GENETIC TEST2

Central Dogma

• DNA replication

• translation

• translation

Template strand is also called

• Noncoding strand

• Antisense strand

Noncoding strand is also called

• Template strand

• Antisense strand

Antisense strand is also called

• Template strand

• Noncoding strand

Coding strand is also called

• Nontemplate Strand

• Sense strand

Nontemplate stand is also called

• Coding strand

• Sense strand

Sense strand is also called

• Coding strand

• Nontemplate strand

What is RBS?

Ribosome binding site on mRNA

What is an open complex?

• Once the TF binds, the TATA box is unwound

• RNAP uses it to initiate transcription

What is a closed complex?

RNAP binds to promoter (does not transcribe yet)

where are the 2 small DNA sites in the promoter, and what are they?

TATA box: -10bp

TTGACA - consensus sequence: -35bp

What is the core enzyme of the RNAP holoenzyme?

α2ββ’ω

• 2x alpha

• beta

• beta prime

• omega

What is the sigma factor of the RNAP holoenzyme?

σ

• sigma

• contains helix-turn-helix structure involved in tighter binding to DNA

Describe the initiation stage of bacterial transcription

• sigma factor slides along DNA and recognizes the promoter

• binds to the promoter (called closed complex)

• the open complex is made and short RNA is made

• the TATA box is opened, and the Open complex is formed

  • short RNA is made

Describe the elongation stage of bacterial transcription

• Sigma factor released and core enzyme is able to proceed down the DNA

• Open complex is 17 bp long

• RNA synthesis rate is ~43bp/s

What are the different types of bacterial termination

Rho-dependent termination

Rho-independent termination

What is rho dependent termination

• rho binds to rut (rho recognition site)

• stem loop forms and causes a pause

• rho catches up to open complex and separated RNA-DNA hybrid

What is rho independent termination

Uracil rich sequence located at 3’ end of RNA

Stem loop structure upstream of the uracil-rich sequence

What is TFIID

TATA-binding protein (TBP) and TBP associated factors (TAFs)

• TBP + TAF

What is TFIIB

• binds to TFIID and enabled RNAP II to bind to the core promoter

• helps TFIIE and TFIIH bind to RNAP II

what is TFIIF

• binds to RNAP II and plays a role in its ability to bind to TFIIB and core promoter

• helps TFIIE and TFIIH bind to RNAP II

What is TFIIE

Plays a role in formation and/or maintenance of open complex

what is TFIIH

a subunit protein that has multiple roles:

• Act as helicases and promote open complex formation

• Phosphorylate the carboxyl terminal domain (CTD) of RNAP II

• Interaction with TFIIB, allowing RNAP II to proceed to elongation

What is a mediator

• Multisubunit complex that mediates the effects of regulatory TF on function of RNAP II

• Can influence ability of TFIIH to phosphorylate CTD, and subunits within the mediator have the ability to phosphorylate CTD

• CTD phosphorylation is needed to release RNAP II from TFIIB, and mediator plays a key role in RNAP II to switch from initiation to elongation

How does RNAP move?

it moves from 3’ to 5’, synthesizing RNA in 5’ to 3’ using triphosphates as nucleotide precursors

Nuclear DNA is transcribed by _____

3 different RNAP

function of RNAP I

Transcribe all rRNA (except 5s)

function of RNAP II

• Transcribe all protein-encoding genes (structural, all mRNAs)

• Transcribes some snRNA genes for splicing

Function of RNAP III

• Transcribe all tRNA genes

• Transcribe 5S rRNA

• MicroRNA genes

Core promoter contains:

TATA box and transcriptional start

what is basal transcription

core promoter’s level of transcription

features of eukaryotic genes

• core promoter

• regulatory elements

cis-acting factors

DNA sequences that exert effect only over a particular gene

trans-acting factors

regulatory proteins that bind to such DNA sequences

what is required for eukaryotic basal transcription?

• RNAP II

• 5 GTPs

• Mediator complex

what does the mediator do?

• Large protein complex

• It mediated interactions between RNAP II and various regulatory TF that bind enhancers or silencers

• Subunit composition is complex and variable

• Core subunits partially wraps around RNAP II

• May phosphorylate the CTD of RNAP II and it may regulate the ability of TFIIH to phosphorylate the CTD

  • Plays a role in transcriptional initiation and elongation

allosteric model

transcriptional termination

• RNAP is destabilized and falls off

• Can be due to release of Elongation factors

Torpedo model

transcriptional termination

• Degradation of 5’ end that RNAP is transcribing until it catches up, causing termination

Colinearity of gene expression

sequence of codons in genes provides the instructions for the sequence of amino acids in polypeptides

RNA splicing occurs in

eukaryotes, and sometimes bacteria

how are nonstructural genes created?

they are transcribed as a long RNA, and then cleaved into small precursors