Enzymes and Protein Structure and inhibitor

Flashcards covering key vocabulary from the Biology 211 lecture on Biomolecules and Cellular Systems, including protein structure, enzyme function, kinetics, and regulation.

Proteins

Polymers of amino acids that are folded into specific 3D shapes.

Amino Acids

The 20 building blocks of proteins, each containing an amino group, a carboxyl group, an alpha carbon, and a variable R group.

Peptide Bond

A covalent bond formed through a dehydration reaction between the carboxyl group of one amino acid and the amino group of another.

N-terminus (Amino Terminus)

The end of a polypeptide chain with a free amino group.

C-terminus (Carboxyl Terminus)

The end of a polypeptide chain with a free carboxyl group.

Hydrogen Bond

A weak, noncovalent interaction important in stabilizing protein structures.

Hydrophobic R-groups

Non-polar amino acid side chains that do not form hydrogen bonds and are 'water-hating'.

Hydrophilic R-groups

Polar amino acid side chains that can form hydrogen bonds and are 'water-loving', including uncharged polar, negatively charged (acidic), and positively charged (basic) types.

Polypeptide

A polymer consisting of more than 10 amino acids joined together.

1° Structure (Primary Structure)

The unique sequence of amino acids in a polypeptide chain, connected by peptide bonds.

2° Structure (Secondary Structure)

Local folded structures like helices (alpha-helix) and sheets (beta-sheet) formed by hydrogen bonds between atoms of the polypeptide backbone.

Helices

A common secondary structure where the primary structure is coiled and stabilized by hydrogen bonds between main chain (backbone) atoms.

Sheets

A common secondary structure where the polypeptide backbone is stabilized into sheet-like formations through hydrogen bonds between main chain atoms of adjacent strands.

3° Structure (Tertiary Structure)

The overall 3D shape of a single polypeptide chain, resulting from interactions between the R-groups (e.g., hydrophobic( vandaal wall interactions, disulfide linkages, ionic bonds, hydrogen bonds).

• example: Hexokinase: tertiary structure with overalll shape of protein which result fromt eh organizaition of secondary structural regions relative to one another .

4° Structure (Quaternary Structure)

The arrangement of multiple polypeptide subunits (each with its own tertiary structure) to form a functional protein complex.

Homotrimer

A protein composed of three identical polypeptide subunits.

Heterotrimer

A protein composed of three different polypeptide subunits.

Activation Energy (Ea)

The initial energy barrier that must be overcome to destabilize bonds in reactants and allow a chemical reaction to proceed.

Transition State

The high-energy, unstable intermediate in a chemical reaction where reactant bonds are breaking and product bonds are forming.

Enzymes

Biological catalysts, mostly proteins, that significantly increase the rate of chemical reactions by lowering the activation energy. Influence:

• rate of chemical reaction

• the Deal of chemical reaction

• not infleunce DG

Active Site

A specific region on an enzyme that binds to the substrate and is responsible for forming the transition state and initiating catalysis.

Induced Fit Model

A model describing how an enzyme's active site changes shape slightly upon binding to its substrate, forcing the substrate into a transition state conformation.

1. an enzyme has an active site - where interact with substrate

2. substrate enter active site, then the enzyme change shape to become enzyme substrate complex

3. Es force reactant tot eh trasition state,

4. by forcing reactant to the trasition state, enezyme reduce the need as much activation energy

5. product is released and enxyme change back to orginal confomation, ready to bind to anotehr substrate

Vmax

The maximum rate of an enzyme-catalyzed reaction when the enzyme is fully saturated with substrate.

• All active sites are occupied by substrate

• When presence of inhibitor, only reversible competitive inhibitor can reach this Vmas, noncompetitive cannot

Reversible Competitive Inhibitor

A molecule that is chemically similar to the substrate and noncovalently binds to the enzyme's active site, competing with the substrate. So that if substrate need to increase concentration to outcompete this inhibitor, this is why Vmax can be reached

Reversible Noncompetitive Inhibition

A type of inhibition where an inhibitor binds noncovalently to an allosteric site on the enzyme (not the active site), altering the enzyme's conformation and reducing its affinity for the substrate.

• If noncompetitve inhibior bind to the allosteric site of enzyme, than it will make the enzyme become less active, then it does not work anymore, leading the decrease in amoung of enzyme, and then decrease rate of reaction

Regulatory (Allosteric) Enzymes

Enzymes that control the rate of entire biochemical pathways by changing their shape and activity upon binding to activators or inhibitors at sites other than the active site.

• quanternaty ( more than 1 active site)

• both active forma nd inactive is revesrible and change

Allosteric Activator

A molecule that binds to an enzyme at an allosteric site, changing its shape to a more active form.

Allosteric Inhibitor

A molecule that binds to an enzyme at an allosteric site, changing its shape to a less active form.Le tthe subsstrate then cannot fit with active site

Feedback Inhibition

A regulatory mechanism where the final product of a biochemical pathway inhibits an enzyme early in the same pathway, thus controlling its own production.

• End of product bind to allosteric enzyme and stabilize in active form, it turn down the enzyme activity

ways that enzyme help form the transition state

1. binding reacting molecules close togeether in correct orientation for reaction to occur

2. Charge interaction stabilized the trasition state through ionic reaction with charged R-group

3. Physcially distort the bonds of substrate to help form the trasition state

Infleunce hwo calls can convert substrate to product

• temperature

• concentration of reactant

• concentration of enzyme

• pH

How pH can alter enzyme function

Protein is hold together by Hydrogen bond, which can be affected by changes in pH. Changes in pH can lead to denaturation of the protein or alter the charge of the R-groups. Protein cahanges shape then enzyme function decreases

How temperature affect enzyme

at low temp, enzyme activity is slow to to slow motion of molecules. As temp increase, activation energy increase until temperature become too high ( optimal range) and the protein denatures. As it denatures because it cannot withstand thermal jostling of atoms at high temp