chapter 8 metabolism
TRANSCRIPT
Chapter 8An Introduction to Metabolism
Overview: The Energy of Life• The living cell is a miniature chemical factory
where thousands of reactions occur• The cell extracts energy and applies energy to
perform work• Some organisms even convert energy to light,
as in bioluminescence• Metabolism is the totality of an organism’s
chemical reactions• Metabolism is an emergent property of life that
arises from interactions between molecules within the cell
Enzyme 1
A BReaction 1
Enzyme 2
CReaction 2
Enzyme 3
DReaction 3
ProductStartingmolecule
•A metabolic pathway begins with a specific molecule and ends with a product•Each step is catalyzed by a specific enzyme
•Catabolic pathways release energy by breaking down complex molecules into simpler compounds
Anabolic pathways consume energy to build complex molecules from simpler ones
Forms of Energy• Energy is the capacity to cause change• Energy exists in various forms, some of which
can perform work
• Bioenergetics is the study of how organisms manage their energy resources
• Kinetic energy is energy associated with motion– Heat (thermal energy) is kinetic energy associated with random
movement of atoms or molecules• Potential energy is energy that matter possesses because
of its location or structure– Chemical energy is potential energy available for release in a
chemical reaction• Energy can be converted from one form to another• Solar energy
– Light energy can be converted to chemical energy by photosynthesis
On the platform,the diver hasmore potentialenergy.
Diving convertspotentialenergy to kinetic energy.
Climbing up convertskinetic energy ofmuscle movement topotential energy.
In the water, the diver has lesspotential energy.
Add solar, potential, & chemical energy for this
picture.
The Laws of Energy Transformation
• Thermodynamics is the study of energy transformations
• A closed system, such as that approximated by liquid in a thermos, is isolated from its surroundings
• In an open system, energy and matter can be transferred between the system and its surroundings
• Organisms are open systems
The First Law of Thermodynamics• According to the first law of thermodynamics, the energy of the
universe is constant– Energy can be transferred and transformed– Energy cannot be created or destroyed
• The first law is also called the principle of conservation of energy
The Second Law of Thermodynamics• During every energy transfer or transformation, some energy is
unusable, often lost as heat• According to the second law of thermodynamics, every energy
transfer or transformation increases the entropy (disorder) of the universe
Chemical energy
Heat CO2
First law of thermodynamics Second law of thermodynamics
H2O
•Living cells unavoidably convert organized forms of energy to heat•Spontaneous processes occur without energy input; they can happen quickly or slowly (very slowly in order to get over EA)•For a process to occur without energy input, it must increase the entropy of the universe
Biological Order and Disorder
• Cells create ordered structures from less ordered materials
• Organisms also replace ordered forms of matter and energy with less ordered forms
• The evolution of more complex organisms does not violate the second law of thermodynamics
• Entropy (disorder) may decrease in an organism, but the universe’s total entropy increases
• The change in free energy (∆G) during a process is related to the change in enthalpy, or change in total energy (∆H), and change in entropy (T∆S):
∆G = ∆H - T∆S• Energy in reactions with a negative G can be
harnessed to perform work
• A living system’s free energy is energy that can do work when temperature and pressure are uniform, as in a living cell
1. The oxidation of glucose to CO2 and H2O is highly exergonic: G 636 kcal/mole. This is possible, but why is it very slow?a. Few glucose and oxygen molecules have the
activation energy at room temperature.b. There is too much CO2 in the air.
c. CO2 has higher energy than glucose.
d. The formation of six CO2 molecules from one glucose molecule decreases entropy.
e. The water molecules quench the reaction.
1. The oxidation of glucose to CO2 and H2O is highly exergonic: G 636 kcal/mole. This is possible, but why is it very slow?
a. Few glucose and oxygen molecules have the activation energy at room temperature.
b. There is too much CO2 in the air.
c. CO2 has higher energy than glucose.
d. The formation of six CO2 molecules from one glucose molecule decreases entropy.
e. The water molecules quench the reaction.
LE 8-5
Gravitational motion Diffusion Chemical reaction
More free energy
Change in Free Energy
• Free energy of the products – free energy of reactants = negative, then products have a greater stability than reactants
• Products have less free energy; in open system, must include environment
• An exergonic reaction proceeds with a net release of free energy
• An endergonic reaction absorbs free energy from its surroundings and reactants are more stable than products
LE 8-6a
Reactants
EnergyProducts
Progress of the reaction
Amount ofenergy
released(G < 0)
Free
ene
rgy
Exergonic reaction: energy released
LE 8-6b
ReactantsEnergy
Products
Progress of the reaction
Amount ofenergy
required(G > 0)
Free
ene
rgy
Endergonic reaction: energy required
2. Firefly luciferase catalyzes the following reaction:luciferin ATP adenyl-luciferin pyrophosphate Then the next reaction occurs spontaneously:adenyl-luciferin O2 oxyluciferin H2O CO2 AMP light What is the role of luciferase?
a. Luciferase makes the G of the reaction more negative.
b. Luciferase produces a transition state with a lower free energy
c. Luciferase alters the equilibrium point of the reaction.
d. Luciferase makes the reaction irreversible.e. Luciferase creates a phosphorylated intermediate.
2. Firefly luciferase catalyzes the following reaction:luciferin ATP adenyl-luciferin pyrophosphate Then the next reaction occurs spontaneously:adenyl-luciferin O2 oxyluciferin H2O CO2 AMP light What is the role of luciferase?
a. Luciferase makes the G of the reaction more negative.
b. Luciferase produces a transition state with a lower free energy.
c. Luciferase alters the equilibrium point of the reaction.
d. Luciferase makes the reaction irreversible.e. Luciferase creates a phosphorylated intermediate.
Equilibrium and Metabolism• Reactions in a closed system eventually reach
equilibrium and then do no work• Cells are not in equilibrium; they are open
systems experiencing a constant flow of materials
• A catabolic pathway in a cell releases free energy in a series of reactions
• Closed and open hydroelectric systems can serve as analogies
LE 8-7a
G = 0
A closed hydroelectric system
G < 0
LE 8-7b
An open hydroelectric system
G < 0
LE 8-7c
A multistep open hydroelectric system
G < 0G < 0
G < 0
Concept 8.3: ATP powers cellular work by coupling exergonic
reactions to endergonic reactions
• A cell does three main kinds of work:– Mechanical– Transport– Chemical
• To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one
Phosphate groupsRibose
Adenine
ATP (adenosine triphosphate) is the cell’s energy shuttle
ATP provides energy for cellular functions
• The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis
• Energy is released from ATP when the terminal phosphate bond is broken
• This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves
LE 8-9
Adenosine triphosphate (ATP)
Energy
P P P
PPP i
Adenosine diphosphate (ADP)Inorganic phosphate
H2O
+ +
• In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction
• Overall, the coupled reactions are exergonic
LE 8-10Endergonic reaction: G is positive, reactionRequires input of energy
Exergonic reaction: G is negative, products have less free energy than reactants
G = +3.4 kcal/mol
G = –7.3 kcal/mol
G = –3.9 kcal/mol
NH2
NH3Glu Glu
Glutamicacid
Coupled reactions: Overall G is negative;together, reactions give off heat
Ammonia Glutamine
ATP H2O ADP P i
+
+ +
How ATP Performs Work• ATP drives endergonic reactions by
phosphorylation, transferring a phosphate group to some other molecule, such as a reactant
• The recipient molecule is now phosphorylated• The three types of cellular work (mechanical,
transport, and chemical) are powered by the hydrolysis of ATP
LE 8-11
NH2
Glu
P i
P i
P i
P i
Glu NH3
P
P
P
ATPADP
Motor proteinMechanical work: ATP phosphorylates motor proteins
Protein moved
Membraneprotein
Solute
Transport work: ATP phosphorylates transport proteins
Solute transported
Chemical work: ATP phosphorylates key reactants
Reactants: Glutamic acidand ammonia
Product (glutamine)made
+ +
+
Pi
ADP
Energy for cellular work(endergonic, energy-consuming processes)
Energy from catabolism(energonic, energy-yielding processes)
ATP
+
The Regeneration of ATP•ATP is a renewable resource that is regenerated by addition of a phosphate group to ADP•The energy to phosphorylate ADP comes from catabolic reactions in the cell•The chemical potential energy temporarily stored in ATP drives most cellular work
Enzymes speed up metabolic reactions by providing an alternative
pathway with a lower EA
• A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction
• An enzyme is a catalytic protein or RNA• Hydrolysis of sucrose by the enzyme sucrase is
an example of an enzyme-catalyzed reaction
LE 8-13
SucroseC12H22O11
GlucoseC6H12O6
FructoseC6H12O6
The Activation Energy Barrier• Every chemical reaction between molecules
involves bond breaking and bond forming• The initial energy needed to start a chemical
reaction is called the free energy of activation, or activation energy (EA)
• Activation energy is often supplied in the form of heat from the surroundings
LE 8-14
Transition state
C D
A B
EA
Products
C D
A B
G < O
Progress of the reaction
Reactants
C D
A B
Free
ene
rgy
How Enzymes Lower the EA Barrier
• Enzymes catalyze reactions by lowering the EA barrier—provide an alternative transition state
• Enzymes do not affect the change in free-energy (∆G); instead, they hasten reactions that could occur eventually
3. In the energy diagram below, which of the energy changes would be the same in both the enzyme-catalyzed and uncatalyzed reactions?
ab cde
3. In the energy diagram below, which of the energy changes would be the same in both the enzyme-catalyzed and uncatalyzed reactions?
ab cde
LE 8-15
Course ofreactionwithoutenzyme
EA
without enzyme
G is unaffectedby enzyme
Progress of the reaction
Free
ene
rgy
EA withenzymeis lower
Course ofreactionwith enzyme
Reactants
Products
Substrate Specificity of Enzymes
• The reactant that an enzyme acts on is called the enzyme’s substrate
• The enzyme binds to its substrate, forming an enzyme-substrate complex
• The active site is the region on the enzyme where the substrate binds
• Induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction
LE 8-16
Substrate
Active site
Enzyme Enzyme-substratecomplex
If reversible, what are the possible types of bonds utilized by enzymes in their active sites?
Catalysis in the Enzyme’s Active Site
• In an enzymatic reaction, the substrate binds to the active site
• The active site can lower an EA barrier by– Orienting substrates correctly– Straining substrate bonds– Providing a favorable microenvironment– Covalently bonding to the substrate
LE 8-17
Enzyme-substratecomplex
Substrates
Enzyme
Products
Substrates enter active site; enzymechanges shape so its active siteembraces the substrates (induced fit).
Substrates held inactive site by weakinteractions, such ashydrogen bonds andionic bonds.
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.
Substrates areconverted intoproducts.
Products arereleased.
Activesite is
availablefor two new
substratemolecules.
Effects of Local Conditions on Enzyme Activity
• An enzyme’s activity can be affected by:– General environmental factors, such as
temperature and pH– Chemicals that specifically influence the
enzyme• Each enzyme has an optimal temperature in
which it can function• Each enzyme has an optimal pH in which it
can functionWe can find these in lab the next few weeks!
LE 8-18
Optimal temperature fortypical human enzyme
Optimal temperature forenzyme of thermophilic (heat-tolerant bacteria)
Temperature (°C)Optimal temperature for two enzymes
0 20 40 60 80 100
Rat
e of
reac
t ion
Optimal pH for pepsin(stomach enzyme)
Optimal pHfor trypsin(intestinalenzyme)
pHOptimal pH for two enzymes
0
Rat
e of
reac
t ion
1 2 3 4 5 6 7 8 9 10
Explain what is happening at each
section of the curve.
Cofactors• Cofactors are nonprotein enzyme helpers• Coenzymes are organic cofactors
Enzyme Inhibitors• Competitive inhibitors bind to the active site of
an enzyme, competing with the substrate• Noncompetitive inhibitors bind to another part
of an enzyme, causing the enzyme to change shape and making the active site less effective
LE 8-19Substrate
Active site
Enzyme
Competitiveinhibitor
Normal binding
Competitive inhibition
Noncompetitive inhibitorNoncompetitive inhibition
A substrate canbind normally to the
active site of anenzyme.
A competitiveinhibitor mimics the
substrate, competingfor the active site.
A noncompetitiveinhibitor binds to the
enzyme away from theactive site, altering the
conformation of theenzyme so that its
active site no longerfunctions.
Concept 8.5: Regulation of enzyme activity helps control
metabolism
• Chemical chaos would result if a cell’s metabolic pathways were not tightly regulated
• To regulate metabolic pathways, the cell switches on or off the genes that encode specific enzymes
Allosteric Regulation of Enzymes
• Allosteric regulation is the term used to describe cases where a protein’s function at one site is affected by binding of a regulatory molecule at another site
• Allosteric regulation may either inhibit or stimulate an enzyme’s activity
Allosteric Activation and Inhibition
• Most allosterically regulated enzymes are made from polypeptide subunits
• Each enzyme has active and inactive forms• The binding of an activator stabilizes the active
form of the enzyme• The binding of an inhibitor stabilizes the
inactive form of the enzyme
LE 8-20a
Allosteric enzymewith four subunits
Regulatorysite (oneof four) Active form
ActivatorStabilized active form
Active site(one of four)
Allosteric activatorstabilizes active form.
Non-functionalactive site
Inactive form Inhibitor Stabilized inactive form
Allosteric inhibitorstabilizes inactive form.
Oscillation
Allosteric activators and inhibitors
• Cooperativity is a form of allosteric regulation that can amplify enzyme activity
• In cooperativity, binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits
LE 8-20b
Substrate
Binding of one substrate molecule toactive site of one subunit locks allsubunits in active conformation.
Cooperativity another type of allosteric activationStabilized active formInactive form
Michaelis-Menton
Lineweaver-Burk analysis is one method of linearizing substrate-velocity data so as to determine the kinetic constants Km and Vmax. One creates a secondary, reciprocal plot: 1/velocity vs. 1/[substrate]. When catalytic activity follows Michaelis-Menten kinetics over the range of substrate concentrations tested, the Lineweaver-Burk plot is a straight line with
Y intercept = 1/Vmax,X intercept = -1/Kmslope = Km/Vmax
4. Which choice best describes what the H ATPase does in terms of flow of energy in many cells?
a. It converts light energy into energy in a concentration gradient.
b. It converts matter into energy in the form of an electrochemical gradient.
c. It pumps protons up their pressure gradient.
d. It converts chemical energy to energy in an electrochemical gradient and heat.
e. It converts energy in a concentration gradient to energy in an electrical gradient.
4. Which choice best describes what the H ATPase does in terms of flow of energy in many cells?
a. It converts light energy into energy in a concentration gradient.
b. It converts matter into energy in the form of an electrochemical gradient.
c. It pumps protons up their pressure gradient.
d. It converts chemical energy to energy in an electrochemical gradient and heat.
e. It converts energy in a concentration gradient to energy in an electrical gradient.
Feedback Inhibition
• In feedback inhibition, the end product of a metabolic pathway shuts down the pathway
• Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed
LE 8-21
Active siteavailable
Initial substrate(threonine)
Threoninein active site
Enzyme 1(threoninedeaminase)
Enzyme 2
Intermediate A
Isoleucineused up bycell
Feedbackinhibition Active site of
enzyme 1 can’tbindtheoninepathway off
Isoleucinebinds toallostericsite
Enzyme 3
Intermediate B
Enzyme 4
Intermediate C
Enzyme 5
Intermediate D
End product(isoleucine)
Specific Localization of Enzymes Within the Cell
• Structures within the cell help bring order to metabolic pathways
• Some enzymes act as structural components of membranes (oxidative phosphorylation in Ch.9; photsynthetic phosphorylation in Ch.10)
• Some enzymes reside in specific organelles, such as enzymes for cellular respiration being located in mitochondria— next chapter
LE 8-22
Mitochondria,sites of cellular respiration
1 µm