RNA Polymerase, Transcription, and Translation Mechanisms in Molecular Biology

RNA polymerase

Synthesizes RNA from a DNA template during transcription; involved in transcription initiation, elongation, and termination.

Nucleosome Remodeling Complexes

Use ATP to reposition or remove nucleosomes, making DNA accessible for transcription, replication, and repair.

Histone Chaperone Proteins

Assist in assembling and disassembling nucleosomes without covalent modification; important in chromatin assembly and DNA replication.

Histone modifying enzymes

Add or remove chemical groups (acetyl, methyl, phosphate) to histones to regulate chromatin structure and gene expression.

RNA Polymerase I, II, III, IV, V

Pol I synthesizes rRNA; Pol II synthesizes mRNA and snRNA; Pol III synthesizes tRNA and 5S rRNA; Pol IV/V in plants regulate siRNA-mediated gene silencing.

Sigma Factor

Directs bacterial RNA polymerase to specific promoter sequences; binds −10 and −35 consensus regions to initiate transcription.

Mediator Complex

Bridges transcription factors and RNA Polymerase II to regulate eukaryotic gene transcription initiation.

TATA Binding Protein (TBP)

Binds TATA box in eukaryotic promoters; essential for pre-initiation complex formation.

General Transcription Factors (TFIID, TFIIB, TFIIA, TFIIF, TFIIE, TFIIH)

Work together to position RNA Pol II at promoters and unwind DNA to start transcription.

Bacteriophage lambda cI, cII, Cro, RecA

Regulate switch between lysogenic and lytic cycles; RecA triggers cleavage of cI during SOS response to induce lysis.

Bacteriophage lambda N and Q proteins

Antiterminators that allow RNA polymerase to read through termination sites and express late phage genes.

snRNPs (U1, U2, U4, U5, U6), U2AF65/35, BBP

Form the spliceosome to remove introns via two transesterification reactions during RNA splicing.

E. coli DNA gyrase and Topoisomerase I

Gyrase introduces negative supercoils; Topoisomerase I relaxes them to maintain DNA topology.

Bacterial Rho enzyme

Helicase that terminates transcription in Rho-dependent termination.

Bacterial RF1, RF2, RF3

Recognize stop codons and release polypeptide chains during bacterial translation termination.

Eukaryotic eRF1

Recognizes stop codons and promotes release of nascent peptide from ribosome.

Eukaryotic eRF3-GTP

GTPase that assists eRF1 in translation termination and peptide release.

eIF4E, eIF4G, PABPs, PIC

Bind mRNA cap and poly(A) tail, bringing mRNA and ribosome together for translation initiation.

Gcn2 and tRNAiMet

Gcn2 senses uncharged tRNA to downregulate global translation; tRNAiMet initiates translation.

RelA

Synthesizes (p)ppGpp ('magic spot') during amino acid starvation to regulate bacterial translation.

eEF2

An elongation factor that moves the ribosome and delivers aminoacyl-tRNAs during translation elongation.

eEF1A-GTP

An elongation factor that moves the ribosome and delivers aminoacyl-tRNAs during translation elongation.

Ribosome recycling factors

Disassemble post-termination ribosome complexes so they can be reused for new translation cycles.

Transcription initiation

RNA polymerase binds promoter, elongates RNA chain, and stops at termination signal; mechanisms differ between bacteria and eukaryotes.

Promoter escape

RNA polymerase breaks free from promoter after forming short abortive transcripts.

RNA transcription elongation reaction

Nucleotides added to 3' end of RNA; pyrophosphate released each step.

5' capping

Addition of 7-methylguanosine cap to nascent RNA for stability and translation initiation.

3' to 5' proofreading

RNA polymerase removes mismatched bases to ensure fidelity.

Allosteric transcription termination

Conformational change in RNA Pol II and loss of elongation factors cause termination.

Torpedo model

Exonuclease degrades residual RNA after cleavage, dislodging RNA Pol II to terminate transcription.

Allosteric effectors

Molecules that change enzyme activity by binding at a regulatory site distinct from the active site.

Bacteriophage lytic cycle

Produces new phages and lyses cell.

Bacteriophage lysogenic cycle

Integrates phage DNA into host genome.

Lambda transcription initiation

Controlled by cI, cII, Cro, and Q proteins to decide between lysogeny and lysis.

5' capping steps

Triphosphatase, guanylyltransferase, and methyltransferase enzymes act sequentially.

Eukaryotic intron splicing

snRNPs catalyze two transesterification reactions to excise introns and ligate exons.

Nonsense mediated decay

Removes mRNAs with premature stop codons.

No-go decay

Targets stalled ribosomes.

Bacterial termination

Intrinsic relies on hairpin + U-rich region; Rho-dependent uses Rho helicase.

Transcriptional attenuation

Regulation by premature termination in response to metabolite levels.

Bacterial translation termination

Stop codons recognized by RF1/RF2 and assisted by RF3.

Eukaryotic NMD

Degrades faulty mRNAs containing premature stop codons.

Translation regulation

Global control via factors like Gcn2; specific mRNA regulation via 5'/3' UTRs and microRNAs.

Viral translation hijacking

Viruses degrade host mRNAs or alter initiation factors to favor viral mRNA translation.

Translation elongation regulation

Factors like eEF2 are regulated via phosphorylation.

Ribosome recycling

Post-termination complex disassembled for new rounds of translation.