measurements.
D.hybridization.

15.The 70S ribosome contains about 50 separate proteins and one

clearly definable enzymatic activity in protein synthesis. The name of
that activity is
A.30S dependent ATPase.
B.aminoacyl-tRNA synthetase.
C.elongation factor G.
D.peptidyl transferase.
E.None of the others answers is correct.

16.Which one of the following classes of histones is not a component

of the core particle?
A.H1
B.H2A
C.H2B
D.H3
E.H4

17.Dolicohol phosphate-mediated glycosylation of proteins occurs on

which amino acid residue?
A.Serine
B.Asparagine
C.Tyrosine
D.Glutamine
E.Arginine

18.Which of the following enzymes is needed only for lagging strand

synthesis at a replication fork?
A.DNA ligase
B.DNA polymerase III
C.Helicase
D.SSB
E.Topoisomerase II

Answer the following questions using the key outlined below:

A if 1, 2 and 3 are correct
B if 1 and 3 are correct
C if 2 and 4 are correct
D if only 4 is correct
E is all four are correct

19.During protein synthesis, movement of peptidyl-tRNA from the 'A'

to 'P' ribosomal sites
1.requires GTP hydrolysis.
2.is catalyzed by EF-G or eEF-2.
3.is inhibited by diphtheria toxin in eukaryotes.
4.involves removal of one tRNA molecule from the ribosome.

20.Histones are not found in

1.human erythrocytes.
2.human liver cells.
3.E. coli.
4.human nerve cells.

21.Which of the following statements concerning nucleosomes is/are

true?
1.The "core" structure contains a piece of DNA about 140
base pairs long along with proteins.
2.The "core" structure contains 8 histone molecules along
with DNA.
3.DNA is believed to be wrapped around the outside of a
histone cluster.
4.Approximately two turns of chromatin DNA exists per
nucleosome core.
22. The genetic code
1.consists of a three letter code referred to as codons.
2.displays degeneracy; that is, in certain cases there are
multiple codons for the same amino acid.
3.is universal, except for mitochondria which use several
codons differently.
4.also specifies modified amino acids that are found in
proteins.

23.A typical cytoplasmic mRNA molecule

1.of eukaryotes encodes multiple proteins.
2.of prokaryotes lacks a polyadenylic acid poly (A)
sequence.
3.of eukaryotes has 50% of its nucleotides methylated in the
2' position.
4.of eukaryotes was most likely modified by a spliceosome
during processing in the nucleus.

24.Okazaki fragments
1.are found primarily on the leading strand during
replication.
2.could contain short sequences of RNA on their 5' end.
3.are products whose base sequences are primarily due to the
action of DNA polymerase I.
4.could be isolated from a system where DNA ligase was
inhibited.

25.The G1 phase of the cell cycle is characterized by

1.highly variable duration.
2.sensitivity to mitogens.
3.production of factors necessary for the S phase to begin.
4.a restriction point termed Go.

26.Puromycin inhibits protein synthesis because

1.its structure is analogous to aminoacyl-tRNA.
2.it can react with a peptidyl-tRNA to yield
peptidyl-puromycin.
3.it causes premature termination of the chain.
4.it blocks the codon recognition step.

27.cDNA which is complementary to the complete mRNA molecule for a

specific protein
1.can be produced by RNA-dependent DNA polymerase.
2.will always contain the sequence CAT.
3.can be used to identify the gene for the specific protein.
4.can be used to determine the sequence of amino acids in
 the specific protein.

28.Excision repair of DNA

1.replaces both strands of the DNA in the damaged region.
2.uses high energy phosphate bonds.
3.utilizes RNA polymerase to make a primer.
4.requires DNA ligase.

29.RNA differs from DNA

1.in that it occurs more frequently as a single rather than
a double-stranded structure.
2.in the type of common purine bases it contains.
3.in the type of common pyrimidine bases it contains.
4.in that all RNAs contain unusual purine bases.

30.Regarding splicing of RNAs,

1.splicing may involve an RNA molecule functioning as an
enzyme.
2.during splicing, introns are precisely removed and exons
joined by 3', 5' phosphodiester bonds.
3.a structure known as a lariat is formed during splicing.
4.poly A tail addition is required for splicing to occur.

ANSWERS

1B 2C 3C 4A 5E 6C 7C 8E 9E
10B 11C 12C 13D 14D 15D 16A 17B 18A
19E 20B 21E 22A 23C 24C 25E 26A 27E
28C 29B 30A

Each of the following statements is followed by five suggested

answers or completions. On the answer sheet, mark the one which is best in
each case.

31. An intracellular target of the cancer chemotherapeutic drug

camptothecin is:
A. histone H1
B. DNA gyrase
C. topoisomerase I
D. RNA polymerase II
E. elongation factor I
32. Which of the following is a true statement?
A. DNA polymerase adds nucleotides to the 3' phosphate group of an
existing strand
B. When read in the same direction (5' to 3'), the sequence of
nucleotides in the newly synthesized DNA strand is the
same as in the parental template strand
C. Synthesis of the new DNA strand occurs in the 5' to 3'
direction on the leading strand but in the 3' to 5' direction
on the lagging strand
D. Bidirectional replication means that one strand must be
synthesized in a discontinuous manner
E. A mutation in the 3'-5' exonuclease of DNA polymerase would
affect the fidelity (accuracy) of DNA synthesis

33. Which of the following processes occur only in cells that are actively
replicating their DNA?
1.excision repair
2.mismatch repair
3.photoreactivation
4.recombinational repair

A. 1 only
B. 1 and 3
C. 2 and 4
D. 1, 2, and 3
E. all of them

34. Which of the following is not true of the prokaryotic (E. coli)
transcriptional process?
A. specific sequences in the promoter are necessary for stable binding of RNA
polymerase
B. A separate helicase enzyme is necessary for unwinding the DNA
template to create an open complex
C. during transcriptional elongation base pairing between the new
RNA molecule and the template strand of DNA is important
D. sigma factor is required only during the initiation process
E. termination requires special sequences (signals) in the nascent
RNA chain

35. In eukaryotes, 28S, 5.8S, and 18S ribosomal RNAs

A. are all encoded by separate genes that are transcribed by RNA
polymerase I
B. are all synthesized as one large precursor molecule that is
subsequently cleaved to release the 3 RNAs
C. are encoded by one large gene that undergoes splicing to
 produce the final RNA products
D. are encoded by a single copy gene that is expressed at
extremely high levels because of its localization to
the nucleolus
E. are assembled into ribosomes as part of the translation
initiation process in the cytosol
36. The most important step in maintaining fidelity of the translation
process is
A. joining of the correct amino acid and tRNA by aminoacyl-tRNA
synthetases
B. proper methylation of tRNAs
C. correct base pairing between the codon and anticodon
D. peptide bond formation by peptidyl transferase
E. none of the above are involved

37. Which of the following are useful antibacterial agents since they block
protein synthesis in prokaryotes but not eukaryotes (in vivo)?

1. streptomycin
2. cycloheximide
3. puromycin
4. diphtheria toxin
A. 1
B. 1 and 3
C. 2 and 4
D. 1, 2 and 3
E. all of them

38. Mannose-6-phosphate receptors in the lumen of the Golgi function

A. in the delivery of lysosomal enzymes to lysosomes

B. to return proteins, such as signal peptidase, back to the ER
C. to add phosphates to mannose residues of lysosome-bound enzymes
D. to activate mannose by coupling it to UDP
E. in the delivery of secreted proteins to secretory vesicles

39. In E. coli the lac operon is expressed at low levels when both glucose and
lactose are available because:

A. no inducer is available to inactivate repressor binding to the

operator
B. glucose is an allosteric activator of repressor DNA-binding
activity
C. CRP, which can enhance RNA polymerase binding to the promoter,
remains in its inactive state
D. beta-galactosidase is unavailable for converting lactose to
 allolactose
E. attenuation causes premature termination of the transcription
process

40. The proto-oncogene encoded protein c-jun is a leucine zipper

containing transcription factor. Therefore it:
A. requires zinc to stabilize the proper conformation for
DNA-binding
B. requires dimerization for activity
C. probably functions as a steroid hormone receptor
D. binds directly to TATA boxes
E. does not require an activation domain for transcriptional
activation
41. Important features of a plasmid cloning vector include:
1. unique restriction enzyme sites for inserting DNA molecules
2. an origin of replication that allows amplification of the clone
in host cells
3. an antibiotic resistance gene that allows for selection of host
cells that carry the clone
4. a middle section that can be removed and replaced by the
DNA insert

A. 1
B. 1 and 3
C. 2 and 4
D. 1, 2 and 3
E. all of them
42. A collection of recombinant DNA clones representing all of the
various mRNA molecules from a certain cell type is a:
A. probe
B. genomic library
C. cDNA library
D. vector
E. restriction digest

43. Which of the following would you expect to enhance the hybridization
between a mouse DNA probe and a human DNA fragment that was 90%
identicalin a Southern Blot experiment:
1. increased temperature
2. increased Mg++ concentration
3. high (alkaline) pH
4. increased NaCl concentration
A. 1
B. 1 and 3
C. 2 and 4
D. 1, 2 and 3
E. all of them
44. A nucleosome core particle consists of
A. two copies of histones H2A, H2B, H3, and H4 organized as an
octamer and associated with about 140 bp of genomic DNA
B. linker DNA between two nucleosomes associated with histone H1
C. a complex of histones H2A, H2B, H3, H4, and H1
D. a 30 nm fiber wound into a solenoid-like structure
E. a complex of the proteins dnaA, dnaB, and dnaC

45. Telomerase:
1. is an enzyme containing an important RNA component
2. is required for initiation of replication in eukaryotes
3. is required for replicating ends of eukaryotic chromosomes
4. is found in all eukaryotic cells
A. 1
B. 1 and 3
C. 2 and 4
D. 1, 2, and 3
E. all of them
46. The concept of "wobble" involves:

A. base pairing between the first (5') base of the codon and the
third (3') base of the anticodon
B. base pairing between the first base of the codon and the first
base of the anticodon
C. base pairing between the third base of the codon and the first
base of the anticodon
D. base pairing between the third base of the codon and the third
base of the anticodon
E. none of the above are correct
47. Which of the following is a true statement?
A. since AUG serves as the start codon methionine is generally
found only at the N terminus of a protein
B. in eukaryotes the same aminoacyl-tRNA is used for the start
codon as for internal AUG sequences
C. in E. coli the same aminoacyl-tRNA is used for the start codon
as for internal AUG sequences
D. in translation of a eukaryotic mRNA the first AUG sequence
almost always serves as the start codon
E. since AUG serves as the start codon methionine is always the
N-terminal amino acid in mature proteins
48. For O-linked glycosylation of secreted or membrane proteins:

A. a complex oligosaccharide is synthesized on dolichol phosphate

and then transferred to the protein
B. sugars are linked to the side chain of asparagine
C. sugars are linked to the side chain of tyrosine
D. sugars are added to the carbohydrate chain one at a time in the
Golgi
E. the necessary enzymes are localized to lysosomes
49. Control by attenuation (as in the trp operon) can occur only in
prokaryotes because:
A. it requires coupling of transcription and translation
B. hairpin loops in RNA are more stable in bacteria
C. prokaryotic genes are often organized as operons
D. eukaryotic transcription does not have specific termination
signals
E. repressor molecules are only found in prokaryotes

50. Initiation of mRNA transcription in a eukaryote

A. involves a group of basal transcription factors that are
required to position RNA polymerase at the transcriptional
start site
B. does not require specific DNA sequences
C. is not a regulated step for determining the level of gene
expression
D. requires canonical -10 and -35 sequences
E. requires sequence specific binding by the RNA polymerase itself

51. Steroid hormone receptors

A. are transmembrane receptors that bind the hormone and nitiate
signals that lead to gene activation
B. are soluble proteins that directly bind the hormone and act as
transcription factors
C. are basal transcription factors that can bind directly to TATA
boxes
D. are transcription factors that bind to DNA but become activated
by phosphorylation in response to hormone
E. are transcription factors that are synthesized when steroid
hormones bind to cell surface receptors
52. Restriction enzymes are required for which of the following
recombinant DNA techniques:

1. RFLP analysis
2. Southern blotting of genomic DNA
3. Preparation of a genomic library
4. Polymerase chain reaction (PCR)
A. 1
B. 1 and 3
C. 2 and 4
D. 1, 2, and 3
E. all of them
53. Since the cloning of the HD (Huntington's Disease) gene and
identification of the specific defect, a genetic screen can be utilized
that does not depend on access to samples from other family members. This
screen utilizes which of the following methods:
A. RFLP analysis
B. DNA sequencing
C. Southern blotting with an ASO (allele specific oligonucleotide)
probe
D. SSC (single strand conformational analysis)
E. PCR (polymerase chain reaction)

54. Processing of a tRNA molecule includes all of the following except:

A. removal of nucleotides from the 5' end
B. removal of nucleotides from the 3' end
C. addition of nucleotides to the 3' end
D. methylation and other base modifications
E. removal of introns by spliceosomes

55. Peptidyl transferase

A. is an intrinsic enzymatic activity of the large ribosomal
subunit and requires an RNA component
B. utilizes the energy of GTP hydrolysis to catalyze peptide bonds
C. transfers peptidyl-tRNA from the P site to the A site
D. recognizes signal peptides for transfer of nascent polypeptides
to the RER
E. mimics an aminoacyl transferase and binds to the A site to
cause termination of translation

56. A common property of DNA polymerase, pyruvate kinase, and aconitase is

that:
A. they are all made on RER bound ribosomes
B. they are all made on soluble ribosomes in the cytosol
C. they all have nuclear translocation signals
D. they are all synthesized by mitochondrial ribosomes
E. none of the above

57. One function of the small protein ubiquitin is:

A. to recognize abnormal proteins so they can be degraded
B. to degrade proteins within the lysosome
C. to become covalently linked to proteins to "mark" them for
degradation
D. to sort endocytosed proteins to the lysosome for degradation
E. to add PEST sequences to proteins to promote their turnover

58. An activation domain for stimulating transcription of a eukaryotic

gene
A. is a specific DNA sequence that is recognized by a
transcription factor
B. is an allosteric site that enhances transcription factor
binding to DNA
C. often contains a homeobox motif
D. is a hydrophobic surface that promotes transcription factor
dimerization
E. is a domain, separate from the DNA binding domain, of a
transcription factor that functions by contacting some
component of the basal transcription machinery

59. An important feature of an origin of DNA replication is:

A. a specific sequence recognized by DNA polymerase
B. a specific sequence recognized by topoisomerase
C. an AT-rich region
D. a GC-rich region
E. a sequence containing a nick at a specific site
60. Which of the following is not a true statement concerning the genetic code
A. some amino acids are coded for by more than one triplet
B. the same code is used by humans and E. coli
C. all 64 possible triplet sequences code for amino acids
D. the code is non-overlapping in an mRNA
E. the there are no gaps between successive codons in an mRNA
(i.e. it is comma-less)

ANSWERS

31C 32E 33C 34B 35B 36A 37A 38A 39C

40B 41D 42C 43C 44A 45B 46C 47D 48D
49A 50A 51B 52D 53E 54E 55A 56B 57C
58E 59C 60C

1)tRNA
P A
C---A
G---C
C---G
G--C
 G--C
G--C
G--C U A
C A U C-G-G-C-C A
C G G ||||| A
C C-G-A-G G-U-C-G-G U C
U |||| C $
G G-C-U-C U
G A G 7mG
D U---A
C---G
G---C
G---C
G---C
Cm A
U A
C U
A

Above is the sequence of tRNA that specifies methionine.

A. Identify the site of attachment of the amino acid (X).

B. Identify the 5' end(Y).

C. Identify the anticodon.(Z)

2) RFLP ANALYSIS

blood of blood of blood on

victim #1 victim#2 suspect

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A.The above results were obtained in a Chief chemists crime laboratory.

Explain how the general RFLP procedure is done. Include any needed
enzyme(s), how the bands are separated.
B.What is the basis of the differences in banding patterns
in individuals?
C. What is your analysis of the results of this RFLP?