Module 2: Section 4 - Enzymes

• Enzymes are called biological catalysts because they speed up metabolic reactions in living organisms
• Catalysts speed up chemical reactions and remain unchanged at the end of the reaction, able to be used again
• A small amount of catalyst can catalyse the conversion of a large number of substrate molecules into product molecules
• The number of reactions that an enzyme molecule can catalyse per second is known as its turnover number

Intracellular enzymes - work within cells eg. catalyse breaks down hydrogen peroxide (by product of several cellular reactions)

Extracellular enzymes - occurs outside the cell eg. digestive enzymes such as amylase (catalyses the hydrolysis of starch into maltose in the mouth) and trypsin ( produced by the pancreas and secreted into the small intestine, catalyses the hydrolysis of peptide bonds)

Enzymes work by lowering the activation energy of a reaction - reactions can occur at much lower temperatures

If two substrate molecules need to be joined, attaching the enzyme holds them close together, reducing repulsion so they can bond more easily

If the enzyme is catalysing a breakdown reaction, fitting into the active site puts a strain on the bonds in the substrate so the substrate breaks up more easily

Lock and Key model

1. Enzyme's active site = complementary to the shape of the substrate molecule.

2. The substrate collides with the active site so the substrate ‘key’ fits into the active site ‘lock’. The substrate is then held in place so the reaction can go ahead, forming an ES-complex.

3. Products are formed - becomes the EP-complex. Products no longer fit so they move away.

Induced fit model

1. The substrate molecule collides with the active site. The enzyme changes shape slightly to make the active site fit more closely around the substrate. The substrate is held in place by oppositely charged groups on the substrate and the active site which found near each other.

2. The ES-complex is formed. The change in enzyme shape places a strain on the substrate molecule so that is destabilized it and the reaction occurs more easily

3. Products are formed - becomes the EP-complex. Products no longer fit so they move away.

As the temperature increases, the kinetic energy increases so the substrate and an enzyme molecules move around more quickly 

This makes the substrate collide with the enzymes active site more often, increasing the frequency of the formation of enzyme-substrate complexes

Applying heat makes the molecules vibrate 

These vibrations put strains on the hydrogen and ionic bonds, causing them to break 

The tertiary structure and the active site of the enzyme will change shape, as the bonds that are responsible for holding the tertiary structure in place break

The substrate can no longer fit the active site of the enzyme - the enzyme has become denatured

All enzymes have their own optimum pH - the pH at which the rate of reaction is highest

At optimum pH, the concentration of hydrogen ions in the solution gives the tertiary structure of the enzyme the best overall shape, so that it is complementary to the substrate

Above and below the optimum pH, the hydrogen ions will interfere with the ionic and hydrogen bonds that hold the enzyme's tertiary structure in place - active site changes shape so the enzyme is denatured

As the concentration of substrate increases, collisions between the enzyme's’ active site and substrate molecules occur more often

More enzyme-substrate complexes form, forming more product - increases the rate of reaction

If the concentration of substrate increases further, the rate of reaction will reach its maximum value (optimum) and stays constant

At this point all the active sites are occupied and so any further increase in substrate concentration will have no effect on the rate of reaction - the concentration of the enzyme becomes the limiting factor 

As the concentration of enzyme increases, more active sites become available 

Therefore it is easier for substrate molecules to collide with the active site so more enzyme-substrate complexes form, forming more product - increases the rate of reaction

If the concentration of enzyme increases further, the rate of reaction will rect its maximum value (optimum) and stays constant 

This is where all the substrate molecules are occupying enzyme active sites, so any further increase in enzyme concentration will have no effect on the rate of reaction - the concentration of the substrate becomes the limiting factor 

Control of enzyme concentration in living cells: 

• Enzyme synthesis - genes for synthesising particular enzymes can be switched on or off depending on a cell's needs
  
• Enzyme degradation - cells degrade old enzymes to regulate the metabolism in the cell and to ensure abnormal proteins are not accumulated in the cell
  

Some enzymes will only work if there is another non-protein substance (cofactor) bound to them 

Some cofactors are inorganic molecules or ions - help the enzyme and the substrate bind together, aren't used up or changed by the reaction eg. chloride ions are cofactors for amylase

Some cofactors are organic molecules - known as coenzymes

Participate in the reaction and are changed by it 

Often act as carriers, moving chemical groups between different enzymes - continually recycled during this process

Vitamins are often a source of coenzymes

If a cofactor is tightly bound to the enzyme, it is known as a prothetic group

For example, zinc ions are a prothetic group for carbonic anhydrase (catalyses the production of carbonic acid from water and carbon dioxide) - zinc ions are a permanent part of the enzyme's active site 

Competitive inhibitor molecules have a similar shape to that of substrate molecules

They compete with the substrate molecules to bind to the active site, blocking the active site so no reaction takes place

How much the enzyme is inhibited is depended on the relative concentrations of the inhibitor and the substrate:

• High concentration of the inhibitor = nearly all of the active sites will be taken up to hardly any of the substrate will get to the enzyme
• Higher conentration of the substrate = increases the substrate's chances of getting to the active site before the inhibitor 

Non-competitive inhibitor molecules bind to the enzyme away from its active site - allosteric site

This causes the active site to change shape so the substrate molecules can no longer bind to it 

They don't 'compete' with the substrate because they are a different shape

Increasing the concentration of the substrate won't make any difference to the reaction rate - enzyme activity will still be inhibited

Inhibitors can be reversible or non-reversible - depends on the strength of the bonds between the enzyme and the inhibitor

If they're strong, covalent bonds, the inhibitor can't be removed as easily and the inhibition is irreverable

If they're weaker hydrogen bonds or weak ionic bonds, the inhibitor can be removed and inhibition is reversable 

Some medicinal drugs are enzyme inhibitors:

• Some antiviral drugs - eg. reverse transcriptase inhibitors inhibit the enzyme reverse transcriptase, which catalyses the replication of viral DNA - prevents the virus from replicating
• Some antibiotics - eg. penicillin inhibihts the enzyme transpeptidase, which catalyses the formation of proteins in bacterial cell walls - weakens the cell wall and prevents it from regulating its osmotic pressure, so the cell bursts and the bacterium is killed

Metabolic poisons interfere with metabolic reactions - often enzyme inhibitors:

• Cyanide is an irreverable inhibitor of cytochrome c oxidase (catalyses respiration reactions - cells that cant respire die)
• Malonate inhibits succinate dehydrogenase (also catalyses respiration reactions)
• Arsenic inhibits the action of pyruvate dehydrogenase (also catalyses respiration reactions)

A metabolic pathway is a series of connected metabolic reactions. The product of the first reaction takes part in the second reaction and so on. Each reaction is catalysed by a different enzyme.

Many enzymes are inhibited by the product of the reaction they catalyse - product inhibition

End product inhibition is when the final product in a metabolic pathway inhibits an enzyme that acts earlier on in the pathway

Enables regulation of the pathway and controls the ablout of end-product that gets made

Both product and end-product inhibition are reversible - when the level of product falls, the level of inhibition will fall and the enzyme can start to function again, so more product can be made