CHAPTER 3 Bioenergetics, Enzymes, and Metabolism.
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Transcript of CHAPTER 3 Bioenergetics, Enzymes, and Metabolism.
CHAPTER 3
Bioenergetics, Enzymes, and Metabolism
3.1 Bioenergetics
• The study of the various types of energy transformations that occur in living organisms.
Energy (thermodinamics)-- the ability/capacity to do work-- the ability to cause specific change
-- Type of EnergyKinetics:energy of movement
(Heat and light energy, 37C)Potential:energy of reorganization of atoms in molecules
(Chemical reaction energy)
02
1.Synthetic
Chemical bonds
Six kinds of workSix kinds of work
Biosynthesis
Six kinds of workSix kinds of work
2.Mechanical
--Muscle
--Cell movement
--Chromosome movement
--Cytoplasmic streaming
Six kinds of workSix kinds of work
3. Concentration
Passive Transport – no energy is expended and molecules move down the concentration gradient.DiffusionOsmosisHypotonicHypertonicIsotonic
Facilitated DiffusionActive Transport – energy (in the form of ATP) must be used to move certain molecules across the membrane.ExocytosisEndocytosisPhagocytosisPinocytosisReceptor mediated endocytosis
Six kinds of workSix kinds of work
4. Electricalspecialized concentration work
Six kinds of workSix kinds of work
5. HeatEspecially important to warm-blooded
animals
Six kinds of workSix kinds of work6. Bioluminescence
Especially important to produce ATPLighting bugs (fireflies) Bacterias
Dinoflagella ( marine algae)
Oxidation-------blue light color
luciferin
The Flow of Energy Through the Biosphere
Aerobic orAnaerobic
Oxidations and Reductions
Oxidations: removal of electrons from substances. (removal of Hydrogen and addition of Oxygen).
Reductions: addition of electrons from substances. (addition of Hydrogen and removal of Oxygen).
C6H1202
C02
CH4
OxidationReduction
C6H1202
CH4
Release of energy (heat)
Chemotrophs Phototrophs
The Laws of Thermodynamics and the Concept of Entropy
• Energy – capacity to do work, or the capacity to change or move something.
• Thermodynamics – the study of the changes in energy that accompany events in the universe.
The First Law of Thermodynamics (1)
• The first law of thermodynamics – the law of conservation of energy.
• Energy can neither be created nor destroyed.
• Transduction – conversion of energy from one form to another.
• Electric energy can be transduced to mechanical energy when we plug in a clock.
The First Law of Thermodynamics (2)
• Cells are capable of energy transduction.
• Chemical energy is stored in certain biological molecules, such as ATP.
• Chemical energy is converted to mechanical energy when heat is released during muscle contraction.
The First Law of Thermodynamics (3)
• Energy transduction in the biological world: conversion is the conversion of sunlight into chemical energy
– Photosynthesis.• Animals, such as fireflies
and luminous fish, are able to convert chemical energy back to light.
- Bioluminescence.
The First Law of Thermodynamics (4)
• The universe can be divided into system and surroundings.– The system is a subset of the universe under
study.– The surroundings are everything that is not
part of the system.– The energy of the system is called the
internal energy (E), and its change during a transformation is called ΔE.
Open and Closed Systems
Biological Systems==== Energy associated with Chemical Reactions ==== Work is the use of energy ( any type) to drive/
produce any process.Example: Oxidation of Glucose at the cellular level
1st Law of Thermodynamics Conservation of Energy (E)
ΔE = Eproducts – Ereactants (reactives)
ΔE = Change in total internal energy of a system
E: total internal energy of any given system
Reactants ProductsTotal Eproducts ; Total Ereactants (reactives)
1st Law of Thermodynamics Conservation of Energy
ΔH = ΔE + Δ(PV)
P = pressure, V = volumeΔH = change in heat content (enthalpy)
Reactants Products
E: H (Q) - PV(W) ; H(heat/enthalpy) = E + PV
1st Law of Thermodynamics Conservation of Energy
ΔH ~ ΔE
---Negative ΔH -- exothermic --heat is released
---Positive ΔH -- endothermic
Reactants ProductsChange on V and P is irrelevant
Heat
ΔH= Hprod - Hreact
---Negative ΔH -- exothermic --heat is released
---Positive ΔH -- endothermic
Example:
Gasoline + 02 (OXIDATION) CO2 + H2O
Heat
Photosynthesis
Heat (sunlight)
(lost)
(gain)
The First Law of Thermodynamics (6)
ΔH~ ΔE
Example 1:Cellulose (paper) + match +O2 burning (heat+glucose monomer +CO2)
ΔH~is simply a meausre of total enthalpy (heat) in any given system.
Example 2:Glucose-6-phospahte Fructose-6-phosphate
Thermodynamically favored (spontaneous?)
Can occur (possible) without input of additional energy
Directionality
Does not predict whether an energy change will be positive or negative.
The Second Law of Thermodynamics (1)
• The second law of thermodynamics: events in the universe tend to proceed from a state of higher energy to a state of lower energy.– Such events are called spontaneous, they
can occur without the input of external energy.– Loss of available energy during a process is
the result of a tendency for randomness to increase whenever there is a transfer of energy.
2nd Law of Thermodynamics
Gain in Disorder
Gain in disorder => entropy (S) ----CHAOS---
ΔS change in entropy between initial & final states
Example 3:
Cellulose (paper) + match +O2 combustion (heat+glucose monomer +CO2)
The Second Law of Thermodynamics (3)
• Every event is accompanied by an increase in the entropy of the universe.
– Entropy associated with random movements of particles or matter.
– Living systems maintain a state of order, or low entropy
heat
ΔG = Free energy (G) = change during a process in energy available to do work
ΔH = ΔG + TΔS
ΔH = change in enthalpyΔS = change in entropy between initial & final statesT = temperature in Kelvins (K= oC +273)
Combining the 1st and 2nd Laws
ΔG = ΔH - TΔS
spontaneity
Combining the 1st and 2nd Laws
ΔG = ΔH - TΔS
Negative ΔG = exergonic(energy production) => spontaneousCAN GO-possible (WILL GO)
Positive ΔG = endergonic (energy requiring) => not spontaneousCAN NOT GO-not possible (WILL NOT GO)
0 ?
+
-
G
Figure 5-9 Dependence of ∆G on the Signs and Numerical
Values of ∆H and the Terms (T∆S)
Negative ΔH -- exothermic (heat)Positive ΔH -- endothermic
Figure 5-10 Changes in Free Energy for the Oxidation and Synthesis of Glucose
Chemotrophs Prototrophs
+ Energy + Energy
Free-Energy Changes in Chemical Reactions (1)
• All chemical reactions are theoretically reversible.
• All chemical reactions spontaneously proceed toward equilibrium (Keq = [P]/[R]).
• The rates of chemical reactions are proportional to the concentration of reactants.
• At equilibrium, the free energies of the products and reactants are equal (ΔG = 0).
R P
At equilibrium, ΔG = 0
[A][B] = [C][D]
k1 = k2
A + B C + Dk1
k2
Free Energy Changes in Chemical Reactions
K1 rate constant of reactantsK2 rate constant of products
AB reactantsCD products
At equilibrium
k1[A][B] = k2[C][D]
k1 = [C][D]
k2 = [A][B] Keq =k1
k2
At equilibrium, free energy to do work – minimumentropy - maximum
Calculating G
Free Energy Changes in Chemical Reactions at standard conditions
T = 298°KP = 1 atmosphereReactants & products = 1MWater = 55.6MpH = 7
ΔG°′ = standard free energy change
?
Free Energy Changes in Chemical Reactions at standard conditions
ΔG°′ = -RT lnK′eq
R = gas constant (1.987 cal/mol-K)T = absolute temperature
ΔG°′ = -2.303RT logK′eq
if equilibrium constant > 1, negative ΔG°′
if equilibrium constant < 1, positive ΔG°′
ln x= 2.303 log x
The Relationship Between ∆G°´ and K´eq
[P] [R]Keq =
R P
Calculating G’
Glu-6-P Fruct-6-P
Keq=0.5
G’ =-954 cal/mol
Products
Reactants
Non equilibrium
Our exp. conditions
G’: Go’ + R T ln [C][D]
[A][B]
R(A and B) P(C and D)
Free Energy Changes in Chemical Reactions in the cell
ΔG′ = ΔG°′ + 2.303RT log[C][D]
[A][B]
Example: ATP hydrolysis: ATP ADP + Pi ΔG°′ = -7.3 kcal/mol
[ATP] = 10 mM, [ADP] = 1 mM, [Pi] = 10 mM
ΔG’ = ΔG°′ + 2.303RT log[ADP][Pi]
[ATP]
ΔG’ = -7.3 kcal/mol + (1.4 kcal/mol) log[10-3][10-2]
[10-2]ΔG’ = -11.5 kcal/mol
The Meaning of ∆G°´ and ∆G´
Coupling Endergonic & Exergonic Reactions
Large Positive ΔG′ energy input
Example:Glutamine from Glutamic acid
Glutamic acid + NH3 GlutamineΔG′ = +3.4 kcal/mol
2 sequential reactions:Glutamic acid + ATP glutamyl phosphate + ADPGlutamyl phosphate + NH3 glutamine + Pi
Glutamic acid + ATP + NH3 glutamine + ADP + Pi
ΔG′ = -3.9 kcal/mol
Coupling Endergonic & Exergonic Reactions
Large Positive ΔG′ energy input
Example:Glutamine from Glutamic acid (glutamine synthase)
Glutamic acid + NH3 GlutamineΔG′ = +3.4 kcal/mol
2 sequential reactions:Glutamic acid + ATP glutamyl phosphate + ADPGlutamyl phosphate + NH3 glutamine + Pi
Glutamic acid + ATP + NH3 glutamine + ADP + Pi
ΔG′ = -3.9 kcal/mol
Common intermediate
Product of the first reaction
becomes
Substrate for the second
Coupling Endergonic & Exergonic Reactions
Free-Energy Changes in Chemical Reactions (2)
• Free energy changes of reactions are compared under standard conditions.– Standard conditions are not representative
of cellular conditions, but are useful to make comparisons.
– Standard free energy changes are related to equilibrium: ΔG°’ = -RT ln K’eq
Calculation of free energy changes (1)
• Non-standard conditions are corrected for prevailing conditions. – Prevailing conditions may cause ΔG to be
negative, even when G°’ is positive.– Making ΔG negative may involve coupling
endergonic and exergonic reactions in a sequence.– Simultaneously coupled reactions have a common
intermediate.– ATP hydrolysis is often coupled to endergonic
reactions in cells.
Coupling Endergonic and Exergonic Reactions
Coupling Endergonic and Exergonic Reactions
ATP hydrolysis
Equilibrium versus Steady-State Metabolism
• Cellular metabolism is non-equilibrium metabolism.
• Cells are open thermodynamic systems.• Cellular metabolism exists in a steady state.
– Concentrations of reactants and products remain constant, but not at equilibrium.
– New substrates enter and products are removed.– Maintaining a steady state requires a constant input of
energy, whereas maintaining equilibrium does not.
Equilibrium vs. Steady State
ΔG°′= At equilibrium, free energy to do work – minimum entropy – maximum
ΔG′ = Steady state – concentrations of reactants and products remain relatively constant, even though individual reactions are not necessarily at equilibrium
Reactions generally don’t reach equilibrium in the cell
Steady State versus Equilibrium
ΔG°’= + 410 cal/mol
Glucose-6-phosphate ? Fructose-6-phosphate
25ºC at a concentration of 1 M of both reagentswith a Keq=0.5 IN VITRO
37ºC at a concentration of 83 uM and 14 uM of reagentswith a Keq=0.169 IN VIVO=CELL
Glucose-6-phosphate Fructose-6-phosphate
Enzymes
ΔG’= - 644 cal/mol
Negative ΔG = exergonic => spontaneousPositive ΔG = endergonic => not spontaneous
CAN GO (WILL GO)
Reactants Products(more energy) (less energy)
Heat
Negative ΔH ---- exothermic --heat is released
Example: Glucose oxidation and ATP hydrolysis
G=-686 kcal/mol -7.3kcal/mol
Enzymes
3.2 Enzymes as Biological Catalysts
• Enzymes are catalysts that speed up chemical reactions.
• Enzymes are NOT always proteins.
• Enzymes may be conjugated with
non-protein components.– Cofactors are inorganic enzyme conjugates.– Coenzymes are organic enzyme conjugates.
RibozymesRibozymes (RNA/protein)(RNA/protein)
Properties of Enzymes (1)• Are present in cells in small amounts.• Are not permanently altered during the course of a
reaction.• Cannot affect the thermodynamics of reactions, only the
rates. Only changes rate at which equilibrium is achieved. Can’t drive endergonic reaction.
• Are highly specific for their particular reactants called substrates. Forms transient complexes with substrate.
• Produce only appropriate metabolic products.• Can be regulated to meet the needs of a cell. Enzymatic activity of EGFR
• Lowers EA allowing reaction to occur without thermal activation.
Properties of Enzymes (2)
*
Overcoming the Activation Energy Barrier
• A small energy input, the activation energy (EA) is required for any chemical transformation.– The EA barrier slows the
progress of thermodynamically unstable reactants.
– Reactant molecules that reach the peak of the EA barrier are in the transition state. ATP+H2O ----- -----ADP+Pi
[ATP:H2O]
Metastable (intermediate chemical) state – condition where reactants are thermodynamically unstable but have insufficient energy to exceed the activation energy barrier for the reaction
Overcoming the Activation Energy Barrier
• A small energy input, the activation energy (EA) is required for any chemical transformation.– The EA barrier slows the
progress of thermodynamically unstable reactants.
– Reactant molecules that reach the peak of the EA barrier are in the transition state. ATP+H2O ----- ---ADP+Pi
[ATP:H2O]
Catalyst – agent that enhances the rate of a reaction by lowering the energy of activation
Enzyme=Catalyst (WILL GO)
Enzymes lower the activation energy
• Without an enzyme, only a few substrate molecules reach the transition state.
• With a catalyst, a large proportion of substrate molecules can reach the transition state.
Kinetic energy is proportional to theTemperature under our exp. conditions
25C
NON-catalyzed reaction
EA
Catalyzed reaction
EA
37C
The Active Site
• An enzyme interacts with its substrate to form an enzyme-substrate (ES) complex.
• The substrate binds to a portion of the enzyme called the active site.
• The active site and the substrate have complementary shapes that allow substrate specificity.
The Active Site (~Motif)
307 amino acidActive siteHis, Glu, Arg, Tyr
130 amino acidActive siteGlu, Asp
Enzyme structure
May have prosthetic groups (small organic molecules or metal ions)
(often electron acceptors)
active (Catalytic) site
Substrate specificity
Temperature dependent
pH sensitivity
The Major Classes of Enzymes with an Example of Each
Mechanisms of Enzyme Catalysis (1)
• Substrate orientation means enzymes hold substrates in the optimal position of the reaction.
Mechanisms of Enzyme Catalysis (2)
• Changes in the reactivity of the substrate temporarily stabilize the transition state.– Acidic or basic R groups
on the enzyme may change the charge of the substrate.
– Charged R groups may attract the substrate.
– Cofactors of the enzyme increase the reactivity of the substrate by removing or donating electrons.
Two Models for Enzyme-Substrate Interaction
Mechanisms of Enzyme Catalysis (3)
• Inducing strain in the substrate.– Shifts in the
conformation after binding cause an induced fit between enzyme and the substrate.
– Covalent bonds of the substrate are strained.
The Catalytic Cycle of an Enzyme
Enzyme KineticsS P enzymes
Ef + S EbS Ef + Pk1 k3
k2
--initial reactions rates (very early in the chemical reactions)
[S]>>>>>>>>>>>>>>>[P]
Enzyme Kinetics (1)
• Kinetics is the study of rates of enzymatic reactions under various experimental conditions.
• Rates of enzymatic reactions increase with increasing substrate concentrations until the enzyme is saturated.
– At saturation every enzyme is working at maximum capacity.
– The velocity at saturation is called maximal velocity, Vmax.
– The turnover number is the number of substrate molecules converted to product per minute per enzyme molecule at Vmax.
Enzyme Kinetics (2)
• The Michaelis constant (KM) is the substrate concentration at one-half of Vmax.– Units of KM are
concentration units.– The KM may reflect
the affinity of the enzyme for the substrate.
Experimental Procedure for Studying the Kinetics of the Hexokinase Reaction
Glu + ATP (1mM) Glu-6-phosphate +ADPEnz=1uM
The Relationship Between Reaction Velocity and Substrate Concentration
--Low substrate concentration [S]<<Km
v is proportional to [S]
--High substrate concentration [S]>>Km
v independent of [S]
--[S] = Km: [S] where v = ½ Vmax
Michaelis-Menten equation
Vmax: maximum velocity of reaction[S]: initial substrate concentrationv: initial velocityKm: Michaelis constant
substrate concentration @ ½Vmax
Vmax is an approximation number (~Vmax)
The Relationship Between Reaction Velocity and Substrate Concentration
Turnover number (K catalysis): Kcat
Kcat = (cat=catalysis) rate at which substrate molecules are converted to product by a single enzyme molecule operating at Vmax
units: time (sec)-1
Kcat = Vmax/[Et]
[Et]. Kcat=Vmax
[Et] = enzyme concentration (Molar [M])
Km and kcat Values for Some Enzymes
KM = Kcat
Double reciprocal plot
v = (Vmax[S])/(Km + [S])
1/v = (Km + [S])/(Vmax[S])
1/v = Km 1 + [S] Vmax [S] Vmax[S]
1/v = Km 1 + 1 Vmax [S] Vmax
Vmax is an approximation number (~Vmax)
Enzyme Kinetics (3)
• Plots of the inverses of velocity versus substrate concentrations, such as the Lineweaver-Burk plot, facilitate estimating Vmax and KM.
• Temperature and pH can affect enzymatic reaction rates.
Enzyme Kinetics (4)
1/v = Km 1 + 1 Vmax [S] Vmax
Experimental Procedure for Studying the Kinetics of the Hexokinase Reaction
Glu + ATP Glu-6-phosphate +ADP
Double-Reciprocal Plot for the Hexokinase
Vmax = 10 µmol/min
-1/Km = -6.7
Km = 0.15mM
The Effect of Temperature and pH on the Reaction Rate of Enzyme-Catalyzed Reactions
Enzyme Kinetics (4)
Enzyme Inhibitors (1)
• Enzyme inhibitors slow the rates for enzymatic reactions.– Irreversible inhibitors bind tightly to the enzyme.– Reversible inhibitors bind loosely to the enzyme.
• Competitive inhibitors compete with the enzyme for active sites
– Usually resemble the substrate in structure.– Can be overcome with high substrate/inhibitor ratios.
Enzyme Inhibitors (2)
Modes of Action of Competitive and Noncompetitive Inhibitors
Reversible – noncovalentE + I EI
Enzyme Inhibitors (3)
• Noncompetitive inhibitors– Bind to sites other
than active sites and inactivate the enzyme.
– The maximum velocity of enzyme molecules cannot be reached.
– Cannot be overcome with high substrate/inhibitor ratios.
Ethanol in Alcoholic beverages (BEER)
Alcohol Dehydrogenase(ADH)
Aldehyde Dehydrogenase
Low Km ---mitochondrial
Low/High Km-- cytosolic/ stomach/ liver
--OH --C=O C00-
ALDH
ALDH
ALDH
Hangover
The Human Perspective: The Growing Problem of Antibiotic
Resistance (1)• Antibiotics target human metabolism without
harming the human host.– Enzymes involved in the synthesis of the bacterial cell wall.
(Penicillin and derivatives=irreversible Inhibitor)– Components of the system by which bacteria duplicate,
transcribe, and translate their genetic information (streptomycin=bacterial ribosomes, ciprofloxacin=bacterial DNA synthesis)
– Enzymes that catalyze metabolic reactions specific to bacteria (Sulfa drugs and folic acid); Protease and reverse transcriptase inhibitors (HIV)
The Human Perspective: The Growing Problem of Antibiotic
Resistance (2)• Antibiotics have been misused with dire
consequences.– Susceptible cells are destroyed, leaving rare and
resistant cells to survive and replicate.– Bacteria become resistant to antibiotics by
acquiring genes from other bacteria by various mechanisms.
3.3 Metabolism
• Metabolism is the collection of bio-chemical reactions that occur within a cell via enzymes.
• Metabolic pathways are sequences of chemical reactions.– Each reaction in the sequence is catalyzed by a
specific enzyme.– Pathways are usually confined to specific locations.– Pathways convert substrates into end products via a
series of metabolic intermediates.
An Overview of Metabolism (1)
• Catabolic pathways break down complex substrates into simple end products.– Provide raw materials
for the cell.– Provide chemical
energy for the cell.
• Anabolic pathways synthesize complex end products from simple substrates.– Require energy.– Use ATP and NADPH
from catabolic pathways.
An Overview of Metabolism (2)
• Anabolic and catabolic pathways are interconnected.– In stage I, macromolecules
are hydrolyzed into their building blocks.
– In stage II, building blocks are further degraded into a few common metabolites.
– In stage III, small molecular weight metabolites like acetyl-CoA are degraded yielding ATP.
Oxidation and Reduction: A Matter of Electrons (1)
• Oxidation-reduction (redox) reactions involve a change in the electronic state of reactants.– When a substrate gains electrons, it is reduced.– When a substrate loses electrons, it is oxidized.– When one substrate gains or loses electrons,
another substance must donate or accept those electrons.
• In a redox pair, the substrate that donates electrons is a reducing agent.
• The substrate that gains electrons is an oxidizing agent.
Oxidation and Reduction: A Matter of Electrons (1)
---SH HS------ ---S-S---
Metabolic Regulation (1)
• Cellular activity is regulated as needed.• Regulation may involve controlling key enzymes of
metabolic pathways.• Enzymes are controlled by alteration in active sites.
– Covalent modification of enzymes regulated by phosphorylation such as protein kinases.
– Allosteric modulation by enzymes regulated (inhibited or stimulated) by compounds binding to allosteric sites # active site.
• In feedback inhibition (negative feedback), the product of the pathway allosterically inhibits one of the first enzymes of the pathway.
Metabolic Regulation (2)
Allosteric effector – small organic molecule that regulates the activity of an enzyme for which it is neither the substrate nor the intermediate product
(Rate limiting enzymes)
Mechanisms of Allosteric Inhibition and Activation
Inhibition Activation
Mechanisms of Allosteric Inhibition and Activation
Catalytic & Regulatory Subunits
Enzyme Regulation
Allosteric regulation
Covalent modification
Enzyme Regulation – Covalent modification
Phosphorylation
Methylation
Acetylation
Proteolytic cleavage
The Regulation of Glycogen Phosphorylase by Phosphorylation
The Regulation of Glycogen Phosphorylase by Phosphorylation
Activation of Pancreatic Zymogens by Proteolytic Cleavage
Autoactivation
Pancreatitis
Basic Concepts on Enzymatic Action
1-Very Active-Powerful
2-Highly Specific-Catalysis
CO2 + H2O CO3H2
1 molecule per sec
Plus enzyme (carbonic anhydrase, CA)
7.7 x 10 6 sec
Time
[P]
A P
Enz
No Enz
Sec Hours
3-Examples
A- transport of CO2 in blood/tissue
CO2 + H2O CO3H2 CO3H- + H+
CO2 + H2O CO3H2 CO3H- + H+
Tissues
Lung
C A in red cells
C A in red cells
3-Examples
B- Sodas
CO2 + H2O CO3H2 CO3H- + H+
--bubbles in soda
--bubbles in mouth after drinking
Time
[P]
A PEnz
[A]
Time
[P]
[Enz]
[P] is proportional to [A] and [Enz]
RNA splicing:removal of introns from pre-RNA
EnzymesEnzymes(Proteins)(Proteins)
RibozymesRibozymes(RNA)(RNA)
(1981)(1981)
CHAPTER 11Pages 449-454
Spliceosomes remove introns from pre-mRNA.Spliceosomes is a particle formed by RNA (snRNA) and Proteins (sm Proteins)
15% diseases(Lupus Erythematosus)
Transcription by RNAPolymerase II and capping
E
I
mG
mG
mG
mGAAA
AAA
AAA
Removal of 3’ end by nuclease and polymerase
Ligation of exons
EndonucleolyticCleavage at splice junctions
Processingintermediate
ISplice site: 5’ Splice site: 3’
EE...G GU...........................A..........................AG G
Branch site sequence
95-99%
5-1%?
...G GU...........................A..........................AG G
hydroxyl, 2’Phosphoryl 5’
Transesterification ........... Required limited amount of ENERGY
Eukaryotes: Prokaryotes: + _
U3?rRNA