Lecture 24. Transcription

Question 1

What is transcription ?

Answer 1

How mRNA is made from a DNA template

Question 2

What is transcriptomics?

Answer 2

Allows us to analyze gene sequences and expression levels of all genes in an organism, often simultaneously

Question 3

What does RNAP II make in eukaryotes?

Answer 3

Makes mRNA

Question 4

What does RNAP I make in eukaryotes ?

Answer 4

ribosomal RNA

Question 5

What does RNAP III make in eukaryotes ?

Answer 5

Transfer RNA

Question 6

What are the three steps in RNA synthesis ?

Answer 6

1. Initiation of transcription
2. Elongation
3. Termination

Question 7

What is a promoter ?

Answer 7

DNA sequences that guide RNAP to the beginning of a gene to start transcription at the initiation site

Question 8

What is the function of a promoter ?

Answer 8

Tell RNA polymerase where and when to initiate transcription

Question 9

What is transcription in eukaryotes regulated by ?

Answer 9

Transcription factors

Question 10

What are the two types of transcription factor ?

Answer 10

1. Repressors

2. Activators

Question 11

What are 4 major differences between eukaryotic and prokaryotic transcription ?

Answer 11

1. Nucleus surrounded by a double membrane
2. DNA is wrapped around histones to give chromatin
3. Promoters have many control sites for transcription factors
4. RNAP has 12 protein subunits and can associate with many different regulatory proteins

Question 12

What is involved in controlling transcription in eukaryotes ?

Answer 12

Opening and closing of chromatin

Question 13

What is regulated by transcription factors and chromatin state ?

Answer 13

Access to core promoter

Question 14

What is a proximal core promoter ?

Answer 14

General transcription factor complex substitute for sigma factor

Question 15

Where is the TATA box analogous to ?

Answer 15

Pribnow box

Question 16

What are distal control elements ?

Answer 16

Enhancer and silencer elements controlled by transcriptional activators/repressors influence general transcription factors an Pol II recruitment

Question 17

What happens during pre-initiation complex assembly ?

Answer 17

1. Binding of TATA binding protein and transcription factor IID

Question 18

Where does the pre-initiation complex assemble around ?

Answer 18

RNA polymerase

Question 19

Where does the TATA binding protein bind to ?

Answer 19

The TATA box in the genes promoter region

Question 20

What does the general transcription factor form ?

Answer 20

A pre-initiation complex that includes RNAP

Question 21

What are general transcription factors a complex version of ?

Answer 21

A sigma factor

Question 22

What is RNA polymerase activated by ?

Answer 22

The phosphorylation of its C-terminal tail and then begins elongation/transcription

Question 23

What does RNA polymerase II begin ?

Answer 23

Elongation

Question 24

What does mRNA precursors contain ?

Answer 24

Exons and introns

Question 25

Where are introns spliced ?

Answer 25

The nucleus

Question 26

What is added to mRNA ?

Answer 26

1. A 5' CAP | 2. 3' PolyA tail

Question 27

How is the mature mRNA transported ?

Answer 27

Transported from the nucleus to the cytoplasm via the nuclear pores

Question 28

What are introns ?

Answer 28

Intervening regions

Question 29

What are exons ?

Answer 29

Coding regions

Question 30

What is splicing ?

Answer 30

Removal of introns

Question 31

What are some things in mRNA in eukaryotes ?

Answer 31

1. Exons 2. Introns 3. Capping 4. Splicing 5. Polyadenylation

Question 32

What does alternative splicing yield ?

Answer 32

Different mRNA's and protein isoforms

Question 33

What is base pairing ?

Answer 33

Two highly negatively charged polymers held together

Question 34

What is DNA hybridisation ?

Answer 34

A velcro type reaction, many low energy linkages multiply their effects to hold DNA together

Question 35

What forms of DNA is unstable ?

Answer 35

Short DNA duplexes

Question 36

What can be used to detect specific mRNAs ?

Answer 36

Northern blotting

Question 37

What does electroblotting do ?

Answer 37

Drives the RNA out of the gel and onto the membrane

Question 38

What is thermal stability of duplex directly related to ?

Answer 38

Perfection of base pair matching

Question 39

What is the zippering effect ?

Answer 39

Longer duplexes hybridise faster and are more stable than short ones

Question 40

What is hybridisation of probes ?

Answer 40

The basis of blotting techniques for detetion

Question 41

What is the hybridisation of primer sequences ?

Answer 41

The basis for targeted DNA replication including PCR

Question 42

What could a hybridised label of DNA of the gene of interest be labelled with ?

Answer 42

1. Radioactive 32p | 2. Biotin labelled nucleotides

Question 43

What is reverse transcriptase ?

Answer 43

Makes DNA from an RNA template

Question 44

What are microarrays used for ?

Answer 44

To measure changes in gene expression across the whole genome

Question 45

How do you measure the abundance of mRNAs ?

Answer 45

Via amplification of cDNA

Question 46

What can reverse transcription PCR be used for ?

Answer 46

Quantifies mRNA indirectly via amplification of cDNA copies

Question 47

What are potential drug targets ?

Answer 47

Genes that are upregulated in cancer cells

Question 48

What does each cells cDNA carry ?

Answer 48

A unique sequence tag

Question 49

What can cell types be identified by ?

Answer 49

Identical transcriptomes