The ONE (RNA Processing & RNA Reverse Transcription)

Transcription Review: Binding/Initiation

- Sigma factor: Binds to help identify the promoter sequence for correct positions for transcription

- Once in correct position, the polymerase opens the double helix to start transcription. Once clear of the promoter, the interaction between sigma-factor and polymerase is broken.

Transcription Review: Elongation

- Once the sigma-factor is released, processivity drastically increases.

- NusA - Helps with elongation and termination

Transcription Review: Termination

- Termination can occur via p-dependent or p-independent. In each case there's is a recognition sequence the initiates the termination

- P-dependent: Increases sequence of A facilitates a hairpin secondary structure that facilitates the release of the polymerase.

- p-independent: The RUT sequence recruits the rho factor for release of polymerase from template (ATP-dependent)

- P-dependent:

Increases sequence of A facilitates a hairpin secondary structure that facilitates the release of the polymerase.

p-independent:

The RUT sequence recruits the rho factor for release of polymerase from template (ATP-dependent)

5' capping is? and where?

Involves the modification of the 5' end of the RNA with a methyl-guanine and occurs near CTD of the RNAP complex

Why is 5' capping important for?

- Ensures RNA is not degraded by nucleases

- Binding site for ribosome in translation

- Methylation is SaM mediated

- Methylation can occur at the subsequent 2' position

Why is intron splicing important

Noncoding regions (introns) must be removed to form the coding mRNA once the terminal are capped ("UTR")

What is intron splicing?

Is a self-catalyzed process mediated through 2 unique hydrolysis process. Splicing mechanism are labeled as Group I or II

Group I

mediated splicing enlists the help of a guanine NUCLEOTIDE cofactor as the nucleophile

Group II

mediated splicing enlists the help of an Adenine NUCLEOSIDE within the intron as the nucleophile

What is Group I introns nucleophile?

Guanine cofactor

What is Group II introns nucleophile?

"A" within intron

the 2 steps in intron type II

- 2'OH of a specific adenosine in the intron attacks the 5' splice site, thereby forming the lariat

- 3'OH of the 5' exon triggers the second transesterification at the 3' splice site thereby joining the exons together

Splice site on the pre-mRNA conatins?

GU at 5' end

AG at 3' end

# of splice products can be increased by?

Using exon cassets "missplicing" is the source of numerous diseases

3' Polyadenylation is?

Process of modifying the 3' of the mRNA with repeating sequence of A

what is 3' poly( A) tails important for?

- Binding site for proteins to coordinate transcription and translation

- May help protect from enzymatic destruction

- Recognition for polyadenylation occurs at 2 site.

- Polyadenylation is protein mediated, polyadenylate polymerase

what are the 2 sites of polyadenylation?

- Upstream of cleavage site at 5'AAUAAA3'

- downstream at a G and U rich region

Micro RNA (miRNA)

utilized for regulation of processes. Small portions of spliced introns that are further processed for activity.

rRNA and tRNA processing is important in?

Activation of ribozymes

Modifications include?

- Splicing of the different sized ribosomes/tRNA from a long pre-rRNA structure

- Base modification

Retrovirus

Virus that utilizes reverse transcription to propagate

Reverse transcription is the?

Ability to utilize RNA as a template to produce DNA

Reactions catalyzed by Reverse transcription

- RNA dependent DNA synthesis

- RNA degradation

- RNA dependent DNA synthesis

Telomeres

Protective, DNA proteins complexes at the end of our chromosomes

Telomorase

Reverse transcriptase enzyme that is responsible for elongation of the telomere region of the chromosome

(Consists of 3 protein domains and a RNA component)

The telomerase activity include?

1. The enzyme binds to the 3' end of the chromosome through complementary binding between the strand and the RNA component of the enzyme.

2. The telomerase extends the sequence 5'à 3'.

3. It then releases and translocate to the "new" 3' end to repeat the process.

4. Extension of the telomere is produced using a Primase and DNA polymerase

1st step of telomerase activity

The enzyme binds to the 3' end of the chromosome through complementary binding between the strand and the RNA component of the enzyme.

2nd step of telomerase activity

The telomerase extends the sequence 5'-> 3'.

3rd Step of telomerase activity

It then releases and translocate to the "new" 3' end to repeat the process.

4th step of telomerase activity

Extension of the telomere is produced using a Primase and DNA polymerase

RNA replicase

Uses RNA as a template to produce mRNA. Initiation of replication is mediated by a viral proteins genome liked primer followed by elongation