Hoatlin:OHSU Genetic Mechanisms Class

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{{HoatlinLab}}
{{HoatlinLab}}
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==Links For Maureen Hoatlin's CON 662 Class Oct 2009==
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==Links for Maureen Hoatlin's CON 662 Class Oct 2013==
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*Lectures: [[Media:HoatlinCON662.pdf|Lecture PDFs]]
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==Bonus Materials==
==Bonus Materials==
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;so many great questions, so many interesting topics, so little lecture time. Here are some additional materials for your interest.
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*[http://www.nature.com/scitable/topicpage/Telomeres-of-Human-Chromosomes-21041 Telomere information]
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*[http://www.ibioseminars.org/lectures/cell-bio-a-med/elizabeth-blackburn.html Telomerase Lectures by Elizabeth Blackburn]
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* Not required, but these are additional reading
<biblio>
<biblio>
#Replisome pmid=19652539
#Replisome pmid=19652539
#Replication pmid=19767190
#Replication pmid=19767190
</biblio>
</biblio>
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*[http://spine.rutgers.edu/cellbio/assets/flash/tel.htm telomere animation]
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;Movies
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*[http://www.youtube.com/watch?v=4jtmOZaIvS0&feature=related DNA Replication]
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*[http://www.youtube.com/watch?v=TC2mYWR8754&p=C9FDF61276AE2050&index=5&playnext=2 Polymerase]
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*[http://www.youtube.com/watch?v=AJNoTmWsE0s Telomere animation]
*[http://www.nature.com/scitable/topicpage/Telomeres-of-Human-Chromosomes-21041 Telomeres on Nature Network]
*[http://www.nature.com/scitable/topicpage/Telomeres-of-Human-Chromosomes-21041 Telomeres on Nature Network]
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==Other Help==
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*[http://www.youtube.com/watch?v=k4fbPUGKurI topoisomerase]
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*[http://www.youtube.com/watch?v=UWNhwceMjfk&p=C9FDF61276AE2050&index=6&playnext=3 Helicase]
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*[http://www.ted.com/talks/lang/eng/paul_rothemund_details_dna_folding.html Crazy Fun with DNA] A TED talk on DNA origami.
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Really.
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*[http://www.ted.com/talks/david_bolinsky_animates_a_cell.html Animation in Science Education] A TED talk to watch during a break from your studies.
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*Enjoy some [http://www.xvivo.net/zirus-antivirotics-condensed/ excellent animations]. The virology animation includes viral replication. Viral styles of replication are complex and fascinating, also providing a target for therapeutic intervention.
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==Other Bonus Material==
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Student Questions from emails
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;Question:
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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?
 +
 
 +
;Answer:
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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.
 +
 
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;Question
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*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?
 +
 
 +
;Answer
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*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.
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;Question
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*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.
 +
 
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;Answer
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*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.
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*[http://www.youtube.com/watch?v=9iaoypSrIT0 Intro genetics lecture by Eric Lander for your ipod/iphone]  
*[http://www.youtube.com/watch?v=9iaoypSrIT0 Intro genetics lecture by Eric Lander for your ipod/iphone]  
*[http://openwetware.org/wiki/BMCB625:Help Managing Literature and Open Science]
*[http://openwetware.org/wiki/BMCB625:Help Managing Literature and Open Science]
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*[http://ibioseminars.org/speaker_index.shtml Great Lectures]
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==Post Test==
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==[[Links For Maureen Hoatlin's CON 662 Class Oct 2009]]==

Revision as of 14:50, 3 October 2013

Equipped with his five senses, man explores the universe around him and calls the adventure Science.  ~Edwin Powell Hubble, The Nature of Science, 1954

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Contents

Links for Maureen Hoatlin's CON 662 Class Oct 2013

Bonus Materials

so many great questions, so many interesting topics, so little lecture time. Here are some additional materials for your interest.
  1. Langston LD, Indiani C, and O'Donnell M. . pmid:19652539. PubMed HubMed [Replisome]
  2. Remus D and Diffley JF. . pmid:19767190. PubMed HubMed [Replication]
All Medline abstracts: PubMed HubMed
Movies

Really.

  • 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

Question

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?

Answer

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.

Question
  • 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?
Answer
  • 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.
Question
  • 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.
Answer
  • 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.


Post Test

Links For Maureen Hoatlin's CON 662 Class Oct 2009

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