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Terms in this set (36)
Major control point in expression of genes is ...
Process of making RNA from DNA.
Which types of RNA does transcription produce?
ALL types of RNA: mRNA, tRNA, rRNA, snRNA, miRNA, siRNA.
Enzyme that catalyzes transcription
DNA-dependent RNA polymerase (moves along template strand in 3' to 5' direction).
Required elements for transcription?
- All 4 ribonucleoside triphosphates (ATP, GTP, CTP, UTP)
- DNA template (which is unchanged in process)
Direction of RNA biosynthesis
5' → 3'
(nucleotide at end of chain retains triphosphate; abbr. ppp)
RNA polymerase in E. coli
Multisubunit; five subunits total. Core enzyme has 4 subunits; holoenzyme consists of all 5.
DNA strand used in RNA synthesis: names
- template strand
- antisense strand
- (-) strand
Non-template DNA strand: names
- coding strand (DNA and RNA sequences will be same, w/exception of U for T)
- sense strand
- (+) strand
DNA sequence that signals start of RNA transcription. Lies upstream of gene.
Promoter regions in prokaryotes (3)
1. -35 region: recognition site; binding site of RNA pol
2. -10 region: TATAAT (Pribnow box); where stable complex of DNA and RNA pol is formed
3. TSS (transcription start site)
Consensus sequences in promoter regions
Many bases in common. I.e., A-T rich (2 H bonds, so easier to break/unwind).
Strong vs. weak promoter
- Strong promoter: binds RNA polymerase tightly; gene transcribed more often
- Weak promoter: binds RNA polymerase weakly; gene transcribed less frequently.
- Strength of promoter decreases as it varies from the consensus sequence.
First phase of transcription, and most controlled. RNA pol binds to prmoter and forms closed complex. β' and σ subunits initiate strand separation (DNA unwinds) to form open complex, melt ~14 b.p.s surround TSS.
Relax supercoils in front of and behind transcription bubble.
First RNA base in transcription
Purine (A occurs more than G)
Topoisomerases relieve supercoiling ahead of and behind transcription bubble as transcription proceeds.
Chain termination: 2 mechanisms (prokaryotes)
Involves specific sequences downstream of gene.
1. Intrinsic termination: controlled by specific sequences called termination sites (complementary repeats that loop back on themselves; hairpin loop of RNA forms, RNA dissociates).
2. ρ-dependent: ρ (rho) protein binds to RNA, another hairpin loop forms, ρ facilitates dissociation of RNA.
Regulation in prokaryotes: alternative σ factors
Different σ subunits cause expression of different genes, i.e., heat shock response in E. coli.
Regulation in prokaryotes: enhancers
DNA sequence that is upstream of promoter (RNA pol does NOT bind to it). Aka response elements. Increases level of transcription. (Silencers decrease level of transcription.)
Regulation in prokaryotes: Operons
Group of genes in prokaryotes that are controlled together. Operator, promoter, and structural genes. Usually not transcribed all the time.
- Repressor protein made by lacI gene
- Repressor protein binds to operator (operator and promoter are control sites)
Regulation in prokaryotes: transcription attenuation
Regulation method in trp operon. Transcription is altered after it has begun by transcription termination or pausing.
Substance that triggers production of proteins (and transcription) in an operon. Called "induction."
Genes that are always expressed
Negative control systems (i.e., operons)
Characterized by fact that if gene for repressor is mutated and the repressor is no longer expressed, the operon is always expressed.
Positive control systems (i.e., operons)
If gene for inducer is mutated, it cannot be expressed (it is uninducible).
Eukaryotic transcription: RNA polymerases (3)
1. RNA pol I: found in nucleolus; synthesizes precursors of most (but not all) rRNAs
2. RNA pol II is found in nucleoplasm and synthesizes mRNA precursors
3. RNA pol III is found in nucleoplasm and synthesizes tRNAs and other small RNA molecules
RNA pol II (B) - eukaryotes
12 subunits; most studied RNA pol; synthesizes mRNA precursors.
RNA pol II promoters - eukaryotes
1. Upstream elements (i.e., enhancers or silencers)
2. -25: TATA box (but it's not always at -25; moves around)
3. Inr: initiator element; not well conserved in terms of sequences.
4. Downstream regulator
NOTE: Inr + TATA box make up core promoter; other elements may be missing. But not all genes even have a TATA box.
Biggest difference between euk. and prok. transcription
Number of proteins involved (MANY more in eukaryotes!)
Protein that regulates transcription in eukaryotes but is not itself a subunit of RNA polymerase.
Initiation - eukaryotes
Many transcription factors bind; allow RNA pol II to bind also (and stabilize). Before transcription can begin, the preinitiation complex must form an open complex, in which the DNA strands are separated.
Elongation - eukaryotes
Pol II synthesizes RNA and leaves the promoter region behind; the GTFs are either left at the promoter or dissociate from pol II.
Note: transcription is much less efficient in vitro than in vivo.
Termination - eukaryotes
Consensus sequence for termination : AAUAAA.
Posttranslational RNA modification
- cap 5' end
- poly-A sequence to 3' end
- splicing out introns
- base modification
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