RNA transcription

Question 1

Three classes of RNA

Answer 1

mRNA
rRNA
small RNA (tRNA, snRNA, 5S rRNA)

Question 2

Promoter

Answer 2

A region of DNA used to activate or repress transcription of a gene

Question 3

Enhancer

Answer 3

Region of DNA that regulates transcription like a promoter, but can be moved relative to the gene it controls (located great distances from their genes)

Question 4

Minimal promoter

Answer 4

smallest region of a full promoter that drives detectable transcription; drive constitutive, low-level transcription

Question 5

TATA box

Answer 5

minimal promoter for pol II that possess TATA sequence

Question 6

Initiation complex

Answer 6

cluster of proteins that assemble around a promoter to initiate transcription

Question 7

TBP

Answer 7

protein that actually binds to TATA box

Question 8

TAFs (TATA associated factors)

Answer 8

assemble around TBP to form the core initiation complex at the minimal promoter

Question 9

start of transcription

Answer 9

usually a purine (A>G), 26-34 bp down from TATA box

Question 10

Mechanism of action

Answer 10

TBP binds a TATA box, TAFs recruited to form core initiation complex, attracts RNA polymerase which “looks” for a purine about 30 bp downstream where it will initiate transcription

Question 11

Recognition sequences

Answer 11

promoters and enhancers clusters of these that are bound by TFs

Question 12

Transcription factors

Answer 12

proteins that bind recognition sequences to control transcription

Question 13

DNA binding domain

Answer 13

a region of TF that recognizes and binds a specific sequence of DNA; usually positively charged; forms bonds with negatively charged phosphates on surface of DNA

Question 14

Activation domain

Answer 14

region of transcription factor that induces RNA transcription by attracting an RNA polymerase; naturally attracted to negative charge of DNA

Question 15

Promoter and enhancer architecture

Answer 15

As TFs bind these sequences they become grouped together on the DNA and stick together (ionic and H bonds); upstream TFs contribute to the initiation complex by binding to the general TFs at the minimal promoter; in this manner the initiation complex becomes a large mass of - charge marking the start of transcription (charge attracts RNA poly)

Question 16

mRNA processing

Answer 16

capping, splicing, polyadenylation

Question 17

primary transcript

Answer 17

RNAs that have not been processed (processing occurs simultaneously with transcription)

Question 18

Capping

Answer 18

a guanosine is added to the first nucleotide of the primary transcript by an unusual 5’-5’ bond; cap is methylated with 2’ OH of 1st and 3rd nucleotides; many others methylated but their location sites vary; capping and methylation increases mRNA stability by resisting its degradation

Question 19

Splicing

Answer 19

removal of a section of primary transcript; region that’s spliced out is an intron and retained regions are exons; introns spliced out by spliceosomes (complexes of snRNPs composed of proteins and snRNAs)

Question 20

Polyadenylation

Answer 20

20-300 adenosines to the 3’ end of the transcript (poly A tail); increase mRNA stability; signaled by AAUAAA but transcription continues 500-2000 bp until pol II falls off the DNA; excess RNA cleaved at a CA 10-30 bp downstream of AAUAAA; Poly A polymerase adds poly A tail; histones lack polyA tail