Biology: Protein Structure, Function, and Synthesis

Vocabulary practice flashcards covering Chapter 5: Protein Structure, Function, and Synthesis, including amino acid properties, structural hierarchy, the genetic code, translation machinery, and protein sorting.

$$\alpha\text{ Carbon}$$

The central carbon atom of an amino acid to which four distinct components are attached: a carboxyl group, an amino group, a hydrogen atom, and a variable R group.

R Group (Side Chain)

The variable chemical group that differs among all 20 amino acids and dictates each amino acid's physical and chemical properties, as well as protein structure, folding, and function.

Hydrophobic Amino Acids

Nonpolar amino acids whose R groups tend to aggregate together in the interior core of a folded protein to avoid contact with the aqueous environment of the cell.

Hydrophilic Amino Acids

Polar or charged amino acids typically positioned on the outer surface of a protein; basic amino acids carry positive charges, while acidic amino acids carry negative charges.

Special Amino Acids

A trio of amino acids with unique structural effects: Glycine provides conformational flexibility, Proline restricts folding and induces bends, and Cysteine forms covalent disulfide bridges ($-\text{S}-\text{S}-$).

Peptide Bond

A covalent bond joining two adjacent amino acids formed via a dehydration synthesis reaction that releases a molecule of water.

Primary Structure

The linear sequence of amino acids in a polypeptide chain, read from the amino end ($\text{N-terminus}$) to the carboxyl end ($\text{C-terminus}$).

$$\alpha\text{ Helix}$$

A stable, right-handed helical secondary structure formed by hydrogen bonds between the backbone carbonyl group of one amino acid and the amide group four residues ahead.

$$\beta\text{ Sheet}$$

A pleated secondary structure consisting of parallel or antiparallel polypeptide strands stabilized by hydrogen bonds between backbone carbonyl and amide groups across adjacent chains.

Tertiary Structure

The overall three-dimensional shape of a single polypeptide chain, governed by secondary structures and interactions among R groups, including hydrogen bonds, ionic bonds, van der Waals forces, and disulfide linkages.

Quaternary Structure

The macromolecular protein structure that results when two or more distinct polypeptide subunits assemble and interact together to form a functional complex.

Four Levels of Protein Structure

The structural hierarchy of proteins progressing from primary sequence to secondary local folds ($\alpha\text{ helices}$ and $\beta\text{ sheets}$), tertiary 3D folding of a polypeptide, and quaternary assembly of multiple subunits.

Protein Chaperone

A specialized helper protein that protects polypeptides against improper folding or denaturation during synthesis and environmental stress.

Codon

A sequence of three consecutive nucleotides in an mRNA molecule that specifies a particular amino acid, a translation initiation signal, or a translation termination signal.

Start Codon

The codon $5'\text{-AUG-}3'$ that marks the start of translation and codes for the incorporation of the amino acid methionine.

Stop Codons

The three codons ($\text{UAA}$, $\text{UAG}$, and $\text{UGA}$) that do not code for an amino acid and instead act as signals to terminate translation.

Redundancy of the Genetic Code

The characteristic of the genetic code wherein multiple distinct codons can specify the same single amino acid.

Unambiguous Nature of the Genetic Code

The property of the genetic code where each individual codon designates one, and only one, specific amino acid or stop command.

Open Reading Frame (ORF)

A continuous stretch of non-overlapping codons that begins with an $\text{AUG}$ start codon and ends with a stop codon.

Anticodon

A three-nucleotide sequence within a tRNA loop that forms antiparallel, complementary base pairs with an mRNA codon.

Aminoacyl tRNA Synthetase

An enzyme that selectively attaches the correct amino acid to the $3'$ hydroxyl end of its corresponding uncharged tRNA molecule.

Ribosomal tRNA Binding Sites (A, P, and E)

The three internal functional pockets of the large ribosomal subunit: the aminoacyl (A) site accepts incoming charged tRNA, the peptidyl (P) site holds the tRNA with the growing chain and catalyzes peptide bond formation, and the exit (E) site discharges uncharged tRNA.

Translation Initiation in Eukaryotes

The process whereby initiation factors and the small ribosomal subunit bind the $5'$ cap of mRNA, scan downstream to identify the start codon ($\text{AUG}$), and subsequently recruit the large ribosomal subunit.

Shine–Dalgarno Sequence

A conserved sequence ($5'\text{-AGGAGGU-}3'$) located upstream of start codons on prokaryotic mRNA that directly recruits the ribosome to initiate translation.

Translation Elongation

The cyclical phase of protein synthesis where an rRNA in the large subunit catalyzes peptide bond formation between the P-site and A-site amino acids, followed by ribosome translocation along mRNA in a $5' \rightarrow 3'$ direction ($\text{E} \leftarrow \text{P} \leftarrow \text{A}$).

Release Factor

A protein that binds to the ribosomal A site upon encountering a stop codon, promoting hydrolysis and release of the completed polypeptide chain and dissociation of the ribosome.

Protein Sorting Signal Sequences

Amino acid sequences within a newly synthesized polypeptide that direct its cellular destination: no signal sequence leaves the protein in the cytosol, an amino-terminal sequence directs it to chloroplasts or mitochondria, and an internal sequence directs it to the nucleus.