Cell Biology: Transcription, the Genetic Code, and Translation

Vocabulary practice flashcards covering eukaryotic and prokaryotic transcription, post-transcriptional processing, genetic code properties, and translation mechanisms.

Promoter

A cis element located in the DNA sequence at the $3'$ end of a gene's template strand where the initiation machinery assembles.

t f two d (TFIID)

A general transcription factor containing the TATA-binding protein subunit that binds first to the promoter's TATA box to help recruit RNA polymerase II.

t f two h (TFIIH)

A general transcription factor that acts as a helicase to unzip DNA and form the transcription bubble, and phosphorylates RNA polymerase to transition from initiation to elongation.

Sigma Subunit

A protein subunit in prokaryotes that binds to RNA polymerase to form the holoenzyme, enabling it to reliably locate and bind to the promoter.

Euchromatin

The accessible state of chromatin required at the promoter region so that transcription machinery can assemble.

Template Strand

The strand of DNA read by RNA polymerase in the $3'$ to $5'$ direction to build RNA in the $5'$ to $3'$ direction.

Terminator (Termination Sequence)

A cis element in DNA that, once transcribed, forms a hairpin loop followed by a string of uracils held by weak base pairings to adenines, causing the RNA to detach.

Five Prime ($5'$) Capping

The addition of a methyl-G nucleotide to the $5'$ end of eukaryotic pre-mRNA via a unique $5'$ to $5'$ bond, marking the site where ribosomes initiate translation.

Three Prime ($3'$) Tailing (Polyadenylation)

The post-transcriptional addition of a long string of adenine nucleotides to the $3'$ end of an mRNA transcript.

Splicing

The post-transcriptional modification process where non-coding introns are excised and protein-coding exons are ligated together.

Exon Junction Complexes

Protein complexes deposited where exons are ligated together that, along with cap-binding and poly-A tail-binding proteins, signal to nuclear pores that mRNA is mature.

Universal (Genetic Code Characteristic)

The property stating that with few exceptions, all prokaryotes and eukaryotes translate the same three-nucleotide codons into the identical amino acids (e.g., AUG coding for methionine).

Specific (Genetic Code Characteristic)

The property stating that a particular three-letter codon assignment is permanent and codes for only one specific amino acid (e.g., GAA only codes for glutamate).

Degenerate (Genetic Code Characteristic)

The property stating that multiple different codons can specify the same single amino acid (e.g., leucine having $6$ codons).

Reading Frame

One of three possible ways to chunk an uninterrupted single-stranded RNA sequence into sequential triplets of nucleotides.

Open Reading Frame (ORF)

The single correct reading frame of an mRNA molecule, typically identified empirically by researchers as the frame with the longest sequence between start and stop codons.

Anticodon

A three-nucleotide sequence situated on a tRNA molecule that base pairs complementarily to a specific codon on an mRNA molecule.

Acceptor End

The $3'$ terminal end of a tRNA molecule to which a specific amino acid is covalently attached.

tRNA Synthetase

One of $20$ enzymes that charges an uncharged tRNA by coupling it to its specific amino acid via a high-energy bond powered by breaking ATP down to AMP.

Nucleolus

The region within the nucleus containing rDNA where ribosomal RNA is transcribed and ribosomal subunits undergo partial assembly.

A Site (Aminoacyl Binding Site)

The ribosomal site where incoming charged aminoacyl-tRNAs enter and are tested for base pairing with the mRNA codon.

P Site (Peptidyl Binding Site)

The ribosomal site that holds the tRNA attached to the growing polypeptide chain.

E Site (Exit / Empty Site)

The ribosomal site where an uncharged tRNA that has transferred its amino acid is positioned before exiting the ribosome.

Scanning

The process where the small ribosomal subunit and initiator methionine-tRNA move along mRNA one nucleotide at a time from the $5'$ cap until encountering the AUG start codon.

Peptidyltransferase

A catalytic RNA molecule (ribozyme) located in the large ribosomal subunit that synthesizes peptide bonds between amino acids in the N-to-C direction.

Ribosomal Translocation

The two-part movement of the ribosome down mRNA by three nucleotides, wherein the large subunit moves first followed by the small subunit.

Release Factors

Proteins that enter the ribosomal A site upon encountering a stop codon, catalyzing the hydrolysis of the bond between the polypeptide and tRNA to terminate translation.

Five Prime Untranslated Region ($5'$ UTR)

The segment of mRNA preceding the start codon, which is constrained in length and typically around $200$ nucleotides long.

Polycistronic mRNA

A bacterial mRNA transcript containing coding sequences and instructions to synthesize multiple distinct proteins.

Monocistronic mRNA

A eukaryotic mRNA transcript containing the genetic sequence to encode only one single protein.

Schein Del Barneau Sequences

Internal ribosome binding sequences found on prokaryotic mRNA transcripts that allow ribosomes to bind directly and translate individual open reading frames.