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Metabolism
Chapter 8
I. Thermodynamics
Metabolism
• All the chemical reactions in an organism
Catabolic pathways
• Break down complex molecules into simpler molecules– Releases energy– Examples?• Digestive enzymes break down food to release energy
Anabolic pathway
• Build complex molecules from simple molecules– Consume energy– Example: Body links amino acids to form muscle in
response to exercise
Energy
• The ability to do work
Kinetic energy
• Energy of movement
Potential energy
• Stored energy as a result of position or structure– Chemical energy – form of potential energy stored
in molecules. On the platform, a diverhas more potential energy.
Diving converts potentialenergy to kinetic energy.
Climbing up converts kineticenergy of muscle movement to potential energy.
In the water, a diver has less potential energy.
Figure 8.2
• An example of energy conversion
Figure 8.3
First law of thermodynamics: Energy can be transferred or transformed but Neither created nor destroyed. For example, the chemical (potential) energy in food will be converted to the kinetic energy of the cheetah’s movement in (b).
(a)
Chemicalenergy
Thermodynamics
• Study of energy transformation in matter• First law: energy cannot be created or
destroyed, only transferred or transformed• 2nd law: Energy that is transferred or
transformed increases entropy or the amount of disorder or randomness in the universe
The Second Law of Thermodynamics
Figure 8.3
Second law of thermodynamics: Every energy transfer or transformation increasesthe disorder (entropy) of the universe. For example, disorder is added to the cheetah’ssurroundings in the form of heat and the small molecules that are the by-productsof metabolism.
(b)
Heat co2
H2O+
II. Free energy
III. ATP
Figure 8.8
O O O O CH2
H
OH OH
H
N
H H
ON C
HC
N CC
N
NH2Adenine
RibosePhosphate groups
O
O O
O
O
O
-
- - -
CH
Energy coupling
• Use of exergonic process to drive an endergonic one
ATP
• Primary source of energy for coupling– Made up of adenine bound to ribose and three
phosphate groups– When ATP is hydrolyzed energy is released in an
endergonic reation
Figure 8.9
P
Adenosine triphosphate (ATP)
H2O
+ Energy
Inorganic phosphate Adenosine diphosphate (ADP)
PP
P PP i
• Energy is released from ATP– When the terminal phosphate bond is broken
• ATP drives endergonic reactions– By phosphorylation,
transferring a phosphate to other molecules
ADP• When ATP is hydrolyzed it become ADP– How many phophates does ADP have?
ATP synthesis from ADP + P i requires energy
ATP
ADP + P i
Energy for cellular work(endergonic, energy-consuming processes)
Energy from catabolism(exergonic, energy yieldingprocesses)
ATP hydrolysis to ADP + P i yields energy
Figure 8.12
IV. Enzymes
Catalyst
• Changes the rate of a chemical reaction without being altered in the process
Enzymes
• Macromolecules that are biological catalysts– Considered proteins
Activation energy
• Amount of energy it takes to start a reaction, or the amount of energy it takes to break the bonds of reactant molecules– Enzymes speed up reactions by LOWERING
activation energy
Progress of the reaction
Products
Course of reaction without enzyme
Reactants
Course of reaction with enzyme
EA
withoutenzyme
EA with enzymeis lower
∆G is unaffected by enzymeFr
ee e
nerg
y
Figure 8.15
Exergonic reaction – energy released
Endergonic reaction – energy required
Parts of enzymes
• Substrate: enzyme reactants• Active sites: site where substrate binds• Enzyme substrate complex: formed when the
substrate and enzyme bind– After substrate binds it is converted into products
which are released from the enzyme
Figure 8.16
Substate
Active site
Enzyme
(a)
• Induced fit of a substrate– Brings chemical groups of the active site into
positions that enhance their ability to catalyze the chemical reaction
Figure 8.16 (b)
Enzyme- substratecomplex
• The catalytic cycle of an enzyme
Substrates
Products
Enzyme
Enzyme-substratecomplex
1 Substrates enter active site; enzymechanges shape so its active siteembraces the substrates (induced fit).
2 Substrates held inactive site by weakinteractions, such ashydrogen bonds andionic bonds.
3 Active site (and R groups ofits amino acids) can lower EA
and speed up a reaction by• acting as a template for substrate orientation,• stressing the substrates and stabilizing the transition state,• providing a favorable microenvironment,• participating directly in the catalytic reaction.
4 Substrates are Converted intoProducts.
5 Products areReleased.
6 Active siteIs available fortwo new substrateMole.
Figure 8.17
Enzyme activity
• Activity of an enzyme can be affected by several factors:– Changes in• Temperature• pH
• Changes in temperature and pH can change the shape of the enzyme, making it less effective
Cofactors
• Non-protein helpers– Include metals like zinc, iron and copper– Function to allow catalysis to occur
Coenzymes
• Organic cofactors such as vitamins
Competitive inhibitors• Reversible inhibitors that compete with the
substrate for the active site– Very similar to normal substrate
Figure 8.19 (b) Competitive inhibition
A competitiveinhibitor mimics the
substrate, competingfor the active site.
Competitiveinhibitor
A substrate canbind normally to the
active site of anenzyme.
Substrate
Active site
Enzyme
(a) Normal binding
Noncompetitive inhibitors
• Prevent enzyme activity by binding to anotehr part of the enzyme– Cause change in shape
Figure 8.19
A noncompetitiveinhibitor binds to the
enzyme away fromthe active site, altering
the conformation ofthe enzyme so that its
active site no longerfunctions.
Noncompetitive inhibitor
(c) Noncompetitive inhibition
V. Enzyme activity regulation
Allosteric site
• Specific binding site other than the active site where regulators bind and change the shape of the enzyme. – Can either stimulate OR inhibit the activity
Stabilized inactiveform
Allosteric activaterstabilizes active fromAllosteric enyzme
with four subunitsActive site(one of four)
Regulatorysite (oneof four)
Active formActivator
Stabilized active form
Allosteric activaterstabilizes active form
InhibitorInactive formNon-functionalactivesite
(a) Allosteric activators and inhibitors. In the cell, activators and inhibitors dissociate when at low concentrations. The enzyme can then oscillate again.
Oscillation
Figure 8.20
Feedback inhibition
• The end product of an enzymatic pathway can switch off the pathway by binding to the allosteric site (the result!)– Increases efficiency of pathway by turning off
when the end product accumulates in the cell.
• Feedback inhibition
Active siteavailable
Isoleucineused up bycell
Feedbackinhibition
Isoleucine binds to allosteric site
Active site of enzyme 1 no longer binds threonine;pathway is switched off
Initial substrate(threonine)
Threoninein active site
Enzyme 1(threoninedeaminase)
Intermediate A
Intermediate B
Intermediate C
Intermediate D
Enzyme 2
Enzyme 3
Enzyme 4
Enzyme 5
End product(isoleucine)
Figure 8.21