Lecture 2 Flashcards
What does Chromatin Condensation inactivate?
Gene Transcription
What type of eukaryotic DNA does transcription on?
One that is wrapped in chromatin
Why does chromatin need to be opened?
For a gene to be activated and transcription to proceed.
What is Chromatin Mediated Regulation often called?
Epigenetic Regulation of gene Expression
What is Heterochromatin?
Regions of chromosomes that are intensely stained
How is DNA packed in a heterochromatin?
Densely Packed
What is a Heterochromatin rich in?
Repetitive DNA (transposons, centromeres, and telomeres)
What is a heterochromatin not accessible to?
Transcriptional machinery
What is found in a heterochromatin?
Inactive genes
What is a Euchromatin?
Lightly stained chromosome regions
What is found in a Euchromatin?
Active Genes
What is a Euchromatin accessible to?
Transcriptional machinery
What happens once the gene is in open chromatin?
A very elaborate system and a variety of factors regulate the expression of each individual gene: far more complicated as compared to prokaryotes
What does RNA polymerase I synthesize?
Only pre-rRNA
What does RNA polymerase II synthesize?
mRNAs, some small nuclear RNAs (mRNA splicing), micro and small interfering RNAs that regulate translation and stability of mRNA’s
What does RNA polymerase III synthesize?
tRNA’s, 5S rRNA, and several other small stable RNAs
What is the RNA transcribed from from RNA polymerase I
Pre-rRNA (28S, 18S, 5.8S rRNAs)
What is the function of pre-rRNA?
Ribosome components, protein synthesis
What is mRNA transcribed by?
RNA polymerase II
What is the RNA function of mRNA
Encodes proteins
What is snRNAs transcribed by?
RNA polymerase II
What is the RNA function of snRNAs?
RNA splicing
What is siRNAs transcribed by?
RNA pol II
What is the RNA function of siRNAs?
Chromatin-mediated repression, translation control
What is miRNAs transcribed by?
RNA pol II
What is the RNA function of miRNA’s?
Translation Control
What is tRNAs transcribed by?
RNA pol III
What is the RNA function of tRNAs
Protein Synthesis
What is 5s rRNA transcribed by?
RNA pol III
What is the RNA function of 5s rRNA?
Ribosome component, protein synthesis
What is snRNA U6 transcribed by?
RNA pol III
What is the function of snRNA U6?
RNA splicing
What is 7S RNA transcribed by?
RNA pol III
What is the function of 7S RNA?
Signal recognition particle for insertion of polypeptides into the ER
What are other small stable RNAs transcribed by?
RNA pol III
What is the function of small stable RNAs?
Various functions
What is a characteristic of the crystal structure of the yeast RNA pol II?
Has been resolved at a High resolution (very active)
How many polypeptides does RNA pol II consist of?
12 polypeptides called RPB1, RPB2, etc..
What does all other eukaryotic RNA polymerases share?
Very high level of homology with the yeast RNA pol II
What does the Clamp Domain in the polymerase (RPB1) do?
Accommodate DNA.
After positioning over DNA what happens to the clamp?
It is closed by a bridge
Where does the synthesis of RNA take place in?
The catalytic centre with the participation of Mg++
Where does the synthesized RNA exit through?
A “channel” and is immediately capped by 7m Guanosine
What does Eukaryotic RNA polymerase II contain?
A unique Carboxy-Terminal Domain (CTD) of its RPB1 subunit
What is the Carboxy-Terminal Domain?
A specialized domain not found in any other polymerases, prokaryotic, or eukaryotic.
What is the CTD involved in?
Multiple regulatory interactions and plays a key role in initiation, elongation, and processing of mRNAs
What does the CTD in yeast contain?
26 repeats of Tyr- Ser - Pro - The - Ser- Pro - Ser
What does the CTD in mammals contain?
52 repeats
What happens to the Ser residue?
It gets phosphorylated during transcription from initiation to elongation
What is the structure like of the CTD?
Not structured (can’t be seen under crystallography)
When is CTD of RNA Pol II phosphorylated?
During in vivo transcription
How is RNA Pol II genes regulated?
- Core Promoter Sequences*
- Promoter-Proximal binding sites for activators
- Distal Enhancers or Repressors
- Chromatin Structure
What is the BRE?
- 37 to - 32 sites
RNA Pol II TFIIB Recognition Element
What is the TATA Box?
- 32 to - 26 sites
A Tight consensus sequence
What is the site of the Initiator
- 2 to +4
What is the site of the downstream promoter element?
+ 28 to +32
Where does transcription start?
At a defined point called the initiator site
- Usually an A on the coding strand
What does BRE and DPE influence?
The activity of the promoter
What does DNA helicase help?
The polymerase initiate transcription.
What does Kinase help?
Release the polymerase
What are RNA Pol I General Txn. Factors labelled as?
TFIA and TFIB
What are RNA Pol II General Txn. Factors labelled as?
TFIIA, TFIIB, TFIID, TFIIE, TFIIH
What are RNA Pol III General Txn. Factors labelled as?
TFIIIB, TFIIIS
