CLASS: Fundamentals I 11:00-12:00
DATE: 8/24/2010
PROFESSOR: Deivanayagam
I.
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VI.
Thermodynamics of Biological Systems
Scribe: Ashley Tate
Proof:
Page 1 of 4
OUTLINE [S2]
a. Today, going to talk about thermodynamics in all biological systems.
b. Parameters to define thermodynamics are all abstract and difficult to define.
c. Also we are going to look at the 3 law of thermodynamics, term of enthalpy, entropy, Gibbs free energy, and
examples of these.
WHAT YOU NEED TO KNOW FOR EXAM [S3]
a. Thermodynamics studies the flow of heat energy from one system to another system. Why do we need to
study the flow of heat energy? Every process that you look at that happens in this world. Is simply based on
the transfer of energy. It’s mostly in the form of heat.
b. If you take simple example of driving your car, is a great example of Thermodynamics. You put in gas and it’s
combusted. Then there is a large amount of heat released, which is pushing your pistols up and down, which
is how you are able to put your leg on the pedal, and not realize how much of thermodynamics is happening
within the system. Therefore, the efficiency of your car is decided by the amount of miles traveled and the
amount of gas you put in; energy is the amount of gas you put in.
c. The laws of thermodynamics rule the universe. This is a basic appreciation one must have about
Thermodynamics. Laws were formulated more than 150 years ago, much before quantum chemistry and
physics came to be. Therefore, people looked at things at a macro-level, not at a micro-level. Marco-level
made things much more complicated.
d. Entire approach of thermodynamics is on macro-states. Systems have many macro-states and with them
there are many micro-states.
ENERGY [S4]
a. Within this lecture, will look at how energy is used. Basically without energy nothing could happen.
b. Energy is defined with 2 parameters, in terms of kinetic energy and potential energy.
c. Kinetic energy is always in motion. An example is flow of water in a river, the molecules are moving at a
certain rate. Molecules in movement have kinetic energy.
d. Potential energy example is water contained in a dam. It has energy but is staying a certain state.
e. Every molecule, every atom, even in its static state has a certain amount of energy, which is called the
internal energy of a system.
THERMODYNAMICS [S5]
a. Thermodynamics is study of how energy is transferred in a particular system.
b. This is defined in 3 different systems: Isolated, Closed, and Open.
c. Isolated System: No exchange of matter or energy. This system does not exist in reality.
d. Closed System: Energy exchange may occur, but transfer does not. Example is closed bottle of water, you
can heat the bottle of water and give energy to it but you cannot take water out. Everything is contained in the
system.
e. Open System: Both energy and matter is exchanged. All biological systems adhere to the open system.
FIRST LAW OF THERMODYNAMICS:[S6]
a. First Law of thermodynamics says energy is neither created nor destroyed. Energy of the universe is a
constant. Every molecule, every atom, everything you see all has energy.
b. Total energy in an isolated system is always conserved. Closed system, in which you are able to create an
energy change. Therefore, the change in energy can be defined as the summation of the heat absorbed by
the system as well as the work done on the system by the surroundings.
c. When you give energy to any system, it is not going to stay there; it is going to start absorbing energy and
doing some work. This sequential defines that.
d. Work can be defined as mechanical. Mechanical is work. If you apply a certain amount of force and distance
traveled that is always defined as work. Work=Force x Distance (Force=Mass x acceleration). The work done
by the little boy in the photo is zero, because he is not able to push anything.
e. Given any state where the molecules are, the internal energy only defines the present state. Internal energy
will never tell you how it acquired energy in the first place.
f. The Law has a lot of subclasses, it will never tell you how a system came to that particular state, It can only
define what the parameters are of that particular system.
MECHANICAL WORK [S7]
a. If you have a system that is bottle up in some molecules, that is a constant pressure system, you can define
work in terms of change in volume. V = V2-V1
b. Work can be defined in multiple terms: Mechanical, Electrical, magnetic, and chemical
c. Calories are the traditional units that energy is defined. SI recommends to use Joules. Also there are other
units such as Avogadro’s number and Coulomb.
d. This slide just for your information.
CLASS: Fundamentals I 11:00-12:00
Scribe: Ashley Tate
DATE: 8/24/2010
Proof:
PROFESSOR: Deivanayagam
Thermodynamics of Biological Systems
Page 2 of 4
VII. SLIDE TITLE [S8]
a. Enthalpy can be a constant pressure system and defined as the summation of a system + the pressure and
volume.
b. If there is an increase in energy of a system: (H = E + PV), you will find that H is nothing but the heat
energy of the system. The first law of thermodynamics tells you enthalpy is directly related to the energy of
the system.
c. For a system at equilibrium, enthalpy can be defined in terms of a gas constant as well as the temperature.
VIII. PROETIN DENATURATION [S9]
a. A good example where enthalpy will play a big role is if you have a protein molecule, and increase the
temperature, at a certain point it must stop. This is the point, where the protein begins to get denatured. If you
had high salt concentrations or urea, it will also begin unfolding because of the electrostatic interactions and
breaking the hydrogen bonds present in protein molecules.
IX. STUDY OF TEMPERATURE.. [S10]
a. From a folded to unfolded state, if you measure the equilibrium constants. In this example they have done it
at pH 3. They are plotted it in this graph, van’t Holf Plot.
b. van’t Holf Plot: plots temp as respect to the equilibrium. Slope at any point gives you the equilibrium. At 54.5,
if you calculate the enthalpy is turns out to be 533kj/mol. It is the breaking point of chymotrypsinogen and
denature at this point.
c. If you do an experiment, with a lot of enthalpy, it tells you it is beginning to break hydrogen bonds and
beginning to expose hydrogen surfaces.
d. Proteins fold in a manner to shield hydrophobic on the inside and keep the hydrophilic on the outside.
e. Large amount of enthalpy means large amount of internal energy. Any system can only without a certain
amount of energy, beyond a certain amount that system is going to break. As you increase the temp, the
system begins to break.
X. SECOND LAW OF THERMODYNAMICS [S11]
a. Second law states energy transfer increase entropy of the universe.
b. Things in order are very unstable state. They have to in disorder, which is very stable state.
c. Any system when gets an energy transfer and gets heated up, the change in order that it looses is the
measure of entropy.
d. Equilibrium is when molecules will start traveling back and forth, which is a change in volume, and the
molecules will spread out almost evenly. However, when the molecules move from one place to another they
will loose some energy.
e. In general all nature processes, tend to achieve equilibrium given any set of circumstances. Equilibrium is
necessary for every process to function properly.
XI. ENTROPY [S12]
a. Entropy can be defined as W, number of microstates.
b. Ice (solid) at ) degrees, once you heat it up, it starts to break the bonds because it is getting energy in them.
Same idea in boiling water, molecules escape from one phase to another phase as the water heats up. This
is called phase transition.
c. Phase transition, complicated process and very poorly understood. Then he talks about in his lab how they
are trying to take protein molecules and convert them to crystals, (which is trying to take energy out of the
system.)
d. Entropy always tries to tell you how energy is dispersed.
e. Enthalpy is the energy of the system. Entropy is disorder of the system.
XII. THIRD LAW OF THERMODYNAMICS [S13]
a. Third law deals with absolute entropies. Means even at 0K, there is a certain amount of entropy. As it
approaches zero. However, we will never deal with these in biological systems.
XIII. GIBB’S FREE ENERGY [S14]
a. Gibb’s free energy is a combination of both entropy and enthalpy in one equation. It is relates to the entropy
and enthalpy of the system. If you define the change in Gibb’s, it also can be measured in terms of change in
entropy and change in enthalpy.
b. G is negative then exergonic (release of energy in the form of work) and G is positive then endogonic
(absorbing energy in the form of work).
c. We can measure enthalpy and entropy with this one equation
XIV.
EXAMPLES OF CHYTRYPSINOGEN... [S15]
a. Mentions the van’t Holf Plot. From earlier.
XV. FOR A PROCESS TO OCCUR SPONTANOUSLY [S16]
a. For a system to occur spontaneous, a system must either give up energy (decrease enthalpy) or give up
order (entropy will increase), or sometimes both.
CLASS: Fundamentals I 11:00-12:00
Scribe: Ashley Tate
DATE: 8/24/2010
Proof:
PROFESSOR: Deivanayagam
Thermodynamics of Biological Systems
Page 3 of 4
b. In general for the process to be spontaneous, G must be negative. An example of this is cellular respiration,
it is giving up -686 kcal/mol.
c. G is also defined as the activation energy that is required.
d. Some reactions are endergonic and they require a large amount of input of energy. Example of this is
photosynthesis. In photosynthesis, energy is derived from the sun.
e. This slide summaries about entropy and enthalpy in one term, which is called Gibb’s free energy. Gibb’s free
energy has to be negative for a reaction to be spontaneous.
XVI.
TABLE [S17]
a. This table summaries many different parameters. You will see in reading this table that only one set of
parameters are actually favored
XVII. ATP [S18]
a. Everyone talks about energy and how cells are derived in energy and form ATP. Large amount of ATP is
required. Cells are very smart and are able to not release much energy.
XVIII. ENERGY IS RELEASED… [S19]
a. ATP is broken down, and the release of the phosphates tend to give off energy, and that is how most of the
life around the cell cycle is revolved.
b. This equation (ATP + H2O → ADP + Pi ) tell you how ATP is hydrolyzed, and how it makes an ATP and how
it gives off a phosphate
c. The G for this equation is -35.7 kJ/mol because there is a little more complication and it’s just not ATP
alone.
d. For this reaction to take place, the Keq is defined exactly how it looks.
XIX.
THE ACTIVATION ENERGIES FOR… [S20]
a. If you look at the energy that is required, for the ATP, it requires an activation energy of 200-400 kj/mol.
b. So if you take an ATP molecule and just leave it like that, it is not going to convert. It requires a certain
amount of work and effort. This amount of work is normally the work that the enzymes in our body do.
Enzymes cut this down to a must lower level and are able to do this much faster and efficient.
XX.
IONIZATION STATES OF ATP [S21]
a. ATP has 5 dissociable protons.
b. *Also need to know how many ionization states are there for ATP.
c. Free energy of hydrolysis of ATP is constant from pH 1-6, can see this in the next graph. but pretty much a
constant up to 6.5
XXI.
CHART [S22]
a. pH is pretty much a constant all the way to 6-6.5, then around 7 goes up real fast. If pH goes beyond a
certain level, it will not be able to break it down. The physiological pH is about 7, and around 35.7 is the
amount of energy required to break the ATP bond.
XXII. No title, TABLE [S23]
a. Most of the enzymes do not just use ATP alone. This graph depicts addition of Mg2+ ion.
b. When you add extra complements into the system, they tend to change the system in an unpredictable
manner. If you plot these with Mg2+, you see the result on the graph is very strange. Typically they are high
concentrations. Every time you add something else to the system, it complications the system.
XXIII. No title, TABLE [S24]
a. If you just plotted a concentration of [C], it would also result a different kind of straight line.
b. In thermodynamics, it is very difficult to determine the results. We do not know the interactions that happen.
One can make some very good guesses but it is more complicated than it looks. Most of the time in
thermodynamics studies people try to predict what is happening but one cannot clearly say this is what is
happening.
XXIV. No title, TABLE 3.3 [S25]
a. SKIPPED
XXV. WHAT IS THE DAILY HUMAN REQUIREMENT FOR ATP [S26]
a. If you look at ATP required for a given day, average adult consumes 11,7000 kJ of food
b. 65 kg of ATP per day
c. The typical adult human body contains 50 g of ATP/ADP
d. ATP is recycled so many times in a day. About 1300 times per day just recycled. It is being used to generate
energy.
XXVI. ISOTHERMAL TITRATION CALORIMETRY [S27]
a. How do we measure these het changes? With protein molecules. Now we can calculate small amounts of
energy that are being released with a calorimetry. Calorimetry measures the amount of heat released.
CLASS: Fundamentals I 11:00-12:00
Scribe: Ashley Tate
DATE: 8/24/2010
Proof:
PROFESSOR: Deivanayagam
Thermodynamics of Biological Systems
Page 4 of 4
b. Have 2 cells: reference cell and experimental cell. In reference cell typically have water at certain temp. In
experimental cell, you allow reaction to take place. Then you start measuring the temperature changes.
These are maintained.
c. This is an isothermal titration caliometry, and in this it measures changes in heat and it is kept in an isolated
system. By doing so in an isolated system, it helps you calculate what kind of entropy is created and what
kind of enthalpy is released.
XXVII. ITC STUDIES ON… [S28]
a. In our lab, we have been studying molecules with a very long alpha helix. The structure wanted to confirm
whether the primary sequence….(continues to talk about his lab and there experiment)
XXVIII. No title [S29]
a. What happens in a cell if G = 0 ? Dead.
[End 47:51 mins]