Transcription, RNA processing and control of Gene expression Flashcards
What are the four rRNA molecules, and where do each of them come from?
There is 28S, 18S, 5.8S and 5S. All except for 5S come from Pol I, 5S is made by Pol III
What does Pol III synthesize?
The 5S rRNA, as well as tRNAs.
True or false: G, U, A, C, and inosine are common to tRNAs
True
What does pol II synthesize?
mRNA
What is the function of the TATA boxes, CAAT box, and GC region?
Generally a promoter region for Pol II (TATA especially)
How do the promotor regions help Pol II begin synthesis?
bind proteins which help Pol II bind
True or false: Pol II can bind to promotor regions without the help of general transcription factors
False (for our purposes at least)
What is TFDII?
A complex of binding proteins that help RNA Pol II bind
TBP is what?
The TATA binding protein, part of TFDII, the specifically binds to the TATA box and acts as a signpost for other proteins to bind
What are the other transcription complexes besides TFIID?
TFIIE, TFIIF, and TFIIH
Which pairs are easier to pull apart, A-T or G-C?
A-T
Which general transcription factor has DNA helicase activity?
TFIIH
True or false: the transcription factors stay attached to RNA Pol II once transcription begins
False
What is the basal transcription complex?
The complex of RNA and general transcription factors that help pol II bind
What does SP-1 bind to? What does it do?
GC-rich sequences
Increases Pol activity above the basal rate
What does NF1 bind to? What does it do?
CAAT boxes
Increases Pol activity above the basal rate
What is required for transcription of tightly bound chromatin?
Chromatin remodeling
What is the primary mechanism for Death Cap Mushroom?
Inhibition of Pol II, blocking the synthesis of mRNA
What is the mechanism by which the abx Rifampicin works? What notable disease is the used as treatment for?
Inhibits the prokaryotic RNA polymerase II
TB
What does pre-mRNA contain? How are these removed?
Exons and introns
By splicing
What are the enzymes that catalyze RNA splicing?
Spliceosomes
What are the three important sites involved in RNA splicing?
5’ splice site
3’ splice site
a branch point
What is the base that is at the branch point in RNA splicing? What does it attack (5’ or 3’ splice site)?
Adenine
Attacks the 5’ splice site
How does tropomyosin have a wide variety of isozymes (hint: think about exons)
Different branch points produce different exons
What molecules is used in the 5’ cap?
Methylguanasine
What is the polyadenylation signal?
The DNA encoded part of the RNA that specifies where the poly A tail should be placed
What does the Poly A tail consist of?
around 200 Adednine nucleotides
Export of mRNAs out of the nucleus is highyl regulated–what do mRNAs NEED to have, in order to leave the nucleus?
Poly A tail, and 5’ cap
Which is degrated first: the 5’ cap or the poly A tail?
Tail first, then cap
What are the enzymes that degrade the mRNA molecule?
Ribonucleases
What is beta-thalassemia? What is it caused by?
It is the reduced synthesis of the b-globin chain of Hb, leading to profound anemia.
This is caused by a gene mutation that alters the base at the boundary of the first exon, leading to incorrect splicing. The correct protein is NEVER produced.
PKU is the result of defective phenylalanin hydroxylase. How is this defect brought about?
There is a single change in the 5’ splice dnor site culminating in a truncated mRNA and thus non-functioning protein
What are chromatin remodeling complexes?
large, multisubunit complexes that use ATP to change structure of nucleosomes temporarily so that DNA is less tightly bound to the histone.
What do histone acetyltransferases (HATs) do?
acetylate various particular K residues in the histones, reducing the positive charge of the histone, and thereby reducing the association with DNA
What do histone deacetylases (HDACs) do?
Opposite of HATs
What sort of chemical change to histones would you expect very active regions of DNA transcription to have?
Hyperacetylation
What does the methylation of cytosine do?
Inhibits transcription of the DNA it is associated with, by binding transcription silencing proteins.
(no effect on base pairing)
Where do DNA binding proteins bind to?
To exposed portion of bases in the major groove of the helix
What are the three types of gene regulartory proteins?
Helix-turn-helix
Zinc finger
Leucine zipper
The helix-turn-helix proteins consist of a helix, small polypeptide chain, and another helix. What part of the protein is involved in binding to the DNA?
The amino acids in the more C-terminal side of the protein
What is the structure of Leucine zippers like?
Two alpha helicies join together to form a coiled-coil.
Each helix has a hydrophobic residue (usually K) at every 7th position
What, generally, is the action of the leucine zipper, zinc finger, and helix-turn-helix proteins?
Bind to DNA and recruit HATs (or HDACs)
The promoter region of the LDL-receptor gene contain what particular region of DNA? What does it do?
SRE-1 (sterol responsive element-1)
Promotes cholesterol affiliated gene synthesis
What is CRSP?
A protein that helps SP-1 bind to the GC boxes, and aid in the transcription of LDL receptor gene
What is SREBP-1a? What does it do?
The sterol responsive binding protein 1a.
It is maintained outside the nucleus unless cholesterol levels falls–then goes in to bind to SRE-1 and recruit a HAT–increases transcription
What is rubinstein_taybi syndrome?
A disease characterized by MR, and other abnormalities, due to the genes encoding EP300 or CBP
PKA is able to gain transcriptional control of PEP carboxykinase via what mechanism? (describe it, there are 3 additional proteins utilized)
PKA phosphorylates CREB which then binds To CRE, which recruits EP300.
CRE/EP300 act as HATs for the PEP carboxykinase gene
What is tamoxifen, and how does it exert its effects?
Inhibits cancer growth by competitivly inhibiting the DNA-binding receptor proteins.
Where is the thyroid hormone receptor usually found?
Bound to the DNA–it represses transcription
What is the protein that the thyroid hormone receptor bound to
RXR, which binds an HDAC
What happens when the thyroid hormone binds to thyroid hormone?
THR undergoes a conformational change, and binds a HAT
Which enzymes does PKA increase the transcriotion of?
Hormone Sensitive Lipase and PEPCK
What is the DNA binding site that is involved in the PKA pathway to increase transcription?
CRE
PKA phosphorylates what protein to attach to CRE?
CREB
What is the protein that attaches to a phophorylated CREB protein sitting on a CRE?
CBP and EP300
What is the function of CBP/EP300 complex?
Recruit a HAT protein to the CRE site and allow fro transcription of PEPCK
What is Rubinstein-Taybi syndrome?
MR due to mutations in the CBP or EP300 proteins.
Where is the cortisol receptor found?
The cytoplasm
What prevents the cortisol receptor from entering the nucleus and activating transcription?
It is masked until cortisol binds to it.
Then conformational change
What is the promoter element for cortisol called?
GRE (glucocorticoid responsive element)
The LCL receptor gene recognizes what protein signals on the outside of VLDLs/LDLs?
Apoprotein E and B
Basal transcription of the LDL receptor gene involves what promoter region, with what protein?
GC rich region with SP-1/CRSP binding to it.
