Lecture notes
Enzymes
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- University Of Southampton (UOS)
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Enzymes CharacteristicsDefi nitions
Enzyme- One or more polypeptide chains forming catalytic active site
Substrate- Molecule which binds active site and undergoes chemical reaction
Product- Result of enzyme action
Critical aspects of Enzymes
Enzyme usually bind substrates with high specificity
o Enzyme active sites are clefts in enzyme where substitute binds and catalytic reactions take place
Substrate binding to active site if often associated with structural changes in enzyme
o When substrate binds to enzyme active site- large number of weal interactions occur between
substrate and enzyme
And facilitate formation of product
Hydrogen bonds
Ionic interactions
Van der Waals
o Structural changes may be minor or may involve significant changes in backbone conformations of
enzyme that are induced by substrate
o In most enzymes- substrate binding leads to more subtle changes in protein structure- most
significant changes occurring in vicinity of enzyme active site
Enzyme activity is highly regulated in cells
o Enzyme regulation- Necessary to maximise energy balance between anabolic and catabolic
reactions and To alter cell behaviour in response to environmental stimuli
o Two primary modes of enzyme regulation:
Bioavailability- amount of enzyme present in cell as a result of regulated gene expression
and protein turnover
Activity of enzyme- controlled by binding of regulatory molecules of by covalent
modification
Types of product
Light- Firefly, Enzyme- Luciferase
Heat- Bombadier beetle, Enzyme- Catalase
What do enzymes do?
Enzyme increases rate of reaction inside cells in 3 major ways:
1) Stabilise transition rate – Lower activation barrier
2) Provide alternative path for product formation – involve formation of stable reaction intermediates –
covalently attached to enzyme
3) Orient substrates appropriately for reaction to occur- reducing entropy change of reaction
Example roles
Digestion of food- Pepsin
Clotting of blood- Thrombin
Blood pressure- ACE
, Defence- Lysozyme
Breakdown of drugs- Cytochrome P450
Routine cell process
Types of reaction
Anabolic - smaller→ larger
o e.g. A+B→C
o e.g. A+A→AA
Catabolic- larger →smaller
o e.g. X→Y+Z
o e.g. XX→X+X
Interconversions
o D+E↔F+G
Enzyme Classifi cation
Most enzyme names end in -ase- denote protein is enzyme
Some have common names- e.g. trypsin
Typically named for reaction they catalyse or their substrate/ product
o e.g Glycogen Synthase→ synthesis of glycogen
Can have category names
o e.g. Proteases→ breakdown of proteins
o Lipases→ breakdown of lipids
Enzyme commission number (Molecular Biology Enzyme Classification system):
o CLASS
Oxidoreductases- Oxidation/ Reduction- transfer electrons (H - and H)
Transferases- Transfer of functional (chemical) groups e.g. methyl
Hydrolases- Break bonds with water- form two products
Lyases- Reactions involving double bonds
Cleavage of C-C, C-O, C-N and other bonds (other than hydrolysis and oxidation)
Isomerases- Transfer of groups within molecule- Intramolecular rearrangements
Ligases- Formation of bonds using energy from ATP
Formation of C-C, C-O, C-S, or C-N bonds using ATP hydrolysis
o SUBCLASS
o SUB-SUBCLASS
o SERIAL NUMBER
e.g. Classification number of hexokinase- EC 2.7.1.1.
- ‘2’- Transferase, subclass ‘7’- transfers phosphoryl group, sub-subclass ‘1’- phosphoryl transfer involves alcohol
acceptor group on glucose
Last digit ‘1’- first enzyme activity named in this category
Why are enzymes necessary?
Enzymes alter rates of reaction- without changing ratio of substrates and products at equilibrium
- Decrease time taken to reach equilibrium
- Increase rates of reaction in both directions by same amount- rates of reactions are affected without changing
final equilibrium or overall change in free energy (∆G) of reaction
Pace of life
o 2H2O2→2H2O +O2
, Decomposition of H2O2 occurs VERY SLOWLY at RT – would take about 3 years for 1 mole of H 2O2 to decompose to
0.5 mol of H2O and 0.25 mol of O2
- This amount of time represents Half-life (t1/2) of reaction
t1/2 decreases- by adding small amount of free iron as chemical catalyst- t1/2 is only 11.6 minutes- represents increase
in rate of decomposition by five orders of magnitude (rate if 105 times faster in presence of ferric ion)
Enzyme Catalase- catalyses very efficient decomposition reaction. Rate of H 2O2 decomposition in presence of
catalase is fast- millions of molecules of H2O2 are decomposed per second per molecule of catalase
Conditions of life
o Body temperature
o Neutral pH
i.e- no high temperature or harsh treatment to speed up reactions
What aff ects reaction rate?
Rate of reaction depends on:
Speed of 1 reaction- rate constant, k
Number of reactions happening
Enzymes can’t change maximum speed of reaction- make it possible for more reactions to happen
Reduce activation energy
Activation energy ΔG ‡
Activation energy- is difference in energy between ground state of reactant
and transition rate
e.g. A-X +B ⇌ A + B-X
- For reaction to occur- molecules must interact in appropriate orientation and
with sufficient collisional energy – productive reaction will take place
- Higher reactant concentration- productive collision is more likely
- During collision- some of kinetic energy is converted to molecular
vibrations- lead to changes in bond length, higher energy of molecule, larger
vibrations
In enzyme-catalysed reaction
Optimal environment of enzyme active site- provides more favourable reaction conditions
o reduces dependence on chance occurrences of proximity
o reduces orientation - needed in uncatalysed reaction
Enzyme active site provides more favourable conditions- lowers Activation energy ΔG‡
- Lowering transition energy barrier – increasing rate of reaction without altering overall free energy ΔG
- Enzyme readily promotes product formation – as function of reduced transition state energy barrier
Catalysts increases rate of reactions:
- In uncatalysed reaction- substrates need to collide in appropriate orientation and with sufficient energy in order
to react
-Adding catalyst to reaction lowers ACTIVATION ENERGY – by providing alternative path to product formation
How does energy relate to speed?
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