LEC 2: Transcription I

Question 1

Types of Genomic Regions

Answer 1

• Regulatory region - sequence of bases that control the initiation of transcription
• Coding region - sequence of bases that are read into a functional molecule (RNA or protein)
• Termination region - sequence of nucleotides that stops transcription

Question 2

Central Dogma

Answer 2

DNA ->(Transcription)-> RNA ->(Translation)-> Protein

Question 3

Reverse Transcription

Answer 3

Few examples exist that are exempt of Central Dogma, where RNA is enzymatically altered to become DNA
- E.g. Retroviruses (HIV etc.), Retrotransposons

Question 4

Prions

Answer 4

The prion protein (PrP) is normally present in the body and is folded into a specific conformation, a state called PrPC
- Prion diseases are caused by the same protein folded abnormally, a state called PrPSc

Question 5

RNA Polymerase

Answer 5

In bacteria, RNA polymerase consists of five subunits: two copies of alpha, a single copy of β, a single copy of β’ and a single copy of omega
- A sigma factor (σ) joins the core to form the holoenzyme, which is capable of binding to a promoter and initiating transcription

Question 6

The σ (Sigma) Factors

Answer 6

σ factors are required for promoter recognition and transcription initiation in prokaryotes
- σ70 is essential for cell growth in all conditions, while other sigmas are required for special events, like nitrogen regulation (σ54), response to heat shock (σ32), sporulation

Question 7

Initiation of Transcription

Answer 7

1. Initiation beings with Sigma binding to promoter region of DNA
2. Sigma opens the DNa helix, transcription begins
3. Initiation completes when Sigma releases, mRNA synthesis continues

Question 8

Elongation of Bacterial DNA

Answer 8

One strand of DNA serves as the template for RNA synthesis, but multiple rounds of transcription may occur so that many copies of a gene may be produced

Question 9

Termination Transcription

Answer 9

The formation of the Hairpin Loop (RNA secondary structure) disrupts the interaction between RNA polymerase and the RNA transcript resulting in the physical separation

Question 10

Termination of Bacterial Transcription

Answer 10

In prokaryotes two types of transcription termination occur
– rho indepedent termination (RNA secondary structure e.g. RNA stem-loop, required for termination)
– rho dependent termination (Rho protein required for termination)

Question 11

Transcription in Eukaryotes

Answer 11

Rate of initiation of transcription regulated by enhancers and silencer elements (regulators)

The initiation of transcription is accomplished by basal transcription factors
– Function analogous to sigma
– Can interact with DNA independently of RNA polymerase

Question 12

RNA Polymerase I

Answer 12

Transcribes the rRNA precursor gene, composed of 2 elements:

1. Core Element, located -45 to +20
2. Upstream control element (UCE), located -180 to -107

Question 13

RNA Polymerase III

Answer 13

Promoters for RNAP III may be:
• Bipartite Sequences downstream from startpoint (Either boxA separated from box OR boxA separated from boxC)
• Separated sequences upstream of startpoint (Oct, TATA)

Question 14

RNA Polymerase II

Answer 14

The promoters of genes transcribed by RNAPII consist of a core promoter and a regulatory promoter:

• TATA Box: sequences of TATAAA
• InR: Pyrimidines surrounding the start point
• Downstream Promoter Element (DPE): downstream of the start point

Question 15

Initiation of Transcription

Answer 15

Order of binding is: IID + IIB + RNAP II + IIF + IIE + IIH

Finally, the binding of activator factors to DNA sequences (called enhancers) induces high-level transcription.

Question 16

Termination of Transcription

Answer 16

1. The eukaryotic RNA polymerase II transcribes well past the end of the gene.
2. RNA polymerase II passes through one or more AATAAA sequences, which lie beyond the 3’ end of the coding region
3. The pre-mRNA, carrying this signal as AAUAAA, is then cleaved by a special endonuclease