Transcription and RNA Processing Flashcards
coding strand
same sequence as the mRNA
template strand
3’ to 5’ strand of DNA
basic structure of genes
promoter region upstream of start site
start site of transcription
teminator sequence that stops transcription
genes can be overlapping or coded in the opposite direction
prokaryotic RNA polymerase
synthesizes all RNA in bacteria except for the primers used in DNA replication
five subunit core enzyme, one that binds template, one that has polymerase activity, and two copies of another necessary for complex formation, role of fifth is unknown
sigma factor
used in prokaryotes, associates with the core RNA polymerase enzyme to form the holoenzyme, recognizes the promoter
Name the three eukaryotic RNA polymerases and describe what they do.
Pol I - ribosomal RNA genes
Pol II - mRNA genes, most snRNA, snoRNAs, and miRNAs
Pol III - tRNAs, 5S rRNA, and some snRNA and snoRNA genes
polyA polymerase and poly ADP-ribose polymerase - two non-template dependent RNA polymerases responsible for synthesizing RNA polymers
prokaryotic gene transcription
promoters 35bp stream of start stie
second site at -10 called the Pribnow box or the TATA box
sequences is where the helix is unwinding, forms a transcription bubble
topoisomerase relieves supercoiling, short RNA molecules made by polymerase until RNA longer than 10 nucleotides is made
polymerase can extend the transcript
termination sequence encodes hairpin structure RNA
Describe the RNA Pol I promoter and how it promotes transcription.
contains the upstream control element (UCE) which binds the upstream binding factor (UBF)
UBF binds UCE and CPE and recruits SL1 which recruits RNA polymerase I
rRNA transcription
greatest mass of RNA in cells is rRNA transcribed by RNAP I
genes linked in tandem with region inbetween containing terminator of one gene and promoter for the next
promoters for rRNA genes are immediately 5’ to the start of transcription and extend into the beginning of the gene
ribosomes assembled with protein structures and processed before export into the cytoplasm where the two subunits of the ribosome are put together
assembly of the 5S subunit happens in the cytoplasm
RNA Pol III promoters
transcribe tRNA genes and recognize DNA sequences near start site, but the actual promoter lies downstream of the start site, split into two segments
processing of tRNAs
synthesized as longer molecules that are trimmed at the ends to form matrue tRNA
uracil residues at the 3’ end are removed and replaced by CCA
some tRNAs also have a small intron in the anticodon loop tha tis removed
other extensive modifications include dihydrouracil, speudocuracil and other methylated bases
structure of an RNA Pol II gene
promoters of some RNAP II genes have a TATA or Hognes Box ~25bp upstream of the start site
constitutively expressed genes usually do not have a TATA box here, replaced by a GC-rich sequence
CAAT boxes often found ~70-80 bps upstream of the start site thatare recognition binding sites for transcription factors
also have start sites, splice sites, stop signals and polyA addition signal
transcription factors
two main categories, general and specific
general TFs bind to the core promoter and are the minimal requirement for recruiting the polymerase and initiating transcription
specific TFs bind within and outside the core promoter and moedulate the frequency of initiation
general TF complex
TFIID binds TATA box, TFIIB binds TFIID, TFIIF recuits the polymerase, and TFIIH acts as a helicase and protein kinase to allow for the promoter to clear
enhancers
can be upstream or downstream of the start site, can also be thousands of bps away in any orientation
bind specific TFs that bend or loop DNA to interact with other TFs and the promoter
can increase or decrease transcription
Describe the transcription rpocess after initiation.
elongation proceeds past stop codon and through 3’ UTR
first a guanine cap is added, then splicing, then polyadenylation
enzyme binds polyadenylation signal, claves mRNA 10-20 nucleotides downstream and then adds ~200 nucleotide polyA tail in a non-templated reaction
all the necessary protein complexes attached to the CTD
RNA splicing
as the lengthening RNA transcript is released from the RNA-DNA duplex, it immediately associates with RNA binding proteins to form a ribonucleoprotein complex
snRNPs facilitate the splicing activity, complex of U1 to U6 excluding U3 is called the spliceosome
processing of rRNA
synthesized in a long rRNA precursor containing the 28S, 18S, and 5.8S rRNAs
eukaryotic 5SrRNA is synthesized separately by RNAP III
pre-rRNA is claved by endoribonucleases, ends of individual rRNAs trimmed and some of the bases modified
ribosomal proteins previously synthesized bind to rRNAs and ribosome assembly occurs
rRNA modifications and assembly are assisted by snoRNAs
processing of tRNA
synthesized as longer molecules
trimmed at their ends to form mature tRNA
uracil residues at the 3’ end are removed and replaced by CCA
some tRNAs have a small intron in the anticodon loop that is removed, extensive base modification
processing of mRNA
collection of all RNAP II transcripts in the nucleus called heterogenous nuclear RNA (assembled with proteins into hnRNPs)
includes transcripts that will become mRNa and transcripts that will be long non-coding RNAs
5’ capping first, 7-methylguanosine cap is added to the 5’ end
introns are removed
polyA tail is added, 40-200 nucleotide long polyA tail is added and interacts with binding proteins to help stabilize the tail against degradation by nucleases
snRNAs
U1-U12, functions in splicing of mRNA, histone mRNA transcription termination
snoRNA
rRNA processing, modification of bases in rRNA
SMN complex
important protein complex for the assembly of snRNPs
miRNA processing
transcribed by RNA pol II, capped at 5’ end and polyadenylated and called primary miRNA
microprocessor complex associates and cuts out pre-miRNA from long precursor
modification by RNA editing include deamination of adenosines to inosines
transported to cytoplasm, cleaved by Dicer to generate mature RNA duplex of 22 nucleotides
one strand of the miRNA duplex is incorporated in to an RNA-induced silencing complex (RISC)
