Biochemical Thermodynamics Flashcards
Definition of Thermodynamics:
Thermodynamics describes the relationship among various forms of energy and how energy effects matter on the
macroscopic level (e.g. temperature, entropy, pressure).
Importance of thermodynamic principles in biochemistry?
Thermodynamics is essential for understanding why
macromolecules fold into their native conformations, how metabolic pathways are designed, why molecules cross biological membranes, etc.
- Thermodynamics tells us which reactions will go forward and which ones won’t.
It is common observation that:
Some processes involving material substances
happen spontaneously, others do not.
Biochemistry studies the changes that occur to material
substances. The sorts of changes or processes that are of interest to biochemists include:
– Phase changes – e.g., melting, boiling, dissolving….
– Chemical reactions – substances change their
chemical nature (by changing the way in which their constituent atoms are bonded together to form
compounds)
– Physical processes – heating, cooling, expansion, compression, etc.
Thermodynamics will NOT tell us…
the rate at which possible processes occur
(that’s kinetics).
The original energy of the gas which
was localised and ordered becomes dissipated into a large number of random molecular motions. It is most unlikely that they will never get back into step.
In what way or ways can a chemical reaction increase the disorder of the system (the reacting substances) or its surroundings?
One way would be if the reaction emits heat (thermal
energy (i.e., if it is exothermic). The heat emitted by the reaction is dispersed in the form of thermal energy in the surroundings. This produces increased disorder and, as we have seen, this is a requirement for spontaneous
change.
entropy:
An increase in disorder
Given the symbol S.
Entropy acts as a measure of
the disorder associated with the atoms or molecules that make up a substance, and the dispersal of energy
associated with those particles.
Any substance, in a defined state…
(specified
values of T, p, etc.), has a specific entropy valueassociated with it.
The entropy of a substance is proportional to…
the number of ways in which the available energy can be distributed over the atoms or molecules of a system.
The entropy of substances..
increases with
increasing temperature.
Relationship between entropy and physical state:
So:
When solids —-> liquids Appreciable increase in S
When liquids —> vapours Very large increase in S
It turns out that there is a very fundamental
relationship between:
Spontaneity of
chemical
reactions and
other processes and entropy change
There exists a thermodynamic function
called…
entropy, denoted S, that has the
property that for any process the change in
entropy of the universe ΔS(univ) ≥ 0
ΔSuniv = ΔSsys + ΔSsur
(>) applies to spontaneous (irreversible)
processes
(=) applies to reversible processes (systems at
equilibrium)
in any spontaneous process there is
always an…
increase in the entropy of the
universe.
Suniv > 0
for a spontaneous process.
Suniv = Ssystem + Ssurroundings
Ssystem
can decrease if Ssurroundings
increases more
We distinguish between
thermodynamics and kinetics:
- Thermodynamics characterizes the
energy associated with equilibrium
conditions in reactions - Kinetics describes the rate at which
a reaction moves toward equilibrium
Equilibrium constant (Keq) is a…
measure
of the ratio of product concentrations to
reactant concentrations at equilibrium
Free energy at the standard state (Go
)
is a
measure of the available energy in
the products and reactants
Equilibrium constant (Keq) and free energy are related through…
Go = -RT ln Keq
Derivation of Go = Go -RT ln Q
The relationship between the free energy of
reaction at any moment in time (G) and the
standard-state free energy of reaction (Go
) is
described by the following equation
- R is the ideal gas constant, J/mol-K,
- T is the temperature in kelvin
- ln represents a logarithm to the base e
- Q is the reaction quotient at that moment in time.
Why we care:
- Free energy is directly related to the equilibrium
of a reaction - It doesn’t tell us how fast the system will come to
equilibrium - Kinetics, and the way that enzymes influence
kinetics, tell us about rates - Today we’ll focus on equilibrium energetics; we’ll
call that thermodynamics
Laws of Thermodynamics:
-Can be articulated in various
ways
- First law: The energy of an
isolated system is constant - Second law: Entropy of an
isolated system increases
A system is the portion of
universe
with which we’re concerned (e.g., an
organism or a rock or an ecosystem)
- If it doesn’t exchange energy or matter
with the outside, it’s isolated. - If it exchanges energy but not matter,
it’s closed - If it exchanges energy & matter, it’s
open
Isolated system:
one in which energy and
matter don’t enter or leave
Enthalpy, H:
- Closely related to energy:
H = E + PV - Therefore changes in H are:
H = E + PV + VP - Most, but not all, biochemical systems
have constant V, P:
H = E - Related to amount of heat content in a
system
Extensive properties:
Thermodynamic properties that are
directly related to the amount (e.g. mass,
or # moles) of stuff present (e.g. E, H, S)
Intensive properties:
not directly related
to mass (e.g. P, T)
- E, H, S are:
state variables;
work, heat are not
Go for hydrolysis of high-energy
phosphate bond in adenosine
triphosphate (ATP):
Hydrogen bond: 4 kJ/mol = 1kcal/mol
- van der Waals force: ~1kJ/mol
Most biochemical reactions involve:
very small (< 10 kJ/mol) changes in
enthalpy
- Driving force is often entropic
- Increases in solute entropy often is at
war with decreases in solvent
entropy. - The winner tends to take the prize.
Apolar molecules in water:
- Water molecules tend to form ordered
structure surrounding apolar molecule - Entropy decreases because they’re so
ordered
Binding to surfaces:
- Happens a lot in biology, e.g.
binding of small molecules to relatively
immobile protein surfaces - Bound molecules suffer a decrease in
entropy because they’re trapped - Solvent molecules are displaced and
liberated from the protein surface
Gibbs:
Free Energy Equation
G = H - TS
- So if isothermal, G = H - TS
Gibbs showed that…
a reaction will
be spontaneous (proceed to right)
if and only if G < 0
