Enzyme

ENZYMES

A protein with catalytic properties due to its power of specific activation

Chemical reactions

Chemical reactions need an initial input of energy = THE ACTIVATION ENERGY During this part of the reaction the molecules are said to be in a transition state.

Reaction pathway

Making reactions go faster
Increasing the temperature make molecules move faster Biological systems are very sensitive to temperature changes.Enzymes can increase the rate of reactions without increasing the temperature. They do this by lowering the activation energy. They create a new reaction pathway “a short cut”

* Enzymes

Free Energy
Progress of the reaction
Reactants
Products
Free energy of activation
Without Enzyme
With Enzyme

Enzyme structure

Enzymes are proteins They have a globular shape A complex 3-D structure Human pancreatic amylase

The active site

One part of an enzyme, the active site, is particularly important The shape and the chemical environment inside the active site permits a chemical reaction to proceed more easily

* Enzyme-Substrate Complex

The substance (reactant) an enzyme acts on is the substrate
Enzyme
Substrate
Joins

Cofactors

An additional non-protein molecule that is needed by some enzymes to help the reaction coenzymes are organic molecules that are required by certain enzymes to carry out catalysis. Many vitamins are coenzymes Cofactors are often classified as inorganic substances that are required for, or increase the rate of, catalysis Fe+3,Fe+2, Zn+2
Nitrogenase enzyme with Fe, Mo and ADP cofactors )

The substrate

The substrate of an enzyme are the reactants that are activated by the enzyme Enzymes are specific to their substrates The specificity is determined by the active site


The Lock and Key Hypothesis
Fit between the substrate and the active site of the enzyme is exact Like a key fits into a lock very precisely The key is analogous to the enzyme and the substrate analogous to the lock. Temporary structure called the enzyme-substrate complex formed Products have a different shape from the substrate Once formed, they are released from the active site Leaving it free to become attached to another substrate

The Lock and Key Hypothesis

Enzyme may be used again
Enzyme-substrate complex
E
S
P
E
E
P
Reaction coordinate

The Lock and Key Hypothesis

This explains enzyme specificity This explains the loss of activity when enzymes denature

The Induced Fit Hypothesis

Some proteins can change their shape (conformation)When a substrate combines with an enzyme, it induces a change in the enzyme’s conformationThe active site is then moulded into a precise conformationMaking the chemical environment suitable for the reactionThe bonds of the substrate are stretched to make the reaction easier (lowers activation energy)


The Induced Fit Hypothesis
This explains the enzymes that can react with a range of substrates of similar types
Hexokinase (a) without (b) with glucose substrate http://www.biochem.arizona.edu/classes/bioc462/462a/NOTES/ENZYMES/enzyme_mechanism.html

Factors affecting Enzymes

Concentration of substrate Concentration of enzyme Temperature pH Inhibitors

Substrate concentration: Non-enzymic reactions

The increase in velocity is proportional to the substrate concentration
Reaction velocity
Substrate concentration

Substrate concentration: Enzymic reactions

Faster reaction but it reaches a saturation point when all the enzyme molecules are occupied. If you alter the concentration of the enzyme then Vmax will change too.
Reaction velocity
Substrate concentration
Vmax

The effect of pH

Optimum pH values
Enzyme activity
Trypsin
Pepsin
pH
1
3
5
7
9
11


The effect of pH
Extreme pH levels will produce denaturationThe structure of the enzyme is changed The active site is distorted and the substrate molecules will no longer fit in itAt pH values slightly different from the enzyme’s optimum value, small changes in the charges of the enzyme and it’s substrate molecules will occur This change in ionization will affect the binding of the substrate with the active site.

The effect of temperature

The effect of temperature

Enzyme activity

0
10
20
30
40
50
Q10
Denaturation

The effect of temperature

Inhibitors
Inhibitors are chemicals that reduce the rate of enzymic reactions. The are usually specific and they work at low concentrations. They block the enzyme but they do not usually destroy it. Many drugs and poisons are inhibitors of enzymes in the nervous system.

The effect of enzyme inhibition

Irreversible inhibitors: Combine with the functional groups of the amino acids in the active site, irreversibly. Examples: nerve gases and containing organophosphorus, combine with serine residues in the enzyme acetylcholine esterase.

The effect of enzyme inhibition

Reversible inhibitors: These can be washed out of the solution of enzyme by dialysis. There are two categories.

The effect of enzyme inhibition

Competitive: These compete with the substrate molecules for the active site.The inhibitor’s action is proportional to its concentration.Resembles the substrate’s structure closely. Enzyme inhibitor complex
Reversible reaction
E + I
EI

The effect of enzyme inhibition

Succinate
Fumarate + 2H++ 2e-
Succinate dehydrogenase
CH2COOH
CH2COOH
CHCOOH
CHCOOH
COOH
COOH
CH2
Malonate


The effect of enzyme inhibition
Non-competitive: These are not influenced by the concentration of the substrate. It inhibits by binding irreversibly to the enzyme but not at the active site.Examples Cyanide combines with the Iron in the enzymes cytochrome oxidase.Heavy metals, Ag or Hg, combine with –SH groups. These can be removed by using a chelating agent such as EDTA.

Applications of inhibitors

Negative feedback: end point or end product inhibition Poisons snake bite, plant alkaloids and nerve gases. Medicine antibiotics, sulphonamides.

Cell processes (e.g. respiration or photosynthesis) consist of series of pathways controlled by enzymes A B C D E F
Enzyme pathways
eF
eD
eC
eA
eB
Each step is controlled by a different enzyme (eA, eB, eC etc)  This is possible because of enzyme specificity

End point inhibition

The first step (controlled by eA) is often controlled by the end product (F) Therefore negative feedback is possible A B C D E F
The end products are controlling their own rate of production There is no build up of intermediates (B, C, D and E)
eF
eD
eC
eA
eB
Inhibition


Example: Phosphofructokinase and ATP
Substrate: Fructose-6-phosphateReactionFructose-6-phosphate + ATP  fructose-1,6-bisphosphate + ADP phosphofructokinase

ATP is the end point

This reaction lies near the beginning of the respiration pathway in cells The end product of respiration is ATP If there is a lot of ATP in the cell this enzyme is inhibited Respiration slows down and less ATP is produced As ATP is used up the inhibition stops and the reaction speeds up again