Enzymes And Metabolism
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Advanced Biology Enzymes and Metabolism
Metabolism
Is the sum of an organism’s chemical reactions Metabolic pathways begin with a specific molecule and end with a product Each step is catalyzed by a specific enzyme Enzyme 1
A
Enzyme 2
Starting molecule
D
C
B Reaction 1
Enzyme 3
Reaction 2
Reaction 3
Product
Metabolism
Catabolic pathways
Anabolic pathways
5.1
Break down complex molecules into simpler compounds Release energy Build complicated molecules from simpler ones Consume energy
Free Energy
5.2
Energy that is free to do work in cells (∆G)
Organisms are continually expending free energy
How is it replaced?
Where is it stored?
Reactions in Metabolism
An exergonic reaction
Proceeds with a net release of free energy and is spontaneous
Free energy
Reactants
5.2
Amount of energy released (∆G <0) Energy Products
Progress of the reaction
Reactions in Metabolism
An endergonic reaction Is one that absorbs free energy from its surroundings and is not spontaneous
Free energy
Products
5.2
Energy Reactants
Progress of the reaction
Amount of energy released (∆G>0)
ATP hydrolysis
Can be coupled to other reactions
Endergonic reaction: ∆G is positive, reaction is not spontaneous
Glu
+
Glutamic acid
NH2
NH3 Ammonia
∆G = +3.4 kcal/mol
Glu Glutamine
Exergonic reaction: ∆ G is negative, reaction is spontaneous
ATP
+
H2O
ADP +
Coupled reactions: Overall ∆G is negative; together, reactions are spontaneous
P
∆G = - 7.3 kcal/mol
∆G = –3.9 kcal/mol
How ATP Performs Work
ATP drives endergonic reactions
By phosphorylation, transferring a phosphate to other molecules
How ATP Performs Work
The three types of cellular work are powered by the hydrolysis of ATP P i
P
Motor protein Protein moved (a) Mechanical work: ATP phosphorylates motor proteins Membrane protein
ADP + P i
ATP P
P
i
Solute Solute transported (b) Transport work: ATP phosphorylates transport proteins P Glu + NH3
NH2 Glu
+ P
i
Reactants: Glutamic acid Product (glutamine) and ammonia made (c) Chemical work: ATP phosphorylates key reactants
Enzymes
A catalyst
An enzyme
5.3
Is a chemical agent that speeds up a reaction without being consumed by the reaction Is a protein catalyst Enzymes speed up metabolic reactions by lowering activation energy
Activation Energy
Is the initial amount of energy needed to start a chemical reaction A
B
C
D
Free energy
Transition state A
B
C
D
EA
Reactants
Exergonic Reaction A
B
C
D
∆G < O
Products
5.4
Progress of the reaction
The effect of enzymes on activation energy and reaction rate
Free energy
Course of reaction without enzyme
EA without enzyme
EA with enzyme is lower
Reactants
Course of reaction with enzyme
∆G is unaffected by enzyme
Products
5.4
Progress of the reaction
Substrate Specificity of Enzymes
The substrate
The enzyme
5.5
Is the reactant an enzyme acts on Binds to its substrate, forming an enzyme-substrate complex
Enzyme Specificity
The active site
Is the region on the enzyme where the substrate binds The active site is designed to fit to a specific substrate
Substrate
Active site
Enzyme
5.5
Induced Fit Model
Induced fit binding of a substrate
Brings chemical groups of the active site into positions that allow them to catalyze the chemical reaction with the substrate
enzyme
substrate
Enzyme- substrate complex
5.6
Induced Fit Model 1 Substrates enter active site; enzyme changes shape so its active site embraces the substrates (induced fit).
Substrates
6 Active site Is available for two new substrate Mole.
5.6/5.7
2 Substrates held in active site by weak interactions, such as hydrogen bonds and ionic bonds.
Enzyme-substrate complex
3 The active site (R groups of its amino acids) can lower EA and speed up a reaction by: 3. 4. 5.
Enzyme
5 Products are Released.
6.
Products
4 Substrates are Converted into Products.
orienting substrates correctly straining substrate bonds providing a favorable microenvironment covalently bonding to the substrate
Effects of Temperature
Each enzyme has an optimal temperature in which it can function Optimal temperature for enzyme of thermophilic (heat-tolerant) bacteria
Rate of reaction
Optimal temperature for typical human enzyme
0
20
40
80
100
Temperature (Cº)
5.8
Effects of pH Each enzyme has an optimal pH in which it can function
Optimal pH for pepsin (stomach enzyme) Rate of reaction
Optimal pH for trypsin (intestinal enzyme)
0
1
2
3
4
5
6
7
8
9
pH
5.8
Cofactors
Cofactors
Coenzymes
5.8
Are nonprotein enzyme helpers such as the metals iron, zinc and copper Are organic cofactors and include most vitamins
Enzyme Inhibitors
Competitive inhibitors
5.8
Bind to the active site of an enzyme and compete with the substrate
A substrate can bind normally to the active site of an enzyme.
Substrate Active site
Enzyme
Normal binding A competitive inhibitor mimics the substrate, competing for the active site.
Competitive inhibitor
Competitive inhibition
Enzyme Inhibitors
Noncompetitive inhibitors
Bind to another part of an enzyme causing a change in the shape of the active site
A noncompetitive inhibitor binds to the enzyme away from the active site, altering the conformation of the enzyme so that its active site no longer functions.
Noncompetitive inhibitor
5.8
Noncompetitive inhibition
Enzyme Regulation
Regulation of enzyme activity helps control metabolism Allosteric enzyme regulation
5.9
Is the term used to describe any case in which a protein’s function at one site is affected by binding of a regulatory molecule at another site
Allosteric Regulation
Many enzymes change shape when regulatory molecules bind to specific sites, affecting function
Allosteric enzyme with four subunits
Regulatory site
Allosteric activator stabilizes active form Active site
Activator
Active form
Stabilized active form Allosteric activator stabilizes active form
Non-functional active site
5.9
Inactive form
Inhibitor
Stabilized inactive form
Allosteric Regulation
Cooperativity
Is a form of allosteric regulation that can amplify enzyme activity
Binding of one substrate molecule to active site of one subunit locks all subunits in active conformation.
Substrate
Inactive form
5.9
Stabilized active form
Feedback Inhibition
In feedback inhibition
5.9
The end product of a metabolic pathway shuts down the pathway
Feedback inhibition The end product binds to the enzyme inhibiting its ability to catalyze the reaction with the initial substrate This is very common in metabolic pathways as a form of regulation
5.9
Metabolism
Is the sum of an organism’s chemical reactions Metabolic pathways begin with a specific molecule and end with a product Each step is catalyzed by a specific enzyme Enzyme 1
A
Enzyme 2
Starting molecule
D
C
B Reaction 1
Enzyme 3
Reaction 2
Reaction 3
Product
Metabolism
Catabolic pathways
Anabolic pathways
5.1
Break down complex molecules into simpler compounds Release energy Build complicated molecules from simpler ones Consume energy
Free Energy
5.2
Energy that is free to do work in cells (∆G)
Organisms are continually expending free energy
How is it replaced?
Where is it stored?
Reactions in Metabolism
An exergonic reaction
Proceeds with a net release of free energy and is spontaneous
Free energy
Reactants
5.2
Amount of energy released (∆G <0) Energy Products
Progress of the reaction
Reactions in Metabolism
An endergonic reaction Is one that absorbs free energy from its surroundings and is not spontaneous
Free energy
Products
5.2
Energy Reactants
Progress of the reaction
Amount of energy released (∆G>0)
ATP hydrolysis
Can be coupled to other reactions
Endergonic reaction: ∆G is positive, reaction is not spontaneous
Glu
+
Glutamic acid
NH2
NH3 Ammonia
∆G = +3.4 kcal/mol
Glu Glutamine
Exergonic reaction: ∆ G is negative, reaction is spontaneous
ATP
+
H2O
ADP +
Coupled reactions: Overall ∆G is negative; together, reactions are spontaneous
P
∆G = - 7.3 kcal/mol
∆G = –3.9 kcal/mol
How ATP Performs Work
ATP drives endergonic reactions
By phosphorylation, transferring a phosphate to other molecules
How ATP Performs Work
The three types of cellular work are powered by the hydrolysis of ATP P i
P
Motor protein Protein moved (a) Mechanical work: ATP phosphorylates motor proteins Membrane protein
ADP + P i
ATP P
P
i
Solute Solute transported (b) Transport work: ATP phosphorylates transport proteins P Glu + NH3
NH2 Glu
+ P
i
Reactants: Glutamic acid Product (glutamine) and ammonia made (c) Chemical work: ATP phosphorylates key reactants
Enzymes
A catalyst
An enzyme
5.3
Is a chemical agent that speeds up a reaction without being consumed by the reaction Is a protein catalyst Enzymes speed up metabolic reactions by lowering activation energy
Activation Energy
Is the initial amount of energy needed to start a chemical reaction A
B
C
D
Free energy
Transition state A
B
C
D
EA
Reactants
Exergonic Reaction A
B
C
D
∆G < O
Products
5.4
Progress of the reaction
The effect of enzymes on activation energy and reaction rate
Free energy
Course of reaction without enzyme
EA without enzyme
EA with enzyme is lower
Reactants
Course of reaction with enzyme
∆G is unaffected by enzyme
Products
5.4
Progress of the reaction
Substrate Specificity of Enzymes
The substrate
The enzyme
5.5
Is the reactant an enzyme acts on Binds to its substrate, forming an enzyme-substrate complex
Enzyme Specificity
The active site
Is the region on the enzyme where the substrate binds The active site is designed to fit to a specific substrate
Substrate
Active site
Enzyme
5.5
Induced Fit Model
Induced fit binding of a substrate
Brings chemical groups of the active site into positions that allow them to catalyze the chemical reaction with the substrate
enzyme
substrate
Enzyme- substrate complex
5.6
Induced Fit Model 1 Substrates enter active site; enzyme changes shape so its active site embraces the substrates (induced fit).
Substrates
6 Active site Is available for two new substrate Mole.
5.6/5.7
2 Substrates held in active site by weak interactions, such as hydrogen bonds and ionic bonds.
Enzyme-substrate complex
3 The active site (R groups of its amino acids) can lower EA and speed up a reaction by: 3. 4. 5.
Enzyme
5 Products are Released.
6.
Products
4 Substrates are Converted into Products.
orienting substrates correctly straining substrate bonds providing a favorable microenvironment covalently bonding to the substrate
Effects of Temperature
Each enzyme has an optimal temperature in which it can function Optimal temperature for enzyme of thermophilic (heat-tolerant) bacteria
Rate of reaction
Optimal temperature for typical human enzyme
0
20
40
80
100
Temperature (Cº)
5.8
Effects of pH Each enzyme has an optimal pH in which it can function
Optimal pH for pepsin (stomach enzyme) Rate of reaction
Optimal pH for trypsin (intestinal enzyme)
0
1
2
3
4
5
6
7
8
9
pH
5.8
Cofactors
Cofactors
Coenzymes
5.8
Are nonprotein enzyme helpers such as the metals iron, zinc and copper Are organic cofactors and include most vitamins
Enzyme Inhibitors
Competitive inhibitors
5.8
Bind to the active site of an enzyme and compete with the substrate
A substrate can bind normally to the active site of an enzyme.
Substrate Active site
Enzyme
Normal binding A competitive inhibitor mimics the substrate, competing for the active site.
Competitive inhibitor
Competitive inhibition
Enzyme Inhibitors
Noncompetitive inhibitors
Bind to another part of an enzyme causing a change in the shape of the active site
A noncompetitive inhibitor binds to the enzyme away from the active site, altering the conformation of the enzyme so that its active site no longer functions.
Noncompetitive inhibitor
5.8
Noncompetitive inhibition
Enzyme Regulation
Regulation of enzyme activity helps control metabolism Allosteric enzyme regulation
5.9
Is the term used to describe any case in which a protein’s function at one site is affected by binding of a regulatory molecule at another site
Allosteric Regulation
Many enzymes change shape when regulatory molecules bind to specific sites, affecting function
Allosteric enzyme with four subunits
Regulatory site
Allosteric activator stabilizes active form Active site
Activator
Active form
Stabilized active form Allosteric activator stabilizes active form
Non-functional active site
5.9
Inactive form
Inhibitor
Stabilized inactive form
Allosteric Regulation
Cooperativity
Is a form of allosteric regulation that can amplify enzyme activity
Binding of one substrate molecule to active site of one subunit locks all subunits in active conformation.
Substrate
Inactive form
5.9
Stabilized active form
Feedback Inhibition
In feedback inhibition
5.9
The end product of a metabolic pathway shuts down the pathway
Feedback inhibition The end product binds to the enzyme inhibiting its ability to catalyze the reaction with the initial substrate This is very common in metabolic pathways as a form of regulation
5.9
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