Protein Synthesis, Structure, and Translation

Vocabulary practice flashcards covering protein structure, genetic code mechanics, translation initiation, elongation, termination, and post-translational modifications.

Translation

The biological process in which a linear sequence of codons in mRNA is converted into a linear sequence of amino acids to synthesize a protein.

Functional RNA

Classes of RNA that are not translated into proteins but perform cellular functions, notably rRNA and tRNA, which account for $95\%$ of total RNA in actively dividing eukaryotic cells.

Peptide bond

A covalent linkage formed between the amino group ($\text{NH}_2$) of one amino acid and the carboxyl group ($\text{COOH}$) of another, releasing one molecule of water ($\text{H}_2\text{O}$).

Primary structure

The linear sequence of amino acids in a polypeptide chain, extending from a free amine-terminal end to a free carboxyl acid-terminal end.

Secondary structure

Local geometric folding of a polypeptide backbone (such as $\alpha$ helices and $\beta$ pleated sheets) stabilized by intramolecular and intermolecular hydrogen bonding of amide groups.

Tertiary structure

The three-dimensional conformation of a single polypeptide chain formed by the folding of secondary structures through interactions such as salt bridges and disulfide bonds.

Salt bridge

An electrostatic interaction stabilizing protein tertiary structure that results from the neutralization between an acidic and a basic amino acid side chain.

Disulfide bond

A covalent bond in protein tertiary structure produced by the oxidation of sulfhydryl groups on two cysteine residues.

Quaternary structure

The structural level resulting from the association of two or more individual polypeptide chains or subunits, forming complexes such as homodimers, heterodimers, globular proteins, or fibrous proteins.

Protein domain

A continuous sequence and structural region within a protein associated with a distinct, defined biological function, typically encoded by a distinct exon.

Genetic code

The set of rules by which genetic information stored in nucleotide sequences (DNA or mRNA) is translated into proteins by living cells.

Codon

A specific sequence of three DNA or RNA nucleotides that corresponds to a particular amino acid or translation stop signal during protein synthesis.

Degeneracy

The property of the genetic code in which multiple different codons can specify the same amino acid, such as GAA and GAG both encoding glutamic acid.

Stop codons

The three terminal codons—UAG (amber), UGA (opal or umber), and UAA (ochre)—that signal the end of translation.

Transfer RNA (tRNA) structure

An adapter molecule exhibiting a cloverleaf arrangement with four double-helical stems and three single-stranded loops, containing an anticodon loop at one end and a $3^\prime$ amino acid attachment site at the other.

Aminoacyl-tRNA synthetase

An enzyme that attaches a specific amino acid to the $3^\prime$ hydroxyl terminus of its cognate tRNA through a two-step, ATP-dependent charging reaction; cells contain 20 distinct varieties, one for each amino acid.

Wobble

The ability of the nucleotide at the $5^\prime$ end of a tRNA anticodon to form alternative non-standard base pairings with the nucleotide at the $3^\prime$ end of an mRNA codon, permitting a single tRNA to recognize multiple codons.

Ribosome

A ribonucleoprotein machine consisting of one small and one large subunit composed of rRNA and proteins, responsible for synthesizing proteins by coordinating mRNA and tRNA interactions.

Ribosomal subunit composition

The structural makeup of the prokaryotic 70S ribosome (50S subunit containing 23S and 5S rRNAs plus 31 proteins; 30S subunit containing 16S rRNA plus 21 proteins) and the eukaryotic 80S ribosome (60S subunit containing 28S, 5.8S, and 5S rRNAs plus 49 proteins; 40S subunit containing 18S rRNA plus 33 proteins).

A (aminoacyl) site

The ribosomal site that receives the incoming aminoacyl-tRNA whose anticodon complements the codon presented in the small subunit.

P (peptidyl) site

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

E (exit) site

The ribosomal site that transiently retains the deacylated tRNA before it dissociates from the ribosome.

Decoding center

A region within the small ribosomal subunit made of rRNA that verifies correct codon-anticodon pairing before permitting an aminoacyl-tRNA to be accepted into the A site.

Peptidyltransferase center

The catalytic active site located in the large ribosomal subunit, composed of catalytic rRNA, that synthesizes peptide bonds between amino acids.

Shine-Dalgarno sequence

A conserved mRNA sequence located within the $5^\prime$ UTR of prokaryotes that base-pairs with 16S rRNA in the 30S subunit to position the initiator codon directly in the P site.

Prokaryotic initiation factors

Proteins (IF1, IF2, and IF3) essential for bacterial translation initiation; IF3 prevents premature association of the 30S and 50S subunits, while IF1 and IF2 ensure that only the initiator tRNA enters the P site.

Elongation factors (EF-Tu and EF-G)

Bacterial proteins involved in translation elongation; EF-Tu delivers aminoacyl-tRNA to the ribosomal A site, and EF-G facilitates ribosomal translocation along the mRNA.

Release factors

Proteins (such as bacterial RF1, RF2, and RF3) that bind stop codons at the A site to catalyze the cleavage of the peptidyl-tRNA bond and release the completed polypeptide chain.

Proteome

The entire complement of proteins expressed in an organism, organ, tissue, or cell at a given time.

Protein isoforms

Distinct but related functional forms of a protein produced from a single gene through alternative splicing of pre-mRNA, differing in their combination of functional domains.

Molecular chaperones

A ubiquitous family of proteins that facilitate the proper non-covalent folding, unfolding, assembly, or disassembly of other macromolecular structures without being components of the final active structure.

Phosphorylation

A reversible post-translational modification in which kinases covalently add a phosphate group to the hydroxyl group of serine, threonine, or tyrosine, and phosphatases remove it.

Ubiquitinylation

A post-translational modification in which the terminal glycine carboxyl group of activated ubiquitin forms an amide bond with the $\epsilon$-amine of a lysine residue on a target protein, marking it for degradation.

26S proteasome

A large multi-protein complex that targets ubiquitinylated proteins, recycles the ubiquitin molecules, and hydrolyzes the polypeptide substrate into oligopeptides.