Enzymes

Enzyme

A substance produced by a living organism which acts as a catalyst to bring about a specific biochemical reaction.

What are enzymes made of?

Usually protein, but can be RNA. Often contain other chemical groups in order to function.

Catalyst

A substance that makes a chemical reaction happen more quickly without being produced or consumed within the reaction

Catalytic power

A numerical measure of the ratio of the catalysed vs uncatalysed rate of reaction

Rate enhancement

General term meaning that enzymes are making pre-existing chemistry happen faster

Reaction coordinate

An arbitrary measure of progress through a reaction

How do enzymes make reactions faster?

By lowering activation energy

kinetics

How fast A goes to B. Depends on the size of the energy barrier that the enzyme needs to overcome to make the reaction happen.

Things that effect activation energy

enzymes, a higher temperature

Regardless of whether an enzyme is present or not...

The amount of energy released in the reaction stays the same.

Induced fit model

When the protein binds to the substrate the protein changes its conformation to accommodate the substrate. This puts some energy into the system and destabilises the substrate and protein, driving the reaction

The rate of formation of products depends on..

How much enzyme substrate complex there is

How much more substrate compared to enzyme is there

Around 1000x

When is there no capacity to increase rate of reaction?

When all of the enzyme has bound to the substrate

Vmax

Maximum rate the enzyme can achieve

KM

the Michealis constant- the substrate concentration that gives a rate of Vmax/2. The amount of substrate required to reach half of Vmax.

What does Km tell you about an enzyme?

Substrate affinity for the enzyme

Competitive inhibition

A molecule of similar shape to the substrate binds to the active site where the substrate wants to bind

Competitive inhibition example

Tamiflu- targets neuraminidase and cleaves sialic acid off of host cells, increasing KM

Non-competitive inhibition

Inhibitor binds to the allosteric site of the enzyme and brings about conformational change in the enzyme, inhibiting it. Changes the shape of the active site so the substrate is no longer able to bind. Decreases KM.

Non competitive activators

Make the enzyme more active

How can competitive inhibition be overcome?

Increasing substrate concentration

How is the gradient of the line on the graph determined?

KM/Vmax

Active site

3 dimensional cleft where the substrate can bind. Often made from amino acids that come from various parts of the primary structure of the protein

Serine proteases

Family of enzymes which break peptide bonds.

Serine protease in digestion

chymotrypsin

serine protease in blood clotting

Factor X

Serine

Usually an inert amino acid with a hydroxyl group on it. They are not usually particularly reactive.

How does serine become activated

By being adjacent to the carboxylic acid and imidazole group

acid-base catalysis

Making the transition state more stable by bonding back to the enzyme

Chymotrypsin

Breaks down proteins that have got aromatic amino acids and this is enabled by binding into the pocket

How is specificity defined

Amino acids adjacent to the active site

Convergent evolution

Evolved independently but has the same amino acid arrangement

Carbonic Anhydrase

catalyzes the conversion of carbon dioxide gas and water into carbonic acid

What can absence of carbonic anhydrase lead to

osteopetrosis and cerebral calcification

What is carbonic anhydrase needed for

efficient carbon dioxide transport in the body

catalysis by approximation

The enzyme is able to the stabilise the intermediate in a reaction by bringing the substrates closer together. In solution, substrates may not meet very often.

CTP

acts as a non competitive inhibitor of aspartate carbamoylase