Bio 400 final

Does RNA need a primer for transcription?

What are the three phases of the RNA transcription?

When looking at the DNA strand there are -34 or +34 for example (number doesn?t matter) what do they represent?

What is it that binds to the promoter sequence for Polymerases?

This is the ore enzyme complex, plus a sigma factor that binds to promoter sequences.

What is another name for sigma factor? And what is the most common in E. coli?

This is an extra sequence to help promote RNA pol recruitment; binds to flexible CTD of alpha subunit of core enzyme.

Describe the initiation stage of RNA pol?

Melting of the DNA duplex in the promoter is mediated by?

Where does the melting happen?

This promoter element can promote or discourage RNA pol binding via s factor, making promoters stronger or weaker?

The -10 motif where DNA melts is rich with what and why?

Fist steps of elongation: this domain is displaced by DNA duplex. Slightly negative like the DNA backbone and will only open when the charged active site arrives.

Initial to elongation: RNA strands up to 10bp are easy to make longer are harder. This blocks the RNA chair until it reaches 10bp. Must be displaced to make way for a longer RNA chain to proceed through the exit.

What are the ways to terminate transcription?

This method of termination involves making a stem and loop in the RAN transcript. Structure disrupts elongation by RNA pol, triggering release

RNA transcript has sequence (poorly defined) that recruits Rho ATPase (another hexamer). Rho uses energy from the ATP hydrolysis to disassemble RNA pol elongation complex.

What are some regulatory proteins?

Changes in protein conformation in response to binding another molecule.

DNA binding proteins that promote/repress RNA pol actively; these must identify and bind specific sequences, so transcription factors commonly bindin the major groove of DNA.

Region of DNA that directs RNA polymerase activity toward downstream coding sequences to be transcribed.

Region immediately upstream of coding sequence that most directly regulates RNA pol activity, mostly by physically positioning RNA pol.

DNA region that binds repressor proteins to inhibit transcription

Region of DNA downstream of coding sequence that directs RNA polymerase to stop transcription and release.

Multiple discrete protein coding sequences under control of a common promoter.

Eukaryotes transcription: What are the similarities to prokaryotes?

Eukaryotes transcription: What is different from prokaryotes?

What are some characteristics to the GTF?

Main focus on RNA transcription in Eukaryotes is on?

Eukaryotes transcription: describe the RNA pol II promoter site.

Eukaryotes transcription: what are all the components for the promoter site?

What is the Inr?

What is the BRE?

What is the TATA?

What is the TBP?

What is the DCE?

What is the DPE?

Eukaryotes transcription: transciption factor that contains TBP as subunit. Other subunits are TAFs. Is the first to bind ; provides a platform to recruit.

Eukaryotes transcription: Transcription factor that makes contacts with both TBP and DNA. Also contracts pol II. Bridge from TBP to pol II.

Eukaryotes transcription: transcription factor that enters the complex at the same time as pol II. Required before TFIIR and TFIIH can join.

Eukaryotes transcription: transcription factor that binds next and recruits TFIIH

Eukaryotes transcription: transcription factor that is helicase to unwind the DNA and has kinase to phosphorilare CTD of the pol II.

These are critical triggers for the initiation of transcription in eukaryotes.

Eukaryotes transcription: this helps position RNA pol II, integrates signals from many possible activators/repressors, etc.

Phosphorylation of the RNA pol II tail CTD controls many steps like?

What are the three steps of capping?

Eukaryotes transcription: what are the models of termination?

Eukaryotes transcription: mode of termination 5? to3? RNase enzyme attacks remain in transcript after cleavage. RNase enzyme ?bumps? RNA pol II and forces dissociation.

Eukaryotes transcription: mode of termination inherent dissociation when RNA transcription is shortened, conformational change in RNA pol.

Eukaryotes transcription: transcription activators almost always have at least 2 functional domains.

Eukaryotes transcription: promoters commonly have redundancies for?

Eukaryotes transcription: DNA binding domain example 1. Dimer of two long helices; look like pinchers. Hydrophobic side chains pack between the two helices at the dimer inaction interface. Both helices extend and occupy the major grooves on either side.

Eukaryotes transcription: DNA binding domain example 2. Another dimer. One helix stabilizes dimer interface. One helix fits into major groove, side chains identify specific DNA sequence.

Eukaryotes transcription: making gene sequences permanently inaccessible to transcription factors. Methylated cytosine in a promoter region.

Eukaryotes transcription: Methylated signals are often maintained as cells replicate. Freshly synthesized daughter strands would not be methylated, so duple is hemimethylated.

Eukaryotes transcription: enzymes probe for hemimethylated sites, add more methyl groups to local cytosines.

Eukaryotes transcription: basic mechanism of removing exons and introns. Splicing machinery.

Eukaryotes transcription: these are what code for proteins.

How are exons ad introns marked to guide splicing?

These proteins mark exons (short stretches)

The proteins tend to mark introns (long stretches)

What is the inventory of Mature RNA?

What is the difference between Prok and Ek mRNA?

Big cytotoxic ribonucleoprotein complexes that execute translation

What are the parts of the ribosome?

How fast is transcription?

How fast is translation?

Adaptor molecules to connect specific codons to specific amino acids.

This is in prokaryotes that is immediately upstream of start codon AUG

Pairing of 16s rRNA to RBS sequence positions the ribosome P-site?

Initiator tRNA (tRNAi). This has just one codon.

Determine the reading from of a coding sequence

Initiator amino acids: Prokaryote and eukaryote

These help prep he small subunit in Prok. Ribosomes to initiate translation.

How my different Ifs are there?

This IF blocks the big subunit assembly

This IF blocks A-site

This IF helps recruit initiator tRNA; blocks non-initiator tRNAs ? Gtpase

Prok: Phase of translation 30s initiation complex. Small subunit, mRNA, fMet-tRNAi, IF1-3

Prok: phase of translation. 30s initiation complex shed IF3. Big sub unit assembles. Assembly triggers GTP hydrolysis by IF2. IF1 and 2 exit. A-site ready

Initiation in EUK: two sets of eIFs doing two jobs?

There are many components for the prep of initiation in EUK they have some jobs what is it?

EUK: mRNA preparations. Tell meeessss?

EUK: elongation. These proofread the codon-anticodon pairing

EUK: elongation. These power translocation

EUK: this resets the ribsomal complex after a peptidyletransferase reaction

Often calla a robot witch RNA molecule whose #D folding creates a binding pocket for a specific ligand; naturally occurring riboswitches frequently bind to a molecule related to function of the protein encoded by the mRNA

An apt amber (RNAmolecule)that posses catalytic activity, so it can covert substrate into product.

Bacterial/prokaryotic, short RNA that binds to protein ormRNA to regulate function. Typically 80 to 110 bases of non-coding sequences.

Eukaryotic, process whereby double-stranded RNA sufficient length is targeted for destruction (by Dicer), the resulting cleavage products are used to probe and destroy more mRNA of compatible sequence by 9RISC complex)

Eukaryotic, endogenously produced (chromomally encoded) short RNA molecule that can base pair with mRNA for post-transcriptional regulation of gene expression.

Same as miRNA, but exogenously produced and delivered to cells/organism, typically with the purpose of triggering RNAi for a selected gene/mRNA

Bind a lot of common metabolites. MRNA sequence makes predictable 3D structure based on intramolecular base pairing. Ligand is often a substrate or product of the enzyme encoded by the mRNA. Translation can be inhibited or activated.

What happens when a riboswitch binds its ligand molecule?

Thought to have evolved as a defense mechanism vs retroviruses, many of which dsRNA genomes.

This loads siRNA from dicer cleavage, surveys cytoskeleton fro complimentary RNA molecules to destroy.

In many EUK this extends the siRNA using the complimentary, longer RNA as a template, making a longer dsRNA

Where do miRNA come from?

Encodes a protein that, if over-produced, promotes cancer

MicroRNA reduces abundance or translation of onogenic mRNA