Protein Structure and Binding (Video Notes)

Vocabulary flashcards covering key protein structure concepts, noncovalent interactions, binding, and real-world examples from the video notes.

Primary structure

The linear sequence of amino acids in a protein, held together by peptide bonds.

Peptide bond

The covalent bond linking the carboxyl group of one amino acid to the amino group of the next in a protein backbone.

Secondary structure

Local folding into alpha helices and beta sheets, stabilized mainly by hydrogen bonds between backbone atoms.

Alpha helix

A common right-handed helical secondary structure stabilized by intra-strand hydrogen bonds.

Beta sheet

A secondary structure formed by beta strands aligned side-by-side with inter-strand hydrogen bonds.

Tertiary structure

The overall three-dimensional arrangement of a single polypeptide, driven by noncovalent interactions among side chains (and some covalent bonds in places).

Quaternary structure

The arrangement of multiple polypeptide chains into a functional protein, held together by noncovalent bonds (with some covalent contributions).

Noncovalent bonds

Weak interactions that hold protein structure together and mediate binding, including electrostatic, hydrogen bonds, van der Waals, and hydrophobic interactions.

Electrostatic interaction

Attractions between opposite charges (charged amino acids) that help fold proteins and mediate binding.

Hydrogen bond

A noncovalent attraction between a partially positive hydrogen and a electronegative atom (N or O) in polar bonds.

Hydrophobic effect

Tendency of nonpolar side chains to cluster away from water, contributing to protein folding.

Hydrophobic core

The interior of a folded protein where nonpolar residues pack away from the aqueous environment.

Van der Waals interaction

Weak attractions between nonpolar atoms when they are in very close proximity, aiding close packing.

Binding site

The specific region on a protein where a ligand binds, formed by the protein’s 3D folding and shape complementarity.

Ligand

A molecule that binds to a protein at its binding site.

Enzyme

A protein that speeds up a chemical reaction by lowering activation energy.

Phenylalanine hydroxylase

An enzyme that converts phenylalanine to tyrosine; defects can lead to PKU.

PKU (phenylketonuria)

A genetic disorder caused by disrupted phenylalanine metabolism, leading to phenylalanine buildup and potential neural damage.

CAP (metabolite activator protein)

A bacterial regulatory protein that, when bound by cyclic AMP, activates alternative metabolic pathways.

Cyclic AMP (cAMP)

A signaling molecule that binds CAP in bacteria, indicating low energy and triggering metabolic responses.

Aspartame

An artificial sweetener made from aspartic acid and phenylalanine that binds sweet taste receptors more strongly than sugar.

Taste receptor

Receptors on taste cells that detect sweet compounds; aspartame can bind and elicit a sweet sensation.

Denaturation

Loss of a protein’s three-dimensional structure (unfolding) due to heat, acid, or other factors.

Cross-linking

Formation of bonds between protein molecules (or within a protein) leading to gelation or solidification when unfolded.

Disulfide bond

A covalent bond between cysteine residues that can stabilize protein structure; an exception to the predominantly noncovalent folding.theme.

Binding affinity

The strength of the interaction between a protein and its ligand; closer shape match yields stronger binding due to more noncovalent bonds.

Mutation effect

Genetic changes that alter amino acid sequence and charge, potentially disrupting folding and function.