Evolution and Structure of RNAPs Flashcards
What are some notable exception to Crick’s central dogma of biology?
Retroviruses with an RNA genome, RNA use as a structural, regulatory and catalytic molecule and the ‘RNA World’ hypothesis.
What is the RNA World hypothesis?
The life began as just RNA, with RNA genomes able to replicate using ribozyme RNAPs, with ribozymes also being used for any other catalytic need.
In the RNA World hypothesis, why is DNA use thought to have evolved?
As a more stable way of storing information.
According to the RNA World hypothesis, how are molecular machines such as RNAPs thought to have evolved?
Proteins that evolved for use as transcription factors eventually became permanent and then vital stability aids. These ‘invaded’ the machine performing more and more roles until eventually the active site is transferred to the proteins.
How well is RNA suited to catalysis compared to proteins and why?
Proteins are hugely superior in binding and catalytic activity as they possess twenty different possible monomers with very different properties, as opposed to only four similar ones that must be used to create the same thing.
What provides evidence for the way in which proteins take over the roles of ribozymes in evolution according to the RNA world theory?
The Ribosome, which is thought to have originated as a purely RNA structure but now uses a variety of proteins as integral parts of its structure, despite not having transferred the active site to the protein components (yet?)
How are RNAPs thought to have evolved?
By use of a homodimeric protein that stabilised it, which through gene duplication began to evolve separately, becoming the two largest subunits in the RNAP (eg B and B’). Continued accretion of other proteins to form current multi-subunit structure.
What provides evidence of the evolution of RNAPs from ribozyme replicases?
The complex interactions possible between RNAPs and RNA.
Bacterial RNAPs use RNA as a template for 6SRNA.
Pol II is inhibited by B2 RNA and can replicate the hepatitis D RNA genome.
Which directions can RNAPs transcribe in?
5’-3’ only, they are unidirectional
How many times are RNAPs believed to have evolved separately, and what is the evidence for this?
Emerged 6 different times, six different fold structures found in the active site.
What is the highest classification RNAPs?
Single or Multi-Subunit
Where are Single-Subunit RNAPs generally found?
Simple phages (Eg T7 and SP6)
What family do Single-Subunit RNAPs belong to?
DNAPs, they have the same fingers-palm-thumb structure and are capable of performing DNA-DNA conversion as well as DNA-RNA and even RNA-RNA.
What other enzymes are Single-Subunit RNAPs?
Reverse transcriptases and RNA-dependent RNA polymerases.
Where are multi-subunit RNAPs found?
Used by all three domains of life.
What are the main differences between the RNAPs found in the three domains of life?
Prokaryotes use only the five subunits conserved within all multi-subunit RNAPs. Eukarya an archaea also use a wide variety of other subunits.
What subunits comprise the prokaryotic RNAP?
2a, B. B’ and w, with the sigma factor also being required.
How many kind of archaeal RNAP are there?
Only one
How many kinds of eukaryotic RNAP are there?
Five, RNAP I, II, III, IV and V.
The last two are found only in plants.
How are subunits named in archaeal RNAPs?
Rpo1, 2, 3 etc.
Also given letters, RpoA, B and D resp.
How are subunits named in eukaryotic RNAP II?
RPB1, 2, 3 etc
Which archaeal RNAP subunits make up the five conserved subunits?
Rpo1, 2, 3, 6 and 11.
AKA RpoA, B, D, K and L.
Which eukaryotic Pol II subunits make up the five conserved subunits?
RPB1, 2, 4, 6 and 11
Which prokaryotic subunit do Rpo1 and RPB1 correspond to?
B’
Which prokaryotic subunit do Rpo2 and RPB2 correspond to?
B
Which prokaryotic subunit do Rpo3 and RPB3 correspond to?
a subunits
