Molecular Biology 6 : Prokaryotic transcription, different types of RNA, prokaryotic RNA regulation and processing, into to eukaryotic transcription Flashcards
How is transcription regulated in prokaryotes ?
- Primarily through initiation of transcription
- Sigma factor acts as initiation factor
- Most bacterial genes regulated by the sigma70 factor
- Other sigma factors are available !
- General mechanism involves a repressor that binds to the operator region of a gene or operon and blocks transcription.
- The repressor is regulated through the binding of a small molecule ligand(s) which controls it’s DNA binding activity.
- Some bacterial genes also respond to activators (positive regulation) (e.g. CAP in lac operon). (Other activators are available!)
- Activators also regulated by binding of small molecule ligands (e.g.cAMP)
In E Coli, what is the steady state level of :
- rRNA ?
- tRNA ?
- mRNA ?
- RNA primers ?
- other RNA molecules ?
What is the synthetic capacity (relative amount of each type of RNA being synthesized at any instant) for each type of RNA ?
rRNA : steady state level 83%, synthetic type capacity 58% tRNA : 14% and 10% mRNA : 03% and 32% RNA primers : < 1% and < 1% Other RNA molecules : < 1% and < 1%
Endonucleolytic cleavage of ribosomal RNA precursors in E. coli happen ?
16S rRNA first cleaved by RNase III then by M16.
23S rRNA first cleaved by RNase II then by M23
5S rRNA cleaved by M5
What is the structure of tRNA ?
- the D arm (left)
- the anticodon arm
- the T-psi-C (right)
- sometimes a variable arme (right)
How is prokaryotic tRNA processed ?
- RNase P and other endonucleases cleave the primary transcript at the 5’ end.
- RNase D trims the 3’ end
- tRNA nucleotidyl transferase adds CCA to the 3’ end via the following reaction : 2 CTP + ATP –> CCA + 3PPi
Why did Severo Ochoa and Arthur Kornberg win the Nobel Prize in Physiology or Medicine in 1959 ?
“for their discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid”
Why did Roger Arthur Kornberg win the Nobel Prize in Physiology or Medicine in 2006 ?
“for his studies of the molecular basis of eukaryotic transcription”
How many RNA Pols do prokaryotes have ?
What about eukaryotes ?
Prokaryotes have only one RNA polymerase.
Eukaryotes have five.
What are the sub-units of T. aquaticus RNA Pol ?
B, B’, sigma, alpha, w (omega)
What are the sub-units of the yeast RNA Pol II ?
RPB1, RPB2, RPB3, RPB11, RPB6
What do crystal structures of prokaryotic and eukaryotic RNA polymerases ?
Structural conservation.
What are the 5 different eukaryotic RNA Pols ?
Which are sensitive to alpha-amanitin ?
RNA Pol I : - ribosomal RNA (45S precursor of 28S, 18S and 5.8S rRNA) - insensitive to alpha-amanitin RNA Pol II : - all protein-coding genes, small nuclear RNAs, U1, U2, U3, etc. - very sensitive to alpha-amanitin RNA Pol III : - transfer RNA, 5S rRNA, snRNA U6, some repeated sequences (Alu) - medrately sensitive to alpha-amanitin Mitochondrial RNA Pol : - all mitochondrial genes Chloroplast RNA Pol : - all chloroplast genes
How does the size of the eukaryotic transcription unit of rRNA-Pol I differ between :
- the human
- X laevis (frog)
- D melanogaster (fruit fly)
- S cerevisiae (yeast)
Human ~ 13.7 kb X laevis (frog) ~ 7.9 kb D melanogaster (fruit fly) ~ 7.7 kb S cerevisiae (yeast) ~ 6.6 kb
How is pre-rRNA processed ?
- Primary transcript is cut to yield the mature rRNAS found in ribosomes.
- Modification by methylation of specific ribose 2’ OH
- Conversion of specific uridine (ribonucleoside of uracil) residues to pseudouridine, an isomeric form.
What genes does RNA Pol III transcribe ?
Why are promoters for this enzyme a special case ?
tRNA, 5S RNA, snRNA U6
Promoters come in various forms and are usually downstream from transcription start site.
Use different types of promoter.
