DNA Transcription

1.Define DNA transcription as the synthesis of RNA

2.List four major kinds of RNA

3.Identify prokaryotic RNA polymerase and its subunit structure

4.identify the function of the σ subunit of prokaryotic RNAP as a promoter binding protein

5.Describe the position and general structure of the prokaryotic RNAP promoter

general structure above
'activators' bind in the -35 region, upstream from the TATA box (aka Pribnow)
'activators' facilitate binding of RNAP and regulate the frequency of transcription.

6.Recognize that RNAP does not require a primer

7.Describe the sequential process whereby RNAP adds nucleotides to the growing RNA chain

core RNAP reads template strand of DNA in a 3' to 5' direction
generates a 5' to 3' RNA transcription
uses ribonucleotide triphosphates
the 5' phosphate of the incoming nucleotide attaches to the 3' hydroxyl of the growing chain.

8.Identify the mechanism of termination of prokaryotic transcription

Elongation continues until a termination signal is encountered
signal can be a 'hairpin' loop preceding a number of U residues
can be a protein called 'rho' (ρ), which causes the release of the transcript from the template.

9.List the functions of eukaryotic RNAP I to III

10.List several differences between prokaryotic and eukaryotic RNAP promoters

Prokaryotic RNA promoters
- RNAP initiates transcription at a high frequency at “strong promoters” and at low frequency at “weak promoters. The sequences of prokaryotic promoters are similar in two regions – one at -10 and another at -35. These regions are called boxes. At =10, the sequence is called the TATA or Pribnow and is recognized by a specific sigma. Repressors bind to a region of the promoter called the 'operator' and inhibit transcription by preventing the binding of RNAP. 'activators' bind in the =35 region or upstream from it to facilitate the binding of RNAP and regulate the frequency of transcription

Eukaryotic RNA Promoters
- Structural regulatory regions in the DNA are called 'cis-acting' because they exist on the same molecule of DNA and near to where RNAP works
- In addition to the TATA box, there are several regions extending -110 nucleotides upstream of the transcriptional start site that include a CAAT box and 'GC rich' regions
- There are other cis-acting 'enhancer' and 'silencer' sequences which are structurally different and located far away from the start point of transcription.

11.Define 'cis acting' and 'trans acting' transcription regulators

Cis-acting: exist on the same molecule of DNA and near to where RNAP acts
Trans-acting: proteins encoded by genes that are distinct from the ones they regulate. Can bind to cis-factors

12.Identify the structure and function of the 5' 'cap' in mRNA

function: the binding of the mRNA to the ribosome during protein synthesis
structure: methylated guanosine nucleotide (7-methyl-GTP) that attaches to the 5'-OH of the RNA.

13.Describe the process of polyA 'tailing' of mRNA

During transcription, a polyadenylation signal (AUAAA) appears in the sequence
It is a signal for enzymatic cleavage of the mRNA 10-20 nucleotides downstream
Additional adenosine nucleotides are then added one at a time to the 3' end of the RNA from ATP
Can be several hundred nucleotides long.

14.Define 'introns' and 'exons'

Introns: Non-coding, intervening sequences of DNA that are transcribed, but are removed from within the primary gene transcript and rapidly degraded during maturation of messenger RNA. Most genes in the nuclei of eukaryotes contain introns, as do mitochondrial and chloroplast genes.

Exons: Coding regions of messenger RNA included in the genetic transcript which survive the processing of RNA in cell nuclei to become part of a spliced messenger of structural RNA in the cytoplasm. They include joining and diversity exons of immunoglobulin genes.

15.Describe 'spliceosome' structure and function