Mod4 - DNA to RNA (Transcription)

Question 1

Function of a promoter (prokaryotes)?

Answer 1

Indicates where transcription starts (by binding to RNA polymerase), and which direction the RNA Pol should face

Question 2

What are leaders/spacers in DNA (prokaryotes)?

Answer 2

Sections of DNA which are NOT translated (leaders are between the promoter and the first cistron, spacers are between cistrons)

Question 3

What are cistrons (prokaryotes)?

Answer 3

Coding regions of DNA (each one codes for one polypeptide)

Question 4

What are Class II genes?

Answer 4

Eukaryotic Genes which are transcribed to mRNA, which is then translated into proteins.

Question 5

Briefly describe the structure of a prokaryotic promoter

Answer 5

There are two sequences (one centred at -10bp and one at -35bp), which together form the Pribnow Box - RNA Pol recognises this sequence and binds to it

Question 6

Name the 6 sub-units of prokaryotic RNA Polymerase

Answer 6

1 sigma, 2 alpha, 2 beta (ß and ß’), and 1 omega

Question 7

Which factor of RNA Polymerase interacts with the promoter sequence?

Answer 7

ONLY the sigma factor

Question 8

In prokaryotic transcription, which sub-unit(s) are involved in catalysis and form the main part of the RNA Pol apparatus?

Answer 8

The ß sub-units

Question 9

What happens as prokaryotic transcription is initiated?

Answer 9

As RNA Polymerase moves off the promoter, the sigma factor is released, leaving just the core enzyme, so that RNA Pol becomes non-specific

Question 10

Which types of genes do the different Eukaryotic RNA Polymerases
transcribe?

Answer 10

RNA Pol I = large rRNA genes
RNA Pol II = protein-encoding genes (mRNA) and snRNA
RNA PolIII = tRNA and 5S rRNA

Question 11

In the RNA Pol II initiation complex, which is only first transcription factor to interact directly with the DNA, and what does this factor consist of? (And which part of the DNA?)

Answer 11

TFIID -> TATA-binding protein (TBP) and TBP-associated factors (TAFs)
TFIID binds to the promoter sequence

Question 12

Which two TFs bind adjacently to TFIID and what are their functions?

Answer 12

TFIIB - measures distance from the core promoter sequence to the transcription start site
TFIIA - helps TFIID to bind

Question 13

Name the 5 TFs that join the complex after the initial 3, and name 3 of their functions

Answer 13

TFIIE - helps to recruit TFIIH
TFIIF - binds to RNA Pol II and helps it to bind to the TFs already in place (D, B and A)
TFIIH - contains helicase and kinase subunits (the helicase prises open the DNA and exposes the template sequence; later, the kinases phosphorylate RNA Pol II and allow it to release from other TFs) -> ALSO I THINK TRANSCRIPTION-COUPLED DNA REPAIR??
TFIIJ and TFIIK - not much info available

Question 14

Summarise the two main stages of Transcription Initiation for RNA Pol I

Answer 14

1. Upstream Binding Factor (UBF) binds to both the Upstream Control Element (UCE) and and the Core Element, then interacts with itself, causing the DNA to loop.
2. A further TF is recruited - SL1 (a Pol1-specific TF, consisting of TBP surrounded by several Pol1-specific TAFs) “the Pol1 equivalent of TFIID”

Question 15

What is unusual about the configuration of RNA Pol III (tRNA) genes?

Answer 15

The promoter sequence is DOWNSTREAM of the transcription start site

Question 16

What is the first binding that takes place for RNA Pol III (tRNA) genes?

Answer 16

TFIIIC binds to the B box of the promoter

Question 17

What are the second and third steps in Translation Initiation for tRNA genes?

Answer 17

Once TFIIIC has bound, it recruits TFIIIB (which consists of TBP and two Pol3-specific TAFs).
Once TFIIIB is recruited, TFIIIC is dispensable - RNA Pol III must start transcription without being blocked by downstream TFIIIC

Question 18

How are snRNA genes different from other genes transcribed by RNA Pol III?

Answer 18

They have an upstream promoter (like Pol II genes)

Question 19

Describe how negative feedback affects the function of the Lac Operon

Answer 19

When Lactose is present, it induces the Operon, so ß-Galactosidase is synthesised, which digests the lactose, decreasing lactose availability, so the repressor is able to bind to the Operator again and repress the operon.

Question 20

Describe how Glucose regulates the Lac Operon through Catabolite Repression

Answer 20

For transcription to occur, CRP (Catabolite Repressor Protein) must be bound to the Promoter. When glucose is present, cAMP production stops, so no cAMP can bind to CRP, so CRP is unable to bind to DNA. Therefore the Lac Operon cannot be transcribed

Question 21

Describe how negative feedback affects the function of the Trp Operon

Answer 21

When no Tryptophan is present, the Trp Operon is transcribed, and the enzymes produced synthesise Tryptophan (biosynthetic product). Tryptophan then binds to the trp repressor, activating it, and causing the operon to be repressed so no further Tryptophan is synthesised (Tryptophan is a co-repressor)

Question 22

Describe how lactose activates/induces the Lac Operon

Answer 22

(The Lac repressor normally holds RNA Polymerase in place a prevents transcription from beginning.) Allolactose binds to the repressor, which then dissociates from the operator, allowing RNA Polymerase to transcribe the genes.