Eukaryotic Gene Expression and Regulation Flashcards
(26 cards)
How does structure of genome and RNA Pol compare between prokaryotes and eukaryotes?
prok: single, circular, with plasmid, small; 1 RNA Pol
euk: chromosomes in nucleosome large; 3 RNA Pol
How does transcription and translation compare between prokaryotes and eukaryotes?
prok: coupled bc no nucleoid barrier, default is ON for transcription
euk: nuclear transcription and cytoplasmic translation; default is OFF for transcription
How does gene clustering compare between prokaryotes and eukaryotes?
prok: operons where genes with similar functions are grouped
euk: usually no operons; each gene has its own promoter and enhancer elements
How does DNA structure compare between prokaryotes and eukaryotes?
prok: highly supercoiled DNA with some associated proteins
euk: highly supercoiled chromatic associated with histones in nucleosomes
Why is the default for euk transcription off?
genes not frequently expressed are “inactive” region of chromatin, which is packaged to be inaccessible to regulatory factors
What is the rate limiting step of transcription?
difference in rate of initiation (tells abundance of specific mRNA)
all genes require — to recruit RNA Pol to promoters
general transcription factors (GTFs)
What is the location and role of RNA Polymerase I?
- located in nucleolus
- transcribes most rRNA
What is the location and role of RNA Polymerase II?
- located in nucleus
- transcribes most protein-encoding genes (mRNA)
- also does snRNA (for splicing) and miRNA
What is the location and role of RNA Polymerase III?
- located in nucleus
- transcribes other RNAs like 5S rRNA, tRNA, and snRNA
What does alpha-amanitin do?
inhibitor that RNAPII shows the most sensitivity to
What are the activities of RNAP?
- **sequence specific **DNA binding (promoter)
- melts DNA to reveal the template strand
- selects ribonucleotide (not deoxynucleotides) that anneals to template strand
- polymerizes RNA strand
-
translocates on DNA template, during which it must:
-unwind DNA in front of polymerase
-unwinds RNA:DNA hybrid
-rewinds DNA behind polymerase - recognize termination signals in the nascent transcript (or on the DNA template)
RNAP must be what quality?
processive (have a high probability of reaching the end of the gene)
What are the E. coli core RNAP subunits?
B’, B, αI, αII, ω
How do the three eukaryotic RNAPs compare to E.coli RNAP and each other?
- all 3 RNAPs have all 5 E.coli- like subunits + 4 other common subunits
- RNAP I and III have the same 2, non-identical α-like subunits
- RNAP II has a C-terminal domain that needs phosphorylation
- all have 3-7 smaller subunits for promoter class recognition
What is the importance of the CTD of RNAPII?
- seq: YSPTSPS
- 5/7 residues are hydrophilic
- ## phosphorylation at S and T
What happens when increased vs. decreased phosphorylation of CTD of RNAPII?
- low CTP (hypo)phosphorylation = transcription initiation
- high CTD (hyper)phosphorylation = elongation
What are the 3 steps of transcription?
- initiation
- elongation
- termination
How does eukaryotic initiation by RNAPII occur?
- 5 GTFs associate with TATA box in the promoter
- RNAPII attaches to GTFs and initiation region in promoter making a loop
- transcription activators/repressors bind to enhancer/silencer regions that are proximal or distal to promoter
How does eukaryotic elongation by RNAPII occur?
- RNAPII released front initiation complex
- emerging RNA gets 5’ cap
- decide if gene should be aborted or not
How does eukaryotic termination occur?
- there are no termination sequences defined
- torpedo model
- allosteric model
what is the torpedo model
- mRNA cleaved after polyA signal sequence
- RNase digests remaining RNA and disrupts transcription complex
potential eukaryotic termination model
what is the allosteric model?
- polyA sequence causes change in RNAPII processivity
- causes RNAPII to dissociate
potential eukaryotic termination model
How is prokaryotic transcription different from eukaryotic transcription?
- initiation doesn’t need TFs
- RNAP can bind directly to DNA
- in cytoplasm
- no mRNA processing
