Proteins and Their Synthesis Part 1

Vocabulary flashcards covering the key terms and concepts from Chapter 9 on protein structure, the genetic code, translation mechanisms, tRNAs, and ribosomes.

Central Dogma of Molecular Biology

The fundamental biological principle stating that the flow of genetic information within cells proceeds sequentially from DNA to RNA to protein.

Amino Acid

The monomer building block of proteins, structured around a central carbon atom bonded to an amino group ($-\text{NH}_2$ or $-\text{NH}_3^+$), a carboxyl group ($-\text{COOH}$ or $-\text{COO}^-$), a hydrogen atom, and a variable $\text{R}$ group side chain.

Peptide Bond

A covalent chemical bond formed between the carboxyl carbon of one amino acid and the amino nitrogen of an adjacent amino acid via the elimination of a molecule of $H_2O$.

Native Fold

The specific, biologically active three-dimensional conformation adopted by a folded protein that is stabilized by numerous favorable internal interactions.

Primary Structure

The linear sequence of amino acid residues in a polypeptide chain, conventionally read and numbered from the amino terminus ($\text{N}$-terminus) to the carboxyl terminus ($\text{C}$-terminus).

Secondary Structure

Local spatial arrangements and recurring folding patterns of the polypeptide backbone, predominantly consisting of $\alpha$-helices and $\beta$-sheets stabilized by hydrogen bonds.

Tertiary Structure

The complete three-dimensional folding of a single polypeptide chain into an active conformation governed by noncovalent interactions, electrostatic forces, van der Waals forces, and hydrophobic effects among $\text{R}$ groups.

Quaternary Structure

The spatial assembly and structural combination of multiple individual polypeptide subunits into a single functional, multi-subunit protein complex.

Co-linearity

The direct linear correspondence between the sequential order of nucleotide bases in DNA/RNA and the sequential order of amino acids in the resulting protein.

Codon

A three-nucleotide sequence in mRNA that codes for a specific amino acid or functions as a stop signal during translation.

Genetic Code

The specific relationship and translational dictionary between triplet codons in mRNA and the individual amino acids they specify.

Degeneracy (Redundancy)

The property of the genetic code whereby more than one distinct codon can code for the same amino acid, with $61$ coding codons designating only $20$ standard amino acids.

Universality

The characteristic of the genetic code being nearly identical across all living organisms, spanning bacteria to humans, with minor exceptions found in mitochondria and certain microbes.

Non-overlapping Code

The organizational feature of the genetic code where each nucleotide belongs to only one codon, and codons are read sequentially without gaps or shared bases.

Open Reading Frame (ORF)

A continuous portion of a reading frame in mRNA read in the $5'$ to $3'$ direction that initiates with an AUG start codon and concludes with a stop codon (UAA, UGA, or UAG), encoding a polypeptide.

Transfer RNA (tRNA)

The adaptor RNA molecule that links mRNA codons to their specified amino acids during translation by binding an amino acid at its $3'$ end and mRNA through its anticodon loop.

Anticodon

A sequence of three nucleotides on a tRNA molecule that base-pairs antiparallelly and complementarily with a specific mRNA codon via hydrogen bonding.

Aminoacyl-tRNA Synthetase

An enzyme responsible for attaching the correct, specific amino acid onto the $3'$ acceptor site of its cognate tRNA in an ATP-dependent, two-step reaction.

Wobble Base Pairing

Non-standard, flexible base pairing occurring at the third ($3'$) position of the mRNA codon with the first ($5'$) position of the tRNA anticodon, allowing one tRNA to recognize multiple synonymous codons.

Ribosome

A large ribonucleoprotein complex composed of two subunits ($30S$ and $50S$ in bacteria; made of ~$65\%$ rRNA and $35\%$ protein) that coordinates translation and catalyzes peptide bond formation.

Peptidyl-Transferase Center (PTC)

The catalytic site situated within the large ribosomal subunit where ribosomal RNA carries out the catalysis of peptide bond formation.

Decoding Center

The active region located in the small ribosomal subunit ($30S$) that monitors the fidelity of complementary base-pairing between the mRNA codon and tRNA anticodon.

Silent Mutation

A nucleotide alteration in a coding sequence that produces a synonymous codon coding for the exact same amino acid, resulting in an unaltered polypeptide.

Conservative Substitution

An amino acid replacement, often triggered by a single-base mutation in the first position of a codon, that swaps one amino acid for another possessing similar biochemical properties.

$\alpha$-Amanitin

A lethal cyclic octapeptide toxin produced by Death Cap mushrooms (Amanita phalloides) that halts transcription by inhibiting RNA polymerases.