B1.2 Protein

Amino Acid Core Structure

Alpha carbon attached to an amine group, carboxyl group, R-group, and hydrogen atom.

Amine Group Formula

-NH2

Carboxyl Group Formula

-COOH

Variable Group in Amino Acids

The R-group (side chain).

Number of Universal Amino Acids

20 different amino acids coded for in the genetic code.

Polypeptide to Protein Transition

A polypeptide becomes a functional protein when it folds into its specific 3D shape/conformation.

Dipeptide Formation Reaction

Condensation reaction.

Bond Formed Between Amino Acids

Peptide bond.

Byproduct of Peptide Bond Formation

One water molecule (H2O) per peptide bond.

Essential Amino Acids

Amino acids that cannot be synthesized by the body and must be obtained from food.

Non-Essential Amino Acids

Amino acids that can be synthesized by the body from other amino acids.

Vegan Diet Challenge for EAAs

Plant proteins often lack sufficient proportions of specific "limiting" essential amino acids (like lysine or methionine).

Calculating Polypeptide Diversity

20^n (where n is the number of amino acids in the chain).

Reasons for Infinite Polypeptide Variety

Amino acid chains can be any length, use any of 20 amino acids, and link in any sequence.

Types of R-group Properties

Hydrophobic vs. hydrophilic; hydrophilic can be polar, non-polar, acidic (negatively charged), or basic (positively charged).

Hydrophobic R-groups

Non-polar side chains with 0 to 9 carbons, some containing aromatic rings.

Hydrophilic R-groups

Polar or charged side chains (7 can become charged; 4 are polar but uncharged).

Acidic R-groups

Give up a proton (H+) and become negatively charged.

Basic R-groups

Accept a proton (H+) and become positively charged.

Primary Structure Definition

The specific sequence and number of amino acids in a polypeptide chain linked by peptide bonds.

Primary Structure Significance

Determines all higher levels of structure and the final 3D conformation of the protein.

Effect of Single Amino Acid Change

Alters local charge or size, potentially causing the protein to misfold and lose function.

Secondary Structure Definition

Regular, repeating folding or coiling of the polypeptide backbone into alpha-helices or beta-pleated sheets.

Bonds Stabilizing Secondary Structure

Hydrogen bonds between amine (-NH) and carboxyl (-CO) groups of non-adjacent peptide bonds.

Alpha-Helix Structure

Coiled helical structure stabilized by hydrogen bonds parallel to the axis.

Beta-Pleated Sheet Structure

Sheet-like pleated structure stabilized by hydrogen bonds between adjacent polypeptide strands.

Tertiary Structure Definition

The overall 3D folding and complex molecular shape of a single polypeptide chain.

Bonds/Interactions in Tertiary Structure

Hydrogen bonds, ionic bonds, disulfide covalent bridges, and hydrophobic/hydrophilic interactions between R-groups.

Disulfide Bridges

Strong covalent bonds formed between the sulfur atoms of two cysteine amino acid residues.

Ionic Bonds in Tertiary Structure

Form between oppositely charged (acidic and basic) R-groups; broken by pH changes.

Hydrophobic Interactions

Non-polar R-groups cluster together toward the interior/core of the protein away from water.

Water-Soluble Protein Tertiary Structure

Hydrophobic amino acids clustered in the interior core; hydrophilic amino acids on the exterior surface.

Integral Membrane Protein Structure

Non-polar hydrophobic amino acids on the outer surface interact with fatty acid tails; polar amino acids form inner channels.

Quaternary Structure Definition

The arrangement and association of two or more polypeptide chains (subunits) into a single functional protein.

Conjugated Protein

A protein combined with a non-protein prosthetic group (e.g., hemoglobin with heme).

Non-Conjugated Protein

A protein consisting only of polypeptide chains without prosthetic groups (e.g., insulin, collagen).

Prosthetic Group Definition

A non-protein molecule tightly bound to a protein essential for its activity (e.g., iron-containing heme in hemoglobin).

Cryo-Electron Microscopy (Cryo-EM)

Technology allowing 3D imaging of single-protein molecules and ligand interactions at near-atomic resolution.

Globular Protein Shape & Structure

Spherical and rounded shape; irregular amino acid sequence; dynamic tertiary/quaternary structure.

Globular Protein Solubility & Function

Soluble in water; performs functional roles (catalysis, transport, signaling, immunity).

Fibrous Protein Shape & Structure

Long, narrow thread-like shape; repetitive amino acid sequence.

Fibrous Protein Solubility & Function

Generally insoluble in water; performs structural roles (strength, support).

Insulin Function & Form

Globular hormone; 2 polypeptide chains linked by disulfide bonds; hydrophilic exterior lets it travel in blood.

Collagen Function & Form

Fibrous structural protein; triple-helix with covalent cross-links; high tensile strength for skin, bones, and tendons.

Hemoglobin Function & Form

Conjugated globular protein; 4 polypeptide subunits each with a heme group; transports oxygen in blood.

Denaturation Definition

A structural change in a protein causing the permanent loss of its 3D conformation and biological function.

Effect of High Temperature on Proteins

Increases thermal kinetic energy, breaking weak hydrogen/ionic bonds and causing the protein to unfold.

Effect of pH Changes on Proteins

Alters the charge on acidic/basic R-groups, breaking ionic bonds and altering solubility and shape.

Genome vs. Proteome

The genome is the complete set of genes (fixed); the proteome is the complete set of proteins expressed (variable and dynamic).