Biology Paper 2 - 2.4 Enzymes

Biological catalyst. Speeds up chemical reactions by lowering activation energy. They are not used up in the reaction/remain unchanged. Intracellular - act within the cell. Extracellular - act outside the cell. Specific to one substrate(s)/reaction.

Catalase - breaks down hydrogen peroxide, formed during metabolic processes, into water and oxygen.
Four polypeptide chains and a haem group.
Held in vesicles in white blood cells, breaks down ingested pathogens.

Amylase - produced in salivary glands, hydrolysis amylose to maltose.
Trypsin - made in pancreas, released into lumen of small intestine; hydrolysis peptide bonds.

A substance that must be present to ensure enzyme reaction takes places. Prosthetic group or coenzyme.

Molecule permanently bound to enzyme molecule via covalent bond. Carbonic anhydrase has zinc ion bound to active site.

Ion or organic coenzyme not permanently bound to active site. Temporary bonds form between enzyme or substrate to ease formation of enzyme - substrate complex. Co-substrates bind to substrate to enable substrate to form correct complement to active site. Cofactor may change distribution of charges on surface of substrate.

Small organic, non-protein molecule. Binds temporarily to active site of enzyme. Coenzyme altered by reaction and is recycled to original state.

Cleft or pocket on surface of enzyme. Complementary to shape of substrate.

Enzyme with substrate(s) held in active site. Joined by non-covalent forces.

Enzyme with product(s) held in active site. Joined by non-covalent forces.

Tertiary structure of enzyme gives active site a shape that is exactly complementary to specific substrate. Substrate fits exactly into active site. Temporary hydrogen bonds form ESC. Substrate broken into product, products leaves active site.
Note: if more than one substrate enters active site to form larger product, an enzyme product complex forms as an intermediary stage before product is released.

Active site has shape that complements the substrate but is not an exact fit when substrate not bound. On binding of substrate, interactions between R groups lining active site and surface of substrate cause conformational change. Enzyme active site molds around substrate. ESC forms. Hydrogen bonds, ionic interactions and hydrophobic interactions bind substrate to active site. Substrate converted to product, product remains in active site, enzyme product forms. Product has different conformation to substrate, active site relaxes. Product released.

An increase in heat leads to an increase in kinetic energy. Enzyme and substrate gain kinetic energy. An increase in successful collisions leads to an increase in ESC. More product is released. Until an optimum temperature is reached.

Molecules vibrate as kinetic energy increases. Hydrogen bonds break and tertiary structure of enzyme active site alters. Substrate no longer fits into active site and rate of reaction decreases. As temperature rises further ionic interactions and disulphide bonds break and enzyme active site is irreversibly altered. The enzyme is denatured. Heat does not break the peptide binds that hold the primary structure.

For most enzyme catalysed reactions - between 0°C and 40°C the rate of reaction will double for every 10°C increase. Above the optimum temperature the coefficient drops as the enzyme active site denatures.
Q10 = rate of reaction at (x + 10) °C divided by rate of reaction at x °C.

The temperature at which an enzyme reaches its maximum rate of reaction.
Note that optimum temperatures vary according to the conditions in which an organism lives.

A measure of acidity/alkalinity. Acids dissociate into protons, H+ and a negative ion. Alkalis dissociate into hydroxide, OH- and a positive ion.

A chemical or molecule that resists changes in pH. They do this by accepting or donating protons or hydroxide ions.

Protons carry a positive charge and are attracted to negative R groups. Hydroxide ion carry a negative charge and are attracted to positive R groups. Protons and hydroxide ions disrupt hydrogen bonds that hold secondary structures in place. Protons and hydroxide ions disrupt hydrogen bonds and ionic bonds that hold tertiary structures in place. Disruption of secondary and tertiary structures may alter the shape of the active site so that it no longer compliments the substrate. Protons and hydroxide ions may cluster around positive/negative R groups that line the active site and interfere with interactions between the active site and the substrate molecule.

Small changes either side of the optimum alter the shape of the active site. If it is no longer complementary to the shape of the substrate the rate of reaction reduces. If the optimum pH is restored, hydrogen bonds reform and the shape of the active site is restored. The rate of reaction is restored.

Large changes in pH away from the optimum permanently denature the enzyme active site. The rate of reaction stops.
Not all enzymes have the same optimum pH and the range at which they are active also varies depending on where it is found.

The number of molecules per unit volume.

At zero concentration of substrate there is no reaction.
As substrate concentration increase there are more successful collisions between enzyme active sites and substrates.
More enzyme substrate complexes form, more product is released.
The rate of reaction increases until it reaches its maximum tare. This is the turnover number.
Beyond this concentration the rate does not increase.
All enzyme active sites are occupied.
Enzyme concentration is now the limiting factor.

Enzyme synthesis, regulated by transcription and translation.
Enzyme degradation, removes surplus enzymes and abnormally formed enzymes.

At zero concentration there is no rate of reaction.
As concentration increased more active sites are available.
There is an increase in successful collisions between enzyme active sites and substrates.
More enzyme substrate complexes form per unit time.

Increasing enzyme concentration further will of increase rate of reaction.
Substrate concentration becomes a limiting factor.

Greatest chance of successful collisions between substrates and enzyme active sites, more ESC form.
As reaction proceeds substrate is use up, fewer molecules left to react.
Fewer successful collisions, rate decrease.
As product accumulates it impedes successful collisions between enzyme active sites and substrates.
Rate decreases/stops.

Plot a graph - this is usually time, s, on x axis against volume of gas, cm3, on y axis.
Draw tangent to line at steepest point.
Rate is change in y axis divided by change in x axis.
In this example the unit of rate is cm3/s.

Molecule has a shape that is similar to the substrate.
Inhibitor fits into active site and forms enzyme inhibitor complex.
Substrate cannot enter active site.
Rate of reaction decreases.
Increasing substrate concentration overcomes the effect of a competitive inhibitor.

As inhibitor concentration increases there are more collisions between the inhibitor and the enzyme active site.
Inhibition increases, rate decreases.
As substrate concentration increases there are more successful collisions between enzyme active site and substrate.
Inhibition reduces, rate increases.

Inhibitor does not compete with substrate for active site.
Binds to enzyme somewhere other than the active site.
Leads to distortion of active site, prevents binding of substrate.
ESC cannot form, rate of reaction reduced.
Adding more substrate does not overcome effect of inhibitor.
Often irreversible.

Accumulation of end product leads to inhibition of final enzyme in pathway.
Product may remain bound to active site - competitive inhibition.
Product may bind elsewhere on enzyme - non-competitive inhibition.