Lecture 26 - Eukaryotic Transcription

Question 1

What do the different eukaryotic polymerases do?

Answer 1

RNA pol 1: rRNA
RNA pol II: mRNA
RNA pol III: tRNA and 5S rRNA segment

Question 2

How does RNA pol 1 work?

Answer 2

Has 2 transcription factors: TF1B and TF1S to help with Binding the promoter and Stabilizing the binding
Makes rRNA in a 45s segment that is then spliced into three pieces to ensure 1:1 ratio of ribosomal units

Question 3

How does RNA pol II work?

Answer 3

Synthesizes mRNA in the pre-mRNA form, which is then processed. mRNA is monocistronic (no operons, genes for proteins with functions in same pathway are located all over genome)
Has 2 types of transcription factors: 1) promoter-proximal, TF2D binds to the TATA box via the TATA binding protein, allows the RNA pol 2 and other transcription factors to bind
2) Enhancer elements: located upstream, work as activators

Question 4

How does TBP work?

Answer 4

Binds to the minor groove via concave surface, bends and spreads minor groove, TBP intercalats between base pairs and creates kink in DNA to allow for RNA pol 2 docking

Question 5

How are eukaryotic genes regulated?

Answer 5

Only positively regulated through enhancer elements. Negative regulation occurs naturally through the chromatin binding in a solenoid which prevents transcription from occurring. Positive regulation has activators binding to enhancer elements to increase transcription at nearby promoters. Activators linked to promoter TFs through co-activators which form a mediator complex intermediary, which allows activators to communicate with pol and TFs. Activators can help recruit RNA pol2

Question 6

What are the 3 types of mRNA processing?

Answer 6

5’ cap, poly-A tail, splicing the introns out

Question 7

How does 5’ capping work?

Answer 7

7-methylguonosine (methylated guanine) added in 5’-5’ triphosphate linkage to the 5’ end during transcription, protects it from nucleases, helps ribosomes initiate translation

Question 8

How does polyadenylation work?

Answer 8

Synthesize RNA beyond the cleavage signal sequence (contains AAUAAA), protein complex has endonuclease to cleave ~20 bases downstream of cleavage signal, then polyadenylate polymerase adds A residues to protect mRNA from nucleases

Question 9

What are 3 common DNA binding motifs?

Answer 9

Zinc finger domains: alpha helix and loop stabilized by zinc ion, binds to the major groove
homeodomain: 3 alpha helices with hydrophobic interactions, helix 3 interacts with bases in the major groove, helix 1 interacts with bases in the minor groove
Leucine zipper: 2 alpha helices that dimerize via hydrophobic interactions between leucine side chains every 7 residues, interact with DNA in the major groove