lecture 12

Question 1

how does RNA fold

Answer 1

• it is not constrained by the double helix
• so it can fold in many ways by hydrogen bonding to itself

Question 2

what roles does RNA have apart from transcription

Answer 2

• enzymatic activity
• bind to proteins to form ribonucleic complexes
• housekeeping for cellular processes (rRNA and tRNA)
• regulatory RNAs

Question 3

function of regulatory RNAs

Answer 3

• non-coding molecules
• used for splicing
• and control of gene expression

Question 4

describe the proportions different RNAs in a cell

Answer 4

• 2% mRNA
• 96% tRNA or rRNA
• 2% other RNA

Question 5

what makes mRNA

Answer 5

RNA polymerase II - also makes snRNA!

Question 6

what makes tRNA

Answer 6

RNA polymerase III - also makes snRNA!

Question 7

what makes rRNA

Answer 7

RNA polymerase I

Question 8

which RNAs are non-coding

Answer 8

• tRNA
• rRNA
• snRNA

Question 9

structure of mRNA

Answer 9

linear or circular

Question 10

structure of tRNA

Answer 10

T-shaped

Question 11

is mRNA or non-coding RNA less stable

Answer 11

mRNA - more prone to hydrolysis or attack by enzymes

Question 12

describe how to differentiate RNA and DNA

Answer 12

• DNA has one hydroxyl group, RNA has two
• RNA has uracil instead of thymine

Question 13

what RNA polymerases make snRNA

Answer 13

Pol II and Pol III

Question 14

what is transcription

Answer 14

making RNA from DNA instructions

Question 15

steps of transcription

Answer 15

1) initiation
2) elongation
3) termination

Question 16

where does transcription start

Answer 16

• from the +1 site downstream of the promoter
• the promoter is NOT transcribed

Question 17

what direction is polymerisation in transcription in

Answer 17

• 5’ to 3’
• RNA nucleotides are added to the 3’ end
• the DNA template is read in the 3’ to 5’ direction

Question 18

what do we mean by overlapping genes

Answer 18

a single segment of DNA sequence codes for more than one protein

Question 19

what is the template strand

Answer 19

• the DNA strand that RNA polymerase reads to build RNA
• antisense

Question 20

what is the non template strand

Answer 20

• non-template strand is NOT read during transcription
• has the same sequence as the RNA (except T instead of U)
• sense

Question 21

is RNA sense or antisense

Answer 21

sense

Question 22

what sequence helps to start transcription

Answer 22

• initiator sequence

Question 23

describe the initiator sequence

Answer 23

• short consensus sequence (2-7 bp)
• consensus meaning it is the “most common” version of the DNA sequence found when we align many similar sequences from different genes

Question 24

location of the initiator sequence

Answer 24

• specific sequence within the core promoter
• spans the transcription start site, e.g. -2 to +4

Question 25

what base is the transcription start site usually

Answer 25

an A

Question 26

what are core promoters

Answer 26

- short DNA sequences needed to start transcription at the correct place - found in highly transcribed genes

Question 27

where are core promoters found

Answer 27

- small part inside the larger promoter - 26-31 bp upstream of the transcription start site

Question 28

what happens at core promoters

Answer 28

it's where protein complexes assemble to start transcription

Question 29

what are CpG islands

Answer 29

- instead of TATA, CpG islands initiate transcription of 70% of protein-coding genes - rich in Cs and Gs (not base pairing, just on the same strand)

Question 30

size of CpG islands

Answer 30

100-1000 bp long

Question 31

where are CpG islands located

Answer 31

- they are not core promoters, but they are located within the promoter - they can overlap with the transcription start site

Question 32

what can suppress transcription

Answer 32

cytosine methylation of CpG islands prevents transcription factors and RNA Pol from binding, effectively suppressing transcription

Question 33

what proteins perform transcription

Answer 33

RNA Pol II and general transcription factors

Question 34

function of RNA Pol II in transcription

Answer 34

reads the DNA and builds a complementary RNA strand

Question 35

function of general transcription factors

Answer 35

- helicase activity - DNA melting: opening DNA to let it be copied - does everything "non-polymerase" - tells RNA Pol II where and when o express specific genes

Question 36

describe the important unit of RNA Pol II

Answer 36

a beta subunit clamp domain at the C-terminus

Question 37

describe the beta subunit clamp domain of RNA Pol II

Answer 37

- this clamps and grabs the DNA template with the help of serines - serine phosphorylation is the main checkpoint for transcription

Question 38

what are the types of transcription factors

Answer 38

general and specific

Question 39

function of specific transcription factors

Answer 39

tells RNA Pol II where and when to make specific genes

Question 40

function of general transcription factors

Answer 40

- identify template strand - identify promoter - bring RNA Pol II to the correct location - when to speed up transcription

Question 41

what are the main steps of transcription

Answer 41

1) initiation 2) elongation 3) termination

Question 42

main steps of initiation

Answer 42

1) transcription factors + RNA Pol II recognise and bind to the promoter 2) melt the DNA to open the template strand 3) limited polymerisation (slow addition of rNTPs)

Question 43

what is promoter clearance

Answer 43

- the transition from initiation to elongation - this is when the beta subunit clamp domain of RNA Pol II is phosphorylated