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PENN STATE / Bmb001 / Bmb 400 / What is also a transcription factor to expressing genes for dna repair

What is also a transcription factor to expressing genes for dna repair

What is also a transcription factor to expressing genes for dna repair

Description

School: Pennsylvania State University
Department: Bmb001
Course: Molecular Biology of the Gene
Term: Fall 2019
Tags:
Cost: 25
Name: Chapter 9 and Chapter 10
Description: Class and Book Notes
Uploaded: 09/10/2019
11 Pages 27 Views 1 Unlocks
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"}.lst-kix_mulqo9mrb2iu-1 > li:before{content:"- "}.lst-kix_l9arkaghl5q5-6 > li:before{content:"" counter(lst-ctn-kix_l9arkaghl5q5-6,decimal) ". "}.lst-kix_l9arkaghl5q5-7 > li:before{content:"" counter(lst-ctn-kix_l9arkaghl5q5-7,lower-latin) ". "}.lst-kix_t009pzmfibs4-8 > li:before{content:"■ "}.lst-kix_t009pzmfibs4-6 > li:before{content:"● "}.lst-kix_t009pzmfibs4-0 > li:before{content:"● "}ul.lst-kix_ampufltmlahi-1{list-style-type:none}ul.lst-kix_ampufltmlahi-2{list-style-type:none}ol.lst-kix_vtvsy92cccoq-2.start{counter-reset:lst-ctn-kix_vtvsy92cccoq-2 0}ul.lst-kix_ampufltmlahi-0{list-style-type:none}.lst-kix_t009pzmfibs4-4 > li:before{content:"○ "}ul.lst-kix_ampufltmlahi-7{list-style-type:none}ul.lst-kix_ampufltmlahi-8{list-style-type:none}.lst-kix_t009pzmfibs4-2 > li:before{content:"■ "}ul.lst-kix_ampufltmlahi-5{list-style-type:none}ul.lst-kix_ampufltmlahi-6{list-style-type:none}ul.lst-kix_ampufltmlahi-3{list-style-type:none}ul.lst-kix_ampufltmlahi-4{list-style-type:none}ol.lst-kix_vtvsy92cccoq-5.start{counter-reset:lst-ctn-kix_vtvsy92cccoq-5 0}ol.lst-kix_gvrbvmhb6py0-0.start{counter-reset:lst-ctn-kix_gvrbvmhb6py0-0 0}ul.lst-kix_t009pzmfibs4-7{list-style-type:none}ul.lst-kix_t009pzmfibs4-8{list-style-type:none}ul.lst-kix_t009pzmfibs4-3{list-style-type:none}ul.lst-kix_t009pzmfibs4-4{list-style-type:none}ul.lst-kix_t009pzmfibs4-5{list-style-type:none}ul.lst-kix_t009pzmfibs4-6{list-style-type:none}ul.lst-kix_t009pzmfibs4-0{list-style-type:none}ul.lst-kix_t009pzmfibs4-1{list-style-type:none}ul.lst-kix_t009pzmfibs4-2{list-style-type:none}ul.lst-kix_btvj4yxifjo0-0{list-style-type:none}ul.lst-kix_btvj4yxifjo0-1{list-style-type:none}ul.lst-kix_btvj4yxifjo0-2{list-style-type:none}ul.lst-kix_btvj4yxifjo0-3{list-style-type:none}.lst-kix_gvrbvmhb6py0-5 > li{counter-increment:lst-ctn-kix_gvrbvmhb6py0-5}ul.lst-kix_btvj4yxifjo0-4{list-style-type:none}ul.lst-kix_btvj4yxifjo0-5{list-style-type:none}ul.lst-kix_btvj4yxifjo0-6{list-style-type:none}ul.lst-kix_btvj4yxifjo0-7{list-style-type:none}.lst-kix_vtvsy92cccoq-0 > li{counter-increment:lst-ctn-kix_vtvsy92cccoq-0}ul.lst-kix_btvj4yxifjo0-8{list-style-type:none}.lst-kix_f6vmrpcwoxoc-8 > li:before{content:"■ "}.lst-kix_q1jzgae3nlcp-8 > li:before{content:"- "}.lst-kix_f6vmrpcwoxoc-6 > li:before{content:"● "}.lst-kix_xjxilgzetqef-5 > li:before{content:"- "}.lst-kix_f6vmrpcwoxoc-4 > li:before{content:"○ "}.lst-kix_l9arkaghl5q5-4 > li{counter-increment:lst-ctn-kix_l9arkaghl5q5-4}.lst-kix_q1jzgae3nlcp-6 > li:before{content:"- "}.lst-kix_ampufltmlahi-0 > li:before{content:"● "}.lst-kix_xjxilgzetqef-3 > li:before{content:"- "}.lst-kix_gvrbvmhb6py0-0 > li{counter-increment:lst-ctn-kix_gvrbvmhb6py0-0}.lst-kix_q1jzgae3nlcp-0 > li:before{content:"- "}.lst-kix_q1jzgae3nlcp-2 > li:before{content:"- "}.lst-kix_xjxilgzetqef-1 > li:before{content:"- "}.lst-kix_q1jzgae3nlcp-4 > li:before{content:"- "}ul.lst-kix_iggqzswo4w6-6{list-style-type:none}ul.lst-kix_iggqzswo4w6-5{list-style-type:none}ul.lst-kix_iggqzswo4w6-4{list-style-type:none}ul.lst-kix_iggqzswo4w6-3{list-style-type:none}ul.lst-kix_iggqzswo4w6-2{list-style-type:none}ul.lst-kix_iggqzswo4w6-1{list-style-type:none}ul.lst-kix_iggqzswo4w6-0{list-style-type:none}ol.lst-kix_gvrbvmhb6py0-2.start{counter-reset:lst-ctn-kix_gvrbvmhb6py0-2 0}.lst-kix_ampufltmlahi-8 > li:before{content:"■ "}ul.lst-kix_iggqzswo4w6-8{list-style-type:none}ul.lst-kix_iggqzswo4w6-7{list-style-type:none}.lst-kix_ampufltmlahi-6 > li:before{content:"● "}.lst-kix_tmynt5s4ho55-3 > li:before{content:"● "}.lst-kix_f6vmrpcwoxoc-0 > li:before{content:"● "}.lst-kix_f6vmrpcwoxoc-2 > li:before{content:"■ "}.lst-kix_ampufltmlahi-2 > li:before{content:"■ "}ol.lst-kix_l9arkaghl5q5-7.start{counter-reset:lst-ctn-kix_l9arkaghl5q5-7 0}.lst-kix_ampufltmlahi-4 > li:before{content:"○ "}.lst-kix_tmynt5s4ho55-1 > li:before{content:"○ "}.lst-kix_xjxilgzetqef-7 > li:before{content:"- "}ol.lst-kix_vtvsy92cccoq-3.start{counter-reset:lst-ctn-kix_vtvsy92cccoq-3 0}.lst-kix_vtvsy92cccoq-6 > li{counter-increment:lst-ctn-kix_vtvsy92cccoq-6}.lst-kix_gvrbvmhb6py0-3 > li:before{content:"" counter(lst-ctn-kix_gvrbvmhb6py0-3,decimal) ". 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"}ul.lst-kix_kofbqmpt24os-0{list-style-type:none}.lst-kix_vtvsy92cccoq-7 > li:before{content:"" counter(lst-ctn-kix_vtvsy92cccoq-7,lower-latin) ". "}.lst-kix_gvrbvmhb6py0-2 > li:before{content:"" counter(lst-ctn-kix_gvrbvmhb6py0-2,lower-roman) ". "}.lst-kix_bfb31cwo5wj2-4 > li:before{content:"○ "}.lst-kix_bfb31cwo5wj2-3 > li:before{content:"● "}ul.lst-kix_tmynt5s4ho55-8{list-style-type:none}ul.lst-kix_tmynt5s4ho55-7{list-style-type:none}ul.lst-kix_tmynt5s4ho55-6{list-style-type:none}ul.lst-kix_tmynt5s4ho55-5{list-style-type:none}.lst-kix_bfb31cwo5wj2-0 > li:before{content:"● "}ul.lst-kix_tmynt5s4ho55-4{list-style-type:none}ul.lst-kix_tmynt5s4ho55-3{list-style-type:none}ul.lst-kix_tmynt5s4ho55-2{list-style-type:none}ul.lst-kix_tmynt5s4ho55-1{list-style-type:none}ul.lst-kix_tmynt5s4ho55-0{list-style-type:none}.lst-kix_t009pzmfibs4-5 > li:before{content:"■ "}.lst-kix_t009pzmfibs4-1 > li:before{content:"○ "}.lst-kix_l9arkaghl5q5-2 > li{counter-increment:lst-ctn-kix_l9arkaghl5q5-2}.lst-kix_gvrbvmhb6py0-4 > li{counter-increment:lst-ctn-kix_gvrbvmhb6py0-4}.lst-kix_lkgv7m6dq8qh-3 > li:before{content:"● "}.lst-kix_bfb31cwo5wj2-7 > li:before{content:"○ "}.lst-kix_btvj4yxifjo0-6 > li:before{content:"● "}.lst-kix_lkgv7m6dq8qh-7 > li:before{content:"○ "}ol.lst-kix_l9arkaghl5q5-8{list-style-type:none}ol.lst-kix_l9arkaghl5q5-7{list-style-type:none}ol.lst-kix_l9arkaghl5q5-6{list-style-type:none}ol.lst-kix_l9arkaghl5q5-5{list-style-type:none}.lst-kix_btvj4yxifjo0-2 > li:before{content:"■ "}.lst-kix_gvrbvmhb6py0-2 > li{counter-increment:lst-ctn-kix_gvrbvmhb6py0-2}.lst-kix_vtvsy92cccoq-0 > li:before{content:"" counter(lst-ctn-kix_vtvsy92cccoq-0,decimal) ". "}ul.lst-kix_mulqo9mrb2iu-7{list-style-type:none}.lst-kix_xjxilgzetqef-6 > li:before{content:"- "}ul.lst-kix_mulqo9mrb2iu-8{list-style-type:none}ul.lst-kix_mulqo9mrb2iu-5{list-style-type:none}ul.lst-kix_mulqo9mrb2iu-6{list-style-type:none}ul.lst-kix_mulqo9mrb2iu-3{list-style-type:none}ul.lst-kix_mulqo9mrb2iu-4{list-style-type:none}ul.lst-kix_mulqo9mrb2iu-1{list-style-type:none}ul.lst-kix_mulqo9mrb2iu-2{list-style-type:none}.lst-kix_xjxilgzetqef-2 > li:before{content:"- "}ul.lst-kix_mulqo9mrb2iu-0{list-style-type:none}.lst-kix_ampufltmlahi-1 > li:before{content:"○ "}.lst-kix_f6vmrpcwoxoc-5 > li:before{content:"■ "}ol.lst-kix_l9arkaghl5q5-4{list-style-type:none}ol.lst-kix_l9arkaghl5q5-3{list-style-type:none}ol.lst-kix_l9arkaghl5q5-2{list-style-type:none}ol.lst-kix_l9arkaghl5q5-1{list-style-type:none}ol.lst-kix_l9arkaghl5q5-0{list-style-type:none}.lst-kix_q1jzgae3nlcp-1 > li:before{content:"- "}.lst-kix_q1jzgae3nlcp-5 > li:before{content:"- "}.lst-kix_vtvsy92cccoq-8 > li{counter-increment:lst-ctn-kix_vtvsy92cccoq-8}.lst-kix_fujng5vrr5r5-6 > li:before{content:"● "}ul.lst-kix_fujng5vrr5r5-2{list-style-type:none}ul.lst-kix_fujng5vrr5r5-3{list-style-type:none}.lst-kix_fujng5vrr5r5-2 > li:before{content:"■ "}ul.lst-kix_fujng5vrr5r5-4{list-style-type:none}ul.lst-kix_fujng5vrr5r5-5{list-style-type:none}ul.lst-kix_fujng5vrr5r5-0{list-style-type:none}ul.lst-kix_fujng5vrr5r5-1{list-style-type:none}ul.lst-kix_fujng5vrr5r5-6{list-style-type:none}ul.lst-kix_fujng5vrr5r5-7{list-style-type:none}ul.lst-kix_fujng5vrr5r5-8{list-style-type:none}.lst-kix_ampufltmlahi-5 > li:before{content:"■ "}.lst-kix_tmynt5s4ho55-0 > li:before{content:"● "}.lst-kix_tmynt5s4ho55-4 > li:before{content:"○ "}.lst-kix_f6vmrpcwoxoc-1 > li:before{content:"○ "}ol.lst-kix_vtvsy92cccoq-6.start{counter-reset:lst-ctn-kix_vtvsy92cccoq-6 0}ol.lst-kix_l9arkaghl5q5-3.start{counter-reset:lst-ctn-kix_l9arkaghl5q5-3 0}ol.lst-kix_gvrbvmhb6py0-7{list-style-type:none}ol.lst-kix_gvrbvmhb6py0-6{list-style-type:none}ol.lst-kix_gvrbvmhb6py0-8{list-style-type:none}ol.lst-kix_gvrbvmhb6py0-1.start{counter-reset:lst-ctn-kix_gvrbvmhb6py0-1 0}.lst-kix_vtvsy92cccoq-5 > li{counter-increment:lst-ctn-kix_vtvsy92cccoq-5}.lst-kix_slyctkmu0ol9-2 > li:before{content:"- "}.lst-kix_slyctkmu0ol9-3 > li:before{content:"- "}.lst-kix_slyctkmu0ol9-4 > li:before{content:"- "}.lst-kix_slyctkmu0ol9-6 > li:before{content:"- "}.lst-kix_slyctkmu0ol9-5 > li:before{content:"- "}.lst-kix_slyctkmu0ol9-8 > li:before{content:"- "}.lst-kix_slyctkmu0ol9-7 > li:before{content:"- "}.lst-kix_9g6wxym9krsi-0 > li:before{content:"● "}ol.lst-kix_gvrbvmhb6py0-6.start{counter-reset:lst-ctn-kix_gvrbvmhb6py0-6 0}.lst-kix_9g6wxym9krsi-2 > li:before{content:"■ "}.lst-kix_9g6wxym9krsi-1 > li:before{content:"○ "}.lst-kix_kofbqmpt24os-2 > li:before{content:"- 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"}.lst-kix_lkgv7m6dq8qh-8 > li:before{content:"■ "}.lst-kix_btvj4yxifjo0-3 > li:before{content:"● "}ul.lst-kix_q1jzgae3nlcp-8{list-style-type:none}ul.lst-kix_q1jzgae3nlcp-6{list-style-type:none}ol.lst-kix_l9arkaghl5q5-8.start{counter-reset:lst-ctn-kix_l9arkaghl5q5-8 0}ul.lst-kix_q1jzgae3nlcp-7{list-style-type:none}ol.lst-kix_vtvsy92cccoq-4.start{counter-reset:lst-ctn-kix_vtvsy92cccoq-4 0}.lst-kix_gvrbvmhb6py0-6 > li{counter-increment:lst-ctn-kix_gvrbvmhb6py0-6}ul.lst-kix_q1jzgae3nlcp-0{list-style-type:none}ul.lst-kix_q1jzgae3nlcp-1{list-style-type:none}ul.lst-kix_q1jzgae3nlcp-4{list-style-type:none}ul.lst-kix_q1jzgae3nlcp-5{list-style-type:none}ul.lst-kix_q1jzgae3nlcp-2{list-style-type:none}ul.lst-kix_q1jzgae3nlcp-3{list-style-type:none}.lst-kix_fujng5vrr5r5-5 > li:before{content:"■ "}.lst-kix_lkgv7m6dq8qh-0 > li:before{content:"● "}.lst-kix_l9arkaghl5q5-5 > li{counter-increment:lst-ctn-kix_l9arkaghl5q5-5}.lst-kix_fujng5vrr5r5-7 > li:before{content:"○ "}ul.lst-kix_f6vmrpcwoxoc-7{list-style-type:none}.lst-kix_fujng5vrr5r5-1 > li:before{content:"○ "}ul.lst-kix_f6vmrpcwoxoc-8{list-style-type:none}ul.lst-kix_f6vmrpcwoxoc-3{list-style-type:none}ul.lst-kix_f6vmrpcwoxoc-4{list-style-type:none}ul.lst-kix_f6vmrpcwoxoc-5{list-style-type:none}ul.lst-kix_f6vmrpcwoxoc-6{list-style-type:none}ul.lst-kix_f6vmrpcwoxoc-0{list-style-type:none}ul.lst-kix_f6vmrpcwoxoc-1{list-style-type:none}ul.lst-kix_f6vmrpcwoxoc-2{list-style-type:none}.lst-kix_fujng5vrr5r5-3 > li:before{content:"● "}ol.lst-kix_l9arkaghl5q5-6.start{counter-reset:lst-ctn-kix_l9arkaghl5q5-6 0}ol.lst-kix_gvrbvmhb6py0-4.start{counter-reset:lst-ctn-kix_gvrbvmhb6py0-4 0}ul.lst-kix_9g6wxym9krsi-5{list-style-type:none}.lst-kix_gvrbvmhb6py0-4 > li:before{content:"" counter(lst-ctn-kix_gvrbvmhb6py0-4,lower-latin) ". 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Chapter 9: the replication of DNA

  • DNA synthesis
  1. 4 deoxynucleoside triphosphates
  2. Primer: template junction

Don't forget about the age old question of Define sedentism.

If you want to learn more check out What does it mean for an enzyme to be saturated?

  • Adding to 31 end
  • Sn2 reaction
  • Oh attacks os
  • Phosphodiester bond

If you want to learn more check out What are specific bonds between atoms that have characteristic behavior?

XTP + (XMP)n → (XMP)n+1 +        

XTP + (XMP)n → (XMP)n+1+        =

Hydrolysis of phosphate

“Pyrophosphate hydrolysis”Don't forget about the age old question of If two characters are in frame from the torso up, what is that shot called?
We also discuss several other topics like Name the five unifying themes of biocomplexity.

  • DNA Polymerase
  • One active site for all four
  • Maniters ability of nucleotides to pair
  • Incorporation of wrong nucleotide is slower(base pair)
  • Incorporation of rNTPs is slower (steric exclusion)
  • Error rate =
  • Speed of DNA polymerase? Incorporation assay labed aNTP

Don't forget about the age old question of What is the atomic number and what it signifies?

Palm - B sheet, catalytic site, hydrogen bonds metals(two divalent)

  1. One metal reduces affinity of  for its hydrogen making able to attack X
  2. Next metal stabilizes the pyrophosphate

Hydrogen bonds of minor groove only bind to correctly paired nue.

Fingers - residues bind to incoming dNTP, correct? Moves palm near metals turn of phosphodiester backbone to expose one base at a time

Thumb - maintains position of primer and active site maintains strong association between DNA polymerase + substrate

Photoreactivation

  • Pyrimidine dimer is made by an energy from UV light

  • Methyltransferase is also a transcription factor to expressing genes for DNA repairs(coupling between DNA repair and transcription)

DNA Polymerase Steps:

  • Adds nucleotides…
  • Incoming nucleotide base pairs with next available template
  • Interaction causes fingers of polymerase to close around base paired dNTP
  • Catalytic metal ions catalyze formation of next phosphodiester bond
  • Attachment of base - paired nucleotides to primer leads to reopening of fingers and movement of primer: template junction by one base pair

  • 1000 nucleotides/sec
  • Depends on degree of processivity(# bases added each time enzyme bonds) range few → 50,000
  • O-helix = finger domain
  • rotation when binds dNTP
  • Conformations change of finger enhances the fidelity of DNA synth

Processibitty - average 3 of nucleotides added each time the enzyme binds a primer: template junction

  • Speed of DNA synth is much faster than that of DNA binding
  • ↑ processivity = ↑ overall DNA synth

Proof - Reading Endonucleases - degrade / cut DNA from inside

Exonucleases - degrade DNA from end

→ a part of the same polypeptide as a DNA polymerase preference for mismatched pairs! errors!

  • DNA polymerase = two active sites
  1. DNA synthesis
  2. Proof reading exonuclease

Mismatched DNA slows DNA synthesis that gives time for moving end to exonuclease active site

Replication Fork

  • Both strands (leading + lagging) are synthesized at rep. fork
  • DNA always synthesized 5 → 3 (along template 3 - 5)

1000 - 2000 nucleotides in bacteria

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