C1.1 Enzymes and Metabolism

Catalyst

A substance that increases the rate of a chemical reaction. Eg. MnO2

Enzyme

Biological catalysts made by living ells, used for reactions that would proceed too slowly at cellular temperature to sustain life processes. Eg. Digestion

Substrate

Reactants converted to products in enzymes

Outline the structure and function of globular proteins

Have precise quaternary structure so that the folds of the peptide allow certain amino acid side chains to form an active site.

Outline the structure of active sites

Active sites are where substrates bind to be converted into products, typically close to the surface of the enzyme. Has a 3D shape and chemical proteins that match the substrate. Creating specificity for enzymes and substrates, so they vary in size.

Outline the function of active site

Catalyze reactions quickly and release products, so that some enzymes can perform thousands of reactions. If altered by environment or chem changes, results in loss of catalytic function.

Outline cyclical pathways

Chemical transformations in metabolic pathways happen in small steps. Occurs in nine steps, each catalyzed by a different enzyme to convert glucose into pyruvate.

Anabolic Reactions

Reactions that build large larger molecules from smaller ones, requires energy input.

Catabolic Reactions

Reactions that generally break down large molecules into smaller ones, releasing energy.

Transition state

Intermediate stage during which reactant/substrate bonds are being broken, while product bonds are beginning to form.

Activation energy

Energy input required to react the transition state in a chemical reaction

Exothermic

Chemical changes that result in a net release of energy as new bonds are made

Exergonic

Chemical changes that result in a release of energy used to do work. Eg. Use of ATP in a pump protein

Endergonic

Chemical changes that store energy in another molecules eg. making ATP

Outline the functions of heat from metabolic reactions

Heat is used to maintain a body temperature higher than the environment in bird and mammals. Can sometimes require cooling mechanisms such as perspiration.

Enzymes-substrate specificity

The ability of an enzyme’s active site to bind certain substrate molecules but not others.

Define Absolute Enzyme specificity

Specificity to only one substrate.

Define Broad Enzyme specificity

Works on multiple substrates.

Define Denaturation

Small disruptions to an enzyme’s property or shape resulting in the loss of function.

State the function of non-substrate molecules in an allosteric site

These molecules cause an increase or decrease in activity of the enzyme by changing the shape of its active site.

Outline Competitive inhibitors

Somewhat resemble substrates, but cannot be broken down by the enzyme. The temporarily bind to the active site, which blocks substrate molecules from being able to bind, resulting in slowed enzyme activity.

Outline level of inhibition

Relative to the ratio of an inhibitor to a substrate. As substrate concentration increases, inhibition decreases because the likelihood of substrate arriving at the active site before the inhibitor becomes higher. However non-competitive inhibitors stay effective at high substrate concentration due to their allosteric site.

Outline feedback inhibition

Enzyme inhibition is part of the bigger picture of regulating the different pathways of metabolic reactions. Regulation ensures that enough necessary products are produced.

Define end product

Often an intermediate/product towards the end of a pathway acting as an allosteric inhibitor of an enzyme early in the pathway.

Outline irreversible inhibition

Usually bond covalently to an active site, permanently stops its function.

Define mechanism-based inhibitors

Can be specific to an enzyme, where the inhibitor resembles the substrate. Considered to be toxic to biological systems

Outline Mechanism-based inhibitors

Can be lethal if the enzyme is involved in a vital process and in a high concentration.

Summarize Penicillin and its effects

Forms a covalent bond with the active site of transpeptidase. Transpeptidase would otherwise create the cross links needed to keep a bacterial cell wall strong enough to resist busting when in hypotonic solution. In the presence of penicillin, bacteria suffer from cell lysis.

Outline the steps of interactions between substrates and enzymes

(1) Substrate approaches the active site via diffusion, then electrostatic attraction takes place. (2) As the substrate binds, it causes a change in the active site that destabilizes bonds in the substrate and favors bond formation of the product(s). (3) If a second substrate is involved, it will bind in a different part of the active site. (4) Product bonds form, products are emptied out of the active site due to their different properties.

Substrate-active site collision

They encounter each other via the random motion of diffusion

Outline the requirement for effective colllisions

Requires a precise orientation, which enzymes can help achieve if the substrate is in very close proximity.

Outline reactions in cell cytoplasm

Relatively small substrates compared to enzymes, so while both are free-floating, substrate measurement is critical.

Outline the process if a enzyme is immobilized

Substrates must move towards them, usually down a concentration gradient.

Outline intercellular enzymes

Comes from ribosomes. Eg. Glycolysis reactions occurring in the cytoplasm

Outline extracellular enzymes

Made by ribosomes embedded in the endoplasmic reticulum, which forms vesicles that secrete these exoenzymes. Eg. digestive enzymes are secreted into the intestines of animals to break down macromolecules.

Define Metabolism

The complex network of interdependent chemical reactions within an organisms

Outline the steps for metabolic reactions to form pathways

(1) Arranges in chains or cycles, where each product is a substrate for the next step. (2) Catalyzed by enzymes specific to each step, which requires organisms to make many different enzymes. (3) Controlled by regulating the number of enzymes or inhibiting their function.