Chap. 4 Problem 2

1
Chap. 4 Problem 2
The two strands of the double-helical plasmid DNA
separate (melt, denature) at 90C. During cooling
down to 25C, the strands come back together.
However, because the single-stranded DNA
sequencing primer is in great excess, it
hybridizes preferentially to its complementary
region of the plasmid. This prevents the two
complementary strands of the plasmid DNA from
reannealing at the region where the primer binds.
DNA polymerases used in sequencing bind to the
3-OH group of the primer and extend it in the
sequencing reactions. DNA sequencing is covered
in Chap. 5.
2
Chap. 4 Problem 4
Prokaryotic mRNAs are ready to be translated
immediately after they are transcribed.
Prokaryotic mRNAs often are polycistronic, and
contain coding sequences for multiple genes that
are under the control of a common promoter.
Eukaryotic mRNAs typically encode only a single
protein. They further are extensively
post-transcriptionally modified by capping,
intron splicing, and polyadenylation reactions
(Fig. 4.15).
3
Chap. 4 Problem 6
An operon is a collection of tandemly linked
genes that are transcribed in a single
polycistronic mRNA. In the E. coli trp operon,
the five gene products all work together in the
biosynthesis pathway for the amino acid
tryptophan. It is advantageous to link genes
together in an operon, so that only one promoter
must be regulated to coordinate expression of the
related genes. In eukaryotes, the trp genes are
transcribed separately (Fig. 4.13b). Thus,
multiple promoters must be coordinately regulated
to achieve the goal of balanced expression.
4
Chap. 4 Problem 8
DNA polymerases synthesize DNA strands in a 5 ?
3 direction while moving 3 ? 5 relative to a
template strand. While one strand (the leading
strand) can be synthesized continuously as the
replication fork advances, the other strand (the
lagging strand) must be synthesized
discontinuously in segments (Okazaki fragments)
due to the polarity of DNA polymerase chain
elongation. Synthesis of the lagging strand
occurs from primers laid down on the template
strand as it is exposed by movement of the fork.
(See Fig. 4.30)
5
Chap. 4 Problem 15

1. If DNA were unwound by helicases for replication,
   but stabilizing ssDNA binding proteins such as
   RPA were mutated and could not bind to the ssDNA,
   then replication would cease due to reformation
   of dsDNA.
2. If a mRNA molecule formed a hairpin loop on
   itself at the AUG start site, then the AUG start
   codon could not be located by the ribosomal
   initiation complex. Translation of the mRNA would
   be blocked.
3. If a cell were unable to produce functional
   tRNAiMet, then translation of most mRNAs would be
   blocked at the initiation step. tRNAiMet is the
   only tRNA that can be used to initiate
   translation.