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Thermodynamics

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Title: Thermodynamics


1
Thermodynamics ATP
  • Review thermodynamics, energetics, chemical
    sense, and role of ATP

2
Lecture 24
  • Thermodynamics in Biology

3
A Simple Thought Experiment
4
Driving Forces for Natural Processes
  • Enthalpy
  • Tendency toward lowest energy state
  • Form stablest bonds
  • Entropy
  • Tendency to maximize randomness

5
Enthalpy and Bond Strength
  • Enthalpy ?H heat change at constant pressure
  • Units
  • cal/mole or joule/mole
  • 1 cal 4.18 joule
  • Sign
  • ?H is negative for a reaction that liberates heat

6
Entropy and Randomness
7
Entropy and Randomness
  • Entropy S measure of randomness
  • cal/degmole
  • T?S change of randomness
  • For increased randomness, sign is

8
System Definition
9
System Definition
10
System Definition
11
Cells and Organisms Open Systems
  • Material exchange with surroundings
  • Fuels and nutrients in (glucose)
  • By-products out (CO2)
  • Energy exchange
  • Heat release (fermentation)
  • Light release (fireflies)
  • Light absorption (plants)

12
1st Law of Thermodynamics
  • Energy is conserved, but transduction is allowed
  • Transduction

13
2nd Law of Thermodynamics
  • In all spontaneous processes, total entropy of
    the universe increases

14
2nd Law of Thermodynamics
  • ?Ssystem ?Ssurroundings ?Suniverse gt 0
  • A cell (system) can decrease in entropy only if a
    greater increase in entropy occurs in
    surroundings
  • C6H12O6 6O2 ? 6CO2 6H2O
  • complex simple

15
Entropy A More Rigorous Definition
  • From statistical mechanics
  • S k lnW
  • k Boltzmann constant 1.38?1023 J/K
  • W number of ways to arrange the system
  • S 0 at absolute zero (-273ºC)

16
Gibbs Free Energy
  • Unifies 1st and 2nd laws
  • ?G
  • Gibbs free energy
  • Useful work available in a process
  • ?G ?H T?S
  • ?H from 1st law
  • Kind and number of bonds
  • T?S from 2nd law
  • Order of the system

17
?G
  • Driving force on a reaction
  • Work available ? distance from equilibrium
  • ?G ?H T?S
  • State functions
  • Particular reaction
  • T
  • P
  • Concentration (activity) of reactants and
    products

18
Equilibrium
  • ?G ?H T?S 0
  • So ?H T?S
  • ?H is measurement of enthalpy
  • T?S is measurement of entropy
  • Enthalpy and entropy are exactly balanced at
    equilibrium

19
Effects of ?H and ?S on ?G
Voet, Voet, and Pratt. Fundamentals of
Biochemistry. 1999.
20
Standard State and ?Gº
  • Arbitrary definition, like sea level
  • Reactants and Products
  • 1 M or 1 atmos (activity)
  • T 25ºC 298K
  • P 1 atmosphere
  • Standard free energy change ?Gº

21
Biochemical Conventions ?Gº?
  • Most reactions at pH 7 in H2O
  • Simplify ?Gº and Keq by defining H 107 M
  • H2O unity
  • Biochemists use ?Gº? and K?eq

22
Relationship of ?G to ?Gº?
  • ?G is real and ?Gº? is standard
  • For A in solution
  • GA GA RT lnA
  • For reaction aA bB ? cC dD
  • ?G ?Gº? RT ln
  • Constant Variable
  • (from table)

º?
Cc Dd

Aa Bb
23
Relationship Between ?Gº? and K?eq
Cc Dd
  • ?G ?Gº? RT ln
  • At equilibrium, ?G 0, so
  • ?Gº? RT ln
  • ?Gº? RT ln K?eq

Aa Bb
Cc Dd
Aa Bb
24
Relationship Between K?eq and ?Gº?
25
Will Reaction Occur Spontaneously?
  • When
  • ?G is negative, forward reaction tends to occur
  • ?G is positive, back reaction tends to occur
  • ?G is zero, system is at equilibrium
  • ?G ?Gº? RT ln

Cc Dd
Aa Bb
26
A Caution About ?Gº
  • Even when a reaction has a large, negative ?Gº,
    it may not occur at a measurable rate
  • Thermodynamics
  • Where is the equilibrium point?
  • Kinetics
  • How fast is equilibrium approached?
  • Enzymes change rate of reactions, but do not
    change Keq

27
?Gº? is Additive (State Function)
  • Reaction
  • A ? B
  • B ? C
  • Sum A ? C
  • Also B ? A
  • Free energy change
  • ?G1º?
  • ?G2º?
  • ?G1º? ?G2º?
  • ?G1º?

28
Coupling Reactions
  • Glucose HPO42 ? Glucose-6-P
  • ATP ? ADP HPO42
  • ATP Glucose ? ADP Glucose-6-P
  • ?Gº?
  • kcal/mol kJ/mol
  • 3.3 13.8
  • 7.3 30.5
  • 4.0 16.7

29
Resonance Forms of Pi
?
?
?
?
30
Phosphate Esters and Anhydrides
31
Hydrolysis of Glucose-6-Phosphate
?Gº? 3.3 kcal/mol
13.8 kJ/mol
32
High ?Gº? Hydrolysis Compounds
?Gº? 14.8 kcal/mol 61.9 kJ/mol
33
High ?Gº? Hydrolysis Compounds
?Gº? 11.8 kcal/mol 49.3 kJ/mol
34
High ?Gº? Hydrolysis Compounds
?Gº? 10.3 kcal/mol 43 kJ/mol
35
Phosphate Anhydrides (Pyrophosphates)
?Gº? 7.3 kcal/mol 30.5 kJ/mol
36
Thiol Esters
?Gº? 7.5 kcal/mol 31.4 kJ/mol
37
Thiol Esters
Thiol ester less resonance-stabilized
38
High-Energy Compounds
  • Large ?Gº? hydrolysis
  • Bond strain (electrostatic repulsion) in reactant
  • ATP
  • Products stabilized by ionization
  • Acyl-P
  • Products stabilized by isomerization
  • PEP
  • Products stabilized by resonance
  • Creatine-P

39
High-Energy Compounds
  • High-energy compound is one with a ?Gº? below
    6 kcal/mol (25 kJ/mol)

40
High-Energy Compounds
41
Group Transfer Potential
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Lecture 25
  • Chemical Sense in Metabolism

61
Making and Breaking CC Bonds
  • Homolytic reactions
  • Heterolytic reactions

62
Making and Breaking CC Bonds
  • Nucleophilic substitutions

63
Nucleophilic Substitution Reactions
  • SN1

64
Carbocation
65
Common Biological Nucleophiles
66
SN2 Nucleophilic Substitution
?
?
67
Reactivity is SN2 Reactions
68
Leaving Group
  • Must accommodate a pair of electrons
  • And sometimes a negative charge

69
Major Role of Phosphorylation
  • Converts a poor leaving group (OH) into a good
    one (Pi, PPi)

70
Acid Catalysis of Substitution Reactions
This H is often donated by an acidic
sidechain of enzyme
71
Central Importance of Carbonyls
  • 1. Can produce a carbocation
  • 2. Can stabilize a carbanion

72
Biological Carbonyls
73
Aldol Condensation
74
Aldol Condensation
75
Aldol Condensation
76
Aldolase Reaction
  • Glycolysis and gluconeogenesis

77
Claisen Condensation
78
Claisen Condensation
79
Thioesters in Biology
  • In thioesters, the carbonyl carbon has more
    positive character than carbonyl carbon in oxygen
    ester.

80
High-Energy Thioester Compounds
81
Coenzyme A
82
Fatty Acid Metabolism
  • Uses Claisen condensation
  • Thiolase acts in fatty acid oxidation for energy
    production

83
Thiolase Role of Cys-SH
84
Thiolase Role of Cys-SH
85
Energy Diagram for Reaction
  • is the transition state
  • Pentacovalent carbon, for example

86
Functional Groups on Enzymes
  • Amino acid side chains
  • Imidazole

87
Functional Groups on Enzymes
  • Coenzymes/cofactors
  • Pyridoxal phosphate
  • Metal ions and complexes
  • Mg2, Mn2, Co2, Fe2, Zn2, Cu2, Mo3

88
Enzyme Inhibitors and Poisons
  • Chelating agents
  • EDTA (divalent cations)
  • CN (Fe2)
  • Cofactor analogs
  • Warfarin
  • Suicide substrates

89
Lecture 26
  • ATP and Phosphoryl Group Transfers

90
Phosphate Esters and Anhydrides
91
Phosphoryl Group Transfers
92
Phosphoryl (Not Phosphate) Transfers
93
Nucleophilic Displacements
94
ATP as a Phophoryl Donor
  • 2 roles for ATP
  • Thermodynamic
  • Drive unfavorable reactions
  • Mechanistic
  • Offer 3 electrophilic phosphorous atoms for
    nucleophilic attack

95
ATP as Phosphoryl Donor
  • 3 points of nucleophilic attack

96
Adenylyation Attack on ?-P
97
Adenylation Attack on ?-P
98
Pyrophosphorylation Attack on ?-P
99
Phosphorylation Attack on ?-P
100
Amino Acid Sidechains as Nucleophiles
101
Enzymatic Phosphoryl Transfers
  • Four classes
  • Phosphatases
  • Water is acceptor/nucleophile
  • Phosphodiesterases
  • Water is acceptor/nucleophile
  • Kinases
  • Nucleophile is not water
  • Phosphorylases
  • Phosphate is nucleophile

102
Phosphatases Glucose-6-Phosphatase
103
Phosphatases Glucose-6-Phosphate
104
Phosphodiesterases RNAase
105
Phosphodiesterases RNAase
106
Kinases ?-Phosphoryl Transfer
  • Transfer from ATP

107
Kinases P-Enzyme Intermediates
108
Kinases P-Enzyme Intermediates
109
Kinases
110
Pyruvate Kinase
  • Makes ATP (?Gº? 31 kJ/mol) from PEP

?Gº? 62 kJ/mol
111
Phosphoryl-Group Transfer Potential
112
Significance of High-Energy P Compounds
  • Drive synthesis of compounds below
  • Phosphated compounds are more reactive
  • Thermodynamically
  • Kinetically
  • If organism has ATP (etc), it can do work and
    resist entropy
  • ?Cells must get ATP
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