Links for Maureen Hoatlin's CON 662 Class
- so many great questions, so many interesting topics, so little lecture time. Here are some additional materials for your interest.
- Langston LD, Indiani C, and O'Donnell M. . pmid:19652539.
- Remus D and Diffley JF. . pmid:19767190.
- Enjoy some excellent animations. The virology animation includes viral replication. Viral styles of replication are complex and fascinating, also providing a target for therapeutic intervention.
Other Bonus Material
Student Questions from emails
When you were talking about DNA replication a "licensing factor" was mentioned, and I was wondering, is this a protein? And what is it's function?
Yes licensing factor is the old name for a set of proteins that bind to the origins. Licensing factor is now thought to include the proteins Cdc6 and Cdt1. These proteins bind to the origin recognition complex proteins, and are synthesized only in a specific phase of the cell cycle (G1). Once replication origins "fire" (or start) these proteins are degraded or exported and the origin can't be "licensed" for firing again until the proteins are synthesized and enter the nucleus in the next cell cycle. That's how the cell controls replication so that the DNA is replicated once and only once.
- I was reading over your notes and can't quite seem to understand why telomeres have high C-T content. Would it not necessarily be true that they would have high C-A content as well?
- Telomeres usually contain some version of tandem copies of sequences like 5'-CCCCAA-3' on one strand and 5'-TTGGGG on the complementary strand. The GT-rich strand comprises the 3'-end and **sticks out** longer than the CA strand (and forms a loop, sealing the end). Specifically for human telomeres, there are 300-8,000 sets of repeats of the sequence CCCTAA /TTAGGG, then a 100-200 nucleotide extension of single-stranded TTAGGG repeats, hence the comment that telomeres have high GT content. But why? The best way to understand this beautiful system is to watch the very simple but very revealing short animation in the link above called telomere animation of how telomerase works at the telomere (see especially step 5 and later). Note that it is all about the requirements of polymerase for a free 3' -OH (and a ss DNA template strand)! It might also help to scan quickly through the very good article from Nature Network listed above as well.
- I am a bit confused about the DNA polymerases that you mentioned in your lecture. Are the leading and lagging strand synthesied by different polymerases? Secondly, you mention polymerase eta and its role in synthesis of the leading strand. I thought eta was only involved in the bypass mechanism? Thanks for your clarification and help.
- I think I see the confusion. I believe it is partly confusion over greek letters used to name the pols. Pol eta (looks like an italics small n) is a translesion pol---so you are correct about that. However, slide there is also a pol epsilon (Greek letter looks like like an italics e) which is the replicative pol that has recently been shown to primarily replicate the leading strand in eukaryotes. The lagging strand is synthesized primarily by pol delta. This division of labor at the replication fork in eukaryotes is a recent discovery, so many texts will have it backwards. Note that in eukaryotes there are two replicative pols: polymerase delta and epsilon, whereas in prokayotes there is only one main replicative polymerase, Pol III. Primase is required in both systems. Hope this helps.
- Can you explain the difference between XP-V and a mutation in XPA-XPG?
- XP patients have a defect in one of the many genes involved in NER (nucleotide excision repair) e.g., XPA, XPC, XPC, XPG etc. Thus, XP patients cannot repair DNA damage (e.g., photoproducts like cyclobutane pyrimidine dimers) caused by exposure to sunlight. The XP-V patients have a different defect but the same phenotype. They have a defective bypass polymerase, called Pol eta. Normally, Pol eta can synthesize (error-free) past a thymine dimer by inserting two A residues. In XP-V patients, other bypass Pols are substituted that are not error-free for this lesion. Also, in XP-V patients, the upstream XPA-XPG proteins are functional and NER repair is intact. Only the bypass polymerase is defective.
- Intro genetics lecture by Eric Lander for your ipod/iphone
- Managing Literature and Open Science