Download Lecture 4 Enzymes Catalytic proteins Enzymes Enzymes Enzymes

10/21/10
Enzymes
Lecture 4
Enzymes
•  Are a type of protein that acts as a catalyst-speeding up
chemical reactions
•  A catalyst is defined as a chemical agent that changes
the rate of a reaction without being consumed by the
reaction
•  Enzymes are biological catalysts
•  Chemical reactions involve the breaking and forming of
bonds-requires energy
Catalytic proteins
Enzymes
Enzymes
•  Activation energy is the initial investment of energy
needed to start a reaction
• What enzymes do therefore is: Reactants Transi5on state
Products (ready to react) •  In most chemical reactions this is provided in the
form of heat
Enzymes act here • Biochemists call ‘reactants’ substrates Substrate •  humans need to maintain a temperature of 37⁰C
Transi5on state
Products (ready to react) Enzymes act here •  Enzymes provide the activation energy for
reactions to proceed at normal temperatures in
biological systems
• Enzymes are substrate-­‐specific – each substrate fits into the enzyme’s ac5ve site 1
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Eg. Sucrase
1 Active site is available for
a molecule of substrate, the
reactant on which the enzyme acts.
Substrate
(sucrose)
How do they work?
2 Substrate binds to
enzyme.
Transi5on state Glucose
OH
Fructose
Enzyme
(sucrase)
H 2O
H O
4 Products are released.
3 Substrate is converted
to products.
Hydrolysis of sucrose involves the breaking of the bond between glucose and fructose the breaking of a bond in the water molecule the forming of 2 new bonds •  Complex molecules have the
potential to breakdown
spontaneously
(2nd law of thermodynamics= the
universe tends towards disorder)
•  They continue to exist because the
initial activation energy required to
breakdown can’t be reached to
initiate a breakdown reaction
•  An enzyme lowers the activation
energy required for a reaction
enabling the substrates to absorb
enough energy even at a moderate
temperature to reach transition
state
Enzymes “active site”
Enzyme shape
•  Enzymes are substrate specific
–  The substrate fits like a key in a lock
–  When the substrate and enzyme are
joined the catalytic action of the enzyme
converts the substrate to product
•  The specificity of an enzyme for a
substrate results from the shape of the
enzyme –due to a compatible fit between
the active site and the substrate
•  The substrate binds to the “active site” of
the enzyme
-This is the catalytic centre of the
enzyme
- The active site is typically a pocket or
groove on the surface of the enzyme
•  Is usually formed by only a few amino
acids
•  Is not rigid
•  The side chains of the aa’s in the
enzyme interact with the chemical
groups of the substrate- enzyme
changes shape and fits even better
around the substrate- INDUCED FIT
•  Induced fit brings the chemical groups
of the active site into new positions
enhancing the ability of the enzyme to
catalyse the reaction
•  The rest of the protein structure
provides the structural framework that
determines the configuration of the
active site
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Induced fit
Induced fit
Induced fit
Types of Enzymes
6 major types
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Types of Enzymes
•  ATPases - hydrolyse ATP. Many proteins with a wide range of roles have an
energy-harnessing ATPase activity as part of their function, for example,
motor proteins such as myosin and membrane transport proteins such as
the sodium–potassium pump.
•  Kinases - catalyze the addition of phosphate groups to molecules. Protein
kinases are an important group of kinases that attach phosphate groups to
proteins.
•  Nucleases - break down nucleic acids by hydrolyzing bonds between
nucleotides.
Types of Enzymes
•  Simple enzymes composed wholly of protein
•  Complex enzymes-called holoenzymes
–  Composed of protein (apoenzyme)+
a simple small organic molecule (cofactor or prosthetic group)
•  Phosphatases - catalyze the hydrolytic removal of a phosphate group
•  Polymerases - catalyze polymerization reactions such as the synthesis of
DNA and RNA.
–  Metalloenzymes are composed of
protein (apoenzyme) + metal
•  Proteases - break down proteins by hydrolyzing bonds between amino
acids.
6 important features of enzymes
1.  Side chains of amino acids make up the active
site
2.  Substrates bind via weak interactions: hydrogen
bonds, hydrophobic interactions
3.  Act at optimal pH, temperature and substrate
concentration
4.  May require other factors to work
5.  Can be inhibited by drugs
6.  Are activated or inhibited by chemical
modification
Features of enzymes
1.  Side chains of amino acids make up the active
site
–  Dependent on R group chemistry
–  Dependent on final folding
3.  Substrates bind via weak interactions:
–  hydrogen bonds
–  hydrophobic interactions
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Features of enzymes
3.
Enzymes act at optimal pH and temperatures:
Features of enzymes
3.
Enzymes act at optimal substrate concentration
Michaelis Menton Kinetics
Most enzymes are like this Enzyme ac5vity How well the
enzyme is
working = rate
of activity
Enzyme ac5vity 37oC 7.4 temp pH Concentration of substrate
Excep5ons: Thermophiles 70⁰C Excep5ons: pH 2 in stomach – pepsin pH 8 in intes5ne -­‐ trypsin Features of enzymes
3.
Enzymes act at optimal substrate concentration
Features of enzymes
3.
Enzymes act at optimal substrate concentration
Michaelis Menton Kinetics
Michaelis Menton Kinetics
How well the
enzyme is
working = rate
of activity
Concentration of substrate
Initial rate
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Features of enzymes
Can define how well a substrate binds to an enzyme by the Km
value
Km value is the substrate concentration at which the enzyme is
working at 50% activity
Big Km = bad binding
Low Km= good binding
Features of enzymes
4. Many require non-protein helpers to
aid catalysis
- ‘co-factors’
Eg: calcium, iron.
• 
Michaelis Menton Kinetics
• 
Features of enzymes
5. Inhibition of enzymes by drugs or molecules
in the body
•  Irreversible-destroys the
enzyme
•  Reversible
–  Competitive-inhibitor
resembles the substrate
–  Noncompetitive-inhibitor
binds to another site on the
emzyme called an
allosteric site
If the co-factor is organic it is a coenzyme
- Most vitamins are coenzymes Eg:
vitamin C
Vitamin C is used by an enzyme to
cross-link collagen. Vitamin C
deficiency causes scurvy – a disease
of dysfunctional cross-linking of
collagen
Features of enzymes
5. Many drugs inhibit enzymes
•  Drugs can compete with
the substrate and prevent
the reaction happening
HMG-­‐CoA Mevalonic acid Cholesterol ENZYME: HMG-­‐CoA reductase Eg. Statins inhibit HMG-Co
Reductase, a key enzyme
in cholesterol synthesis
HMG-­‐CoA – statins therefore lower
cholesterol and protect
or against heart disease.
Lovostatin competes with
the substrate for the
active site
HMG-CoA
reductase
lovosta5n 6
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Features of enzymes
Features of enzymes
6. Cellular enzymes can be
activated by “phosphorylation”
6. Are activated or inhibited by a chemical
modification
•  Other enzymes add the phosphate group to
the other enzyme,
-these enzymes are called kinases
–  Phosphorylation –addition of
phosphate grp
•  Kinases are said to “phosphorylate” the
protein
–  Acetylation –addition of an acetyl group
•  Eg: Adrenalin activates Phosphorylase kinase
which phosphorylates Glycogen
Phosphorylase.
-This enzyme in turn breaks down
glycogen to release glucose
–  Dephosphorylation-removal of a
phosphate group
–  Deacetylation-removal of an acetyl
group
Signal cascade
In summary...
Receptor protein Adrenaline (hormone protein) signals Phosphorylase Kinase (protein kinase enzyme) P
GP
GP
Glycogen Phosphorylase Glycogen glucose P
=Phosphate group •  Enzymes are catalytic proteins
•  Lower the initial activation energy required
for a reaction to happen
•  Are specific for their substrate – shape
•  The active site is usually made up of only
a few amino acid side chains
•  Induced fit
•  There are 6 important features
Adrenaline results in the release of glucose which allows for rapid produc4on of energy 7