Enzymes

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

© 2007 Paul Billiet ODWS

http://www.saburchill.com/IBbiology/bio_hp.html

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”



An enzyme controlled pathway

Enzyme controlled reactions proceed 108 to 1011 times faster than corresponding non-enzymic reactions.



Enzyme structure Enzymes are

proteins They have a

globular shape A complex 3-D

structure

Human pancreatic amylase© Dr. Anjuman Begum


http://www.chem.ubc.ca/personnel/faculty/withers/group/group/begum/begum.htm

http://www.chem.ubc.ca/personnel/faculty/withers/group/group/begum/begum.htm


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

© H.PELLETIER, M.R.SAWAYA ProNuC Database


http://gibk26.bse.kyutech.ac.jp/jouhou/image/dna-protein/all/small_N9icw.gif


Cofactors An additional non-

protein molecule that is needed by some enzymes to help the reaction

Tightly bound cofactors are called prosthetic groups

Cofactors that are bound and released easily are called coenzymes

Many vitamins are coenzymes Nitrogenase enzyme with Fe, Mo and ADP cofactors

Jmol from a RCSB PDB file © 2007 Steve Cook H.SCHINDELIN, C.KISKER, J.L.SCHLESSMAN, J.B.HOWARD, D.C.REES

STRUCTURE OF ADP X ALF4(-)-STABILIZED NITROGENASE COMPLEX AND ITS

IMPLICATIONS FOR SIGNAL TRANSDUCTION; NATURE 387:370 (1997) © 2007 Paul Billiet ODWS

http://www.steve.gb.com/science/nitrogen_metabolism.html


http://www.steve.gb.com/science/nitrogen_metabolism/nitrogenase.html

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© 2007 Paul Billiet ODWS


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 conformation The active site is then moulded into a precise

conformation Making the chemical environment suitable for the

reaction The 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 substratehttp://www.biochem.arizona.edu/classes/bioc462/462a/NOTES/ENZYMES/enzyme_mechanism.html


http://www.biochem.arizona.edu/classes/bioc462/462a/NOTES/ENZYMES/enzyme_mechanism.html


Factors affecting Enzymes substrate concentration pH temperature 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 denaturation The structure of the enzyme is changed The active site is distorted and the substrate

molecules will no longer fit in it At 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 ionisation will affect the binding of the substrate with the active site.



The effect of temperature Q10 (the temperature coefficient) = the increase in

reaction rate with a 10°C rise in temperature. For chemical reactions the Q10 = 2 to 3

(the rate of the reaction doubles or triples with every 10°C rise in temperature)

Enzyme-controlled reactions follow this rule as they are chemical reactions

BUT at high temperatures proteins denature The optimum temperature for an enzyme controlled

reaction will be a balance between the Q10 and denaturation.



The effect of temperature

Temperature / °C

Enzyme activity

0 10 20 30 40 50

Q10 Denaturation


The effect of temperature For most enzymes the optimum temperature is about

30°C Many are a lot lower,

cold water fish will die at 30°C because their enzymes denature

A few bacteria have enzymes that can withstand very high temperatures up to 100°C

Most enzymes however are fully denatured at 70°C


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. © 2007 Paul Billiet ODWS

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 pesticides, 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 inhibition1. 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 inhibition2. 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,

sedatives and stimulants


Education

Enzymes