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24 Cards in this Set
- Front
- Back
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Name the 3 Steps of Transcription
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Initiation, Elongation, Termination
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Which direction is RNA synthesized?
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5'---3'
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Which direction is the template strand copied/read?
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3'------5'
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What is de novo RNA synthesis?
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Initiated de novo by joining 2 ribonucleotides together to form the first 3'-5- phosphodiester bond.
Primer NOT required |
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Name the 3 Domains of Specific Transcription Factors and their function
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1) Leucine Zipper-Promotes heter/homo dimer formation of transcrip factor by hydrophobic interactions btw R groups of Leucine (Pincers on either side of DNA)
2)Basic Amino Acid (Lys/Arg)=DNA binding domain with cis-acting elements of target genes. Includes enhancers/silencers 3) Transactivation=interacts with proteins in RNAP II to regulate transcription activity (talks to the rest of the polymerase) |
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Zinc Finger, give and example and what is it composed of?
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Steroid Hormone Receptors
Composed of alpha-helix and 2 anti-parallel Beta Sheets |
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Domains of Steroid Hormone Receptor and their functions
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1) Hormone Binding Domain-binding of steroid, confrom change, activates receptor=>heterodimer
2) Zinc Finger-DNA binding domain that binds DIRECTLY to cis-acting elements in steroid responsive genes 3)Transactivation-interacts with proetins in RNAPII to regulate transcription (talks to rest of polymerase) |
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How does DNA Methylation affect transciption? what enzyme is used?
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1) inhibits binding of activator proteins to cis-acting elements in the promoter
2) can promote recruitment of specific repressor proteins to target/red flag cis-areas in promoter DNA Methyltransferase |
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Genomic Impriniting-tegrity. do not understand
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mechanism by gene expression is dependent on whether gene came from the mother or the father's chromosomes. Patterns of methylation are maintained following DNA replication by methyltransferases
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Describe Acetylation of Histones. What enzyme is used?
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Acetylation: HATs-HATs acetylate Lys in amino tails of histones/neutralize pos charged R groups and relax chromatin=gene activtion
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Describe Deactylation of Histones? What enzyme is used? What is the complex called?
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HDACs-deactylate Lys in amino tails of histones, which restores the positive charge on R group
-condenses chromatin structure/decreases accessibilty to TFs -leads to gene silencing/repression -Corepressor Complex |
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What do Remodeling factors do to chromatin?
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Stretch nucelosomes apart/remodel/open up chromatin. they are ATP dependent.
-stretch out linker DNA |
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Inhibitors of Transcription. Give clinical examples.
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Antibiotics
ex.) Actinomycin D: blocks the ability of Polymerase to copy the DNA template strand -Rifampicin prevents formation of first phophosdiester bond by RNA Polymerase alpha-Amanitin: toxin in mushrooms that binds tightly to RNAPII to inhibit elongation |
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Antibiotics:
actinomycin D does what? rifampicin does what? a-amantin does what? |
blocks ability of RNA polymerase
-rifampicin-prevents formation of first phosphodiester bond by RNA polymerase -aplha-amanitin-binds tight to RNA polymerase II to inhibit elongation (mushrooms) also RNAP III at [high] |
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Parts of RNA Polymerase II Holoenzyme
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core RNA polymerase, general and specific transcription factors, mediators
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name the 2 important general transcription factors and their functions
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TFIID and TFIIH
D: binds to TATA box H:helicase unwinds DNA in promoter, phosphorylates C-terminal domain (CTD chain) of RNAP II-tells it to get going and leave mess behind |
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in prokary Transciption bubble. the unwound region is how many bp?
the RNA/DNA duplex is how many bp? |
17
12 |
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What causes the dissocation of RNA from DNA template?
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the weak bond btw A-U, compbined with the hairpin of C-G, disrupts assocation of RNAP with DNA template=termination
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2 methods of termination
describe the 2nd one |
template-directed termination and Rho Protein termination
Rho protein binds to specific sequences in newly synthesizes RNA. has ATP-dep helicase activity that dissociates RNA from template strand. "peels" it off the DNA |
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processtivity is what? how quickly?
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RNA Polymerase stays on template and processes/transcribes DNA at 50 nucleotides/sec
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what is the proofreading enzymes for transcription?
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there is none!
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subunits of the prokary RNA polymerase holoenzyme
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1 omega (w)
2 alpha (a) 1 beta (B) pincer-phosophodiester bond formation/grasps DNA 1 beta prime (B') pincer-grasps DNA 1 sigma (o) important one!-promoter recognition/initiation (sigma marks the spot) |
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sigma subunit binds to promoter due to ______.
how many diff kinds of polymerase in prokary? |
high affinity binding
theres only 1! different sigma subunits though. ex #70 and #32 |
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topoisomerase II does what?
topoisomerase I does what? |
II unwinds the DNA ahead of transcipt bubble to prevent positive supercoiling (aka Gyrase)
type I topo to relaxneg supercoilds behind transc bubble |
