BIO130H1 Study Guide - Midterm Guide: Histone Octamer, Dna Supercoil, Top1

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25 Jun 2016
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Histones: Histone octamer core composed of 2x(H2A, H2B, H3, H4), positively-charged to interact with
DNA. H1 is linker histone, packages nucleosomes together. Histones have amino terminal tails that
control DNA replication and transcription.
Cohesin: Looped domains of DNA wrap around this to form protein scaffolds.
Condensin: Facilitates condensing of chromosomes, especially during mitosis.
Primase: Lays down RNA primers, thus providing 3’ -OH for formation of new strand. Often transiently
forms primosome with helicase. Low fidelity.
Helicase: Unwinds DNA.
Ligase: Catalyzes 5’-3’ phophodiester bonds between adjacent nucleotides.
DNA polymerase: Lays down nucleotides during DNA replication. Also used to fill gap after
exonuclease and endonuclease remove mismatched bases. Held to DNA by sliding (beta) clamp.
Single-strand binding proteins: Bind to single strands of DNA to keep bubble open during DNA
replication.
Topoisomerase I: Only breaks one strand of DNA for tension relief. Also performs DNA supercoiling in
prokaryotes.
Topoisomerase II: Breaks both strands for DNA, often to allow another DNA helix to pass through it
Telomerase: In eukaryotes, elongates 3’ overhangs to allow DNAP to complementarily lengthen the
shortened 5’ end
.
3’ to 5’ exonuclease: Attached to DNAP, immediately corrects mismatched base pairs during replication.
In cytosol, will degrade mRNAs without 5’ caps or poly(A) tails.
MutL (strand-directed mismatch repair): In eukaryotes, detects distortion(nicks) of DNA helix, then
removes the strand surrounding the problematic area. In prokaryotes, MutL does not look for nicks but
rather for methylated adenosines.
Glycosylase (base excision repair): Looks for single mismatched/altered bases. Different glycosylases
look for different modified bases. Will “behead” (remove base component of) offending base, then
endonuclease will cleave away the base’s backbone. DNAP will then fill gap, then ligase seals nicks.
Sigma factor: In prokaryotes only. Binds with RNAP. Different sigma factors identify different
promoters for the holoenzyme (σ-factor + RNAP) to bind to. Release of σ-factor allows RNAP to enter
processive mode.
Transcription initiation in eukaryotes: TBP (TATA-Binding Protein) of the TFIID binds to promoter
(which will let RNAP know which strand to transcribe) and bends DNA, which signals for arrival of
TFIIA and TFIIB which help position RNAPII. TFIIF helps secure RNAPII. TFIIE regulates TFIIH.
TFIIH: Involved with both transcription initiation and excision repair. Possesses helicase activity that
will unwind DNA for lesion removal. Possesses kinase, which allows RNAPII to leave preinitiation
complex by phosphorylating RNAPII’s CTD.
1
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Document Summary

Histones: histone octamer core composed of 2x(h2a, h2b, h3, h4), positively-charged to interact with. Histones have amino terminal tails that control dna replication and transcription. Cohesin: looped domains of dna wrap around this to form protein scaffolds. Condensin: facilitates condensing of chromosomes, especially during mitosis. Primase: lays down rna primers, thus providing 3" -oh for formation of new strand. Ligase: catalyzes 5"-3" phophodiester bonds between adjacent nucleotides. Dna polymerase: lays down nucleotides during dna replication. Also used to fill gap after exonuclease and endonuclease remove mismatched bases. Single-strand binding proteins: bind to single strands of dna to keep bubble open during dna replication. Topoisomerase i: only breaks one strand of dna for tension relief. Topoisomerase ii: breaks both strands for dna, often to allow another dna helix to pass through it. Telomerase: in eukaryotes, elongates 3" overhangs to allow dnap to complementarily lengthen the shortened 5" end.

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