bio

Central Dogma

The flow of genetic information from DNA → RNA → Protein

Transcription

The process of synthesizing RNA from a DNA template

Genome

The complete set of DNA in an organism

Transcriptome

The complete set of RNA transcripts present in a cell at a given time

RNA

Ribonucleic acid; contains ribose sugar and uracil

Uracil

Nitrogenous base used in RNA instead of thymine

Template Strand

DNA strand read by RNA polymerase during transcription

Coding Strand

DNA strand with the same sequence as RNA except T replaces U

RNA Polymerase

Enzyme that synthesizes RNA from a DNA template

Transcription Bubble

Region where DNA strands separate during transcription

RNA-DNA Hybrid

Short region where RNA remains temporarily paired with DNA template

Supercoiling

Twisting of DNA caused during transcription

Sigma Factor

Bacterial protein that directs RNA polymerase to promoters

σ70

Sigma factor for housekeeping genes

σ38

Sigma factor activated during starvation

σ32

Sigma factor activated during heat shock

σ54

Sigma factor involved in nitrogen metabolism

Promoter

DNA sequence where transcription begins

Consensus Sequence

Conserved promoter sequence recognized by sigma factors

-35 Region

Promoter sequence recognized by bacterial sigma factors

-10 Region

TATAAT-containing bacterial promoter sequence

UP Element

AT-rich promoter region that increases transcription

Footprinting Assay

Technique used to identify protein-binding sites on DNA

Closed Complex

RNA polymerase bound to double-stranded DNA promoter

Open Complex

DNA strands separated and loaded into RNA polymerase

Abortive Initiation

Production of short unstable RNA fragments during initiation

Promoter Clearance

Release of sigma factor allowing elongation to begin

Elongation

Stage where RNA polymerase synthesizes RNA

DNA Entry Channel

Polymerase channel where DNA enters

RNA Exit Channel

Polymerase channel where RNA exits

NTP Entry Channel

Polymerase channel where nucleotides enter

Kinetic Proofreading

Error correction using pyrophosphorolysis after mismatches

Pyrophosphorolysis

Reverse reaction removing incorrectly added nucleotides

Nucleolytic Proofreading

Error correction involving RNA cleavage after polymerase backtracking

Backtracking

Reverse movement of RNA polymerase after mismatch detection

Rho-Independent Termination

Bacterial termination using RNA hairpin and U-rich sequence

Hairpin Loop

RNA secondary structure important in termination

Rho-Dependent Termination

Bacterial termination requiring rho helicase

rut Site

RNA sequence where rho binds

Rho Helicase

ATP-dependent helicase involved in rho-dependent termination

Helicase

Enzyme that unwinds nucleic acids

ATP Hydrolysis

Breakdown of ATP to release energy

RNA Polymerase I

Eukaryotic polymerase that synthesizes rRNA

RNA Polymerase II

Eukaryotic polymerase that synthesizes mRNA

RNA Polymerase III

Eukaryotic polymerase that synthesizes tRNA and 5S rRNA

CTD (C-Terminal Domain)

Tail of RNA Pol II that recruits transcription factors

TATA Box

Promoter sequence recognized by TBP

TBP (TATA-Binding Protein)

Protein that binds the TATA box

TAFs (TBP-Associated Factors)

Proteins assisting TBP function

TFIID

Transcription factor complex containing TBP and TAFs

TFIIB

Transcription factor that binds the BRE sequence

BRE

TFIIB recognition element in promoters

Inr (Initiator Element)

Promoter sequence at transcription start site

DPE (Downstream Promoter Element)

Promoter element downstream of start site

UBF (Upstream Binding Factor)

Protein binding Pol I promoters

UCE (Upstream Control Element)

Promoter sequence for RNA Pol I

SL1 Complex

Pol I transcription complex containing TBP and TAFs

TFIIIB

Transcription factor required for Pol III initiation

TFIIIC

Transcription factor that binds downstream Pol III promoter regions

Box A

Internal promoter element for Pol III genes

Box B

Internal promoter element for Pol III genes

Mediator Complex

Large protein complex linking activators to transcription machinery

Preinitiation Complex

Assembly of transcription factors before transcription begins

Initiation Complex

Open transcription complex ready for RNA synthesis

CTD Phosphorylation

Modification of Pol II CTD allowing promoter escape

Elongation Factors

Proteins assisting RNA elongation in eukaryotes

Torpedo Model

Mechanism of Pol II termination involving Xrn2 exonuclease

AAUAAA Signal

Polyadenylation signal in eukaryotic mRNA

CPSF

Cleavage and polyadenylation specificity factor