Chapter 3.5: The Function of a Protein Is Determined by Its Structure

Flashcards from Chapter 3.5 of Principles of Life, 3rd Edition.

Enzymes

Catalytic molecules that increase the rate of biochemical reactions by lowering the activation energy needed

• These can bind to reactants to participate in the reaction yet maintain their chemical form

• Generally specialized to bind to only one or a few closely related reactants in one reaction

• Produced and regulated according to needs of environment and system

Structural and motor proteins

Proteins that provide physical stability and enable movement in the cell

Signal and regulatory proteins

Proteins that control the rates of numerous biological processes

Receptor proteins

Proteins that receive and respond to molecular signals from inside and outside the organism

Protein bonding

This occurs at specific sites on the protein determined by its three-dimensional shape, where side chains bond with molecules or ions

Ligand

A molecule or ion that binds to another molecule, like a protein, through numerous weak bonds that determine binding affinity

• Addition of these can cause conformational changes which affect protein functions

Binding affinity

The interaction strength between a ligand and protein molecule

Conformational change

A change in the shape of a protein following the binding of a ligand, affecting its function

Side chain modification (R group modification)

Protein structure modifications through amino acid and chemical group bonds

Cofactor

An additional molecule that some proteins require to function, varying in bond strength either for tight or loose bonds

• Seen with ATP as it is converted to and from ADP

Prosthetic groups

Cofactors that are tightly bound to a protein with covalent bonds

Coenzymes

Cofactors that are loosely bound to enzymes

Proteolysis

The breaking apart of a bond in a protein for a change in activation state as needed

Reaction rate

This can be affected by temperature, concentrations, free energy, and activation energy

Activation energy (E_a)

The energy needed to successfully start and complete a reaction

• This can be met with higher temperatures or molecular reorganization for higher interaction likelihood

• Most common way of meeting this in living systems is lowering it via enzymes

Catalysis

The ability to increase reaction rates without chemical changes; enzymes can do this repeatedly and rapidly up to a 10³ to 10⁸ speedup

Substrates

The reactants in an enzyme-catalyzed reaction

Active site

The site on the enzyme where specific substrate molecules bind

• Typically only a small part of the protein

• Relies on hydrogen bonds, van der Waals interactions, and charged groups for binding

Conformation

The three-dimensional shape of an enzyme

• With its chemical properties, one enzyme is made to be highly specific

• This may change during a reaction as an example of induced fit

Enzyme-substrate complex (ES)

This is created by the binding of substrates to the active site of an enzyme, held together by chemical bonds, in order to give rise to products

Induced strain

Method of inducing change through an enzyme by stretching bonds in the substrate, making them easier to break with greater potential energy

Substrate orientation

Method of inducing change through an enzyme by orienting two substrates to facilitate reactions

Chemical modification

Method of inducing change via an enzyme via the involvement of the side chains (R groups) in the reaction for manipulation of products

Metabolic pathway

A series of reactions in which the product of one reaction is a substrate for the next for the breakdown or synthesis of molecules

Catabolic pathway

A metabolic pathway that breaks down molecules and releases energy

Anabolic pathway

A metabolic pathway that synthesizes molecules from simpler ones, building up potential energy

Inhibitor

A molecule that prevents the entry of a molecule into the active site, lowering the rate of reaction

Irreversible inhibition

When an inhibitor covalently binds to an active site of an enzyme and fails to leave, disabling the enzyme

• Rare in nature but used in medicines

Competitive inhibitor

An inhibitor of an enzyme that binds to the active site and prevents substrate binding normally, decreasing the rate of reaction as none occur

• These are reversible and can be countered with greater substrate concentration

Uncompetitive inhibitor

An inhibitor of an enzyme that binds to the complete enzyme-substrate complex, preventing the release of products

• Cannot be countered with greater substrate concentration due to attraction to already-bound enzyme

• Can be unbound, allowing for occasional formation of products

Noncompetitive inhibitor

An inhibitor of an enzyme that binds outside of the active site, changing the enzyme structure so that normal binding cannot occur

• Cannot be countered with greater substrate concentration due to attraction to enzyme itself (requires greater enzyme concentration)

• Can be unbound with reversible effects

• Is a type of allosteric regulation

Allosteric regulation

Type of regulation where molecules bind to an enzyme outside of the active site and modify the enzyme’s shape, allowing for a change in activity

• This can be done non-covalently and reversibly

• Seen with noncompetitive inhibitors

Allosteric site

The binding location of molecules involved in the allosteric regulation of enzymes

• These are typically on different peptides of the protein

Phosphorylation

The process of modifying an amino acid by the addition of a phosphate group

• Can induce changes like increased hydrophilicity

• Is reversible

Kinase

A class of enzymes that catalyzes the addition of phosphate groups to proteins

Phosphatase

A class of enzymes that catalyzes the removal of phosphate groups from proteins