Transcription and RNA Modifications Overview

Gene

Segment of DNA coding for a functional product.

RNA

Final product of some genes or translated into proteins.

Transcription

Process of copying DNA into RNA.

mRNA

Messenger RNA that encodes amino acid sequences.

Central Dogma

Path from gene to protein to trait.

Transcription Factors

Proteins that regulate transcription rate.

Promoter

DNA sequence initiating transcription process.

Terminator

Sequence specifying the end of transcription.

Regulatory Sequences

Sites controlling transcription via protein interaction.

Ribosomal-binding Site

Region where ribosome attaches to mRNA.

Codons

Triplets of nucleotides coding for amino acids.

Start Codon

Initiates translation of mRNA into protein.

Stop Codon

Signals termination of protein synthesis.

Initiation

First stage of transcription; RNA polymerase binds.

Elongation

RNA polymerase synthesizes RNA during transcription.

Termination

RNA polymerase stops synthesizing RNA.

Structural Genes

Genes encoding polypeptides and proteins.

Open Complex

Formed during RNA synthesis in elongation.

Bacterial Promoter

Specific DNA sequence for transcription initiation in bacteria.

Negative Numbering

System for numbering bases in promoter sequences.

E. coli

Bacterium used in early transcription studies.

Meselson and Jacob

Researchers who linked RNA to protein synthesis.

Promoter sequences

Regions critical for initiating transcription.

-35 sequence

DNA sequence located 35 bases upstream.

-10 sequence

Also known as Pribnow box, crucial for binding.

Consensus sequence

Most common bases enhancing transcription initiation.

RNA Polymerase

Enzyme synthesizing RNA from DNA template.

Holoenzyme

Complete RNA polymerase complex with all subunits.

Core enzyme

RNA polymerase without sigma factor subunit.

Sigma factor

Subunit that recognizes promoter regions in DNA.

Open complex

Formed when DNA unwinds at the promoter.

Closed complex

Formation after sigma factor binds to promoter.

Initiation

First step of transcription, forming RNA strand.

Elongation

RNA strand synthesis occurs in 5' to 3' direction.

Template strand

DNA strand used for RNA synthesis.

Coding strand

DNA strand with same sequence as RNA transcript.

RNA synthesis rate

RNA is synthesized at 43 nucleotides per second.

Termination

End of RNA synthesis, releasing RNA and polymerase.

Rho-dependent termination

Termination requiring rho protein as helicase.

Helix-turn-helix motif

Structure enhancing sigma factor binding to DNA.

TATAAT box

Specific sequence in the -10 region for initiation.

Open complex length

Approximately 17 base pairs long during transcription.

Antisense strand

Another name for the template strand in transcription.

Sense strand

Another name for the coding strand in transcription.

Rho-independent termination

Termination without rho protein involvement.

Rho-dependent termination

Requires rho protein to terminate transcription.

Rut site

Recognition site for rho protein on RNA.

Stem-loop structure

RNA secondary structure causing polymerase pausing.

Eukaryotic RNA polymerases

Three types transcribing different RNA molecules.

RNA pol I

Transcribes all rRNA genes except 5S rRNA.

RNA pol II

Transcribes protein-coding genes and most snRNA.

RNA pol III

Transcribes tRNA genes and some non-coding RNAs.

TATA box

Core promoter element crucial for transcription initiation.

Basal transcription

Low-level transcription from core promoter alone.

Cis-acting elements

DNA sequences affecting transcription of nearby genes.

Trans-acting factors

Regulatory proteins influencing gene expression from afar.

Enhancers

Cis-acting elements that stimulate transcription.

Silencers

Cis-acting elements that reduce transcription.

General transcription factors

Proteins required for RNA polymerase II activity.

Mediator complex

Protein complex facilitating interactions in transcription initiation.

Open complex

Formed when RNA polymerase binds to the promoter.

Transcriptional start site

Location where transcription begins on DNA.

Preinitiation complex

Closed complex of proteins before transcription starts.

TFIID

Complex that binds to TATA box during initiation.

TBP

TATA-binding protein, part of TFIID complex.

TAFs

TBP-associated factors aiding in transcription initiation.

Phosphorylation

Addition of phosphate groups to proteins.

C-terminal domain (CTD)

Region of RNA Pol II essential for transcription elongation.

Mediator

Protein complex facilitating RNA Pol II interactions.

TFIIH

Transcription factor involved in CTD phosphorylation.

Transcriptional initiation

Start of RNA synthesis by RNA polymerase.

Transcriptional elongation

Phase where RNA polymerase synthesizes RNA.

mRNA termination

Process where transcription ends at polyA signal.

Allosteric Model

RNA cutting leads to transcription complex disassociation.

Torpedo Model

Exonuclease causes RNA polymerase disassociation post-cut.

RNA modifications

Chemical alterations to RNA molecules post-transcription.

Cap and tail

5' cap and 3' polyA tail modifications for mRNA.

RNA editing

Process altering nucleotide sequences in RNA.

Collinearity

Direct correspondence between DNA codons and polypeptides.

rRNA

Ribosomal RNA, essential for ribosome structure.

Nucleolus

Nucleus region for rRNA transcription and processing.

tRNA processing

Cleavage of tRNA precursors into functional tRNAs.

RNaseP

Endonuclease ribozyme involved in tRNA maturation.

Exons

Coding sequences retained after RNA splicing.

Introns

Non-coding sequences removed during RNA splicing.

Splicing

Joining of exons after intron removal.

Group I intron splicing

Self-splicing mechanism found in certain rRNA genes.

Group II intron splicing

Self-splicing mechanism in mitochondrial and chloroplast DNA.

Pre-mRNA spliceosome

Complex facilitating splicing in eukaryotic protein-coding genes.

Self-splicing

Introns splice themselves without enzymes.

Ribozyme

RNA that catalyzes its own splicing.

Group I Introns

Introns that splice using a specific mechanism.

Group II Introns

Introns that splice via a lariat structure.

Maturases

Proteins that enhance splicing rates in vivo.

Spliceosome

Complex that splices pre-mRNA in eukaryotes.

snRNPs

Small nuclear RNA and proteins in spliceosome.

Intron-exon boundaries

Sequences that define splicing sites.

Lariat structure

Loop formed by intron during splicing.

U6 subunit

Ribozyme that cleaves RNA and reconnects exons.

Metalloribozyme

Ribozyme requiring Mg2+ ions for activity.