Transcription

Question 1

stages of initiation of transcription

Answer 1

RNA polymerase II complex binds to promoter and opens DNA double helix

Question 2

what binds to start site in eukaryotes vs prokaryotes

Answer 2

general transcription factors vs sigma factor

Question 3

what is the TATA box

Answer 3

short sequence of T and A nucleotides in the promoter region where general transcription factors bind
recruits protein complex

Question 4

which strand is used as the template strand

Answer 4

antisense

Question 5

TFII

Answer 5

general transcription factor that recruits RNA polymerase II

Question 6

elongation- compared to DNA replication

Answer 6

can be synthesised de novo (no primers needed)
5’-3’

Question 7

true or false: many RNA molecules can be synthesised from the same gene

Answer 7

true
feather like structure seen with short transcripts extending from 5’ end of gene and long transcripts from 3’ end

Question 8

what is transcriptional stress

Answer 8

DNA damage induced by breaks during transcription
can be relieved by topoisomerases

Question 9

how is transcription terminated

Answer 9

termination signal-not same as stop codons (translation)
RNA folds into hairpin secondary structure to aid displacement from DNA

Question 10

3 stages of mRNA processing

Answer 10

capping
polyadenylation
splicing

Question 11

modification of guanine nucleotide that makes the 5’ cap

Answer 11

methyl group added

Question 12

3’ UTR role

Answer 12

mRNA is cleaved after polyA signal in 3’ UTR and polyA tail added
done by polyA complex

Question 13

function of polyA tail

Answer 13

protects mRNA from degradation
exportation from nucleus to cytoplasm

Question 14

what is the spliceosome made of

Answer 14

complex of proteins and snRNPs and snRNA

Question 15

what are snRNPs

Answer 15

small nuclear ribonucleoproteins

Question 16

what is a ribonucleoprotein

Answer 16

complex of protein and RNA

Question 17

snRNA

Answer 17

small nuclear RNA
recognise splice sites
catalyse splicing reaction
ribozymes
complex secondary structure

Question 18

alternative splicing

Answer 18

splice variant proteins (isoforms) can have different functions in tissues

Question 19

cis regulatory elements

Answer 19

DNA sequences around the protein coding regions that control when and how much mRNA is transcribed
eg enhancers, promoters, silencers
can active or repress transcription synergistically or antagonistically

Question 20

role of activators

Answer 20

recruit PIC proteins

Question 21

role of mediator protein complex

Answer 21

links activator transcription factors with PIC

Question 22

co factors

Answer 22

bind to TFs for extra regulation
recruitment of general TFs, modifiers, PIC complex etc

Question 23

chromatin modifiers

Answer 23

facilitate access to DNA by adding/removing modifications from histones
can modify DNA itself

Question 24

nucleosome

Answer 24

147 bps
protein core of 8 histones: 2 tetramers of H2A H2B H3 H4 subunits
forms octamer
H1 associates with linker DNA between histones

Question 25

chromatin remodelling factors

Answer 25

slide along DNA strand to slide nucleosomes relative to each other
exchange histone octamers or subunits (eg is DNA damage is detected, can swap out some histones and put a tag that recruits DNA repair complexes)
remove core histones
alter structure by wrapping more tightly

Question 26

histone tail modification

Answer 26

by chromatin modifiers
methyl groups and acetyl groups mainly added to lysines
also phosphorylation

Question 27

effects of acetylation

Answer 27

causes steric interactions
reduce affinity of nucleosome tails to each other
loosen chromatin
recruitment of PIC

Question 28

effect of methylation

Answer 28

increase affinity of nucleosome tails
recruitment of proteins that repress transcription
attract proteins that pack dna into heterochromatin

Question 29

exception to methylation

Answer 29

lysine 4 of histones
induces gene expression