Bacterial transcription
List the three basic steps of transcription.
Initiation, elongation, termination
Name the polymerase used in eukaryotes to transcribe tRNA.
RNA Pol III
Catabolic operons like lac tend to be ________; biosynthetic operons like trp tend to be ________.
Inducible; repressible
Name the three functional classes of proteins that act on histone modifications.
Writers, readers and erasers
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Gyrase and topoisomerase perform similar roles in transcription, which is to _________.
Relieve supercoiling caused by the advancing RNA polymerase
True or false: The mediator complex directly binds promoter DNA sequences to recruit RNA Pol.
False, the mediator does not bind DNA directly. It interacts with activator proteins and other transcriptional machinery to bridge regulatory signals.
Deleting a regulatory protein makes transcription of its operon go DOWN. Name the type of control that protein was exerting.
Positive control — it was an activator
True or false: The three types of chromatin states are euchromatin, facultative heterochromatin, and constitutive heterochromatin.
Truth nuke
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Intrinsic termination needs no protein other than RNA polymerase itself. Name the two features of the RNA that stop transcription.
A hairpin, and a string of Us
Before a eukaryotic polymerase can start, this ~70-polypeptide assembly must form at the promoter, and it does so in a defined order.
The preinitiation complex (PIC)
lacI encodes the repressor, but it is not considered part of the lac operon. Explain why.
It has its own promoter and terminator and is transcribed separately from the polycistronic lacZYA message.
Name 3 examples of distal regulatory elements.
Possible answers: Enhancers, silencers, insulators, locus control regions
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Explain the role of the σ subunit.
Increase affinity of RNA polymerase to promoters by recognizing their consensus sequences, stabilizing the initiation complex for transcription initiation.
Bacteria stop at a terminator in the DNA. Pol II has no fixed terminator, so termination is instead a consequence of this.
Cleavage of the transcript at the poly(A) signal
Identify the mistake in this explanation: The lac operon has multiple components. The operator is a protein that binds the lac operon to turn transcription off. The activator is a protein that binds the lac operon to turn transcription on.
The operator is not a protein; it’s a sequence of DNA that the repressor (encoded by lacI) binds.
You move a candidate enhancer from 4 kb upstream into an intron downstream, and flip its orientation. Nothing happens to its activity. Care to explain?
Enhancers work at a distance and in either orientation, because they act by looping to the promoter
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E. coli has several sigma factors besides σ⁷⁰. Swapping which sigma factor is loaded accomplishes this.
Redirects polymerase to a different set of promoters, which reprograms the whole transcriptome
You want to quantify how a drug changes expression of a single gene across 96 patient samples. The transcript is present at about two copies per cell. Name the method(s) you would use.
RT-PCR followed by qPCR
In trp attenuation, alternative hairpins in the leader RNA either stop transcription or let it continue, depending on whether the ribosome stalls. Explain why this could not work in eukaryotes.
Bacterial transcription and translation are coupled, whereas in eukaryotes, these are separated both spatially and temporally.
Two active-site mutations abolish Cas9's cutting but leave its binding intact. Name what this turns Cas9 into, and what you could use this for.
A programmable DNA-binding module; whatever you fuse to it is what happens at that binding site, e.g. activator, repressor
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