Protein Biosynthesis and Translation Vocabulary

Vocabulary practice flashcards covering terms, factors, enzymes, structural domains, ribosomal sites, and translation inhibitors from the protein synthesis lecture notes.

Codon

A sequence of three consecutive nucleotides in mRNA that specifies a particular amino acid or translation stop signal, always read in the $5' \rightarrow 3'$ direction.

Open Reading Frame (ORF)

A continuous series of codons in a nucleic acid sequence that begins with a start codon (AUG) and ends with a stop codon, translated in the N-to-C direction.

Transfer RNA (tRNA)

An adapter RNA molecule, typically 72 to 93 nucleotides long with an L-shaped 3D structure, that connects mRNA codon sequence information to a specific amino acid.

DHU Loop

A loop structure in tRNA containing dihydrouridine that serves as the primary recognition site for aminoacyl-tRNA synthetase enzymes.

Aminoacyl-tRNA Synthetase (AARS)

An enzyme that attaches a specific amino acid to its corresponding tRNA molecule via an ester linkage, serving as the true translator of the genetic code.

Aminoacyl Adenylate (Aminoacyl-AMP)

An activated intermediate formed during the first step of amino acid activation when an amino acid reacts with ATP, releasing inorganic pyrophosphate ($PP_i$).

Class I Aminoacyl-tRNA Synthetase

A class of monomeric AARS enzymes that bind ATP and the tRNA CCA arm in a hairpin conformation, acylating the 2'-hydroxyl group of the terminal adenosine.

Class II Aminoacyl-tRNA Synthetase

A class of dimeric or multimeric AARS enzymes that bind ATP and the tRNA CCA arm in a helical conformation, acylating the 3'-hydroxyl group of the terminal adenosine (except for tRNAPhe enzyme).

Wobble Hypothesis

A model explaining how the first two bases of an mRNA codon form strong standard base pairs with the tRNA anticodon, while the third base forms looser, non-traditional base pairs.

Inosine (I)

A modified, non-traditional nucleoside formed by the deamination of adenosine that, when located at the first position of a tRNA anticodon, can base-pair with U, C, or A.

Shine-Dalgarno Sequence

A consensus mRNA sequence upstream of the start codon in bacteria that base-pairs with 16S rRNA in the 30S ribosomal subunit to align the translation initiation site.

IF-1 (Initiation Factor 1)

A bacterial translation initiation protein that prevents premature binding of tRNAs to the ribosomal A site and establishes the reading frame.

IF-2 (Initiation Factor 2)

A GTP-binding protein that facilitates the binding of charged initiator tRNA ($\text{fMet-tRNA}_f^{\text{Met}}$) to the 30S ribosomal subunit.

IF-3 (Initiation Factor 3)

A bacterial initiation factor that binds to the 30S ribosomal subunit to prevent premature 50S subunit association and enhances P-site specificity for fMet-tRNA.

EF-Tu (Elongation Factor Thermo Unstable)

A GTPase elongation factor that binds aminoacyl-tRNA and delivers it to the vacant A site of the ribosome during polypeptide elongation.

EF-G (Elongation Factor G)

A GTPase elongation factor that promotes the translocation of mRNA and tRNAs by one codon toward the $3'$ direction following peptide bond formation.

Ribosomal A Site

The aminoacyl site of the ribosome that receives incoming activated aminoacyl-tRNA molecules during polypeptide elongation.

Ribosomal P Site

The peptidyl site of the ribosome that holds the tRNA carrying the growing polypeptide chain.

Ribosomal E Site

The exit site of the ribosome where uncharged tRNA resides briefly prior to its release.

Peptidyl Transferase

A ribozyme catalytic activity located in the 23S rRNA of the 50S ribosomal subunit that catalyzes peptide bond formation between amino acids.

Release Factor (RF)

A protein that binds to a stop codon at the ribosomal A site during translation termination, prompting GTP hydrolysis and the release of the synthesized polypeptide.

Polysome

A complex comprising an mRNA molecule bound to multiple ribosomes actively translating polypeptides simultaneously.

Streptomycin

An aminoglycoside antibiotic that alters the structure of the bacterial 30S subunit, inhibiting initiation and causing mRNA misreading.

Tetracycline

An antibiotic that binds to the bacterial 30S subunit to prevent aminoacyl-tRNA binding at the A site, forcing EF-Tu to waste energy by hydrolyzing GTP.

Chloramphenicol

An antibiotic that binds to the bacterial 50S ribosomal subunit and inhibits peptidyl transferase activity.

Erythromycin

A macrolide antibiotic that binds to the bacterial 50S ribosomal subunit and prevents ribosome translocation.

Azithromycin

A semi-synthetic antibiotic derived from erythromycin A, discovered by Pliva in 1980, that binds to the bacterial 50S subunit to block translocation.

Puromycin

An inhibitor and structural analog of aminoacyl-tRNA that binds to the ribosomal A site and causes premature polypeptide chain termination in prokaryotes and eukaryotes.

Cycloheximide

An antibiotic that specifically inhibits translation translocation in eukaryotic ribosomes.

Ricin

A potent N-glycosidase toxin from castor oil plant seeds that inactivates the 28S rRNA subunit by removing a critical adenine base, blocking elongation factor binding.

\alpha-Sarcin

A ribonuclease toxin secreted by fungi that inhibits protein synthesis by cleaving a single phosphodiester bond in 28S rRNA.