Becker's World of the Cell: The Genetic Code and Protein Synthesis

Comprehensive vocabulary flashcards covering the genetic code, translation initiation, elongation, termination, molecular chaperones, mutation types, mRNA quality control, and posttranslational processing.

Genetic Code

The set of rules that defines the relationship between the DNA base sequence and the linear order of amino acids in protein products.

One Gene–One Enzyme Hypothesis

The hypothesis proposed by George Beadle and Edward Tatum based on Neurospora crassa mutants, stating that each gene mutation disables a single specific enzymatic step in a metabolic pathway.

One Gene–One Polypeptide Theory

The refined concept stating that the nucleotide sequence of a gene determines the amino acid sequence of a polypeptide chain, supported by findings in hemoglobin and tryptophan synthase.

Sickle-Cell Hemoglobin

A mutant form of hemoglobin identified by Vernon Ingram that differs from normal hemoglobin by a single amino acid substitution, where valine replaces glutamic acid.

Degenerate Code

A characteristic of the genetic code where a particular amino acid can be specified by more than one triplet codon.

Nonoverlapping Code

A genetic reading arrangement in which the reading frame advances three nucleotides at a time, ensuring each nucleotide belongs to only a single codon.

Frameshift Mutation

A mutation caused by the insertion or deletion of one or more base pairs (an indel) that causes the remaining sequence to be read out of phase.

Pseudo Wild-Type

A phenotype produced when a second nearby indel mutation cancels out the effect of an initial frameshift mutation, restoring the triplet reading frame.

Template Strand

The single strand of DNA that is copied during transcription to direct the synthesis of a complementary mRNA molecule.

Coding Strand

The DNA strand that is not copied during transcription, containing a base sequence similar to the synthesized mRNA, with thymine in place of uracil.

Codon

A sequence of three ribonucleotides in mRNA, written in the $5^\prime \rightarrow 3^\prime$ direction, that specifies a particular amino acid or translation stop signal.

Start Codon

The mRNA triplet AUG, which specifies methionine (or N-formylmethionine in bacteria) and defines the reading frame for translation.

Stop Codons

The three codons (UAA, UAG, and UGA) that do not encode amino acids but instead signal the termination of polypeptide synthesis.

Codon Usage Bias

The preferential occurrence of certain synonymous codons over others at higher frequencies in an organism's mRNA.

A (Aminoacyl) Site

The ribosomal binding site that accommodates an incoming aminoacyl-tRNA carrying an activated amino acid to be added to the polypeptide chain.

P (Peptidyl) Site

The ribosomal binding site where the tRNA molecule linked to the growing polypeptide chain resides during protein synthesis.

E (Exit) Site

The ribosomal binding site from which uncharged tRNAs leave the ribosome after donating their amino acid.

Ribosome Binding Sites

The distinct functional regions of the ribosome that direct translation, including the mRNA-binding site on the small subunit and the A, P, and E tRNA-binding sites.

Transfer RNA (tRNA)

An adaptor RNA molecule linked to a specific amino acid via an ester bond that base-pairs with mRNA codons through its anticodon triplet.

Aminoacyl-tRNA Synthetase

One of 20 enzymes that attach specific amino acids to their cognate tRNA molecules via an ester bond using ATP hydrolysis, followed by proofreading.

Wobble Hypothesis

The principle that flexibility exists in base pairing between the third ($3^\prime$) position of an mRNA codon and the first ($5^\prime$) position of a tRNA anticodon.

Inosine

A modified base created by RNA editing of adenosine that often occupies the tRNA wobble position and can pair with U, C, or A in mRNA.

Polycistronic mRNA

An mRNA transcript found in bacteria and archaea that encodes multiple distinct polypeptides, typically grouped together in operons.

Shine-Dalgarno Sequence

A bacterial mRNA sequence consisting of three to nine purines located upstream of the start codon that pairs with the $3^\prime$ end of 16S rRNA to establish the mRNA-binding site.

N-formylmethionine (fMet)

A modified methionine carried by initiator tRNA in bacteria whose amino group is blocked, permitting only its carboxyl group to form peptide bonds.

30S Initiation Complex

The bacterial complex consisting of the 30S ribosomal subunit, initiation factors (IF1, IF2-GTP, IF3), mRNA, and initiator tRNA bound at the P site.

70S Initiation Complex

The complete bacterial ribosome assembled when the 50S subunit binds the 30S initiation complex following the hydrolysis of IF2-bound GTP and factor release.

43S Preinitiation Complex

The eukaryotic translation complex formed by the association of the small ribosomal subunit, initiator tRNA, eIF2-GTP, eIF1, eIF1A, eIF3, and eIF5.

Kozak Sequence

A common eukaryotic consensus sequence around the start codon (typically ACCAUGG) recognized by the scanning small ribosomal subunit.

Internal Ribosome Entry Sequence (IRES)

A specialized nucleotide structure located upstream of the start codon in certain mRNAs that permits 5' cap-independent ribosomal initiation.

Poly(A)-Binding Protein (PABP)

A eukaryotic protein that binds the 3' poly(A) tail of mRNA and interacts with eIF4G to circularize the transcript and stabilize translation initiation.

EF-Tu

A bacterial elongation factor that, when bound to GTP, escorts aminoacyl-tRNA to the ribosomal A site and hydrolyzes GTP upon proper codon pairing.

EF-Ts

A bacterial elongation factor that facilitates the recycling of EF-Tu by catalyzing the displacement of GDP and regeneration of EF-Tu-GTP.

EF-G

A bacterial elongation factor that promotes the translocation of mRNA and tRNAs across the ribosome through the hydrolysis of bound GTP.

Ribozyme Peptidyl Transferase

The catalytic center of the ribosome located in the large subunit rRNA (23S rRNA in bacteria) that catalyzes peptide bond formation.

Polyribosome

A cluster of multiple ribosomes simultaneously translating the same mRNA molecule in the $5^\prime \rightarrow 3^\prime$ direction to maximize protein production.

Release Factors

Proteins that recognize stop codons at the ribosomal A site and trigger the hydrolysis and release of the completed polypeptide chain.

Molecular Mimicry

The structural similarity where protein release factors resemble tRNA shapes to bind directly into the ribosomal A site.

Molecular Chaperones

Proteins that assist nascent or misfolded polypeptide chains in attaining proper three-dimensional conformation by binding hydrophobic regions in an ATP-dependent manner.

GroEL/GroES Complex

A bacterial Hsp60 chaperonin system in which a barrel-shaped GroEL cavity and a GroES cap create an ATP-regulated hydrophilic environment for protein folding.

Missense Mutation

A point mutation where a base-pair substitution changes a codon to specify a different amino acid.

Nonsense Mutation

A point mutation that converts an amino acid-specifying codon into a stop codon, causing premature termination of translation.

Silent Mutation

A base-pair substitution that alters a codon without changing the encoded amino acid, typically occurring at the third nucleotide position.

Nonstop Mutation

A base-pair substitution that alters a normal stop codon into an amino acid-coding codon, resulting in translation continuation beyond the normal termination point.

Suppressor tRNA

A mutant tRNA whose altered anticodon recognizes a premature stop codon and inserts an amino acid, thereby suppressing a nonsense mutation.

Nonsense-Mediated Decay (NMD)

A eukaryotic quality-control mechanism that degrades mRNAs containing premature stop codons identified prior to the final exon junction complex.

Exon Junction Complex (EJC)

A multiprotein complex deposited at exon-exon junctions following pre-mRNA splicing that serves as a marker for detecting premature stop codons.

Nonstop Decay

A eukaryotic surveillance pathway in which an RNA-degrading enzyme binds to the empty A site of a stalled ribosome to destroy an mRNA transcript lacking a stop codon.

Transfer-Messenger RNA (tmRNA)

A specialized bacterial RNA that binds the A site of stalled ribosomes on transcripts lacking stop codons, tagging the incomplete protein for degradation.

Preproinsulin

The precursor precursor polypeptide of insulin from which pre-amino acids are cleaved to yield proinsulin, which after forming disulfide bonds has pro-amino acids excised to form mature insulin.

Protein Splicing

A rare posttranslational modification wherein internal protein sequences called inteins are excised and the flanking segments, called exteins, are joined together.