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35 Cards in this Set

  • Front
  • Back
Transcription in Prokaryotes
Carried out by RNA polymerase. The beta, alpha, and omega subunits form the core enzyme and bind enzyme to random DNA site. The addition of sigma subunit results in formation of a holoenzyme which finds specific promoter regions in DNA (-10 and -35). Once bound, RNA polymerase can unwind helix (no need for helicase here) and replicate strand. Only template (one) strand is replicated from DNA to RNA read 3'-->5'. RNA polymerase releases when reaches terminator region.
RNA Polymerase
Consists of two beta, two alpha, and two other subunits.
Promoter Regions
Site -35 and -10 on DNA where polymerase finds to attach before transcription begins at +1.
Frequency of transcription of prokaryotes
Depends on affinity of RNA polymerase to promoter site. Also responds to internal and external environment of cell.
Transcription Activators
Positive regulators. Bind polymerase near the promoter, increase recruitment of polymerase by protein to protein interactions. Increase likelihood of transcription.
Repressors
Negative regulators. Bind operator sequences that usually overlap with regulated promoter. Prevent polymerase from binding and therefore, repress transcription.
Eukaryote Polymerases
In Eukaryotes, different polymerases are specialized to transcribe specific genes.
RNA Polymerase I
Found in the nucleolus and transcribes rRNA. Transcribes all rRNA except 5S rRNA. These genes are arranged in tandem repeats and group together to form the nucleolar region of the nucleolus.
RNA Polymerase II
Most genes transcribed by this enzyme. Transcribes protein encoding genes in the nucleus, most snRNA (used in splicing), snoRNA (guide chemical modifications of RNAs), and miRNA (small RNA involved in post-transcriptional gene regulation, and other small non-coding, regulatory RNA.
RNA Polymerase III
Transcribes nuclear transfer RNA genes, 5S rRNA genes, snRNA (used in splicing), and 7S RNA for the signal recognition particle.
Eukaryotic Subunits
Some polymerase subunits come from bacteria while there are some eukaryote-specific subunits as well as subunit specific subunits.
Eukaryote Polymerase specific subunit (CTD)
CTD: C-terminal domain of RNA Polymerase II is unique and involved in the regulation of the enzyme. Phosphorylation of Ser in this protein effects the activities of the polymerase.
Weights of Nuclear Eukaryote Polymerases
The molecular weights of nuclear RNA polymerases in eukaryotes ranges from 500-700 kDa.
Organelle Polymerases
Mitochondria and Chloroplasts likely evolved from bacteria. This is supported by fact that their RNA polymerases resemble those of bacteria and bacteriophages.
General Transcription Factors
Required for all eukaryote polymerase enzymes to initiate transcription at specific sites on double stranded DNA. Help polymerases to recognize promoter sites as none of them can do it directly themselves.
RNAP II Transcription Factors
TFIIB, TFIID, TFIIF, TFIIH
TFIIB and TFIID
RNAP II Transcription Factors that recognize specific sequences in promoter region of DNA and bind there. TFIID is the main one of these two TFs. TFIID interacts with three different consensus sequence elements: the TATA box, the initiator element (INR), and the DPE (Downstream Promoter Element).
TFIIF
Delivers RNAP II to TFIIB and TFIID complex bound to promoter region.
TFIIH
A multimeric transcription factor that consists of 10 subunits. One of the subunits is a ATP-dependent helicase that is used to unwind DNA at the transcription start site.
Nomenclature for TF
For RNAP II, all transcription factors will have a TFII. RNAP I will be TFI, RNAP III is TFIII.
RNAP II Core Promoters
Core promoter sequences direct initiation of transcription. There are focused and dispersed core promoters. We understand more about focused.
Focused Promoters
Either a single or a cluster of transcriptional start sites over several nucleotides. TFIID is the main transcription factor responsible for attracting RNAP II to the promoter sites. Not all are necessary at once to attract polymerases.
TATA Box
A consensus sequence found around -30 relative to transcription start site. Usually TATAWAAR where W is a purine and R is either A or T. Bound by TATA Binding Factor (TBP), a subunit of TFIID. When TBP binds to TATA box, unwinds DNA 80 degrees and relaxes helix. TFIID also has TAF (TATA Associated Factors), which modifies the histones and therefore relaxes the nucleosome.
INR
Most common consensus sequence that is 8bp long. Surrounds transcriptional start site.
DPE
Downstream Promoter Element is found at +28 to +33 relative to the transcriptional start site. Position to INR is crucial for optimal transcription initiation.
BRE
Often sit adjacent to TATA box and bind TFIIB. Along with TFIID, greatly enhance ability to attract RNAP II. Often important if TATA is weak. TFIID works with or without this extra promoter region.
Eukaryotes vs. Vertebrates
While most eukaryotes use focused and TATA related promoter sites, vertebrates (specifically humans) use mostly dispersed promoters.
Dispersed Promoters in vertebrates
Promoters range from 50-100 nucleotides and are often found in regions known as CpG Islands.
Sp1 like proteins
Used in transcription promotion in dispersed promoters. Usually in absence of TATA regions, but not always. Interact and recruit TFIID, and therefore, TFIIB, RNAP II, TFIIH, etc.
Promoter Proximal Elements
Additional promoter regions found within 200pm upstream of transcriptional start site.
Enhancers
Additional promoter regions. Lie in regions greater than 200bp and can be tens of thousands of bps away from the transcriptional start site. Can be up or downstream, or within introns from the start site.
Additional promoter regions
Use direct protein to protein interactions, or multi-protein complexes (Mediators) to help attract RNAP or TF to core promoter regions.
Mediator
A multi-protein complex that binds many components of transcription initiation and acts as a bridge between factors and gene. Also histone acetylase and other modifying enzymes that effect chromatin and make gene available for transcription.
Mutations and promoters
Mutations in and around promoter regions (or upstream of) can severely change and reduce transcription. Beta-globin gene is a good example. Beta Thalassemia is disease associated.
Mutations and Core Transcription Factors
Mutations in TBP causes spinocerebellar ataxia 17, sort of like Huntington's. Mutation is an expansion of trinucleotide (GAC) repeats in the amino terminal region of TBP.