Short answers
1
The majority of sequence-specific DNA-binding proteins make contact
with the DNA molecule in the major groove as opposed to the minor groove. Explain
why this is so.
The major groove, is 22 Å wide and the other, the minor groove, is 12 Å wide.
The diameter of the α helix is 1.2 nanometres allowing it to fit into the major groove but
not the minor groove.
Transcription factor' make multiple contacts to the edges of the DNA bases,
allowing them to "read" the DNA sequence. Most of these base-interactions are made in
the major groove, where the bases are most accessible.
2
Given the following partial sequence for the sense strand of a doublestranded DNA:
5’-ATGGTAAGGCTTTAG-3’
(a)
(b)
Write down the sequence for the complementary DNA strand.
Write down the sequence of the mRNA corresponding to the DNA shown
above.
3
What is an amphipathic compound? Explain how such compounds
contribute to the structure of biological membranes.
Ans: An amphipathic compound has one region or domain that is hydrophilic and
another that is hydrophobic. When added to water, amphipathic compounds tend to
arrange in a way that exposes their hydrophilic regions to the solvent and hides their
hydrophobic domains. One structure that accomplishes this is the lipid bilayer, which
forms spontaneously with phospholipids in water.
4
Describe the two substrate level phosphorylation reactions in glycolysis?
What is the payout for these reactions?
Ans. Substrate level phosphorylation reactions generate ATP by capturing the
high phosphate transfer potential of the substrate in a coupled reaction with ADP. The
enzymes phosphoglycerate kinase and pyruvate kinase catalyze the two substrate level
phosphorylation reactions in stage 2 of glycolysis. Since two molecules of
glyceraldehyde-3-P are generated for every molecule of glucose metabolized, each of
these substrate level phosphorylation reactions yield 2ATP/glucose. Phosphoglycerate
kinase (reaction 7) provides the payback of 2ATP invested in stage 1 of glycolysis to
generate fructose-1,6-BP, whereas, reaction 10 catalyzed by pyruvate kinase represents
the ATP earnings step in the pathway by generating 2 net ATP.
5
Explain why all mono- and disaccharides are soluble in water.
Ans: These compounds have many hydroxyl groups, each of which can hydrogen
bond with water.
1. What kind of linkages are present between glucose units in glycogen
A)
a1,4 only
B)
b 1,6 only
C)
b1,6 and b1-4
D)
a1,4 and b1,6
E)
a 1,4 and a 1,6
2. There are three main points of regulation in glycolysis. They all have what in
common?
A)
all involve reactions before the 6 carbon backbone is split into 3 carbon
molecules
B)
they all involve oxidation-reduction reactions
C)
they all involve large negative free energy changes
D)
They all involve reactions coupled to synthesis of ATP
E)
They all involve reactions where the Go value is close to zero
3. Of the DNA sequences shown below, which one will have the highest melting
temperature (Tm) when annealed to its complementary sequence under otherwise
identical conditions?
A)
AGTCTTAGTTC
B)
CTCTAATCAGG
C)
GACCTAGGACC
D)
TACAGTTACAA
E)
ATGTAATACTA
4. Membrane structures are maintained primarily by:
a.
hydrophobic interactions.
b.
covalent bonds.
c.
hydrogen bonds.
d.
non-spontaneous assembly.
A)
ionic interactions.
5. The reference compound for naming D and L isomers of sugars is:
A)
fructose.
B)
glucose.
C)
glyceraldehyde.
D)
ribose.
E)
sucrose.
6. When the linear form of glucose cyclizes, the product is a(n):
A)
acetal.
B)
glycoside.
C)
hemiacetal.
D)
lactone.
E)
oligosaccharide.
7. In B-DNA each deoxyribose is in the C-2' endo conformation. This means that
it is
A)
B)
C)
D)
E)
the furanose ring is completely planar
the 2' carbon is in the same plane as the 5' carbon
the 2' carbon is in the same plane as the furanose ring oxygen
the 2' carbon is on the same side of the furanose ring as the 5' carbon
the 2' carbon is on opposite side of the furanose ring from the 5' carbon
8. The feature(s) of DNA deduced by Watson and Crick included:
A)
two parallel polynucleotide chains form a helix around a common axis.
B)
the pyrimidine and purine bases are parallel to the helix axis.
C)
the deoxyribose sugars are on the inside of the helix.
D)
All of the above.
E)
None of the above.
9. If an unfavorable biochemical reaction is coupled to ATP hydrolysis, the
reaction will probably be
A)
stopped
B)
driven forward
C)
reversed
D)
non-spontaneous
E)
not affected
10. How many stereoisomers are possible for a hexoaldose monosaccharide?
A)
2
B)
4
C)
8
D)
16
E)
32
True/False
1
FALSE Phosphofructokinase1 converts fructose6phosphate to fructose 1,6
bisphosphate. ADP binds this enzyme at a site other than the active site and increases the
reaction velocity. Therefore ADP is a competitive inhibitor.
2
fastest step
FALSE The control enzyme in a metabolic pathway usually catalyzes the
3
True If an RNA molecule forms a base-paired double helix with a DNA
molecule, then the RNA is complementary to the DNA molecule.
4
False The temperature (Tm) at which 50% of the hydrogen bonds between
base pairs of a DNA molecule are broken and the two DNA strands separate is
independent of the %GC base pairs of the DNA.
5
True In double-stranded DNA-RNA hybrids, base pairing occurs between
A and T, if A is in the RNA strand and T is in the DNA strand.
6.
False DNA replication proceeds in the 3’ to 5’ direction
7.
False Telomeres are replicated by the regular DNA replication machinery
8
False Histones interact with DNA primarily in a sequence specific manner