2 and 3, Transcription, Translation, and Protein Trafficking

Vocabulary practice flashcards covering transcription, mRNA processing, translation mechanisms, genetic code features, ribosomal sites, antibiotic actions, protein post-translational modifications, and cellular trafficking pathways based on Dr. Jonathan Lerner's lecture.

Central Dogma of Molecular Biology

The framework describing the unidirectional flow of genetic information from DNA to RNA via transcription, and from RNA to protein via translation.

Messenger RNA (mRNA)

Single-stranded transcripts that carry genetic instructions from DNA in the nucleus to the cytosol for protein synthesis, representing approximately $5\%$ of total cellular RNA.

Ribosomal RNA (rRNA)

Non-coding RNA molecules that associate with proteins to form ribosomes; they are the most abundant RNA type, representing approximately $80\%$ of total cellular RNA.

Transfer RNA (tRNA)

Non-coding RNA molecules that carry specific amino acids to the ribosome during translation, representing approximately $15\%$ of total cellular RNA.

Xist

A $19\,\text{kb}$ long noncoding RNA that interacts with one X chromosome to induce its inactivation for dosage compensation in mammals.

RNA Polymerase I

A eukaryotic DNA-dependent RNA polymerase that synthesizes most rRNAs in the nucleolus.

RNA Polymerase II

A eukaryotic DNA-dependent RNA polymerase that synthesizes messenger RNAs (mRNAs) and certain noncoding RNAs, including miRNAs.

RNA Polymerase III

A eukaryotic DNA-dependent RNA polymerase responsible for synthesizing tRNAs and some rRNAs.

Pre-Initiation Complex (PIC)

A protein complex composed of six general transcription factors (TFIIA, TFIIB, TFIID, TFIIF, TFIIE, and TFIIH) that recruits RNA polymerase II to the promoter at the transcription start site.

TFIIH

A general transcription factor with helicase activity (XPB/XPD) to unwind DNA and kinase activity (CDK7) to phosphorylate the C-terminal domain of RNA polymerase II, allowing promoter clearance.

Polyadenylation Signal Sequence

An AAUAAA consensus sequence in the $3'$ UTR of pre-mRNA that signals site-specific cleavage and subsequent addition of a poly(A) tail.

5' Cap

A modified 7-methylguanosine nucleotide added to the $5'$ end of nascent pre-mRNA that protects it from exonuclease degradation and facilitates ribosome binding.

Poly(A) Tail

A stretch of up to approximately $250$ adenine ribonucleotides added to the $3'$ end of pre-mRNA that facilitates nuclear export, mRNA stability, and translation.

Spliceosome

A large ribonucleoprotein complex composed of five small nuclear RNAs (snRNAs) and over $50$ proteins (snRNPs) that removes introns and joins exons in pre-mRNA.

Exon Skipping

A splicing mutation outcome where an exon adjacent to a mutated splice site is omitted from the mature mRNA.

Intron Retention

A splicing mutation outcome where an intron adjacent to a mutated splice site is incorrectly retained in the mature mRNA.

Cryptic Splice Site

An abnormal splice site activated by a mutation, leading to improper exon/intron joining and truncated exons.

Codon

A sequence of $3$ nucleotides in mRNA, written and read in the $5'$ to $3'$ direction, specifying a specific amino acid or translation stop signal ($64$ total possible codons).

AUG

The start codon that specifies methionine and serves as the universal signal to initiate protein translation.

Stop Codons

The three codons (UAG, UGA, and UAA) that do not code for amino acids but signal the termination of translation.

Degenerate (Genetic Code)

The property of the genetic code wherein multiple distinct codons can specify the same single amino acid.

Aminoacyl-tRNA Synthetases

Enzymes that catalyze the specific attachment of each amino acid to its corresponding tRNA at the $3'$ end.

A Site (Ribosome)

The aminoacyl binding site on the ribosome that receives incoming aminoacyl-tRNA carrying the next amino acid.

P Site (Ribosome)

The peptidyl binding site on the ribosome that holds the peptidyl-tRNA attached to the growing polypeptide chain.

E Site (Ribosome)

The exit site on the ribosome where uncharged tRNAs reside before being released.

eukaryotic Initiation Factors (eIFs)

A group of at least $10$ protein factors required in eukaryotes to assemble the $40\text{S}$ subunit, initiator tRNA, and $60\text{S}$ subunit onto mRNA during translation initiation.

eukaryotic Release Factor (eRF)

A protein factor that binds to a stop codon in the A site of the ribosome, causing the newly synthesized polypeptide chain to be released.

Streptomycin

An antibiotic that targets bacterial ribosomes to inhibit translation initiation and induce misreading of the mRNA.

Tetracycline

An antibiotic that binds to the $30\text{S}$ subunit of bacterial ribosomes, preventing incoming aminoacyl-tRNAs from binding to the A site.

Erythromycin

An antibiotic that binds to the $50\text{S}$ subunit of bacterial ribosomes and inhibits translocation during elongation.

Signal Recognition Particle (SRP)

A cytosolic protein-RNA complex that binds the N-terminal leader sequence of a growing polypeptide and directs the ribosome complex to the ER membrane receptor.

N-linked Glycosylation

A co-translational modification in the ER lumen where a $14$-sugar branched oligosaccharide is transferred from dolichol to an asparagine (Asn) residue within Asn-X-Ser or Asn-X-Thr sequences.

Mannose-6-phosphate

A post-translational sugar modification added in the Golgi complex that targets newly synthesized acid hydrolase precursor proteins to lysosomes.

Constitutive Secretion

A continuous secretory pathway where transport vesicles budding from the trans-Golgi network fuse with the plasma membrane to release contents extracellularly without requiring an external signal.

Regulated Secretion

A secretory pathway where proteins are stored in cytoplasmic secretory granules until an extracellular signal triggers exocytosis.

Preproinsulin

The initial translation product of the insulin gene, containing an N-terminal leader signal peptide that directs it into the ER lumen.

Proinsulin

The precursor protein formed in the ER lumen after proteolytic cleavage of the N-terminal signal peptide from preproinsulin.

Insulin Synthesis and Secretion Pathway

The multi-step pathway involving nuclear transcription/splicing, ER translation/signal peptide removal (preproinsulin to proinsulin), Golgi cleavage into mature insulin and C-peptide, and regulated secretion from vesicles.