Tuesday September 8

  1. What is the difference between a nucleoside and a nucleotide?
  2. Which parts of a mature mRNA molecule do not transmit information for the synthesis of protein?
  3. If perfect Watson-Crick base pairing were required between codons and anticodons, cells would need 61 different tRNAs, although there are only 20 amino acids encoded. How does the cell recognize all codons with fewer than 61 tRNAs?

Monday September 14

  1. What are the three substrate requirements for DNA polymerase I?
  2. Which component of the replication machinery cleaves and re-ligates double-stranded DNA to allow untangling?
  3. What is the role of glycosylase in the base excision repair of nucleotide mismatches and damaged bases?

Thursday September 17

  1. A Southern blot of digested human genomic DNA produces a single band when hybridized at high stringency but 6 bands at low stringency. Describe one hypothesis explaining the result.
  2. Using the same pair of PCR primers, you obtain a product with a different molecular weight if you amplify from cDNA instead of genomic DNA. Give one explanation for this difference. Which condition is more likely to give a larger product?

Monday September 21

  1. How does RNA interference inhibit the function of a specific gene? That is, what molecule does RNAi affect and how does this in turn affect gene expression?
  2. Why do we add G418 and ganciclovir to culture medium when we're selecting recombinant ES cells during construction of a knockout mouse? What does each drug do to help us find the correct type of ES cells?

Monday September 28

  1. How might mobile DNA elements contributed to the evolution of higher organisms?
  2. What are the components of a core nucleosome?
  3. Is heterochromatin more likely or less likely to be transcribed than euchromatin? Why?

Thursday October 1

  1. In the example of microarrays given in the textbook (see Fig. 5-29), what does it mean when a spot is more red-colored in the presence of serum?
  2. What is one reason why "deep sequencing" may be advantageous over microarrays to screen effects on gene expression?