Transcript Metabolism - Anderson School District One

Metabolism
Campbell and Reece
Chapter 8
Metabolism
• total sum of all chemical reactions
in an organism
Metabolic Pathways
• begin with specific molecule which
is altered in series of defined steps,
resulting in certain product(s)
• each step has own specific enzyme
• mechanisms that regulate enzymes
balance metabolic supply & demand
Pathways can have >1 starting
material &/or product)
Catabolic Pathways
• break down complex molecules into
simpler one releasing nrg
• example: cellular respiration
Anabolic Pathways
• build complex molecules out of
simpler ones
• require nrg
• example: protein synthesis
• nrg released from catabolic
pathways used to fuel anabolic
pathways
Bioenergetics
• study of how
energy flows
through living
organisms
Forms of Energy
(capacity to do work)
1. KE
2. Thermal Energy
3. PE
4. Chemical Energy
KE
(energy of motion)
Thermal Energy
(heat)
• KE ass’c with random movement of
atoms or molecules
Light Energy
PE
(energy matter possesses due to
its position)
Chemical Energy
(type of PE)
• in catabolic pathways
Laws of Energy Transfer
• thermodynamics: study of energy
transfer that occurs in a system
• system: matter being studied
• surroundings: everything else in the
universe
• isolated or closed system: has no
interaction with surroundings
• open system: energy & matter can be
transferred between system &
surroundings
1st Law of Thermodynamics
(Law of Conservation of
Energy)
• amt of energy in universe is constant
• Energy can neither be created or
destroyed
1st Law of Thermodynamics
2nd Law of Thermodynamics
(Entropy)
• in most nrg transfers, some nrg is
lost to the system, usually in form of
heat nrg
• in case of digesting food, most of
chemical nrg is lost as heat
• logical consequence of losing nrg
with each transfer: universe is
becoming more disordered
2nd Law of Thermodynamics
• entropy : a measure of the disorder
or randomness of the universe
• 2nd Law: every nrg transfer or
transformation increases the
entropy of the universe
• (there is an unstoppable trend
toward randomization of the
universe)
2nd Law of Thermodynamics
• spontaneous process: a process that
can occur w/out input of energy
▫ will always increase entropy of the
universe
• Biologists use the Laws of
Thermodynamics to predict which
chemical reactions will happen
spontaneously & which one require
an input of nrg
J. Willard Gibbs
• Yale professor, 1878
Gibbs Free-Energy (G)
• is the part of a system’s nrg that can
perform work when the T & P are
uniform thru out the system (living
cell fits this description)
Gibbs Free Energy
• system is the chemical reaction
• enthalpy = total energy (in biologic
systems)
• ΔH = change in system’s enthalpy
• ΔS = change in system’s entropy
• absolute temperature (K) = ºC + 273
Free-Energy Change (ΔG)
ΔG = ΔH - TΔS
• 0nce you know ΔG you can say whether a
reaction will be spontaneous or require
an input of nrg
• *to be spontaneous ΔG must be (-)
• for ΔG to be (-), either ΔH must be (-)
(enthalpy decreases) or TΔS must be (+)
(entropy increases)
Spontaneous Reactions
• all spontaneous reactions have a –ΔG
which decreases the system’s free nrg
• reactions with a (+) G or G = 0 are never
spontaneous
Another Way to Look at ΔG
• ΔG = G (final state) - G(initial state)
• because G(final state) has less free nrg it will
be less likely to change thus the system
will be more stable
• think of free nrg as a measure of a
system’s instability
• unstable systems have higher G tend to
change in such a way as to end with a
more stable, lower G
example
Less Stable
More Stable
Equilibrium
• state of maximum stability
• as a chemical reaction moves toward
equilibrium the free nrg of reactants &
products gradually decreases
• free nrg increases if reactants & products
somehow pulled away from equilibrium
(removing products from system)
• for a system @
equilibrium, G is @ its
lowest possible value
in that system
• any change from that
equilibrium position
will have a (+) ΔG &
so will not be
spontaneous
• *because a system @ equilibrium cannot
spontaneously change, it cannot do work
• A process is spontaneous & can
do work only when it is moving
toward equilibrium.
Free Energy & Metabolism
• exergonic reaction: energy outward
▫ proceeds with net release of free nrg
• endergonic reaction: energy inward
▫ proceeds only if absorption of free nrg
▫ reversible chemical reactions must be
endergonic in one direction & exergonic in
the other direction
Exergonic Reactions
• reactions that occur spontaneously
• ΔG is always (-) (reaction loses free nrg)
• example:
• 1M C6H12 O6 + 6 O2  6 CO2 + 6 H2O
+ 686 kcal (2,870 kJ)
• BREAKING BONDS OF
REACTANTS DOES NOT
RELEASE ENERGY…
(IT REQUIRES ENERGY)
ENDERGONIC REACTIONS
• absorbs free energy from surroundings
• G increases so can think of it as reaction
that stores free energy
• ΔG is always (+) (amount of G tells you
how much energy needed to drive
reaction)
• nonspontaneous reactions
Endergonic Reactions
• example:
▫ if cellular respiration of glucose yielded
686 kcal of energy
then….
▫ plants had to add 686 kcal energy to make
the glucose
Great Explanation
• http://www.youtube.com/watch?annotation_id
=annotation_654505&feature=iv&src_vid=JBm
ykor-2kU&v=DPjMPeU5OeM
Equilibrium & Metabolism
• reactions that have reached equilibrium
cannot do work
• chemical reactions of metabolism would
reach equilibrium if they occurred in
isolation (like in a test tube)
•If a cell reaches
equilibrium it is dead!
How do Cells Avoid Equilibrium?
• products of
reactions do not
accumulate
because they are
used as reactants
in the next
reaction
How do Cells Avoid Equilibrium?
• Sequence of
reactions keeps
going because
there is a large
free-energy
difference
between the
original
reactant(s) and
final product(s)
Catabolic Pathways
• energy released in “little packets”
• if reaction simply started with original
reactant(s ) final product(s) in a single
step releasing all the energy at once
would probably be catastrophic for the
cell (and maybe the body)
ATP Couples Exergonic Reactions
with Endergonic Reactions
3 Kinds of Work Done by Cells
1. Chemical Work
2. Transport Work
3. Mechanical Work
Chemical Work
• pushing endergonic reactions that
do not occur spontaneously
• example: monomers  polymers
Transport Work
• moving substances across
membranes against their
concentration gradients
• example:
Mechanical Work
• action of cells moves something
• examples: cilia beating, muscle
fibers contracting, chromosomes
moving in anaphase
• http://biology.berkeley.edu/bio1a/topic/
Muscle_Motility/actin_myosin.html
Energy Coupling
• * cells use an exergonic process to
drive an endergonic one
• example: ion pump:
ATP
• ADENOSINE TRIPHOSPHATE
ATP
• hydrolysis reaction breaks a
phosphate group off
Hydrolysis of ATP
• exergonic reaction
• releases 7.3 kcal / mole ATP so…
the free energy change measured
under standard conditions:
• ΔG = -7.3 kcal/mol
ATP Hydrolysis in Cells
• not under standard conditions & not
at concentrations of 1 M
• under cellular conditions:
▫ ΔG = - 13 kcal / mol
Phosphate Bonds in ATP
• are called “high-energy bonds” but
that does not mean they are strong
bonds
• release of nrg comes from chemical
change to a state of lower free
energy (not from bonds themselves)
Energy Change in Hydrolysis
of ATP
Why so much Energy in ATP?
• 3 phosphate groups all (-) charged &
close together so their mutual
repulsion contributes to instability
of this part of the ATP molecule
• ATP w/all 3
phosphate groups
How Hydrolysis of ATP
Performs Work
• proteins harness the nrg in
hydrolysis of ATP to perform the 3
types of cellular work:
1. Chemical
2. Transport
3. Mechanical
Coupling Reactions
• if ΔG of endergonic reaction is < the
amt of nrg released by ATP
hydrolysis the 2 reactions can be
coupled so…overall the reaction is
exergonic
Coupling Reactions
Coupling Reactions
• key involves formation of a
phosphorylated intermediate which
is more reactive (less stable) than
the original unphosphorylated
molecule
Phosphorylated Intermediates
Transport Work
▫ usually involves protein becoming
phosphorylated  changing shape
Mechanical Work
▫ ATP usually
binds
noncovalently
to a motor
protein
▫ ATP is
hydrolyzed 
ADP + P
▫ another ATP
binds etc.
Regeneration of ATP
• free energy required to rephosphorylate ADP  ATP comes
from exergonic breakdown
reactions (catabolic reactions)
ATP Cycle
How Enzymes Work
• Laws of Thermodynamics tell us
which rxs will occur spontaneously
but do not tell us how quickly
• many rxs occur spontaneously but
so slowly it is imperceptable
▫ example: sucrose + H2O glucose +
fructose + 7 kcal/mol would have no
perceptable change for years unless
you add sucrase (then takes seconds)
Enzymes
• biologic catalysts that speed up
chemical rxs w/out being consumed
by the rx
• macromolecules
▫ proteins
▫ ribozymes (RNA enzymes)
Activation Energy Barrier
• to review:
▫ chemical rx involve breaking old
bonds & making new one
▫ changing 1 molecule  another
usually involves contortion of
reactant molecule into a highly
unstable state b/4  reactants
Unstable State
Activation Energy Barrier
• to reach the contorted state where
bonds can change, reactants must
absorb nrg from their surroundings
• when new bonds formed in products
nrg is released as heat & molecules
return to stable shapes with lower
nrg than they had in their contorted
shape
Free Energy
0f
Activation Energy
(EA )
• is nrg required to contort reactant
molecules so bonds can break
• often supplied in form of thermal
nrg (absorbed by reactant from their
environment)
Activation Energy/ Unstable
Transition State
• as reactants absorb thermal nrg 
move faster  collide more often &
with more force
• atoms w/in the reactant molecules
more agitated so more likely bonds
will break
• both happen in the unstable
transition state
Exergonic Reaction:
occurs spontaneously (ΔG <0)
Activation Energy
• in most cases EA is so high &
transition state is reached so rarely
that rx hardly ever  product
How Enzymes Lower EA
• many complex molecules (proteins,
DNA) high in free nrg so you would
think they have the potential to
spontaneously decompose
• doesn’t happen because
temperatures typical for most cells
do not provide enough energy to get
over the EA hump
How Enzymes Lower EA
• enzymes lower EA enabling
reactants to absorb enough nrg to
reach the transition state even at
normal temperatures
• *enzymes cannot change the ΔG for
a reaction
Substrate Specificity of Enzymes
• substrate:
▫ reactant an enzyme acts on
• enzyme-substrate complex
▫ when enzyme is bound to subtrate
▫ enzyme
+

substrate
enzymeenzyme
substrate 
+
complex
product
Specificity of Enzymes
• results from its shape (result of it’s
a.a. sequence)
• active site: restricted region of
protein enzyme that binds to
substrate
Active Sites
• proteins alter between different
shapes in a dynamic equilibrium
with slight differences in free nrg in
each “pose”
• shape that best fits the substrate not
always the one with lowest free nrg
Active Sites
• induced fit: when substrate fits into
active site the enzyme changes shape
slightly so as to fit even more snug
(protein not rigid with fixed shape)
Catalysis in the Active Site
• enzymes can catalyze either the
forward or reverse reaction:
depends on which direction has a
(-)G
• which depends on the relative
concentrations of reactants &
products
• net effect: reaction will move in
direction that favors equilibrium
Mechanisms Used by
Enzymes to Lower EA
1. if 2 or more reactants, active site
positions them in proper
orientation for rx to occur
Mechanisms Used by
Enzymes to Lower EA
2. remember EA is proportional to
the difficulty of breaking bonds, so
having the active site stretch & bend
the bonds toward their transitionstate form helps reduce the amt of
free nrg that must be absorbed to
achieve transition-state
Mechanisms Used by
Enzymes to Lower EA
3. active site might provide a
microenvironment more conducive to
reaction than the solution would be w/out
the enzyme
if enzyme has acidic a.a. it would lower pH
of the solution in otherwise neutral cell
Mechanisms Used by
Enzymes to Lower EA
4. direct participation of active site in
chemical reaction
(subsequent reactions restores active
site to original state so active site
same before & after)
When Enzyme Becomes
Saturated
• can increase rate of reaction initially
by increasing [substrate] up to point
where every enzyme has its active
site occupied then increasing amt
substrate will have no further effect
• when that happens only way to
increase rate of rx is to add more
enzyme
Enzyme Animations
• http://highered.mcgrawhill.com/sites/0072495855/student_view0/cha
pter2/animation__how_enzymes_work.html
• http://bcs.whfreeman.com/thelifewire/content/
chp06/0602002.html
Effects of Local Conditions on
Enzyme Activity
1. Temperature
2. pH
3. cofactors
4. Enzyme Inhibitors
Effects of Temperature
on Enzyme Activity
• rate of enzyme activity increases
with increasing temperature up to a
point
• as T increases so does KE of
molecules so more collisions..more
likely substrate will find active site
• when point reached speed of
reaction drops sharply
Effects of Temperature
on Enzyme Activity
Effects of Temperature
on Enzyme Activity
• each enzyme has its optimal T @
which its rx rate is greatest
• above some point the protein
denatures
• most human enzymes have optimal
T @ 35 – 40 ºC
• some thermophilic bacteria have
enzymes with optimal activity
@ 70 ºC
Effects of pH on Enzyme
Activity
• each enzyme has optimal pH
• most enzymes have optimal pH
of 6 -8
Cofactors
• nonprotein helpers for enzymes
• might be
1. bound to the enzyme as permanent
fixtures
2. bound loosely & reversibly like the
substrate
Inorganic Cofactors
• Zn++
• Fe++
• Cu++
Organic Cofactors
• called: coenzymes
• most vitamins are essential because
they act as coenzymes or are the raw
material that a coenzyme is made
from
Enzyme Inhibitors
certain chemicals that inhibit action
of specific enzymes
reversible: if inhibitor has weak,
transient attachment
irreversible: if inhibitor forms
covalent bond with enzyme
Types:
1. Competitive
2. Noncompetitive
Competitive Inhibitors
• inhibitor mimics substrate
• can be overcome by increasing
[substrate]
Noncompetitive Inhibitor
• do not compete with substrate @
active site
• bind to another part of enzyme 
causes enzyme to change shape so
active site becomes less effective
• http://biologyanimations.blogspot.com/search/label/enzymes
Evolution of Enzymes
• accepted Model:
▫ naturally occurring mutations that
change a.a. in active site or some
other crucial position
▫ then changes in environment so
natural selection could tend to favor
the mutation
Evolution of Enzymes
Artificial Selection
Evolution of Enzymes
Artificial Selection
Regulation of Enzyme Activity
• Cells must control which metabolic
pathways are active when or there
would be mass chaos.
• control is achieved by controlling
which enzymes are active when
Allosteric Regulation of Enzymes
• allosteric regulation describes any
case in which a protein’s function @
1 site is affected by the binding of a
regulatory molecule to a separate
site
Allosteric Activation &
Inhibition
Allosteric Regulators
• few of many known metabolic
enzymes have been shown to be
regulated this way
• pharmaceutical research uses this
model to design medications to act
as regulators (usually bind to
enzyme longer than real regulators
so are more effective)
Allosteric Regulators
• ADP & P play role in balancing the
flow of traffic between anabolic &
catabolic pathways by their effects
on key enzymes
• ATP binds to several catabolic
enzymes allosterically, lowering
their affinity for substrate & so
inhibiting their activity
• ADP & P activate same enzymes
• http://programs.northlandcollege.edu/biology/
Biology1111/animations/enzyme.html
Cooperativity
• substrate binds to 1 active site on
multisubunit  shape change in all
subunits  increases catalytic
activity@ other sites
• in effect, amplifies the response of
enzymes to substrates
Cooperativity
Cooperativity also in Hgb
• Hemoglobin (Hgb) made of 4
polypeptides (subunits)
• each 1 has oxygen-binding site
• O2 binds to 1 site  increases
affinity for O2 to other 3 sites
Hemoglobin
• when Hgb in oxygen-poor capillary
affinity of oxygen-binding sites
decreases & O2 released
• as 1 O2 leaves the affinity for others
continues to decrease
• http://www.youtube.com/watch?v=WXO
BJEXxNEo
Feedback Inhibition
• end product of metabolic pathway
binds to enzyme early in pathway
and switches off the pathway
Cells are Compartmentalized
• organelles bring order to metabolic
pathways
▫ some have enzymes for several steps
of pathway assembled in a
multienzyme complex
▫ some have fixed locations in certain
membranes
▫ some w/in membrane spaces