11: Transcription of Genes Flashcards
Sense/antisense strand
Sense:
Not used as template. Equivalent in the sequence to the mRNA (same as plus strand, coding strand, nontemplate strand)
Antisense:
DNA strand that is complementary to the coding sequence and is used as a template for synthesizing mRNA (same as noncoding or template strand).
Constitutive / housekeeping genes
Genes that are switched on all the time because they are needed for essential life functions.
Often used as controls in experiments, as they are not affected by the changes.
Cistron
Denotes a structural gene:
Sequence of DNA (or RNA) that encodes a protein or a nontranslated RNS molecule.
Monocistronic mRNA:
- In eukaryotes.
- mRNA carrying the information of a single cistron, which is a coding sequence for only a single protein.
Polycistronic mRNA:
- In prokaryotes
- mRNA carrying the coding sequences (cistrons) for several proteins.
- Operon organization: genes with similar function organized together.
Open reading frame, ORF
Any base sequence in DNA or RNA that could encode a protein.
Does not contain any stop codons that would interrupt the translation.
Recognition of the beginning of a gene
Major difference between prokaryotes and eukaryotes occur in the initiation and regulation of transcription, not in RNA synthesis.
Upstream, 5’ side:
Promoter region (-10, -35) binds RNA pol.
5’-UTR: noncoding region between the 5’ end (transcription start site, +1) and the translation start site.
Bacterial RNA pol: core enzyme (RNA synthesis) + sigma unit (promoter recognition, -10 + -35) = holoenzyme.
Consensus sequences:
-10: TATAAT
-35: TTGACA
Weaker bindings, easier to part strands.
The strength of a promoter depends partly on how closely it matches the ideal consensus sequence.
Manufacturing the message: production of mRNA
Sigma unit binds to promoter => core enz opens the DNA => transcription bubble
Sigma detaches after DNA pol is bound and new strand is 8-9 bases. Only core enz left.
First base is usually an A, almost never a pyrimidine (C/T).
5’ -> 3’
40 nt per second
Prokaryotic RNA pol:
- 2xα, β, β’ and ω subunits
- β and β’: catalytic site
- α: assembly and recognition of promoters.
- ω: binds to β, stabilize it and aids in its assembly into the core enz.
- Inhibited by the antibiotic rifampicin. Blocks elongation of RNA. Binds to β-subunit.
- DNA gyrase inserts negative supercoils ahead of RNA pol and topoisomerase I removes negative supercoils behind.
Termination of RNA synthesis
Terminator sequence:
At the end of a gene. Tells RNA pol to stop transcribing.
Two inverted repeats (on opposite strands) separated by ca. 6 bases, followed by a run of A’s.
Stem and loop (hairpin) structure forms => RNA pol pauses and detaches.
Rho-dependent (ρ) requires protein factor ρ.
Rho-independent. Most
- Rho: specialized helicase that uses ATP to unwind DNA/RNA hybrid double helix. Binds mRNA after the rut recognition regions have been synthesized.
Causes allosteric changes in the catalytic subunits of RNA pol => termination.
Activator protein
Positive regulation: switches on a gene.
Change shape in response to small molecules; inducers. Only one conformation binds to DNA.
Repressor protein
Negative regulation: repressor keeps a gene switched off until it is removed.
Binds to an operator sequence.
Binding of inducer to repressor changes its conformation from DNA-binding to nonbinding form.
Eukaryotic transcription
10 times as many genes => more complex.
Have multiple RNA pol:
Typically 3 in nucleus. Mitochondria and chloroplasts have their own.
RNA pol II: most protein encoding seq. 5% of cellular RNA.
RNA pol I+III: tRNA + rRNA
Transcription factors
Protein that regulates gene expression by binding to DNA and/or to RNA pol.
General
- Required for transcription of all genes.
- TFI, TFII, TFIII (RNA pol I, II, III)
- Recognition of promoter and initiation of transcription by RNA pol II.
Specific:
- Needed for transcription of particular gene(s) under specific circumstances.
Enhancer:
- Regulatory seq that binds TFs but that is outside, and often far away from, the promoter.
Transcription of rRNA and tRNA
rRNA by RNA pol I localized in nucleolus.
RNA pol III makes rRNA and tRNA, in addition to small nuclear RNAs (snRNAs). These oversee the splicing of mRNA in the nucleus.
RNA pol II
Transcription of most of the protein-encoding genes.
General TFs bind to the promoter region.
Some specific TFs bind to promoter, others bind to the enhancer.
Promoters:
- Initiator box
- TATA box: binding site of TF that guides RNA pol II to the promoter region that guides RNA pol to the promoter in eukaryotes.
- Upstream elements: upstream of TATA, recognized by specific proteins. Make contact with activator.
