Chapter Five Flashcards
(31 cards)
Is the genome unwound when it is transcribed?
No, only certain, specific sections are kept unwound
Why, like DNA, can RNA only be copied from DNA in the 5’ to 3’ direction?
Because it needs to attach to the 3’ hydroxyl
What are the five types of RNA that we discussed?
- mRNA
- tRNA
- rRNA
- snRNA
- miRNA
What is mRNA?
messenger RNA “genes”
it is the message for the order of amino acids
includes 3000 ish base pairs (1500-8000)
What is tRNA?
transfer RNA
it transfers or escorts amino acids to the ribosome complex to convert mRNA to the chain of amino acids
91 bases long
they fold in on themselves making clover like structures.
What is rRNA?
Ribosomal RNA
RNA structurally important for the ribosomal complex
it connects the protein complexes of the ribosome
What is snRNA?
small nuclear RNA
it interacts with proteins to form snURP’s, which play a role in RNA processing
usually a few hundred bases long
What is miRNA?
micro-interference RNA
21 bases long (used in gene regulation)
What stage of the cell cycle does transcription take place?
G2 (cell growth)
What is the first step of DNA transcription?
Initiation
How is it recognized that a certain bit of DNA needs to be transcripted?
There exists sequences adjacent to the DNA that act as promoter sites.
What is the core promoter?
It is a region of DNA adjacent to the gene, that encompasses the lnr and TATAAA box
What is the TATAAAA box?
It is a region of the DNA upstream from the gene within the core promoter and is about 25-30 base pairs away from the TSS
What is the CATT box?
It is a region of DNA that exists around 75 base pairs upstream from the gene that helps in promotion of transcription
If there is a mutation within this region, only 4/10 times will the gene that lies further downstream be transcribed
What is the GC box?
It is a region of DNA that exists around 90 base pairs upstream from the gene that also helps as a promoter.
Explain the initiation step in transcription in as much detail as possible.
TFII D which is a protein involved in initiation is bouncing around within the nucleus and binds to the TATAAAA box. This flexes the protein and allows other proteins that assist in initiation (TFII A & B) to come along and bind to TFII D. This is the start of the assembly of the pre-initiation complex.
The entire point of the these proteins, is to orient themselves so that TFII F attached to RNA Polymerase can come along and add to the complex. This is now the minimal transcription complex.
Finally, TFII E and H come along and bind tightly to the complex to stabilize the RNA Polymerase, completing the pre-initiation complex.
Describe the elongation step in transcription in detail.
The RNA polymerase II has its own helicase activity. So RNA poly II is able to embed in between the DNA strands and move along. There is no need to SSBP to hold it open. As RNA Polymerase II is moving down and copying, it has no proofreading activity. The RNA Polymerase II makes these chains of RNA that drag behind it as nucleotides are added. The ten most recently made RNA nucleotides are still adhering to the single strand of DNA being copied, and as nucleotides are added, the mRNA breaks off form the pressure of the turns.
This is because RNA is bigger and cannot continue to adhere to the DNA because DNA is smaller and has alpha helix turns that RNA cannot follow bc RNA cannot fold that small.
This tail continues to build. Once the RNA Polymerase II reaches the end of a gene at a stop codon, the RNA stops copying
What things can RNA Polymerase carry out?
- Helicase activity (it unzips)
- 5’ to 3’ polymerase activity (it adds)
- Like DNA primase, it does not require 3’-OH to start a chain of RNA
What does RNA Polymerase not carry out?
- It has no 3’ to 5’ exonuclease activity (proofreading)
- It has no 5’ to 3’ exonuclease activity
(we aren’t running into the back of any DNA)
Why is 3’-5’ exonuclease activity not important for transcription?
Why is it important for DNA replication?
Proofreading is not so important for DNA transcription because RNA is mass produced, and it is very unlikely that the same mistake will exist for all the produced RNA. If some have mistakes, its all good because they will get degraded.
DNA needs to be copied perfectly, or as close as we can get, because it is passed onto progeny, and without exonuclease activity, many mutations could occur that have negative effects for the cell.
Can initiation and elongation happen simulataneously?
Yes!
What are the two ways that transcription can be terminated?
Rho dependent process (termination proteins)
Rho independent process
Explain how a gene that is Rho dependent terminates.
As RNA polymerase II approaches the termination site on the DNA, the Rho protein binds to a specific site on the newly synthesized RNA, known as the rut site past the stop codon. Rho then travels along the RNA toward RNA polymerase and when it catches up, there is no room for RNA polymerase II and it dissociates from the DNA releasing the RNA transcript.
How does Rho independent termination work?
At the end of the RNA transcript, there exists, first, regions with high GC bases going (GCGCGCGC) and second, a region with high TU bases.
As RNA polymerase synthesizes the high GC region, it folds back on itself forming a hair-pin structure due to hydrogen bonding.
Because the only thing left after the high GC bases are TU, and these are weaker, the strand just disassociates from the DNA template given the pull of the hair-pin.
