Eukaryotic Gene Expression Flashcards
what are the differences between prokaryotes and eukaryotes
transcription in eukaryotes takes place on DNA that’s wrapped in CHROMATIN
chromatin needs to open for a gene to be activated and transcription to proceed
chromatin regulation = EPIGENETIC REGULATION of gene expression
what is heterochromatin?
hetero = different
regions of chromosome that are intensely stained
DNA is MORE DENSELY PACKED
rich in repetitive DNA (transposons, centromeres, telomeres)
NOT ACCESSIBLE to transcriptional machinery –> wound up tight
INACTIVE GENES
what is euchromatin?
eu = true
lightly stained chromosome regions
ACTIVE GENES are found in euchromatin
accessible to transcriptional machinery
what are the three RNA polymerases?
I –> pre-rRNA
II –> mRNAs and some small nuclear RNAs
III –> tRNAs, 5S rRNAs, small stable RNAs
what does RNA polymerase I do?
pre-rRNA (28S, 18S, 5.8S, rRNAs)
ribosome components, protein synthesis
what does RNA polymerase II do?
mRNA, snRNAs, siRNAs, miRNAs
encodes protein, RNA splicing. chromatin-mediated repression. translation control
what does RNA polymerase III do?
tRNAs –> protein synthesis
5S rRNA –> ribosome component, protein synthesis
snRNA U6 –> RNA splicing
7S RNA –> signal recognition particle for insertion of polypeptides into the ER
other small stable RNAs
describe the similarities between the RNA polymerases
crystal structure of the YEAST in RNA pol II has been resolved at a high resolution
RNA pol II consists of 12 polypeptides, called RPB1, RPB2…RPB12
all other eukaryotic RNA polymerases share a very high level of homology with the yeast RNA pol II
CLAMP DOMAIN (RPB1) accommodates DNA
after positioning over DNA the clamp is closed by a bridge
synthesis of RNA takes place in the catalytic center with the participation of Mg2+ (propagates production of sulphite bridges)
synthesizes RNA exits through a “channel” and is immediately capped by 7m Guanosine (biomarker)
what polymerase subunits are similar?
prokaryotes: B, B’
eukaryotic: RPB1, RPB2
describe the RNA polymerase complex mechanism
clamp and bridge
channel through which the RNA is extruded from the complex
nascent RNA is processed
describe the CARBOXY-TERMINAL DOMAIN of the RPB1 terminal of RNA pol II
specialized domain not found in any other polymerase
CTD is involved in multiple regulatory interactions and plays a key role in the initiation, release, elongation, and processing of synthesized mRNAs
CTD is YEAST contains 26 repeats of Try-Ser-Pro-Thr-Ser-Pro-Ser
–> mammals 52 repeats
ser residues are PHOSPHORYLATED upon transition
CTD is NOT STRUCTURED –> cannot be analysed by crystallography
what are the red and green regions in the images of CTD?
red = phosphorylated
green = not phosphorylated
what regulates RNA pol II transcribed genes?
CONSERVED BASAL PROMOTER ELEMENTS –> CORE PROMOTED SEQUENCES
promotor-proximal binding sites for transcriptional activators
distal enhancers or repressors
chromatin structure
what are the positions of the core promoter elements?
-37 to -32: TFIIB recognition element (GGG/CCA CGCC)
-31 to -26: TATA box
TATA T/A A A/T A/G
-2 to +4: initiator
drosophila: TCA G/T T T/C
mammals: YYAN T/A YY
+28 to +32: downstream promoter element
A/G G A/T C/T G/A/C
where does transcription start?
INITIATION SITE –> usually an A on the coding strand
what other factors join the preinitiation complex?
DNA helicase –> help intitiate
kinases –> release the polymerase
elongationmove nucleosomes out
what are the RNA pol II GTFs?
TFIIA, TFIIB, TFIID, TFIIE, TFIIH
