Enzymes

Enzymes are proteins that help chemical reactions but are not used up in the process. They catalyze chemical reactions. Molecules involved in catalyzed chemical reactions are known as substrates.

A cofactor is a non-protein molecule that helps in the chemical reaction. An example is the iron Heme used by cytochromes.

Substrates bond with the enzyme's "active site", to form an 'enzyme-substrate complex'. If more than 1 substrate is required then it may also bond at the active site. They are known as the reactants. Active sites are specific to certain substrates and certain reactions.

Once the chemical reaction is complete, products are released, and the enzyme can begin the process again.

Enzymes speed up biochemical reactions.

  • Acid/Base catalysis. acids and bases are proton carriers and help with proton (H+ transfer
  • covalent catalysis. The enzyme will covalently bind to the molecules and help with electron transfer. It acts as an electron carriers or sink.
  • electrostatic catalysis. e.g. to work on negatively charged DNA, a metal ion Mg is used to stabilise charge.
  • proximity and orientation effect. some enzymes will help bump two molecules together in the right way.

References

Intro to enzymes and catalysis at Khan Academy.

Energy

A molecule in a low energy state is in its stable form.

A catalysed reaction has a smaller activation energy than uncatalysed.

Chart of a reaction coordinate diagram. The x-axis is reaction progress or state of molecule, y-axis is energy.

There is a hill to get from A to B, the top of the hill, ‡ is the transition state.

The free energy of activation is the energy required to get from A to the transition state. ΔG

The standard free energy change for the reaction is between B and A. ΔG°

Enzymes and activation energy at Khan Academy.

Induced Fit

There are steps that happen in a catalysed reaction.

  1. enzyme (E) and substrate (S) are separate.
  2. Initial binding. ES together form the 'enzyme-substrate complex'.
  3. Transition state, induced fit. E and S are together and are very tightly bound. This is the highest energy level.
  4. reaction occurs, and S becomes products P1 and P2
  5. Products are released.

Activators or inhibitors (regulating molecules), could bind at allosteric sites (a binding site that is NOT the active site). This causes conformational changes on the enzyme, so the active site's shape is different.

Induced fit model of enzyme catalysis.

Types of enzymes

Transferase

A + BX -> AX + B

Transfers molecule X from B to A.

Ligase

A + B -> AB

Ligate or join. Combine to form a complex. DNA ligase joins DNA strands.

Oxidoreductase

redox reaction.

Dehydrogenase

Removes a hydride functional group.

Isomerase

A -> B, where B is an isomer of A.

There is only 1 product and 1 substrate.

Epimerase

Epimerase is a type of isomerase enzyme.

Hydrolase

A + H2O -> B + C

Hydrolysis uses water to create B and C from A. e.g. cleave peptide bonds.

Lyase

A -> B + C

Doesn't use water, or redox.

Six types of enzymes at Khan Academy.

Co-factor or Co-enzymes

Co-enzymes are organic carrier molecules. NADH may act as an electron carrying co-enzyme.

Co-factors participate in catalysis. e.g. Mg2+ co-factor stabilises electronegative DNA.

Vitamins are organic co-factors and co-enzymes.

Minerals are inorganic co-factors.

Co-factors, co-enzymes and vitamins at Khan Academy.

Enzyme Environment

Certain enzymes will prefer certain pH and temperature.

pH

DNA polymerase

temperature

Fever stops digestive enzymes working.

Enmzymes and their local environment at Khan Academy.