Chapter 5

Amino Acid

The basic building block of proteins, each has a central carbon bonded to an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen, and an R group.

R Group (Side Chain)

The variable part of each amino acid that determines its polarity, charge, and hydrophobicity/hydrophilicity.

Peptide Bond

A covalent bond linking two amino acids, formed via dehydration synthesis.

Primary Structure

The linear sequence of amino acids in a protein determining all higher-level folding and function.

Secondary Structure

Local folding patterns in a polypeptide due to hydrogen bonding, including alpha helices and beta sheets.

Tertiary Structure

The complete 3D folded shape of a single polypeptide chain, stabilized by interactions among R groups.

Quaternary Structure

Protein structure formed by the assembly of multiple polypeptide chains into a functional protein.

Denaturation

The loss of a protein’s shape and function due to heat, pH, or chemicals; often irreversible.

Ribosome

A molecular machine that reads mRNA and assembles proteins, made of rRNA and proteins with A, P, and E sites.

tRNA (Transfer RNA)

A small RNA molecule that matches an anticodon to the mRNA codon and carries the corresponding amino acid.

Codon

A triplet of mRNA bases that codes for a specific amino acid; there are 64 possible codons.

Anticodon

A triplet of bases on tRNA that pairs complementarily and antiparallel with the mRNA codon.

Reading Frame

The way nucleotides are grouped into codons during translation; shifts alter the entire downstream sequence.

Redundant Genetic Code

More than one codon can code for the same amino acid.

Unambiguous Genetic Code

Each codon codes for only one amino acid, preventing confusion.

Signal Peptide (Signal Sequence)

A short amino-terminal sequence on a new polypeptide that signals the ribosome to head towards the ER.

Signal Recognition Particle (SRP)

A protein-RNA complex that recognizes the signal peptide, pauses translation, and directs the ribosome to the ER.

Folding Domain

A part of a protein that folds independently into a stable structure, often shared across proteins.

Protein Family

A group of evolutionarily related proteins with similar structure and function due to shared domains.

Hydrophobic Amino Acids

Amino acids with nonpolar side chains that tend to be found inside proteins.

Hydrophilic Amino Acids

Amino acids with polar side chains, including polar uncharged, acidic, and basic types.

Glycine

The simplest amino acid known for its flexibility.

Proline

An amino acid known for its rigidity and ability to cause bends in protein chains.

Cysteine

An amino acid that forms disulfide bridges, contributing to protein structure stability.

α-Helix

A right-handed spiral structure formed in the secondary structure of proteins through hydrogen bonds.

β-Sheet

A pleated sheet structure formed in the secondary protein structure through hydrogen bonding between chains.

Hydrogen Bonds

Weak bonds that stabilize the secondary structure in proteins.

Ionic Bonds

Attraction between positively and negatively charged side chains that stabilize protein tertiary structure.

Van der Waals Forces

Weak attractions between molecules or parts of molecules that contribute to protein stability.

Disulfide Bridges

Strong covalent bonds that form between cysteine residues stabilizing protein structures.

Chaperones

Proteins that assist in the correct folding or refolding of other proteins.

mRNA (Messenger RNA)

The template molecule responsible for carrying genetic information from DNA to the ribosome.

Anticodon on tRNA

The three-base sequence on tRNA that is complementary to a specific mRNA codon.

Start Codon

AUG; the codon that signals the start of translation and codes for methionine.

Stop Codons

Codons (UAA, UAG, UGA) that signal the termination of protein synthesis.

Frameshift Mutations

Mutations that alter the reading frame, causing changes in all downstream codons.

Peptide Bond Formation

The process through which amino acids are joined in a protein via dehydration synthesis.

Mutation Effects on Protein Structure

Changes in DNA that can affect the structure and function of proteins.

Translation Process

The complex process by which ribosomes synthesize proteins based on mRNA sequence.

Functional Protein

A protein that has folded properly and carries out its biological function.

Gene-Encoded Protein

Proteins that are directly coded for by the sequence of nucleotides in a gene.

Mutations in Signal Peptides

Mutated signal sequences can lead to mislocalized proteins or proteins remaining in the cytosol.

Translation Resume

The continuation of protein synthesis after the SRP directs the ribosome to the ER.

Genetic Code Characteristics

Features of the genetic code such as redundancy and unambiguity that ensure proper translation.

Molecular Machines

Complex structures like ribosomes that perform biochemical functions, such as protein synthesis.

Amino Acid Charge

Refers to whether an amino acid side chain carries a positive, negative, or neutral charge.

Polarity of Side Chains

Determined by the structure and characteristics of the R group of amino acids.

Evolution of Proteins

The adaptation and development of proteins over time due to environmental pressures and genetic changes.

Protein Structure Hierarchy

The levels of protein structure including primary, secondary, tertiary, and quaternary structures.

Structural Domains

Distinct functional or structural units within proteins that can evolve separately.