Term
| When a DNA sequence is represented by a single strand, which strand is given? |
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Definition
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Term
| How does DNA replication and RNA transcription differ with respect to prokaryotic and eukaryotic polymerases? |
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Definition
DNA replication: 5 prokaryotic polymerases; Many eukaryotic polymerases
RNA transcription - 1 prokaryotic polymerase; 3 eukaryotic polymerases |
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Term
| How do DNA-dependent DNA polymerases and RNA polymerases differ with respect to enzymatic functions? |
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Definition
| RNA polymerase has no proof reading (no 5'-3' or 3'-5' exonuclease) |
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Term
| List the 3 steps of prokaryotic RNA synthesis. |
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Definition
1. Initiation - RNA pol binds to the promoter and searches for the 1st and 2nd bases in the gene to form phosphodiester bond.
2. Elongation - RNA pol slides along the gene to incorporate the corresponding ribonucleotides.
3. Termination - RNA pol encounters termination sequence and falls off. Recycles to promoter to start again. |
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Term
| How long are promoters? What are the 2 promoter sequences and where are they located? |
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Definition
| ~40 bp; TTGACA (~35 bp upstream) and TATA (~10 bp upstream) |
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Term
| What is the sigma protein factor? |
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Definition
| Determines promoter specificity |
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Term
| What are the subunits of the RNA polymerase core? |
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Definition
alpha - (2) recognizes the regulatory sequences in the promoter on the DNA
beta - catalyzes phosphodiester backbone formation
beta' - holds onto the DNA template |
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Term
| What is the RNA polymerase holoenzyme composed of? |
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Definition
| The core and the sigma factor (sigma protein) |
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Term
| RNA transcription initiation ends when... |
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Definition
chain reaches ~10 nt
sigma factor is released from the holoenzyme |
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Term
| What 2 topoisomerases work on DNA during RNA transcription? |
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Definition
Gyrase adds neg coils downstream to relax DNA
Topoisomerase 1 removes the neg coils upstream |
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Term
| What are the 2 mechanisms of transcriptional termination? |
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Definition
Intrinsic terminator - G+C rich palindrome followed by U rich sequence
Rho-dependent terminator |
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Term
| How does rifampicin work and what does it treat? |
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Definition
Rifampicin binds to the beta subunit of RNA polymerase causing transcriptional paralysis after the dinucleotide stage. It is less effective if bacteria has a mutation in the gene coding for the beta subunit.
TB |
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Term
| What genes does RNA polymerase I transcribe? |
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Definition
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Term
What genes does RNA polymerase II transcribe?
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Definition
| All protein coding genes and snoRNA, miRNA, siRNA, and most snRNA, but mainly mRNAs |
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Term
What genes does RNA polymerase III transcribe?
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Definition
| tRNA, 5s, and other small RNAs |
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Term
| What is important about the CTD on RNA pol II? |
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Definition
| It is the link between transcription and mRNA processing -- capping, splicing and polyadenylation. |
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Term
| What is alpha-amamitin and what does it affect? |
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Definition
| A hepatotoxin; alpha-amamitin inhibits the largest subunit of RNA polymerase II so essential mRNAs in the liver are degraded but not replaced. |
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Term
| What are the 3 promoter types for the eukaryotic RNA polymerases? |
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Definition
RNAP I - bipartite promoter, overlapping the +1 site and the upstream element
RNAP II - recognizes ~60 bp of DNA in the core promoter and initiates synthesis from the +1 base 25 bps downstream of TATA box
RNAP III - promoter located within the tRNA gene |
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Term
| How do enhancers differ from promoters? |
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Definition
| Enhancers are not required for initiation of transcription; enhancers are not location specific and are orientation independent |
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Term
| What are the 3 transcriptional termination signals for eukaryotic RNA polymerase? |
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Definition
RNAP I - terminator sequence + protein factor
**RNAP II** - termination signal unknown - linked with polyadenylation of RNA
RNAP III - similar to bacteria - GC rich region with run of U residues |
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Term
| What is the sequence at intron-exon boundaries? |
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Definition
5' splice site - AGGUAGAGU
Branch site in middle - A
3' splice site - [Py tract]AGGU |
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Term
| What does RNA editing refer to in mammalian cells? |
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Definition
conversion of C to U via cytidine deaminase
conversion of A to I via adenine deaminase |
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