1. Molecular interactions in cells
Many
Metabolic pathways (biochemical pathways)
Complex often series of enzyme controlled reactions
Energy transformed
Molecules degraded and synthesised

2. ATP - Adenosine Triphosphate
nucleic acid – adenine base, ribose sugar,
three phosphate groups
stores energy and makes it available
energy is used for chemical, transport and mechanical work

3. Catalysis
Metabolism of an organism is the series of complex biochemical reactions that occur within them.
Reactions are sped up (catalysed) by enzymes.

4. Anabolic Reactions
Uses energy to SYNTHESISE large molecules from smaller ones e.g.
Amino Acids Proteins
Also known as endothermic reactions
ENDOTHERMIC REACTION

5. Catabolic Reactions
These release energy through the BREAKDOWN of large molecules into smaller units e.g.
Cellular Respiration:
ATP ADP + Pi
Also known as exothermic reactions
EXOTHERMIC REACTION

6. Enzyme characteristics
made of protein
catalyse reactions
affected by temperature and pH
denatured at high temperature
are specific to a reaction because of their active site.

7. Enzymes
All chemical reactions require energy to enable them this is the activation energy.
Enzymes lower the activation energy.
2 types of reaction are:
Anabolic (synthesis) a dehydration synthesis reaction.
Catabolic (degradation) a hydrolysis reaction.

8. Enzyme types
Proteases - break down proteins into amino acids by breaking peptide bonds (hydrolysis).
Nucleases - break down nucleic acids into nucleotides (hydrolysis).
Kinases - add phosphate groups to molecule.
Phosphatases – remove phosphate groups
ATPases - hydrolysis of ATP.

9. Enzyme activity
Active site is region where the reaction with substrate occurs.
Correct substrate alters the shape of the active sight to allow the substrate to fit perfectly.
This is called the 'induced fit model'.
(Molecules close to shape of substrate may react with differing efficiencies)

10. Control of Enzyme activity
Control of enzyme activity occurs in these ways
number of enzyme molecules present
compartmentalisation
change of enzyme shape by
competitive inhibitors, non-competitive inhibitors,
enzyme modulators, covalent modification
end product inhibition

11. Competitive inhibition
A molecule close to shape of substrate competes directly for active site so reducing the concentration of available enzyme.
This can be reversed by increasing the concentration of the correct substrate unless the binding of competitor is irreversible.

13. Malonate example
Succinate dehydrogenase catalyses the oxidation of succinate to fumarate (respiration)
Malonate is the competitive inhibitor

14. Non-competitive inhibition
An inhibitor binds to the enzyme molecule at a different area and changes the shape of the enzyme including the active site.
This may be a permanent alteration or may not.

16. Inhibition can either be reversible or non-reversible
Some inhibitors bind irreversibly with the enzyme molecules.
The enzymatic reactions will stop sooner or later and are not affected by an increase in substrate concentration.
These are irreversible inhibitors heavy metal ions including silver, mercury and lead ions.

17. Enzyme modulators
Some enzymes change their shape in response to a regulating molecule.
These are called allosteric enzymes
Positive modulators (activators)
stabilise enzyme in the active form.
Negative modulators (inhibitors)
stabilise enzyme in the inactive form.

18. Allosteric Enzymes

19. Covalent modifications
Involves the addition, modification or removal of a variety of chemical groups to or from an enzyme
(often phosphate.)
These result in a change in the shape of the enzyme and so its activity.
These include phosphorylation by kinases and dephosphorylation by phosphatases.
Conversion of inactive forms to active forms e.g. trypsinogen and trypsin

20. An example of activation is trypsinogen to trypsin
trypsinogen activated by
enterokinase in duodenum

21. Trypsin is synthesised in the pancreas, but not in its active form as it would digest the pancreatic tissue
Therefore it is synthesised as a slightly longer protein called TRYPSINOGEN
Activation occurs when trypsinogen is cleaved by a protease in the duodenum
Once active, trypsin can activate more trypsinogen molecule

22. An example of phosphorylation activating an enzyme is the skeletal muscle enzyme GLYCOGEN PHOSPHORYLASE
Glycogen is converted to glucose when heavy demands are placed on muscle tissue
Glycogen phosphorylase must be activated when sugar is needed and quickly deactivated when glucose is plentiful.

23. Glucose and ATP act as negative modulators
AMP (adenosine monophosphate) acts as a positive modulator
This is useful, because AMP is a product of ATP breakdown and will be more plentiful when energy levels are low and more glucose is needed
A further complication is that there is a hormonal control mechanism by adrenaline and glucagon

24. End product Inhibition
Often seen in pathways that involve a series of enzyme controlled reactions.
The end product once produced has an inhibiting affect on an enzyme in the reaction.
Example:
Bacterial production of amino acid isoleucine from threonine.
5 stages enzyme controlled
Threonine Isoleucine

25. End-Product Inhibition
Metabolism is organised as a series of metabolic pathways, and control of these pathways is an important feature of cell biochemistry
End-product inhibition is energetically efficient as it avoids the excessive (and wasteful) production of the intermediates of a pathway
This is a form of NEGATIVE FEEDBACK

26. describe the catalytic functions of proteases, nucleases, ATPases and kinases
describe the induced fit model of enzyme activity
explain how competitive and non-competitve inhibitors affect enzyme activity
describe allosteric enzymes
explain the effect of positive and negative modulators binding to allosteric enzymes
explain what is meant by covalent modification of enzymes and how they control enzyme activity
explain the role of end-product inhibition in the control of metabolic pathways