L01

Question 1

What is ‘gene expression’?

Answer 1

The process by which information in genes (DNA) is decoded into protein

Question 2

Name the process DNA -> RNA

Answer 2

Transcription

Question 3

Name the process RNA -> Protein

Answer 3

Translation

Question 4

Define ‘transcription’

Answer 4

Transfer of genetic information from ds DNA to ss RNA (mRNA)

Question 5

What is the purpose of DNA

Answer 5

Encode proteins

Question 6

Role of gene expression

Answer 6

Determines the function of the cell/primary specifier of cell identity

Question 7

How do cells respond to changes in the environment?

Answer 7

Gene expression is altered

Question 8

What is the DNA sequence for -35 promoter in prokaryotes?

Answer 8

TTGACA

Question 9

What is the DNA sequence for the -10 promoter in prokaryotes?

Answer 9

TATAAAT

Question 10

How far is the TATA box from the TSS?

Answer 10

-31 ~ -26 (about 30 base pairs)

Question 11

Why is it called the TATA box?

Answer 11

First 4 bases often, TATA

Question 12

What is the pyrimidine rich sequence?

Answer 12

Inr (initiator)

Question 13

Where is the initiator often located

Answer 13

-2 ~ +4

Question 14

Does DNA have all the core (basal) promoter elements?

Answer 14

No

Question 15

In mammals what percentage of protein coding genes lack obvious TATA & Inr?

Answer 15

60-70

Question 16

How does methylation affect transcription in CpG islands?

Answer 16

Methylation of CpG islands = silencing txn
Non-methylation of CpG islands = promoting txn

Question 17

What is methylation?

Answer 17

Addition of a methyl group

Question 18

What residues are methylated in mammalian CpG islands?

Answer 18

Most C residues followed by a G (5-methyl C)

Question 19

What is the catch when it comes to CpG methylation?

Answer 19

C residues are hypomethylated

Question 20

UAS

Answer 20

Upstream Activating Sequences

Question 21

URS

Answer 21

Upstream Repressing Sequences

Question 22

What tools do we use for identifying promoter elements?

Answer 22

Sequence comparison and Reporter Analysis

Question 23

What are the type of RNA polymerases in eukaryotes?

Answer 23

RNA pol I,II, III

Question 24

What does RNA pol I do?

Answer 24

Transcribes rRNA which is used to make ribosomes

Question 25

Where is the RNA pol I located?

Answer 25

Nucleolus

Question 26

What does RNA pol II do?

Answer 26

Transcribes mRNA

Question 27

Where is the RNA pol II located?

Answer 27

Nucleus

Question 28

What does RNA pol III do?

Answer 28

Transcribes tRNA which is used to translate mRNA genetic code into a sequence of amino acids

Question 29

What are the differences between prok. and euk. RNA polymerase?

Answer 29

Overall similar structure, euk. RNA polymerase is bigger (consists of 12 subunits). Prok. have one RNAp. that carry out all the functions compared to euk (3)

Question 30

What is the role of a sigma factor in bacterial prokaryotic transcription?

Answer 30

Helps bacterial RNA polymerase recognise promoter DNA

Question 31

What is the eukaryotic equivalent of sigma factors in prokaryotic transcription?

Answer 31

Transcription factors!

Question 32

Order of TFII in eukaryotes

Answer 32

TFIID, TFIIA, TFIIB, TFIIF, TFIIE, TFIIH

Question 33

What is the function of TFIID

Answer 33

Binds to TATA

Question 34

What is the function of TBP?

Answer 34

Binds to TATA

Question 35

What is the function of TAF?

Answer 35

Helps TBP fx when no TATA & in the presence of activator proteins. When not present does not work.

Question 36

What is the function of TFIIA?

Answer 36

Further stabilises complex

Question 37

What is the function of TFIIB?

Answer 37

Further stabilises complex

Question 38

What is the function of TFIIF?

Answer 38

Recruits RNA Polymerase II

Question 39

What is the function of TFIIE?

Answer 39

Recruits TFIIH & promotes promoter melting

Question 40

What is the function of TFIIH?

Answer 40

Unwinds DNA, repairs DNA, & phosphorylates

Question 41

What are the components of TFIIH and what are they responsible for?

Answer 41

CAK (Kinase) - phosphorylation XPB/SsL2/helicase - ATPase used in promoter melting. unwinding DNA and DNA repair

Question 42

What are the elements present in eukaryotic promoters?

Answer 42

TATA/Initiator (Inr - pyrimidine rich)

Question 43

What are the functions of the eukaryotic promoters?

Answer 43

TATA - binding site for TFIID Inr - start site for when there's no TATA box / enhancing txn

Question 44

How can reporter genes be used to analyse promoter sequences?

Answer 44

By measuring the activity of a promoter in a cell

Question 45

How many major RNA polymerases are there in eukaryotic cells?

Answer 45

3

Question 45

How do the General Txn Factors (GTF) assemble on the promoter to form PIC?

Answer 45

TFIID - binds to TATA/promoter TFIIA&TFIIB - bind to TFIID to stabilise complex TFIIF - assembles with RNA polymerase to form the Polymerase II complex TFIIE - recruits TFIIH TFIIH - contains helicase units that unwind DNA/cause promoter melting & contains kinase units = phosphorylation

Question 46

Describe the major events during transcription initiation.

Answer 46

- RNA polymerase binding to the DNA promoter template. - unwinding of DNA = creating separate strands = INITIATION