Practice Problems for Molecular Biology, Session 4: Alternative Approaches to
Molecular Biology

Question 1 

All known DNA polymerases extend DNA chains in the 5' to 3' direction and require a primer. As the fork approaches the end of a linear chromosome, synthesis of the leading strand continues to the end of the DNA template strand, completely replicating the leading strand template. However, the lagging strand template is copied in a discontinuous fashion and cannot be replicated in its entirety.

a) Diagram or describe the lagging strand template and the newly synthesized discontinuous strand at the end of the chromosome.

b) Diagram or describe what will happen to the length of the chromosome upon multiple rounds of replication. Explain why this may have undesirable consequences.

c) Some organisms such as bacteria and viruses have circular, not linear, chromosomes. Explain how having a circular chromosome could solve the problem discussed above.

d) Other organisms have non-coding sequences at the ends of linear chromosomes called telomeres. A telomere is simply a long stretch of repeated nucleotides. Why does the telomere lessen the impact of the incomplete replication of lagging strand templates?

Question 2

You are studying a very short protein-encoding region whose sequence is shown below. The region of sequence shown is from the transcriptional start site to the transcriptional stop site. This region encodes two different polypeptides. The region’s one small intron is shown for you in bold.

5’-CTACGTACTATGTATTCCGATCTATACTCGATCTAGTCGCATTCCGATAAGATCGTAC-3’

3’-GATGCATGATACATAAGGCTAGATATGAGCTAGATCAGCGTAAGGCTATTCTAGCATG-5’

a) What are the sizes of the two polypeptides?

b) Which strand is used as a template in transcription for the smaller polypeptide, the upper strand or the lower strand?

c) How many nucleotides long would the final processed mRNA made from this gene be (not including the 5’ cap and the 3’ poly A tail)?

d) What is the sequence of the smaller polypeptide

f) Say that the C:G base pair that is underlined in the sequence above were changed to an A:T basepair to make a mutant form of this gene.

i) Which kind of mutation would this be for the smaller polypeptide? Your choices are: a frameshift mutation, a nonsense mutation, a silent mutation, or a missense mutation.

ii) Which kind of mutation would this be for the larger polypeptide? Your choices are: a frameshift mutation, a nonsense mutation, a silent mutation, or a missense mutation.

Question 3

Below is a schematic of gene Y, which encodes protein Y. The promoter region is indicated by the dotted box.

a) The transcript first produced by this gene would be approximately how many nucleotides long?

b) The transcript from this gene that is used for translation would be approximately how many nucleotides long?