Hoatlin: Fundamentals: Difference between revisions
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==Links for Maureen Hoatlin's CSF 2014 Class== | ==Links for Maureen Hoatlin's CSF 2014 Class== | ||
*[http://www.youtube.com/watch?v=aVgwr0QpYNE Splicing animation] | |||
*[http://www.youtube.com/watch?v=SMtWvDbfHLo transcription animation] | |||
*[http://www.youtube.com/watch?v=4jtmOZaIvS0&feature=related DNA Replication] **note: mute the idiotic sound and voiceover and imagine instead the original soundtrack of a machine perking along. | *[http://www.youtube.com/watch?v=4jtmOZaIvS0&feature=related DNA Replication] **note: mute the idiotic sound and voiceover and imagine instead the original soundtrack of a machine perking along. | ||
*[http://www.youtube.com/watch?v=TC2mYWR8754&p=C9FDF61276AE2050&index=5&playnext=2 Polymerase] | *[http://www.youtube.com/watch?v=TC2mYWR8754&p=C9FDF61276AE2050&index=5&playnext=2 Polymerase] | ||
*[http:// | *[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] | ||
*[http://www.youtube.com/watch?v=k4fbPUGKurI topoisomerase] | *[http://www.youtube.com/watch?v=k4fbPUGKurI topoisomerase] | ||
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==Questions and Answers== | ==Questions and Answers== | ||
*Taken from emailed questions: | *Taken from emailed questions: | ||
;Question | |||
*I had one question about the study guide. It says HATs acetylate and therefore neutralize a negative charge. I was taught that lysine is positive, and putting an acetyl group on it neutralized a positive charge. | |||
;Answer | |||
*I think I see the confusion. In the sentence you got confused by (II. A.4a), the charge referred to is the negative charge on the DNA phosphate backbone. This is a problem with wording because the study guide and slides are so condensed that they make a general case for both HATs and HDACs. Other students had the same question. I hope this clears it up: | |||
Reversible modification of the ε-amino group of lysine by acetylation neutralizes a negative charge on DNA. | |||
*The longer version for the study guide that would be better is: | |||
*Histone tails contain amine groups on lysine and arginine. These positively charged residues interact with the negatively charged phosphate groups on the DNA phosphate backbone. Acetylation by HATs neutralizes the positive charges on the histone tails thus reducing histones binding to DNA, leading to chromatin expansion. HDACs remove acetyl groups resulting in a positive charge of histone tails increasing binding between the histones and DNA backbone, condensing chromatin. | |||
;Question | ;Question | ||
*Are transcription factors, basal transcription factors, basal factors all the same thing? | *Are transcription factors, basal transcription factors, basal factors all the same thing? | ||
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Transcription factors can be constitutively-active – present in all cells at all times or can be conditionally-active – requires activation (e.g., cell specific or signal-dependent). | Transcription factors can be constitutively-active – present in all cells at all times or can be conditionally-active – requires activation (e.g., cell specific or signal-dependent). | ||
* | *Lecture Slides have the overview of the list of proteins that regulate transcription (as follows): | ||
**Basal transcription factors | **Basal transcription factors | ||
***TATA-binding protein TFIIB, TFIIA, TFIIE, TFIIH etc. | ***TATA-binding protein TFIIB, TFIIA, TFIIE, TFIIH etc. | ||
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*Cis elements- these are regulatory sequences on DNA. Can they be both enhancers and silencers? Does their proximity to the gene matter to still be considered "cis"? | *Cis elements- these are regulatory sequences on DNA. Can they be both enhancers and silencers? Does their proximity to the gene matter to still be considered "cis"? | ||
;Answer | ;Answer | ||
*Yes, they can be both enhancers and silencers, and can be very far away from the promoter, but on the same piece of DNA. | *Yes, they can be both enhancers and silencers, and can be very far away from the promoter, but on the same piece of DNA. Enhancers can even be located on a different chromosome than the promoter. Here’s a recent paper that is nteresting to scan briefly because it describes the complexities in transcription control. de Laat, W., & Duboule, D. (2013). Topology of mammalian developmental enhancers and their regulatory landscapes. Nature, 502(7472), 499–506. doi:10.1038/nature12753 | ||
;Question | ;Question | ||
*Regarding constitutive and inducible enhancer elements, it was my understanding that enhancer refers to the DNA sequence, whereas activator refers to the DNA binding protein, so I’m not sure of what a constitutive and inducible enhancer is. | *Regarding constitutive and inducible enhancer elements, it was my understanding that enhancer refers to the DNA sequence, whereas activator refers to the DNA binding protein, so I’m not sure of what a constitutive and inducible enhancer is. |
Revision as of 11:04, 27 January 2014
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Links for Maureen Hoatlin's CSF 2014 Class
Really.
Questions and Answers
Reversible modification of the ε-amino group of lysine by acetylation neutralizes a negative charge on DNA.
Transcription factors can be constitutively-active – present in all cells at all times or can be conditionally-active – requires activation (e.g., cell specific or signal-dependent).
That's how PARP1 inhibitors are relatively selective in killing the HR deficient tumor cell but not the wild-type cell (which is competent for HR)
Other Stuff |