BIO 3.2-3.5 - Biochemical pathways and enzymes

Biochemical reaction

A reaction occurring in a cell that leads to the formation of a product from a reactant

Biochemical pathways

A series of linked biochemical reactions

Enzyme

A protein that acts as a biological catalyst that speeds up chemical reactions by decreasing the activation energy required for the reaction to occur

Catalyst

A factor that causes an increase in the rate of reaction

Activation energy

The minimum amount of energy required to initiate a chemical reaction

Substrate

The reactant that an enzyme acts on

Active site

The region of an enzyme that temporarily binds with the specific substrate of the enzyme

Intracellular enzymes

Enzymes that are made inside the cell and remain inside to speed up and control metabolism

Extracellular enzymes

Enzymes that are made inside the cell but are activated outside of the cell

Catabolic reaction

A reaction in which complex molecules are broken down into simple molecules

Anabolic reaction

A reaction in which complex molecules are built from simple molecules

Exergonic reaction

A reaction where energy is released (catabolic reactions are exergonic)

Endergonic reaction

A reaction where energy needs to be absorbed (anabolic reactions are endergonic)

The lock-and-key hypothesis

• Each enzyme has an active site with a distinct shape which only the specific substrate molecules can fit

• The active site is the ‘lock’ and the substrate is the ‘key’

• The enzyme puts pressure on the bonds of the substrate, catalysing the reaction

The induced fit model

• When the substrate binds to the active site, the active site changes shape slightly to accommodate the substrate molecule (induced form)

• This puts strain on the bonds within the substrate, therefore reducing the activation energy required to catalyse the reaction

• The active site returns to its relaxed form after releasing the substrate

Properties of enzymes (5)

1. Enzymes speed up chemical reactions that would otherwise be too slow

2. Enzymes are specific to a particular reaction

3. Enzymes can be reused after catalysing a reaction

4. Enzymes are denatured at high temperatures (loses its shapes and becomes inactivated)

5. Enzymes have an optimum pH range

Cofactor

Small inorganic ions or organic molecules that alter the active site of an enzyme

Coenzyme

A non-protein organic molecule that acts with an enzyme to alter the rate of reaction

Roles of coenzymes

• Transfer particles such as phosphates, hydrogens and electrons

• Transfer energy

Loaded form

A high energy form of a coenzyme that can donate electrons and hydrogen ions

Unloaded form

A low energy form of a coenzyme that accepts electrons and hydrogen ions

Denaturation

The loss of enzyme structure and function due to the breaking of bonds upon heating, causing the active site to permanently change shape

Factors that impact enzyme function (6)

1. Temperature

2. pH

3. Substrate concentration

4. Enzyme concentration

5. Cellular compartmentalisation

6. Enzyme inhibitors

How is rate of reaction affected by temperature?

• Enzymes have an optimum temperature at which they work best

• As temperature increases from 0 to the optimum, the rate of reaction increases because the kinetic energy of molecules increases and causes more frequent collisions

• Above the optimum temperature, the rate of reaction declines and then ceases due to the denaturation of enzymes

How is rate of reaction affected by pH?

• Different enzymes have different optimum pH levels

• The enzyme will denature if the pH is too high or too low

How is rate of reaction affected by substrate concentration?

• As substrate concentration increases, the rate of reaction increases until it reaches a maximum and plateaus

• A higher concentration increases the frequency of collisions

• The plateau occurs because the system becomes saturated when all the enzyme molecules are working at maximum efficiency

How is rate of reaction affected by enzyme concentration?

As enzyme concentration increases, the rate of reaction increases linearly if there is unlimited substrate and other factors remain constant

Cellular compartmentalisation

Having separate organelles in eukaryotes allows for the creation of an optimal environment for specific enzymes to function

Inhibitor

A molecule that binds to an enzyme to slow down or stop the enzyme’s function

Reversible inhibition

The bonds that form between the enzyme and the inhibitor molecule are very weak hydrogen bonds that can be easily broken

Irreversible inhibition

The bonds that form between the enzyme and the inhibitor molecule are strong covalent bonds that will not break

Competitive inhibitors

• Competitive inhibitor molecules have a similar shape to the enzyme’s normal substrate molecules

• The inhibitor and substrate molecules compete for the active site. If the inhibitor binds first, it prevents the substrate from binding and reacting.

• The concentrations of the inhibitor and substrate molecules determine which is more likely to enter the active site

Non-competitive inhibitors

• Non-competitive inhibitor molecules bind to a site that is not the active site

• This causes the shape of the active site to change, meaning the substrate can no longer bind to the active site

Why do biochemical pathways need to be regulated? (3)

• To prevent waste of resources and energy

• To prevent build-up of harmful products

• To prevent depletion of substrates

The two directions that biochemical pathways are regulated

• Down-regulated - slowing or stopping enzymes in the pathway (inhibition)

• Up-regulated - increasing the activity of enzymes in the pathway

Allosteric enzymes

Enzymes consisting of two or more polypeptide chains that can exist in an active form and an inactive form

Allosteric inhibition

• An inhibitor can bind to the allosteric site, changing the enzyme from active to inactive form

• The inactive form of the enzyme is shaped so that the substrate will not fit into the active site

• This is an example of non-competitive inhibition because the inhibitor does not bind to the active site

Allosteric activation

• An activator can bind to the allosteric site, changing the enzyme from inactive to active form

• The active form of the enzyme enables the substrate to bind to the active site, allowing the enzyme to catalyse the reaction

Feedback inhibition

• The end products of certain metabolic pathways can act as inhibitor molecules by binding to enzymes further back in the pathway

• The amount of product produced is regulated by how much product is currently present (negative feedback loop)