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Transcription: The process by which the information contained in a template strand of DNA is
copied into a ssRNA molecule of complementary base sequence
Transcription process
1.The process by which mRNA is made from a DNA template (or “antisense”)
2.Carried out by RNA polymerase in a 5’-3’ direction (RNA) Polymerase moves along DNA in 3'
—> 5' direction (toward 5' end)
3.Only 1 strand of DNA duplex serves as the template for a given gene
6. 2 short stretches of DNA that are similar from one gene to another (-35 region TTGACA
& -10 region TATAAT )
The resulting mRNA molecule has the same sequence as the non-template (or “sense”) strand,
except for replacing thymine with uracil.
Only one DNA strand is transcribed for any one gene
Different genes can be transcribed on different strands though
Transfer RNA (tRNA) brings amino acids to the ribosomes during translation
Ribosomal RNA (rRNA) complexes with ribosomal proteins to make the ribosome, the organelle
that translates the mRNA
Small nuclear RNA (snRNA) complexes with snRNPs, involved in eukaryotic splicing
3 stages of transcription
1.Chain initiation
RNA polymerase binds to initiate transcription
Initiation - binding of RNA polymerase to double-stranded DNA. RNA polymerase binds
at a sequence of DNA called the promoter
2.Chain elongation
Only the template strand is transcribed
The transcription bubble is ~15 nt long with 8-9 nt paired with the 3' end of the RNA
Elongation - the covalent addition of nucleotides to the 3' end of the growing
polynucleotide chain
3.Termination
RNA polymerase reaches a terminator sequence and the RNA and polymerase are released
Termination - the recognition of the transcription termination sequence and the release
of RNA polymerase
Prokaryotic Gene Structure
Gene: Transcriptional Unit
RNA transcript
Template strand
5’ UTR 3’ UTR
Elongation
Termination
Self-Termination
Termination Stem-Loop
Termination
Rho-dependent:
Absence of poly U sequence
Has a G-C rich region upstream of termination, may or may not be palindromic
Hexamer of 6 identical units
Rho binds to rut (rho utilization) site in 3’ UTR
Travels along mRNA at same speed as RNA polymerase
When polymerase pauses at the G-C rich region, rho catches up to it and unwinds DNA-RNA
hybrid causing polymerase to fall off
Eukaryotic Transcription
Similar but more complicated process than in prokaryotes
4 RNA polymerases
Pre-mRNA molecule that is modified and processed to produce a functional mRNA molecule
Prokaryotes have one type RNAP that carry out all transcriptional reactions
Eukaryotic organisms have 4 types of RNAPs
RNAP I: transcribes most of the rRNAs genes
RNAP II: transcribes the structural genes (most important)
RNAP III: transcribes the tRNAs genes, 5S rRNA genes and snRNA genes
RNAP IV: transcribes some siRNA’s in plants
• General TFs - bind at core promoter sites in association with RNA polymerase
– Comprised of TBP (TATA binding protein) and TAFs (TBP associated factors)
(TFs) play a role in virtually every aspect of transcription process from binding
polymerase to DNA template, initiation of transcription, elongation &termination
Enhancer Elements
Enhancers are regulatory elements that when bound by Activators, a type of transcription
factor, result in increased transcriptional activity
Enhancers can be upstream, downstream or within the gene, can function in either orientation
and can be VERY far away
Protein binding to DNA is achieved by a specific combination of van der Waals forces,
ionic bonds & H bonds between amino acid residues & various parts of DNA, including
backbone
Distal promoter elements to distinguish them from the proximal elements situated
closer to the gene
Enhancers even more distant DNA elements (than proximal or distal promoter elements)
Variations in the level of activators and repressors in different cell types give tissue
specific expression of genes
Prokaryotic vs Eukaryotic
Prokaryotes have Polycistronic mRNAs
pre-rRNA
The primary transcript, which is cleaved to form individual ribosomal RNAs (the 28S,
18S, and 5.8S rRNAs of eukaryotic cells).
pre-tRNA
The primary transcript, which is cleaved to form transfer RNAs.
promoter
A DNA sequence at which RNA polymerase binds to initiate transcription.
repressor
A regulatory molecule that blocks transcription.
ribozyme
An RNA enzyme.
RNA editing
RNA processing events other than splicing that alter the protein coding sequences of
mRNAs.
RNA polymerase
An enzyme that catalyzes the synthesis of RNA.
RNase P
A ribozyme that cleaves the 5′ end of pre-tRNAs.
self-splicing
The ability of some RNAs to catalyze the removal of their own introns.
small nuclear ribonucleoprotein particle (snRNP)
Complex of an snRNA with proteins.
small nuclear RNA (snRNA)
A nuclear RNA ranging in size from 50 to 200 bases.
spliceosome
A large complex of snRNAs and proteins that catalyzes the splicing of pre-mRNAs.
steroid hormone receptor
A transcription factor that regulates gene expression in response to steroid hormones.
TATA box
A regulatory DNA sequence found in the promoters of many eukaryotic genes
transcribed by RNA polymerase II.
TATA-binding protein (TBP)
A basal transcription factor that binds directly to the TATA box.
TBP-associated factor (TAF)
A polypeptide associated with TBP in the general transcription factor TFIID.
transcription factor
A protein that regulates the activity of RNA polymerase.
transcriptional activator
A transcription factor that stimulates transcription.
zinc finger domain
A type of DNA binding domain consisting of loops containing cysteine and histidine
residues that bind zinc ions.