Lesson 1: Protein Structure/Function Key Terms

polypeptide backbone

repeating sequences of atoms along the core of the polypeptide chain

side chain

the part of an amino acid that differs between amino acid types; give each type of amino acid its unique chemical and physical properties

conformation

the folded, 3D structure of a polypeptide chain

alpha helix

common folding pattern in proteins, in which a linear sequence of amino acids folds into a right-handed helix stabilized by internal hydrogen bonding between backbone atoms

beta sheet

common structural motif in proteins which different sections of the polypeptide chain run alongside each other, joined by hydrogen-bonding between atoms of the polypeptide backbone

primary structure

linear sequence of monomer units in a polymer (amino acid sequence of a protein)

secondary structure

regular local folding pattern of a polymeric molecule; a helices and b sheets

tertiary structure

complex 3D form of a folded polymer chain, especially a protein or RNA molecule

ligand

any molecule that binds to a specific site on a protein or other molecule

equilibrium constant (K)

the ratio of forward and reverse rate constants for a reaction, equal to the association/affinity constant for a simple binding reaction

enzyme

protein that catalyzes a specific chemical reaction

substrate

molecule on which an enzyme acts

catalyst

substance that can lower the activation energy of a reaction, thus increasing its rate, without being consumed by the reaction

transition state

structure that forms transiently in the course of a chemical reaction and has the highest free energy of any reaction intermediate

coenzyme

small molecule tightly associated with an enzyme that participates in the reaction that the enzyme catalyzes, often by forming a covalent bond to the substrate

feedback inhibition

the process in which a product of a reaction feeds back to inhibit a previous reaction in the same pathway

phosphorylation

reaction in which a phosphate group is covalently coupled to another molecule

active site

region of an enzyme surface to which a substrate molecule binds in order to undergo a catalyzed reaction

regulatory site

region of an enzyme surface to which a regulatory molecule binds and thereby influences the catalytic events at the separate active site

linkage

in ligand binding, the conformational coupling between two separate ligand-binding sites on a protein, such that a conformational change in the protein induced by binding of one ligand affects the binding of a second ligand

cooperativity

regulatory phenomenon in multi-subunit enzymes where the binding of a substrate to one active site affects the binding affinity of other sites, enhancing or inhibiting further substrate binding

protein kinase

enzyme that transfers the terminal phosphate group of ATP to one or more specific amino acids (serine, threonine, or tyrosine) of a target protein

protein phosphatase

enzyme that catalyzes phosphate removal from amino acids of a target protein

scaffold protein

protein that binds groups of intracellular proteins into a complex, often anchoring the complex at a specific location in the cell

proteomics

study of proteomes (similar to genome, set of proteins produced) and their functions