environmental cycles of metabolism carbon is fixed (incorporated) by autotrophs (co 2 ) and...
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Environmental Cycles of Metabolism
• Carbon is fixed (incorporated) by autotrophs (CO2) and heterotrophs (complex such as carbohydrates)
• Nitrogen (N2) is solely introduced into biological systems through microbes
• Also phosphate cycle, sulfur cycle, etc.
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Modes of metabolism
• Catabolism – nutrient breakdown
• Anabolism – macromolecule synthesis
• Both are linked via carriers of chemical energy NADH, ATP, NADPH, FADH2
• These sources of chemical energy allow cells to perform “work” (synthesis, etc…)
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Consider the cell a “system”
• Isolated system – cannot exchange energy or matter with its surroundings (not a cell)
• Closed system – can exchange energy, but not matter with its surroundings (still not a cell)
• Open system – can exchange energy and matter in and out (A Cell!)
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Internal energy is a state function• The thermodynamic state is defined by
prescribing the amounts of all substances present, and two of these variables: temperature (T), Pressure (P), and Volume (V) of the system.
• The internal energy (E) of the system reflects all of the kinetic energy of motion, vibration, and rotation and all of the energy contained within chemical bonds and non-covalent interactions
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How do cells make and use chemical energy?
• Bioenergetics must follow the laws of thermodynamics
• First Law: the total amount of energy in the universe remains constant; energy may change form or location, but cannot be created or destroyed.
• Second Law: Entropy is always increasing
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First Law of Thermodynamics
E = q – w
q = heat; positive q indicates heat is absorbed by the system, negative q indicates heat given off by system
w = work; positive w means the system is doing work, negative w means work is being done on the system
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Oxidation of palmitic acid
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A “bomb” calorimeter allows reactions to be carried out at constant volume
• Because the reaction in (a) is carried out at constant V, no work is done on the surroundings
• Therefore, E = q
• In this case, E = -9941.4 kJ/mole
• The negative sign indicates the reaction releases energy stored in chemical bonds and transfers heat to the surroundings
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Reactions at constant pressure
• In reaction (b), the reaction proceeds at 1 atm pressure
• The system is free to expand or contract, the final state has contracted because the amount of gas has changed from 23 moles to 16
• The decrease in volume means that work has been done on the system by the surroundings
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PV work appears as extra heat released
• When volume is changed against a constant pressure, w = PV
• Assumptions: constant T, gases are ideal, which allows us to use PV = nRT
• w = nRT = -17.3 kJ/mol• SO, under constant pressure q = E + w = E + nRT =
-9941.4 kJ/mol – 17.3 kJ/mol
= -9958.7 kJ/mol – In (b) the surroundings can do work on the system, this (PV) work looks like extra heat
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Most biochemical reactions occur under constant pressure, not constant volume
• Because q does not equal E, we need to account for PV work done
• We define a new quantity, enthalpy (H) – H = E + PV
H = E + PV– When the heat of a reaction is measured at
constant pressure, H is determined
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E and H measurements are useful for biochemists
• Although oxidation of palmitic acid occurs very differently in the human body than in a calorimeter, the values of E and H are the same regardless of the pathway
• Average human expends ~6000 kJ or roughly 1500 kcal for bodily function, with exercise that figure easily doubles
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E, H, is there a big distinction?
• For most chemical reactions the difference between these two quantities is negligible
• Typically, PV is a tiny quantity
• For instance, it’s about 0.2% difference for palmitic acid oxidation
H is generally considered a direct measure of the energy change in a process and is the heat evolved in a reaction at constant P
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Entropy and the second law
The minimal value
of entropy is a
perfect crystal at
absolute zero
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Diffusion is an entropy driven process
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Increase in entropy can lead to -G
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Thermodynamic quantities
H = enthalpy, the heat content of the systemexothermic = negative, endothermic =
positive; Units: Joules/moleS = entropy, randomization of energy and matter;
positive sign indicates increased entropy; Units: joules/mole(K)
G = Gibbs Free energy, amount of energy that is available to do work at constant T and P; Units: Joules/mole
Note 1 calorie = 4.184 Joule
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Gibbs-Helmholtz equation
G = H – TS
Positive G is endergonic, requires energy for reaction to occur, this is unfavorable
Negative G is exergonic, releases energy, this is a favorable process; spontaneous but not necessarily rapid
A decrease in energy (-H) and/or increase in entropy (+S) make favorable processes
G =0 indicates the system is at equilibrium
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Thermodynamics of melting ice
Ice is a crystal lattice held together by H-bonds, bonds must be broken to form water
Energy for breakage of H-bonds is almost entirely the H for this reaction and this term is positive
Entropy favors water over ice
But recall G is also temperature dependent
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Entropy and Enthalpy contributions to melting ice
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Biochemical reactions can have different contributions
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Why is G called “free” energy?
G represents the portion of an energy change H that is available or free to do useful work.
TS is amount of energy that is unavailable to do work
G = H – TS
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A G Warning!
• You will see many different G’sG – Gibbs Free Energy
G’o or Go – Standard State Free Energy
energy per mole in standard state (1M)
Go – Standard state Free Energy of Activation
enzyme catalysis