1. The B-DNA structure found in solution is a
right-handed double helix of antiparallel chains (11 bp/turn).
left-handed double helix of antiparallel chains (~10 bp/turn).
right-handed double helix of antiparallel chains (~10 bp/turn).
left-handed zig-zag helix of antiparallel chains (12 bp/turn).
right-handed double helix of parallel chains (~10 bp/turn).
2. DNA differs from RNA in the following features
DNA is resistant to base catalyzed hydrolysis; RNA is hydrolyzed by OH-.
DNA residues are linked by 3'-->5' phosphodiester bonds; RNA is 2'-->5' linked.
DNA has deoxyribose residues; RNA has ribose residues.
DNA contains the A, C, G and T bases; RNA contains A, C, G, and U.
All but the second choice are correct differences
3. Because DNA is a highly charged polyanion, its stability to heat denaturation ("melting"):
does not depend on hydrophobic interactions.
increases with increasing [salt].
decreases with increasing [salt].
is independent of G + C content.
increases with increasing pH.
4. The glycosidic bonds in DNA and RNA
can be hydrolyzed by OH-.
are free to rotate over about 180?
are restricted to one of four possible orientations.
connect the sugar to the base.
stabilize Watson-Crick H-bonds.
5. Polyacrylamide and agarose gel electrophoresis separate nucleic acids based primarily on their
length.
ratio of mass/charge.
(G+C)/(A+T) content.
organismal origin.
content of 15N (buoyant density).
6. Nucleotide bases absorb light at __ nm, while aromatic amino acids absorb light at __ nm.
280, 260.
260, 280.
280, 280.
260, 260.
None of the above are correct
7. Thymidine
is equal to the adenosine concentration in double-stranded DNA.
is replaced by Uracil in RNA.
normally forms 2 hydrogen bonds with adenosine.
can participate in hydrophobic interactions due to its methyl group.
All of the above are correct.
1. Tm refers to:
a) a registered trademark.
b) the temperature at which 50% of a DNA molecule is denatured.
c) the temperature at which 50% of a protein molecule is denatured.
d) the temperature at which membranes are 50% fluid.
e) b, c, and d correct.
2. DNA with a GC content of 50% will melt at approximately __ degrees C under typical conditions for PCR.
a) 60
b) 70
c) 80
d) 90
e) 100
3. In solution, the grooves of nucleic acid helices
a) are filled with H2O and counterions.
b) expose the H-bonding groups of the bases.
c) expose the hydrophobic surfaces of the bases.
d) are about equal in width.
e) The first two choices are both correct.
4. The force, or energetic term, that is most stabilizing for nucleic acids is:
a) hydrophobic effects.
b) hydrogen bonds.
c) electrostatics.
d) van der Waals (base stacking).
e) conformational entropy.
5. The unfavorable free energy associated with not satisfying a hydrogen bond after formation of the double helix is approximately
a) 1 kJ/mol.
b) 5 kJ/mol.
c) 10 kJ/mol.
d) 20 kJ/mol.
e) 30 kJ/mol
. Amino acids whose side chains interact with the DNA or RNA backbone (i.e. phosphate) include the following:
a) Glu and Asp.
b) Leu and Ala.
c) Lys and Arg.
d) Ile and Val.
e) Cys and Met.
7. Amino acids whose side chains can interact with the DNA or RNA nucleotide bases via H-bonding include the following:
a) Asn and Gln.
b) Val and Ala.
c) Lys and Leu.
d) Ile and Val.
e) Cys and Met
8. The type II restriction endonucleases, such as Eco RI, bind to DNA sites:
a) that are usually palindromic.
b) using H-bonds for specificity.
c) using non-sequence-dependent backbone interactions.
d) that are two-fold symmetric in the complex.
e) All four choices are correct
1. An expression vector or plasmid:
always contains an origin of replication.
usually contains a gene that confers antibiotic resistance to the bacterial host.
always contains DNA segments for the regulation of mRNA production.
usually contains one or more restriction sites.
all of the above
2. Cleavage of DNA by EcoRI endonuclease results in the formation of
two 3'-OH ends and two 5'-phosphate ends.
one 3'-OH end and one 5'-phosphate end.
two 3'-phosphate ends and two 3'-OH ends.
one 3'-OH end and one 5'-phosphate end.
four ends, all with -OH groups.
3. The enzyme that joins DNA cut by restriction enzymes is called
Joinase.
Polymerase.
Ligase.
DNA phosphorylase.
Reverse transcriptase.
4. Which of the following statements is incorrect about most DNA polymerases?
They require a primer.
They synthesize in the 5' to 3' direction.
They require a template.
They synthesize in the 3' to 5' direction.
They have 3'-5' exonuclease activity.
5. DNA Gel electrophoresis is similar to SDS-PAGE of proteins because
in both cases a plot of log (Molecular weight) versus distance migrated is linear.
both techniques rely on a constant charge to mass ratio.
both techniques utilize the sieving properties of gels.
molecules migrate to the anode in both cases.
All of the above are correct.
1. Replication in E. coli is initiated by the generation of short RNA primers using
RNA polymerase.
primase.
DNA polymerase II.
reverse transcriptase.
The first and second choices are both correct
2. The RNA primers used to initiate replication in E. coli
result in Okazaki fragments on the leading strand.
are removed by Pol I "nick translation".
are joined together by DNA ligase.
are removed by helicase + ATP.
The first and second choices are both correct.
3. The nicks, or gaps, between fragments on the lagging strand are eventually sealed by
Crazy glue.
DNA ligase.
RNA ligase.
Restriction endonucleases.
Gyrase.
4. The two exonuclease activities of DNA polymerase I
occur at two different active sites.
are coupled during the formation of "gapped DNA".
degrade DNA in a 5' --> 3' direction.
degrade DNA in a 3' --> 5' direction.
are not essential for viability of E. coli.
5. The differences between Pol I and Pol III are:
one is an RNA polymerase, the other is a DNA polymerase.
one has a 3'-5' exonuclease activity, the other does not.
one has a 5'-3' exonuclease activity, the other does not.
one utilizes RNA primers, the other does not.
Pol I and Pol III are different names that describe the same enzyme.
6. During replication, overwinding or overtightening of DNA is caused by __ and removed by __.
DNA ligase, Gyrase
DnaB, DNA polymerase
DnaB, Gyrase
DnaA, Gyrase
Single Stranded Binding Protein, DnaA
1. The RNA polymerases that transcribe bacterial DNA or eukaryotic nuclear DNA are
multisubunit enzymes and partially homologous.
monomeric and very large.
multimeric and interchangeable.
only active inside the cell.
highly glycosylated in their active forms.
2. A promoter is
a manager for a sports team.
a specific sequence of DNA to which RNA polymerase binds.
a specific sequence of DNA to which a catabolic repressor binds.
a specific DNA sequence to which a restriction endonuclease binds.
not found in eukaryotic cells.
3. The binding of lac repressor to DNA could be considered to be analogous to
competitive inhibition of an enzyme.
allosteric effects in enzyme regulation.
uncompetitive inhibition of an enzyme.
mixed-type inhibition of an enzyme.
none of the above.
4. The frequency of incorrect nucleotide incorporation into RNA is about one error for every ___ nucleotides polymerized.
1,000
10,000
100,000
1,000,000
106
. The "closed complex" at bacterial promoters:
is in equilibrium with free RNA polymerase and the promoter.
is not affected by promoter mutations.
is bound more tightly when repressors are present.
is not affected by activator proteins.
is a dead-end product.
. In a cell, DNA transcription is halted when
RNA polymerase falls off of the DNA.
The end of the DNA is reached.
When a rho site is reached.
When a stop codon is reached.
When a restriction site is reached
1. Ribosomes select the correct tRNAs
and then charge them using the appropriate synthetase.
then bind to the appropriate mRNA.
solely on the basis of their anticodons.
with the least abundant anticodons
depending on their abundance in the cytosol.
2. Degenerate codons differ mostly in
the identities of their first base.
the identities of their second base.
the identities of their third base.
the wobble position.
The third and fourth choices are both correct
3. The tertiary structure of yeast tRNAPhe
is maintained mostly by non-Watson-Crick base pairing.
involves extensive base stacking interactions.
resembles the 3-dimensional structure of other tRNAs.
is depicted in the cloverleaf diagram.
All of the choices except the fourth are correct.
4. On the ribosome, mRNA binds __ and the peptidyl transferase reaction occurs __.
between the subunits; on the large subunit.
between the subunits; on the small subunit.
to the large subunit; on the small subunit.
to the small subunit; on the large subunit.
to the small subunit; between the subunits.
5. The pathway of a tRNA during polypeptide elongation on the ribosome is:
A site --> P site --> E site.
P site --> A site --> E site.
A site --> P site --> entry site.
P site --> entry site --> exit site.
none of the above.
6. The accurate charging of tRNAIle by IleRS with Ile and not Val (50,000:1)
requires a two-step editing process.
requires the binding of Ile to be 50,000-fold tighter than Val.
requires the hydrolysis of 2 ATPs for each Ile charged.
requires the presence of a small protein, fidelity-factor.
The first and third choices are both correct
7. Hydrolytic editing of incorrectly charged tRNAs
involves attack of PPi on the aminoacyl-AMP intermediate.
occurs at a second active site on the synthetase.
is a waste of ATP, that could be used for other cellular functions.
is a necessary step for all of the aminoacyl-tRNA synthetases.
occurs when the incorrect tRNA binds to the synthetase
8. The two features of the tRNA molecule involved in converting the triplet codon to an amino acid are:
in the anticodon stem and the 3' CCA end.
in the T Loop and the D stem and loop.
in the anticodon and the acceptor stem.
solely in the anticodon.
distributed throughout the structure