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Enzymes and biological reactions Cheat Sheet (DRAFT) by

Core principles 4 Enzymes and biological reactions

This is a draft cheat sheet. It is a work in progress and is not finished yet.

Key Terms

Primary Structure
Formed from the order of amino acids
Conden­sation
Reaction occurs joining 2 molecules together into a larger one with the elimin­ation of water
Secondary Structure
Formed from the folding of the primary structure into 2 main forms: the alpha helix or beta pleated sheet
Tertiary Structure
Formed from the folding of the secondary structure into a 3D shape
Hydrolysis
The breaking down of large molecules into smaller ones by the addition of a molecule of water

Metabolism Terms

Metabolism
A series of enzyme­-co­ntr­olled reactions in the body. There are 2 main types:
Anabolic Reactions
Protein synthesis where amino acids are built up into more complex polype­ptides
Catabolic Reactions
Digestion of proteins where complex polype­ptides are broken down into simple amino acids

Key Terms

Enzyme­-su­bstrate complex
An interm­ediate structure formed during an enzyme­-ca­talysed reaction in which the substrate and enzyme bind tempor­arily, such that the substrates are close enough to react
Activation energy
The minimum energy that must be put into a chemical system for a reaction to occur

Key Points about Enzymes

They are proteins that speed up chemical reactions
They lower the activation energy needed for the reaction to take place
They don't actually take part in the reaction
They are only needed in small quantities
They can be re-used
They convert substrates into products
Therefore they can be described as biological catalysts

Inhibitors

Enzymes can be inhibited by other substa­nces, which can either combine with the active site directly or bind to another part of the enzyme to prevent the formation of an enzyme­-su­bstrate complex.
2 forms of inhibition exist, compet­itive and non-co­mpe­titive inhibi­tion, which may be either reversible (where inhibitor binds tempor­arily) or irreve­rsible (where the inhibitor binds perman­ently).

Compet­itive Inhibition

This is where a molecule has a similar shape to the substrate and so it also has a compli­mentary shape to the active site.
The first molecule to collide succes­sfully with the active site will form a complex.
By increasing the concen­tration of substrate, the inhibition is overcome, so long as the inhibition is reversible, as it is more likely that a substrate molecule will form an enzyme­-su­bstrate complex.

Compet­itive Inhibition diagram

Compet­itive Inhibition Summary

The substrate and compet­itive inhibitor both 'compete' for the active site. It can be overcome by increasing substrate concen­tra­tion.

Biosensors

Contain immobi­lised enzymes that can be used to detect small concen­tra­tions of specific molecules in a mixture, e.g. glucose in a sample of blood.
A biosensor consists of a specific immobi­lised enzyme, a select­ively permeable membrane, and a transducer connected to a display.
The select­ively permeable membrane allows the metabolite to diffuse through to the immobi­lised enzyme, whilst preventing the passage of other molecules.
The metabolite binds to the active site of the enzyme, and is converted into a product, which in turn combines with the transducer turning the chemical energy into an electrical signal.
The higher the concen­tration of metabolite present, the greater the electrical signal.
This technique is used to accurately measure the blood glucose of diabetic parents whose blood glucose should normally be kept between 3.89 and 5.83mmol dm-3.
 

Enzyme Structure

Complex folded polype­ptide chains that are held together in a complex 3D shape
each amino acid in primary structure is joined to the next by a conden­sation reaction which forms a peptide bond
This structure is then folded into an alpha helix or beta pleated sheet, held together by hydrogen bonds called the secondary structure
The secondary structure is folded again to form a 3D shape that is held together by hydrogen, ionic and disulphide bonds
This creates an active site where substrates can bind
The bonds that hold the tertiary structure in place are suscep­tible to changes in temper­ature, pH and the action of reducing agents
Enzymes act in an aqueous enviro­nment because they are soluble and catalyse many reactions including hydrolysis

How enzymes work

In a catabolic reaction, the substrate binds to the active site, forming the enzyme­-su­bstrate complex.
The reaction proceeds and products are released, the active site is now free to catalyse another reaction.
In anabolic reactions, several substrates bind and one or more products are released.
As biological reactions, enzymes lower the activation energy needed to start a reaction by providing energy to break bonds in existing molecules so new ones can form in new molecules. By doing so, chemical reactions are sped up.

Enzyme work

Intrac­ellular and Extrac­ellular

Enzymes may act intrac­ell­ularly, e.g. during protein synthesis where the formation of a peptide bond between 2 amino acids is catalysed.
Or extrac­ell­ularly e.g. when pancreatic amylase is released from pancreatic cells and travels to the small intestine via the pancreatic duct where it catalyses the breakdown of starch to maltose.

Factors affecting the rate of reaction

Rate of reaction = number of reactions that occur per second or unit time
Enzyme action is affected by 5 things:
1. Substrate concen­tration
2. Temper­ature
3. pH
4. Enzyme concen­tration
5. Presence of inhibitors

Product formation

Product formation is different from the rate of reaction as it shows the total product made.
Once a plateau is reached, no more product is formed and the reaction has stopped.
With a rate of reaction graph, the rate would drop to zero at this point.

Product formation diagram

Non-co­mpe­titive inhibition

An inhibitor binds to another site on the enzyme (the allosteric site).
This binding changes the shape of the active site, preventing substrate molecules from forming an enzyme­-su­bstrate complex.
An example is cyanide that binds to cytochrome oxidase inhibiting respir­ation.

Non-co­mpe­titive inhibition diagram

Non-co­mpe­titive inhibition summary

The inhibitor binds to an allosteric site deforming the shape of the enzyme's active site. It cannot therefore be overcome by increasing substrate concen­tra­tion.

Biosensor definition

A device that combines a biomol­ecule such as an enzyme, with a transducer, to produce an electrical signal which measures the concen­tration of a chemical.

Biosensor diagram

  

Lock and Key Model

The substrate has a compli­mentary shape to the enzyme's active site, like a key fitting into a lock.
This explains the specif­icity of many enzymes i.e. that many only catalyse one substrate.

Lock and key diagram

Induced fit model

Many observ­ations show that the enzymes active site was being altered by the binding substrate molecule.
The induced fit theory suggests that the active site is able to change slightly to accomm­odate the substrate.
This change places strain on the substrate molecule, helping to break bonds and so lowering the activation energy.
This explains why in some cases several molecules with similar shapes are able to bind to the active site.
This is shown by the enzyme lysosome, which is an anti-b­act­erial enzyme found in human tears and saliva.
The active site consists of a groove, which closes over the polysa­cch­arides found in the bacterial cell walls, and the enzyme molecule changes shape, which allows hydrolysis to occur.

Induced fit diagram

Substrate concen­tration

When the substrate concen­tration increases in an enzyme­-co­ntr­olled reaction, there is a greater chance of a successful collision between the substrate and the enzyme resulting in more enzyme­-su­bstrate complexes forming which increases the rate of reaction.
When all the enzyme active sites are occupied, a plateau is reached which represents the maximum rate of reaction for their condit­ions.

Substrate concen­tration diagram

Enzyme concen­tration

When the substrate concen­tration increases in an enzyme­-co­ntr­olled reaction, there is a greater chance of a successful collision between the substrate and enzyme so more enzyme­-su­bstrate complexes are formed, thus increasing the rate of reaction.
As long as substrate is present in excess this will continue to rise so long as there are no limiting factors.

Enzyme concen­tration diagram

End product inhibition

Often seen in complex metabolic pathways where several enzymes are involved.
It is an example of compet­itive inhibition at work in cells, and prevents the build-up of the end product in the pathway, which could become harmful.
In essence, the product of one reaction acts as the substrate for the next, and the end product acts as a compet­itive inhibitor for an enzyme earlier in the pathway.
In the example below, the end product inhibits enzyme 1: as the end product is used up in the cell, the concen­tration of end product falls and the concen­tration of the initial substrate rises, so overcoming the inhibi­tor's effect

End product inhibition diagram

Advantages of immobi­lised enzymes

1. Enzymes can be easily recovered and reused.
2. Product is not contam­inated by the enzyme .
3. More stable at higher temper­ature.
4. Catalyse reactions at a higher range of pH.
The result is that several enzymes with different temper­ature and pH optima can be used at the same time.
Enzymes can also be easily added or removed giving greater control over the reaction.
 

Temper­ature

When the temper­ature of an enzyme and substrate increases in an enzyme­-co­ntr­olled reaction, both the enzyme and substrate molecules gain more kinetic energy and so move faster, increasing the chance of a successful collision between them.
As more enzyme­-su­bstrate complexes are formed, the rate of reaction decreases rapidly as hydrogen bonds in the tertiary structure break due to increased vibrations resulting in a change to the shape of the active site - this is called denatu­ring.

Temper­ature diagram

pH

When the pH of an enzyme increases or decreases either side of the optimum, the rate of reaction decreases.
The charges on the amino acid side chains (R groups) that make up the enzyme's active site are influenced by free hydrogen (H+) and hydroxyl (OH-) ions.
If too many H+ or OH- ions are present, the substrate can be repelled from the active site, preventing it from binding.
If these changes are relatively minor, then it is revers­ible.
More excessive changes in pH will result in the ionic bonds in the tertiary structure breaking which causes denaturing by creating a permanent change to the shape of the active site.

pH diagram

pH Optimum

Use of buffers in enzyme experi­ments

The rate of an enzyme­-co­ntr­olled reaction, is greatly influenced by small changes in pH.
It is therefore essential, when carrying out any enzyme experiment (where pH is not the indepe­ndent variable), that pH is controlled, ideally at its optimum, so it is not limiting the rate of reaction.
This can be achieved by using a pH buffer.
A buffer is a solution that can resist changes in pH by neutra­lising acid/alkalis that are added to the solution.
In the body, we buffer the pH of the blood around 7.4 by using 2 chemicals - carbonic acid and bicarb­onate.

Buffer Summary

A chemical that resists changes in pH.
Neutra­lises excess acids or alkslis.
Can be used to maintain the optimum pH for a given reaction.

Importance of immobi­lised enzymes

Immobi­lised enzymes are enzymes that are fixed to an inert matrix. This can be achieved in 2 main ways:
1. Entrapment - held inside a gel e.g. silica gel.
2. Micro-­enc­aps­ulation - trapped inside a micro-­capsule e.g. alginate beads.
Beads containing the enzyme can be packed into a glass column, and substrate added at one end.
The rate of flow of the substrate over the beads can be controlled: a slow flow rate will give more time for the enzyme­-su­bstrate complexes to form, and therefore yield more product.
Because the enzymes are contained within their own 'micro­-en­vir­onment', the enzymes are less suscep­tible to changes in pH, temper­ature and the action of chemicals such as organic solvents.