Chapter 5: Protein Function Flashcards
Ligand
a molecule bound by a given protein; can be any kind of molecule, including nucleic acid or another protein; transient nature of protein-ligand interaction is essential
Binding Site
a specific site on the protein at which the ligand binds; complementary to the ligand in size, shape, charge, and hydrophobic or hydrophilic character; one protein may have multiple sites
Conformational Flexibility
changes may be subtle or dramatic; frequently essential to protein function
Induced Fit
conformational change in a protein that alters a binding site so that it becomes more complementary to the ligand, making tighter binding
Cooperativity
when a conformational change in one subunit (triggered by the binding of a ligand) can increase or decrease affinity of neighboring protein for same ligand
Regulation of Protein activity
usually accomplished through specific interactions with one or more additional ligands
Equilibrium Expression
a way to describe the reversible binding of a protein and a ligand
P+LPL
Helix-turn-Helix Motif
DNA binding motif crucial to the interaction of many bacterial regulatory proteins with DNA
Cofactor
additional chemical component that allows an enzyme to complete its activity
Coenzyme
complex organic or metallo-organic molecule called a coenzyme; acts as a transient carrier of specific functional groups; most derived from vitamins
Prosthetic Group
coenzyme or inorganic cofactor that is tights or covalently bonded to the enzyme protein
Holoenzyme
complete, catalytically active enzyme with bound coenzyme or cofactor
Apoenzyme/Apoprotein
the protein part of a holoenzyme
Binding Energy (delta Gb)
energy derived from the enzyme-substrate interaction; major source of free energy used by enzymes to increase the rates of reactions; stabilizes enzyme-substrate interaction
Transition State
a transient moment when the alteration in the substrate has reached a point corresponding to the highest energy in the reaction coordinate diagram
Activation Energy
difference between energy of ground state and transition state
Enzyme Kinetics
determining the rate of a reaction and how it changes in response to changes in experimental parameters
Competitive Inhibitor
reversible; competes with a substrate for the active site of an enzyme; usually structurally similar to substrate
Uncompetitive Inhibitor
reversible; binds at a site distinct from the substrate active site; binds to ES
Mixed Inhibitor
reversible; binds at a site distinct from the substrate active site, but binds E or ES
Covalent Modification
a way of modulating protein activity by binding a group to one or more AA residues
Protein Kinase
catalyzes the attachment of phosphoryl groups to specific AA residues of a protein
Protein Phosphatase
catalyzes the removal of phosphoryl groups
Proteolytic Cleavage
inactive precursor protein is cleaved to form the active protein
