Week 5 Part 1: Transcription 1 (Bacteria) Flashcards
What is the molecular definition of a gene
Genes are segments of DNA that are transcribed into RNA
There are two types of genes when transcribed, what are they and what is the corresponding RNAs called?
Two possibilities:
1. The RNA can encode a protein (mRNA)
2. The RNA doesn’t encode a protein and simply works as RNA (tRNA, rRNA)
True or False: more mRNA always means more protein
False. Though this is typically the case, there are ways to control transciption.
RNA polymerase catalyzes the sequential addition of ribonucleotides in what direction?
5’ to 3’
What is the one important difference between the nucleotides RNA uses in comparison to what DNA uses?
While DNA uses dNTPS, RNA uses NTPs (i.e. ATP)
RNA is made ________ and ________ to DNA
anti-parallel; complimentary
What direction is the DNA template that the RNA is created from read in?
3’-5’
By just looking at en example of a strand of RNA and a strnad of DNA, how can you tell which is RNA?
There are two ways to tell, first is if the strand has Uracil (U) then it is most likely RNA. However, DNA can have uracil, so a sure way to tell is the extra O on the 2’ carbon in the ribose sugar.
What are the other names for the the template and non-template strands?
Template strand a.k.a. anti-sense strnad
Non-template strand a.k.a. the sense strand – this is because it has the same directionality and bases (except U) as the RNA
True or False: RNA polymerase does not require a primer
True
What links RNA nucleotides?
Phosphodiester bonds
What is the RNA polymerase also referred to?
The RNAP is also known as the core enzyme
What is the structure that is made up of the sigma factor AND the RNAP called?
Sigma factor + RNAP = holoenzyme
Describe the step of the transcription cycle for bacterial transcritption
- the sigma factor binds to RNAP and finds promoter sequence (forms the holoenzyme)
- **Localized unwinding of DNA, **a few short RNAs synthesized intitially & then RNAP clamps down, sigma factor is then released (sigma factor will rebind when more transcription is needed)
- Elongation
- Termination & release of RNA
What is the promoter sequence?
The promoter sequence is a sequence of nucleotides BEFORE the active site, which also means it is not transcribed. It is where the sigma factor binds.
What is the most common promoter sequence?
(-10, -35) The negative number signify how many nucleotides before the first nucleotide transcribed (+1)
What do the terms upstream and downstram refer to when talking about nucleotides?
If nucleotide 1is upstream to nucleotide 2, nucleotide 1 has a lower number. If nucleotide 1 is downstream to nucleotide 2, nucleotide 1 has a higher number. (E.g.: -10 is downstream to -35)
In bacteria, is there only one sigma factor that recognizes promoter sequences?
No. Different sigma factors recognize different sequences.
Which DNA strand is transcribed?
It depends, both DNA strands can be used as a template for RNA
What happens to the structure of RNA as it begins to form?
As the newly synthesized RNA leaves the RNAP, it can begin to base pair with itself and form structures like loops (e.g. hairpins)
Which nucleotide do terminator sequences near the stop site largely consist of? Why?
Terminator sequences near the stop site largely consist of As as the h-bonds between As and Us are not as strong as that of Gs and Cs.
The initial steps of RNA synthesis are relatively ___________
infefficient
Why is the elongation mode of RNA polymerase considered highly processive?
RNAP moves quickly, synthesizing RNA without falling off the DNA template
What are some of the characteristics of RNA termination signals?
- Hairpin structure formed as a result of GC rich sequences
- AT rich DNA sequences following hairpin sequences
How do termination signals help to dissociate the RNA transcript from the polymerase?
It distrupts h-bonding of new mRNA transcript with DNA template
What is one of the biggest differences between prokaryotic and eukaryotic gene expression?
Prokaryotic gene expression: operations are coupled, meaning that before finishing transcription, you can start translation
Eukaryotic gene expression: because of the nucleus, you cannot couple transcription + translation (however, the preparation operations required to happen before translation can happen even before translation is finished)
