Chapter 15: The Genetic Code and Translation

Vocabulary practice flashcards covering the genetic code, protein structure, tRNA charging, and the stages of translation (initiation, elongation, termination, and surveillance) based on Chapter 15 of Genetics: A Conceptual Approach.

One Gene, One Enzyme Hypothesis

The hypothesis formulated by George Beadle and Edward Tatum proposing that genes function by encoding enzymes, and that each individual gene encodes a separate enzyme.

One Gene, One Polypeptide Hypothesis

The refined version of Beadle and Tatum's hypothesis recognizing that many enzymes and proteins consist of multiple distinct polypeptide chains, each encoded by a separate gene.

Auxotroph

A mutant strain of an organism, such as Neurospora, that is unable to synthesize essential nutritional compounds and requires specific nutrient supplementation to grow.

Minimal Medium

A culture medium containing only the basic nutrients that wild-type organisms need to survive, on which auxotrophic mutants cannot grow without specific supplementation.

Primary Structure

The first level of protein structure, consisting of the unique linear sequence of amino acids joined together by peptide bonds.

Secondary Structure

The local spatial conformation of a polypeptide chain, such as an alpha helix, formed by interactions and hydrogen bonding between amino acids.

Tertiary Structure

The overall three-dimensional folding and geometric shape of a single complete polypeptide chain beyond its secondary structure.

Quaternary Structure

The macromolecular structural organization formed by the association and spatial arrangement of two or more individual polypeptide chains.

Peptide Bond

The covalent bond that links two amino acids together, formed between the carboxyl group of one amino acid and the amino group of another with the release of a water molecule ($H_2O$).

Radical Group (R Group)

The variable side chain attached to the central alpha carbon ($C_\alpha$) of an amino acid that confers its distinctive chemical properties and identity.

Codon

The fundamental unit of the genetic code, consisting of a triplet of three adjacent RNA nucleotides that specifies a single amino acid or a translation stop signal.

Sense Codon

A codon in mRNA that specifies a particular amino acid; there are $61$ sense codons in the standard genetic code.

Degenerate Code

A structural property of the genetic code where multiple different codons specify the same amino acid, containing more physical states than strictly necessary to encode the $20$ amino acids.

Synonymous Codons

Different codons that specify the exact same amino acid, such as UUU and UUC both specifying phenylalanine.

Isoaccepting tRNAs

Different transfer RNA molecules that bind and carry the same amino acid but possess different anticodon sequences.

Wobble Hypothesis

The principle stating that non-standard, flexible base pairing can occur between the third ($3'$) base of an mRNA codon and the first ($5'$) base of a tRNA anticodon.

Inosine

A modified base found at the first position ($5'$ end) of certain tRNA anticodons that can pair with adenine ($A$), uracil ($U$), or cytosine ($C$) at the third position of a codon.

Reading Frame

The specific grouping of nucleotides into consecutive triplets during translation; any single-stranded nucleotide sequence has three potential ways to be read.

Nonoverlapping Code

A genetic coding system where each single nucleotide is part of only one codon and is not shared between adjacent codons.

Initiation Codon

The first codon of mRNA translated by a ribosome (most commonly AUG), which establishes the correct reading frame and codes for methionine.

$$N\text{-formylmethionine (fMet)}$$

A chemically modified methionine derivative that serves exclusively as the initial amino acid incorporated into bacterial polypeptides during translation initiation.

$$tRNA_i^{fMet}$$

The specialized initiator tRNA in bacteria that carries $N\text{-formylmethionine}$ to the initiation codon to initiate translation.

Termination Codons

The three codons (UAA, UAG, and UGA) that signal the end of translation and the release of the polypeptide chain, for which no normal tRNAs possess complementary anticodons.

Universality of the Code

The principle that each codon specifies the exact same amino acid across virtually all living organisms, with only minor deviations occurring in specific organellar or nuclear genomes.

tRNA Charging

The two-step, ATP-dependent chemical process in which an amino acid is covalently attached to the $3'$ acceptor stem of its corresponding tRNA molecule.

Aminoacyl-tRNA Synthetase

An enzyme that specifically attaches a particular amino acid to its cognate tRNA; exactly $20$ distinct varieties exist within a cell, one for each standard amino acid.

Acceptor Stem

The site at the $3'$ end of a tRNA molecule possessing the conserved CCA nucleotide sequence to which an amino acid is covalently linked.

Anticodon

A sequence of three nucleotides located in the anticodon loop of a tRNA molecule that forms antiparallel, complementary base pairs with a specific mRNA codon.

30S Ribosomal Subunit

The small subunit of the bacterial ribosome that binds mRNA and facilitates the alignment of initiator tRNA during translation initiation.

50S Ribosomal Subunit

The large subunit of the bacterial ribosome that joins the initiation complex to create a functional ribosome and contains the peptidyl transferase center.

Initiation Factor 3 (IF-3)

A bacterial translation factor that binds to the 30S ribosomal subunit, preventing the premature association of the 50S subunit until the mRNA and initiator tRNA are assembled.

Initiation Factor 2 (IF-2)

A bacterial initiation factor that binds GTP and delivers the charged initiator tRNA ($fMet\text{-}tRNA^{fMet}$) to the initiation codon on the 30S subunit.

Initiation Factor 1 (IF-1)

A bacterial initiation factor that enhances the dissociation of the large and small ribosomal subunits and assists in assembling the 30S initiation complex.

70S Initiation Complex

The fully assembled, functional bacterial ribosome formed by the association of the 30S and 50S subunits along with mRNA and initiator tRNA positioned at the initiation codon.

Shine–Dalgarno Consensus Sequence

A conserved sequence in bacterial mRNA located upstream of the initiation codon that base-pairs with complementary nucleotides at the $3'$ end of 16S rRNA to position the ribosome.

Kozak Sequence

A consensus sequence ($5'\text{-ACCAUGG-}3'$) surrounding the initiation codon in eukaryotic mRNAs that facilitates start codon recognition by the eukaryotic ribosome.

Aminoacyl (A) Site

The ribosomal site that receives incoming charged tRNAs whose anticodons match the exposed mRNA codon during elongation.

Peptidyl (P) Site

The ribosomal site where initiator tRNA binds during initiation and which holds the tRNA covalently linked to the growing polypeptide chain during elongation.

Exit (E) Site

The ribosomal site from which a deacylated, uncharged tRNA is discharged into the cytoplasm after transferring its amino acid to the growing peptide chain.

Elongation Factor Tu (EF-Tu)

A protein translation factor that forms a complex with GTP and a charged tRNA, delivering the aminoacyl-tRNA into the ribosomal A site.

Elongation Factor Ts (EF-Ts)

An elongation factor that regenerates the active EF-Tu-GTP complex from inactive EF-Tu-GDP so it can bind another charged tRNA.

Elongation Factor G (EF-G)

A translation factor that utilizes GTP hydrolysis to stimulate the translocation of the ribosome along mRNA by one codon in the $5' \rightarrow 3'$ direction.

Peptidyl Transferase Center

The catalytic center residing within the 23S rRNA of the large ribosomal subunit responsible for catalyzing peptide bond formation between amino acids in the A and P sites.

Release Factors

Proteins (such as RF1, RF2, and RF3 in bacteria) that bind to the ribosome when a stop codon enters the A site, promoting translation termination and the release of the polypeptide chain.

tmRNA (Transfer-Messenger RNA)

A specialized bacterial RNA with both tRNA and mRNA properties that rescues stalled ribosomes on mRNAs lacking a stop codon, tagging the defective peptide for degradation.