E.
coli topoisomerase III
I. contains a hole capable of holding duplex DNA
that is
lined with negatively charged residues.
II. binds the sugar-phosphate backbone such that
base
recognition is possible.
III. functions by nucleophilic attack on the binding
phosphate group.
A. I, III
B. II, III
C. I, II
D. II only
E. I only
Which of the following is FALSE about RNA?
A. It may be involved in the control of gene
expression.
B. It may be double stranded in viral genomes.
C. It may form double-stranded stems by binding
its complementary bases within the same strand.
D. It is only synthesized as a single strand.
E. It always forms a single strand that resembles
the structure of B-DNA.
Heat-denatured DNA exhibits ______ UV
absorbance, which is called the ______.
A. decreased; hypochromic effect
B. increased; hypochromic effect
C. increased; hyperchromic effect
D. decreased; hyperchromic effect
E. identical; renaturation effect
How does a nucleotide differ from a nucleoside?
a) nucleosides are found in DNA, whereas
nucleotides are found in RNA
b) purines are only found in nucleotides
c) nucleosides contain only deoxyribose sugars
d) a nucleotide is a nucleoside with a phosphate
ester linked to the sugar
The fundamental differences between RNA and
DNA are
a. the organic bases only
b. bases, ribose units, and the phosphodiester
linkage
c. bases, ribose units, and the glycosidic bond type
d. bases and the ribose units only
Which of the following groups is not found in
nucleosides?
a. phosphates
b. purines
c. pyrimidines
d. sugars
e. all of these are found in nucleosides
The backbone of nucleic acids consists of
a. a phosphodiester bond between the 2' and 5'
hydroxyl groups of neighboring sugars
b. a phosphodiester bond between the 3' and 5'
hydroxyl groups of neighboring sugars
c. a glycosidic bond between a pyrimidine and a
sugar
d. a glycosidic bond between a purine and a sugar
Which of the following statements about the
structure and conformation of DNA is FALSE?
a. DNA binding proteins distort DNA structure
b. Changes in ionic strength can alter DNA
structure
c. Specific sequences can cause deviations in
conformation.
d. Changes in DNA conformation result from
energy minimizations and do not relate to in vivo
conditions.
e. All of the above are true.
Which is a six-membered heterocyclic aromatic
ring?
a) pyrimidine
b) purine
c) sugar portion of DNA
d) ribonucleotide
cAMP and cGMP are _______ with phosphate
esterified as a cyclic ______ and are important
as _____ of cellular metabolism.
a. nucleotides; phosphodiester; inhibitors
b. nucleotides; phosphomonoesters, regulators
c. nucleotides; phosphodiesters, regulators
d. nucleosides; phosphomonoesters, stimulators
e. all of the above

The oligonucleotide AGGUCCAUUGAAp, is best
described as
a. an RNA oligonucleotide with a 3'phosphate
b. an RNA oligonucleotide with a 5'phosphate
c. a DNA oligonucleotide with a 3'phosphate
d. a DNA oligonucleotide with a 5'phosphate
The sugar pucker is___ in the ___form.
a. C2'-endo; A-DNA
b. C3'-endo; B-DNA
c. C2'-endo for pyrimidines and C3'-endo for
purines; Z-DNA
d. C2'-endo for purines and C3'-endo for
pyrimidines; B-DNA
e. C2'-endo for purines and C3'-endo for
pyrimidines; A-DNA
The nucleotide sequence of DNA is which level
of structure?
a. primary
b. secondary
c. tertiary
d. quaternary
Which is the dominant form of DNA found in a
cell?
a) A
b) B
c) Z
d) H
Which best describes the relationship between
the nucleobases in a piece of DNA?
a. they are parallel to the helical axis
b. they are perpendicular to the helical axis
c. they are randomly oriented with respect to the
helical axis
Which of the following statements is true for
double-stranded DNA?
a. the amount of A is the same as the amount of T, and
the amount of G is the same as the amount of C
b. the amount of A is the same as the amount of G, and
the amount of T is the same as the amount of C
c. the amount of A is the same as the amount of C, and
the amount of G is the same as the amount of T
d. more than one of the above is true
Where can drugs or polypeptides bind to DNA?
a. the minor groove only
b. the major groove only
c. either the minor or major groove
d. neither the minor or major groove
Histones are proteins that
a. are frequently associated with eukaryotic DNA
b. are frequently associated with prokaryotic DNA
c. are never found in association with DNA
d. contain a high percentage of residues with
carboxylic acid side chains
Which of the following best describes the
structure of a nucleosome?
a. DNA wrapped around an octomer containing two
each of H2A, H2B, H3, and H4 with H1 on the
outside
b. DNA wrapped around an octomer of H1 with
H2A,B, H3 & H4 on the outside
c. DNA wrapped around a octomer of either
H2A/H2B or H3/H4 with H1 on the outside
d. DNA wrapped around a tetramer of either
H2A/H2B or H3/H4 with H1 on the outside
The outside diameter of a piece of DNA is
closest to
a) 2 Å
b) 20 Å
c) 200 Å
d) 2000 Å
The strands in the double helix
a. both run in the same 5' to 3' direction, i.e., they
are parallel
b. have their 5' to 3' directions opposed, i.e., they
are anti-parallel
c. can be either parallel or anti-parallel
d. are perpendicular to one another
Topoisomerases are associated with
a. production of RNA from DNA.
b. joining of nucleotide monomers to make
polynucleotides
c. supercoiling of DNA
d. ribosomes
RNA is hydrolyzed in basic solution, but DNA is
not. This occurs because
a. thymine is found in DNA, and uracil is not
b. DNA is double stranded, and RNA is single
stranded
c. DNA contains 2'-deoxyribose, but RNA does not
d. RNA has modified bases, but DNA does not
Which of the following statements regarding the
structure of DNA is correct?
a. the two strands are parallel
b. the two strands are held together by intrachain
hydrogen bonds
c. the two strands have complementary base
pairing
d. the hydrogen bonding that holds the helix
together is always between two purines or between
two pyrimidines
e. the ratio of adenine to guanine is the same in all
organisms
The A and B forms of DNA
a. both have 10 base pairs per turn of the helix
b. both have 11 base pairs per turn of the helix
c. are both left-handed helices
d. are both right-handed helices
Supercoiling of DNA
a. is not observed in prokaryotes
b. requires the action of topoisomerase enzymes
c. does not require ATP
d. is not observed in eukaryotes
Two circular DNAs are isolated, both with 1000
bp. One is supercoiled; the other is not. The
two DNAs are placed in an ultracentrifuge
a. the supercoiled DNA should sediment faster
b. the nonsupercoiled DNA should sediment faster
c. they should sediment at the same rate
d. the information provided is not enough to
determine which will sediment faster
Which piece of DNA will have the higher Tm,
one with a cytosine plus guanine content of
30% or
one with a cytosine plus guanine content of
50% if both are heated under the same
experimental
conditions?
a. 30% cytosine plus guanine will have the higher
Tm
b. 50% cytosine plus guanine will have the higher
Tm
c. Their Tm's will be the same
d. There's no way to predict for this information
The Tm for melting the double helix is:
a. The temperature at which the helix starts to
open
b. The midpoint of the range over which the helix
denatures
c. The temperature at which the helix is completely
open
d. The energy needed to melt the DNA
e. None of these is correct
The chemical forces that contribute to the
stability of the DNA due to the base stacking
present in the DNA helix are
a) hydrogen bonds
b) van der Waals
c) disulfide bonds
d) b and c
Prokaryotic chromosomes are typically ___,
while eukaryotic chromosomes are
a. circular; linear and richly protein-associated
b. circular and richly protein-associated; linear
c. linear and richly protein-associated; circular
d. linear; circular and richly protein-associated
e. none are true
All of the following are important
characteristics of DNA EXCEPT:
a. a 1:1 ratio between pyrimidine residues and
purine residues
b. adenine base pairs with uracil
c. hydrogen bonding between base pairs
d. information contained in the sequence of one
strand conserved in the sequence of other strand
e. information is accessed through transcription of
the information into RNA
In a melting profile for DNA, the absorbance at The Z-form of DNA
260 nm increases as a result of the disruption a. does not exist in nature
of the DNA structure. What is the fundamental b. is right-handed
physical basis for the absorbance increase? c. tends to occur in purine-only sequences
a. the effective concentration of DNA changes d. tends to occur in pyrimidine-only sequence
b. denatured DNA absorbs light more strongly than e. tends to occur in alternating purine-pyrimidine
native DNA because the bases have become sequences
unstacked
c. native DNA absorbs light more strongly than
denatured DNA because the bases are stacked The following types of RNA are common to all
d. the absorbance of DNA is highly sensitive to organisms, except:
temperature
snRNA

The melting profile for a DNA is found to differ

in two different salt solutions. In 0.001 M NaCl, Which of the activities of DNA Polymerase I is
Tm most important in its role of proofreading?
= 55o
3' → 5' exonuclease.
C, and in 0.01 M NaCl, Tm = 65o
C. The fundamental reason for this change is
a. higher salt concentration increases the
electrostatic repulsions between phosphates Which of the following enzymes is used to
b. the base stacking is more effective in high salt create AP sites?
c. hydrogen bonding between complementary bases
Glycosylase
in enhanced at high salt
d. higher salt concentration decreases the
electrostatic repulsions between phosphates
Which of the following is not required for optimal
DNA replication?
Hydrophobic bonding via pi-clouds is referred to DNA Polymerase II.
as
a. base stacking
b. propeller twist The direction of synthesis of a DNA strand is
c. hyperchromicity
d. supercoiling from the 5' end to the 3' end on both strands.

The helix can be untwisted by the action of The last nucleotide added to a growing DNA
which type of topoisomerase? chain has a _____ on the sugar.
a. Type I only
3'-hydroxyl
b. Type II only
c. Both types I and II
d. Topoisomerases cannot untwist the helix
The enzyme that attaches the Okazaki
fragments together is called
The feature(s) of DNA deduced by Watson and DNA ligase
Crick included
a) two antiparallel polynucleotide chains coiled in a
helix around a common axis
Single strand binding proteins are important for
b) the pyrimidine and purine bases lie on the
this activity:
inside of the helix
c) the bases are nearly perpendicular to the axis Prevent single-stranded DNA from rewinding and
d) all of the above protect it from degradation.
_____ is an enzyme that introduces supercoiling Aminoacyl-tRNA Synthetases are involved in
into closed circular DNA. which step of translation?
a. activation
DNA Gyrase b. initiation
c. elongation
d. termination
Eukaryotic and prokaryotic ribosomes can be e. none of these
compared in all these ways, except:

Both contain the same number of RNA molecules.

Which of the following is not an advantage of
degeneracy in the genetic code?
a. More than one amino acid can bind to a tRNA.
The hydrogen bonding interactions in a Watson-
b. Each tRNA can bind to more than one codon.
Crick AT base-pair involve what units in the
c. Most codons can bind to more than one tRNA.
adenine base?
d. Fewer tRNA molecules are needed.
N-1 and the amino group on C-6

At which position on tRNA is the wobble base of

Ch12 the triplet anticodon?
a. 1st position (5' letter)
Which category of RNA carries amino acids for b. 2nd position
the process of translation? c. 3rd position (3' letter)
a. mRNA d. Wobble can occur at any position
b. rRNA
c. snRNA
d. tRNA
At which position on the mRNA is the wobble
base of the triplet codon?
a. first position (5' letter)
As in RNA and DNA synthesis, the synthesis of b. second position
proteins follows the following steps, except: c. third position (3' letter)
a. Activation of monomers d. the wobble base can be at any position
b. Initiation
c. Elongation
d. Termination
How many codons are known for each amino
e. All of these are involved in all polymer synthesis
acid?
a. 1 only
b. 2 only
The template for protein synthesis is: c. 2 to 4 depending on the nature of the amino acid
a. a mRNA strand d. 1 to 6 depending on the nature of the amino
b. the DNA coding strand acid
c. the DNA template strand
d. a protein primer
e. none of these
Which amino acids have unique codons?
a. met, gly
b. trp, met
Which of the following statements concerning c. tyr, met
the genetic code is false? d. stop, his
a. It is based on triplets.
b. It is non-overlapping.
c. Commas are used.
d. It is degenerate.
How many codons are possible in a system in Which of the following is not true?
which a sequence of three bases specifies a a. A single activating enzyme can interact with all
single amino acid? the tRNAs for its corresponding amino acid
a. 20 b. The selectivity of the aminoacyl-tRNA
b. 24 synthetases for their tRNA molecules is often called
c. 27 the second genetic
d. 64 code
c. There are two major classes of aminoacyl-tRNA
synthetases
The genetic code is said to be degenerate. This d. aminoacyl-tRNA synthetases link amino acids to
means that tRNA molecules without the need for an energy
a. each codon codes for more than one amino acid. source
b. each anticodon can interact with many different
triplet sequences in the mRNA, which may differ in
any or all Which of following best describes the two-step
of the three nucleotides. process for adding amino acids to tRNAs?
c. many of the amino acids are coded for by AA = amino acid, Pi
different codons. = phosphate, PPi
d. the code is universally used by virtually all = pyrophosphate
species. a. AA + ATP → AA−P + ADP; AA−P + tRNA →
AA−tRNA + Pi
b. AA + ATP → AA−AMP + PPi
The process of amino acid activation ; AA−AMP + tRNA → AA−tRNA + AMP
a. involves the formation of a peptide bond between c. tRNA + ATP → tRNA−P + ADP; tRNA−P + AA →
the amino acid and tRNA AA−tRNA + Pi
b. takes place by formation of a mixed anhydride of d. tRNA + ATP → tRNA−AMP + PPi
the amino acid and tRNA ; tRNA−AMP + AA → AA−tRNA + AMP
c. involves the formation of an ester bond between
the amino acid and tRNA
d. none of these Which linkage best describes the covalent bond
between an amino acid (AA) and its tRNA?
a. Amino group of AA linked to 5' −OH of tRNA.
The initial step in the formation of an b. Amino group of AA linked to 5' phosphate of
aminoacyl-tRNA is tRNA.
a. esterification of the tRNA c. Carboxyl group of AA linked to 3' −OH of tRNA.
b. activation of the amino acid by reaction with d. Carboxyl group of AA linked to 3' phosphate of
ATP tRNA
c. activation of the tRNA by reaction with ATP
d. interaction of the mRNA with the tRNA
Which of the following is not a function of
elongation factors in E. coli?
An aminoacyl-adenylate contains a. Keep the ribosomal subunits bound together.
a. an ester bond b. Lead the incoming tRNA to its correct position
b. an acid anhydride bond on the ribosome.
c. an amide bond c. Carry GTP to provide energy for certain steps in
d. an ether bond the elongation process.
d. Regenerate the elongation factors by replacing
GTP for GDP.
e. The elongation factors do all of these.
The mRNA must contain the following to allow
for initiation of protein synthesis in E. coli.
a. A purine rich sequence to bind to the ribosome.
b. A pyrimidine rich sequence to bind to the
ribosome.
c. A Shine-Delgarno sequence.
d. A purine rich sequence to bind to the ribosome
and a Shine-Delgarno sequence.
e. A pyrimidine rich sequence to bind to the
ribosome and a Shine-Delgarno sequence.
Which of the following is not a function of
initiation factors in E. coli?
a. Prevent the ribosomal subunits from binding
together.
b. Lead the initial tRNA to its correct position on
the large subunit of the ribosome.
c. Help the mRNA to bind to the tRNA.
d. Carry GTP to provide energy for certain steps in
the initiation process.
e. The initiation factors do all of these
An aminoacyl-tRNA is initially bound to the
ribosome
a. at the A site on the 50S subunit
b. at the P site on the 50S subunit
c. at the A site on the 30S subunit
d. at the P site on the 30S subunit
After peptide bond formation takes place, what
step is necessary for continuation of protein
synthesis?
a. binding of uncharged tRNA to the ribosome
b. binding of EF−Tu
c. binding of EF−Ts
d. translocation of the ribosome
In protein synthesis formation of new peptide
bonds is catalyzed by
a. elongation factor EF−Tu
b. elongation factor EF−Ts
c. elongation factor EF−G
d. peptidyl transferase
What is the mode of action of puromycin in the
inhibition of protein synthesis?
a. inhibition of peptidyl transferase
b. inactivation of EF−G
c. termination of the growing polypeptide chain
d. dissociation of mRNA from the ribosome
Which antibiotic confirmed that the growing
peptide chain is transferred to the amino group
of the incoming tRNA?
a. Puromycin
b. Streptomycin
c. Cyclohexamide
d. None of these antibiotics was useful for studying
the mechanism of protein synthesis.
e. None of these antibiotics actually interferes with
peptide transfer.
At what point does the formylation reaction
take place to produce N-formylmethionine?
a. On the free amino acid prior to its addition to a
tRNA.
b. After methionine has been added to a specific
tRNA.
c. After the methionine-tRNA adduct has
complexed with the ribosome.
d. After the first peptide bond is formed on the
ribosome
What is the start codon on the mRNA for
prokaryotic translation?
a. AUG
b. UAA
c. UAG
d. UGA
A polysome is
a. a complex consisting of one mRNA to which
several ribosomes are attached
b. a polypeptide chain in the process of being
formed
c. an intermediate stage in the self-assembly of
ribosomes
d. an aggregate of ribosomal proteins
In bacteria, translation of the mRNA begins
a. during the synthesis of the mRNA.
b. after synthesis of the mRNA has been
completed.
c. after 5' capping of the mRNA.
d. after all processing (capping, polyadenylation,
and removal of introns) has taken place
A Shine-Dalgarno Sequence is a In the process of translation, before an amino
a. sequence of nucleotides in the DNA that acid can be incorporated into a growing protein
interacts with the σ-subunit of RNA polymerase to chain, the activation process of the amino acid
begin transcription. involves _____.
b. sequence of nucleotides in an mRNA that a. mRNA
interacts with the small subunit of a ribosome to b. tRNA
begin translation. c. snRNA
c. sequence of nucleotides in the DNA that d. scRNA
interacts with ρ-protein to terminate transcription.
d. sequence of nucleotides in an mRNA that
functions to terminate translation. Identify the component required for the chain
initiation step of protein synthesis.
a. DNA helicase
During elongation, tRNA binds initially to the b. Release factors
a. "A" site on the ribosome. c. 30S ribosomal subunit
b. "P" site on the ribosome. d. UAA
c. "E" site on the ribosome.

The first tRNA (bearing fmet) binds to the

a. "A" site of the ribosome.
b. "P" site on the ribosome. Which enzyme transcribes genes encoding tRNA
c. "E" site on the ribosome in eukaryotes?
a. RNA polymerase I
b. RNA polymerase II
Leader sequences for protein transport to c. RNA polymerase III
specific organelles are removed by proteases d. Different tRNAs are transcribed by different RNA
associated with the: polymerases.
a. endoplasmic reticulum
b. golgi apparatus c. RNA polymerase III
c. nucleus
d. mitochondria
e. none of these The promoter site is
a. the start site for transcription in DNA
b. the binding site for regulatory proteins that
Degradation of proteins stimulate transcription
a. happens randomly c. the general region of DNA downstream from the
b. frequently makes use of proteasomes start site
c. always requires ubiquitinylation of proteins to be d. the site on DNA at which RNA polymerase binds
degraded to initiate transcription
d. tends to target proteins with basic amino acid e. None of these
residues at their N-terminal ends

The protein which marks proteins for

degradation is called:
a. Chaperonin
b. Ubiquitin
c. Proteasomin
d. Apoptosin
e. None of these names is correct.