Protein Function

Target

This is the protein itself in 3-dimensional space.

Ligand

This is the molecule that the protein binds to, typically resulting in a change in conformation in the target (protein).

Selective

This is when the ligand fits exactly where it is supposed to in the target like a glove.

Non-Selective

This is when the ligand will fit to the target, but not tightly, it moves around a bit.

Binding Site

This is the region of the protein (target) that associates with the ligand (docking).

Structural Specificity

This is when the shape of the lock fits perfectly with the key; the ligand fits to the binding site super well.

Chemical Specificity

This is when the binding is not specific until certain chemical bonds come into play; something other than shape makes it specific.

Complementarity

This is a property that affects ligand binding that depends on the tertiary structure of the protein, creating unique microenvironments; how well they fit.

Flexibility

This is a property that affects ligand binding that depends on the tertiary structure, allowing proteins to adapt to their ligands.

Surfaces

This is a property that affects ligand binding where binding sites can consist of concave, convex, or even flat surfaces; as well as pockets/cavities in the tertiary structure.

Non-Covalent Forces

This is a property that affects ligand binding that are characteristic properties of the binding site (exposed hydrophobic surfaces, water displacement).

Affinity

This is a property that affects ligand binding related to the binding ability of the enzyme to the substrate; how well do the protein & ligand get along?

Surface-String Interaction

This is when an extended loop of one protein makes contact with the surface of another protein (string snaps into cleft).

Helix-Helix Interaction

This is when the helices from two different proteins wrap around each other to form a coiled-coil.

Surface-Surface Interaction

This requires the precise matching of complementary surfaces in two proteins (like a lego😃) .

Non-Covalent

__________________ bonds mediate protein-protein interactions.

function

The _________________ of the protein is defined by the interaction with its ligands.

Specificity

This is the ability of a protein to bind either a single molecule, or at most, a very small group of molecules in preference to all other molecules.

Affinity

This is the strength of the interaction between two proteins.

Active Site

This is the location of substrate binding where a chemical reaction occurs.

Binding Site

This recognizes & binds to the substrate molecule.

Catalytic Site

This is the site of a chemical reaction affecting the substrate; where the activity happens.

Cofactors

This is a non-protein chemical compound or metallic ion that is required for a protein’s biological activity to happen; helper😀.

Non-Specific Inhibition/Activation

In this mechanism of regulation, enzymes react differently to changes in temperature and pH.

Regulation of Substrate/Enzyme Amount

This is when the substrate is competing for binding sites; but enzyme concentration beyond a certain point has no effect if the substrate concentration is limiting.

Compartmentalization of Enzymes

In this mechanism of regulation, certain enzymes only work in their specific compartments; everything has its place.

Inhibitor

This is a molecule that binds to an enzyme

Competitive Inhibitor

This is a molecule binding to an enzyme where the inhibitor & substrate are in direct opposition; all about which the enzyme likes more.

Noncompetitive Inhibitor

This is where the inhibitor has a binding site on the inside that is different from the active site; there’s no competition.

decreases

Increasing the inhibitor _______________ the rate of the reaction.

Reversible Covalent Modification

This is a factor that affects the rate of a reaction (i.e. phosphorylation).

Negative Feedback

This is when a product is produced, and that product prevents the producer from starting the process over again.

Positive Feedback

This is when a precursor for a reaction is made, therefore allowing the reaction to skip steps to get to the end product faster.