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55 Cards in this Set

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What does a eukaryoic respressor do? AKA?
compete with activator for DNA binding site (protein binds directly to DNA)
-inhibits directly through protein-protein interactions
-AKA: active respressor
What does a corepressor do?
modify the chromatin structure
What is chromatin?
Nucleosome core particle
-146 bp DNA wrapped around histones
-1 molecule H1 binds DNA!
-2 molecules each of H2A, H2B, H3, H4
What factors can control transcriptional activity of chromatin?
1. modifications of histones
-methylation
-phosphorylation
-histone acetylation
2. Nucleosome rearrangement
-association of HMGN (non-histone chromosomal proteins) w/nucleosomes
3. Non-coding RNA
4. DNA Methylation
What enzyme is responsible for the actylation of the histone tails?
HAT: histone acetyltransferase
What are the features that HAT imposes on the histone tails?
-acetylates histone tails=
1. recruited by 'elongation factors' during transcription
2. associated with actively transcribed DNA
3. increase accessibility of chromatin
What is HDAC? What does it do?
-histone deacetylase, makes DNA wrap tightly around histones to shut off
What does histone acetylation do? Where does it occur specificity?
-Reduces net postive charge of histones= weak interaction with DNA & facilitates binding of TFs to DNA
*occurs on core histones H2A, H2B, H3 & H4
1. histone domain (DNA wrapping)
2. amino-terminal domain (extends outside nucleosome)
RICH IN LYSINE
What amino acids do mehtylation deal with?
phosphorylation?
ubiquitination?
methylation: lysine and arginine
phosphorylation: serine
ubiquitination: lysine
What is suspected that methylation and phosphorylation do regarding the histone tails?
provide additional TF binding sites??
What are two type of non-coding RNA?
1. RNA interference
-short, dsRNA
-includes degradation of homologous mRNA
2. microRNAs (miRNAs)
-short, non-coding
-regulation gene expression
-recruits methyltransferase for H3 lysine-9
What is the RISC? what does it do?
RISC: RNA induces silening complex
What is RITS? What does it do?
RITS: RNA induced transcritpional silecing complex. forms chromatin so transcription is shut off
What do non-coding RNAs do to the chromatin stucture?
-induces histone modifications that lead to chromatin condensation to form heterchromatin
Ex: involved in X-chromosome inactivation
What does the Xist gene do?
1. transcribe RNA on inactive chromosome
2. coats chromosome
3. induces methylation of H3, leading to chromosome condensation
What is genomic imprinting?
when one of the egg/sperm cells is methylated=inactive during development of germ cells
What does mRNA do?
tRNA?
rRNA?
mRNA=carries genetic information
tRNA=decodes message into sequence of AA
rRNA=enzyme for protein synthesis
List the "Dogma" with enzymes under arrows
DNA transcription with RNA polymerase to mRNA translation with tRNA to protein
Which part of the dogma is most regulated?
transcription
What is on the 5' and 3' end of mRNA that is extensively modified?
7-methyl G on 5'
poly A tail on 3'
(way to control gene expression)
Which end of the mRNA molecule is co-transcriptional? post-transcriptional?
co-transcriptional=7'
post-transcriptional=3'
What is significant about rRNA synthesis?
all cleaved from one molecule of DNA
How does rRNA processing (Pol I) take place?
large precursor transcript is cleaved to form mature rRNA molecules by nucleases
How does tRNA Processing (Pol III) take place?
1. 5' cleaved by RNase P (ribozyme=RNA enzyme)
2. 3' cleaved
3. Addition of CCA
4. Base Modification
Where does eurkaryotic mRNA processing take place?
nucleus
What is the big difference in mRNA processing in eurk. v prok?
euk=separation of transcription/translation so processing possible
prok=couple transcription/translation, mRNA must be mature
Go through the process of mRNA processing to protein
1. Transcription by RNAP II, during this 7meG cap added
2. cleave at 3' poly A addtion site
3.PAP (poly A polymerase) adds tail
4. spliceosome-snRNA+protein take out introns
5. Transported to cytoplasm
6.nucleases trim poly A tail
7. docks to ribosome for translation
Which part of the mRNA is 'junk'?
introns
What is required for translation initiation?
Capping
What is capping and when does it occur?
-occurs during transcription
(co-transcriptionally)
-7methyl guanosine
-linked 5' to 5'
WHat is the poly A tail required for?
-stability
-translation (interacts with 5' cap)
What initiates the PAP complex?
sequences in the RNA chain
-PAP complex associated w/RNA pol II
-GU rich sequence (50 bases downstream of poly A addition site)
What is mRNA splicing? what is this event directed by?
cutting on the introns and ligating together the exons
-directed by the primary transcript (pre-mRNA)
Describe the splicing mechanism? what is this mechanism carried out by?
-requires 2 transesterification rxns
-spliceosome carries it out
-1.cleavage at 5' splice site to form lariat-like intermediate
2. cleavage at 3' splice site
3. ligation of exons
4. degradation of lariat by cell
What is a spliceosome?
carries out splicing in mRNA-
snRNAs
U1: 5' splice junction
U2: branch point
U4-6: complex
U5: stabalization
snRNPs are recycled after splicing occurs and mRNA transported
What is a ribozyme?
an RNA molecule with enzymatic activity
What are the mechanisms of self-splicing?
Group I: self-splicing introns, use GTP co-factor (no lariat formation)
Group II: no GTP(same as splicosome but no snRNPs)
WHat is differential processing referring to?
-splicing patterns regulate gene proudct identity
-some transcripts spliced differently in different cells
-used for tissue specific genen expression
-different tissues make different mRNAs from the same primary transcript
What does alternative splicing refer to?
mechanism where exons of use are selected
What does poly A choice refer to?
multiple poly A sites
What does Calcitonin-CGRP do and where are they made? which exons go to each?
Calcitonin-Ca2+ uptake hormone
-made in thyroid, controls kidney function

*CGRP-neuron transmitter
-made in pituitary, helps detect taste

Calcitonin: 1,2,3,4
CGRP: 1,2,3,5,6
What are two factors that control mRNA stability?
1. Length of poly A tail: long poly A tail=more stable
2. degraduation sequation: n=o=stable, more AUUUA=less stable
What degrades RNA and where can it be found?
exonuclease, on ribosome
What gene is involved in the regulation of AUUUA repeat?
beta-globin gene
What is the enzyme in the final process of gene expression?
ribosome for translation
what decodes the triplet codons?
tRNA
What is at the 5' and 3' end of the polypeptide chain?
5'=amino
3'=carboxy
What is the enzyme that catlyses the peptide bond?
peptidyl transferase
What is the inition codon?
AUG
What is ________?
degenerate
Where is the acceptor stem-attachment of AA?
3' OH
What determines the accuracy of protein synthesis?
1)charging of tRNA
2)decoding of the codon on mRNA
What does the correct pairing of AA to tRNA?
amino-acyl tRNA synthetases
Where does the recognition of tRNA occur?
identity element bases
WHat is special about inosine?
it can substitute as C, U or A