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Water!
Introduction
-Water has everything has to do with life. All the biochemistry reactions occur in aqueous
environment.
-Water is present in a great huge amount.
Q: What is the molar concentration of water? A: 55. M.
 Every time you deal with a reaction with water, you are dealing with a huge
reservoir of water (55 M concentration).
 Products and Reactant are usually in nM, microM or mM, however water is 55 M
concentration. Water is big element that is around. We are going to talk about
acid/base, and hydrophobic.
Water is beautiful. Zoo-freshwater with life and fish.
Slide 4
Water as a chemical molecule
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Water has an unusual angular structure.
It has a huge electronegative oxygen between the two electro-positive hydrogen
atoms giving it polar character giving its functions in reactions.
You can read the details of the slide as well.
It is highly asymmetrical molecule because of oxygen (partially negative) and the
hydrogen (partially negative).
Concentration of water is 55M again.
The bond angle is not as important for our course.
Slide 5 That kind of structure of gives the water the ability to form hydrogen bond (from
previous slide.
 In a water molecule, the hydrogen bond is hydrogen bonded to another to oxygen
in another molecule , and the oxygen is bonded to two other hydrogens from two
other molecule all by hydrogen bonding.
 Hydrogen plays a role in way the molecules bind to each other. =Hydrogen
bonding.
 In case of water, Bonds are weak and are constantly moving, folding occurs in
picoseconds when water is liquid.
 When water is solid the energy is taken away from the system, the hydrogen
bonds are fixed and becomes ice. The bonds are not moving.
 This slide is a good illustration of bonding.
Slide 6. The chemical Functions of Water
 Water is a good solvent.
 It is capable of taking a polar molecule and surrounding it so that ions are in true
(complete) solution.
 Water is an active participant in numerous (all) biological reactions because it is
present in huge quantities.
 In many reactions, water is both a reactant and a product.
 Water forms H-bonds to itself and polar solutes.
 If you master the concept of water, you have 85% biochemistry in your pocket.
 Strange interaction occurs with water because of the hydrophobic interactions
(oil). Many life processes occur because of these interactions. Oil is an example
of non-polar substance. Hydrophobic interactions are “secret of life.”
Slide 7- Hydrophobic Interaction.
Q: What happens when water finds itself in presence of highly non-polar solute?
 The non-polar solute will organize water and the hydrogen bond network
rearranges to make a shell (clathrate) around the non-polar to isolate it.
 Water can’t dissolve the substance. Water isolates it which increases the order of
water.
 This is difficult because it goes against thermodynamics. The second law of
thermodynamics says that universe is going into an increasing disorder state. So,
if water orders itself around the non-polar solute, then it is going against
thermodynamics. It is costly (energetically).
 Will do thermodynamics later.
Slide 8:
 This is a non-polar solute. Water can not dissolve it. Water will organize and form
an ice like structure. Since it causes the water to be ordered, it is unstable.
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Example: take a break and put a drop of oil in it. Shake it up, and the oil will be
dispersed (droplets can’t be seen). However, if you leave it alone, the oil will
congeal back together (can see it). If you have order of a certain kind, and do not
have constant energy (to maintain order) then disorder will occur. The disorder is
that: water molecules will leave, and the lipid molecules will congeal. You will
start again with insoluable lipid and a lake of water.
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You have a clathrate structure, it will be eventually destroyed, which is good for
biochemical reactions.
Slide 9- Amphiphatic molecules
 In biochemistry, we have molecules that are called amphiphatic molecules.
Amphiphatic molecules have a long tail that is hydrophobic (core), and polar
substance which is a carboxyl head that is hydrophilic.
Slide 10
Best example is a fatty acid.
A fatty acid
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Long chain of methylene groups make up the hydrophobic tale.
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It has an end with a carboxyl head has a sodium ion on it making it polar. This
situation creates the huge non-polar tail and the polar head of the molecule. This
is a fatty acid substance that is incorporated into a membrane.
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Q: Why will it be incorporated into a membrane?
A: Because the water will force the hydrophobic tails to join other hydrophobic
tails and form micelles as seen in next slide.
Slide 11-Micelles
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Micelles are formed such that hydrophobic core of the micelle becomes the
hydrophobic tails. The negatively charged carboxyl groups will be on the surface.
Not a good illustration- It should be in 3-D. It would be a sphere with fatty tails
(hydrophobic tails) inside, and the polar heads (carboxyl groups) at the surface.
Basically how the membranes are formed. They are formed by taking advantage
of the hydrophobic activity and water.
Slide 12- The Hydrophobic Effect
Summary:
 The hydrophobic effect is responsible for folding of proteins.
 A long protein chain (globular) it is going fold into a small globular (sphere).
Most soluble proteins look like this (on board).
 There is an acquired spherical concentrated figure b/c of hydrophobic tails wanted
to get away. Folding globular protein is controlled by water.
Assembly of quaternary structures
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There are spherical molecules that will associate with other spheres to form
quaternary structures.
They will come together and are held by Hydrophobic bonds.
There are formed because of the size of proteins molecules because they want to
avoid water (fear water). They leave water part and come together.
Large protein aggregate together.
Assembly of Membranes
The membranes-Already went over.
Binding Phenomena
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Very important in biochemistry. .
Molecules recognize each other and bind because of hydrophobic interaction.
Enzymes recognize their substrate – done b/c of hydrophobic interaction
Antibody/Antigen interaction is also due to Hydrophobic interaction.
If is not a permanent interaction (meaning not covalent), then it is done by
hydrophobic bonding.
Hydrophobic bonding is a very unique type of bonding.
Bond Energies –Review Slide 13
Keep in mind, in biochemistry everything will be listed in joules. This is listed in kJ/mol
or kCal/mol.
1 cal= 4.184 J.
Joules is international designation of energy. Calories have to do more with nutrition.
Keep mind of the two units.
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Covalent bonds like Carbons-Carbon single bonds require 368 kJ/mol. Double
bonds requires greater bonds energy to break 682 kJ/mol.
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The non-covalent dissociations are important in biochemistry.
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Hydrogen bonds in between highly electronegative atoms like oxygen and
nitrogen. The oxygen is more electronegative. The breaking of this bond is 10-40
kJ/mol. These hydrogen bonds are weak and easy to break.
Hydrophobic bonds are listed as negative because you must take away energy (or
cool down) to break them or dissociate them.
Hydrophobic bonds enhanced by warming. But to break them you must cool the
system. Next week: talk about collagen, to break them, you have to cool them
which is evidence they are held by (by hydrophobic bonding.
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Ion-ion interaction is a lot stronger than H-bonding. It is 40-100 kJ/mol.
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Van Der wall
o interactions occur in any substance or molecule has for another molecule
until they get close to each other when attracted and then they repel. For a
while, they have a certain attraction.
o It is a weak interaction but can be important because of the large size of
the biochemical molecules. The large molecules give lots of opportunities
to form Van Der Waals interactions.
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Kinetic Bond Energies
o At 25C, all molecules are moving with an energy (2.5 kJ/mol) Always
some type of agitation with a molecule or an atom in molecule.
o However, No movement (agitation) or energy utilization will occur if it a
perfect crystal in absolute zero temperature.
Slide 14- Acid Base Equilibria
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Water’s role as a chemical. Extreme importance, b/c water has 2 H atoms and
one oxygen atom (highly electronegative) it sets up arrangement that water can
ionize. It can act as either an acid or a base. Get used to it.
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Take two molecules of water together, one is an acid (give a proton ) and donate
it to another water.
o The product of these water molecules ionizing gives a hydronium ion and
hydroxide ion.
o At 25 C, pure water, the ion product is 1 x 10^-14. This the product of the
hydroxide times the hydronium concentrations. The pH scales comes
from this.
o The proton is present at a concentration of 1 x 10^ -7 M. At this
concentration, the negative log of this is pH of 7.
o Because:
So the pH = -log [hydronium or hydrogen concentration]
Molecules interact with water and do things to water.
Slide 15-Conjugate Acid- Base Systems.
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There are many organic acids (acetic acid, proponic acid ect).
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This acid(1), the reason it is an acid is because it is in presence of water. The
water molecule is a base (1).
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The acid gives up the proton to the water making an anion, and hydronium ion.
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So now, what was an acid is a base; what was a base is now an acid. *concept of
conjugate acid-base*.
The base accepts the proton. Acid donates a proton. This is the Bronstend Lowry
concept.
You can set up the lewis structures and know how the arrows in how the electrons move.
I will not go over them but you should know it.
Change in pH can be dramatic because the hydronium ion concentration can change.
Slide 16 Equilibrium Constants
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Equilibrium constant is the product of the products over the reactants of the
equation on the previous slide.
o The denominator is the dissociated acid and water, the numerator the
dissociate acid and water (as H+).
o You can take the water out of this constant because it is present in huge
amounts.
o Then you get a new factor Ka which is dissociation constant of the acid.
o The amount of anion generated by the acid when it dissociates multiplied
by the proton divided by the concentration of the original acid.
o Kd = [A-] [H+] [HA] [H2O]
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o Let Ka = Kd [H2O]
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o Ka = [A-] [H+] [HA]
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The higher the Ka, the larger dissociation. If the acid is strong and it dissociates
90%, then dissociated is 1/10th giving Ka a large number.
Ka , reflects the strength of the acid (how much it dissociates into the anion form
to the proton form ).
o The higher the Ka, the higher the acidity.
o The lower the Ka, the less the acidity
Slide 17- Henderson-Hasselbach equation.
If you take the negative log of the all the factors, then you would the equation:
-Log Ka = -log [H+] – log ([A-]/[HA])
Rearrange and solve for pH (which is also the –log[H+]:
• pH = pKa + log ([A-]/[HA]) ; The Henderson-Hasselbach equation.
[A-]= the anion of dissociate acid
[HA]= the acid
It can help you determine the system, and if you know the numbers you can look at the
system easily.
Slide 18- pH, pKa
Signifacnce.
pH = -Log [H+]
Value is inversely related to the concentration of Hydrogen ion. The higher the
concentration of hydrogen ion, the lower the pH. Two acid: pH=3, pH=7, the strongest
acid (or highest conc of H+) is the one with pH=3. The lower concentration is pH=7.
If :
[H+]=.1;
log (.1)= -1
[H+]=.01 ; log(.01)= (-2)
[H+]=.001; log (.001)= (-3)
This is set-up so it is going down in concentration of H+.
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If you take the negative of the log, then it is 1, 2 , 3 respectively. Therefore, the
higher the number of pH, the lower the concentration of hydrogen ion.
This is an inverse relationship (pH and hydrogen ion).
If the pH of the orange juice is 3.2, and the tea is 7.8. The concentration of
hydrogen ions is greater in the orange juice. Orange juice is highly acid. Too
much tea go into an alkalanie state.
The pKa is –log of the Ka. Therefore, a high Ka is highly acidic. The lower the
pKa, the higher the acidity. For example, if pKa= 4, and pKa=7, then the pKa of 4
is strong acid.
Note:
 When acid is half dissociated then the ratio is 1, at the point pKa=pH because the
log of zero is one.
Slide 19- Titration Curves:
You can force acid and base into different configuration.
Look at Bottom Figure
 Take acetic acid and add OH- equivalents (or adding base).
 The carboxyl group is going to be titrated to the anion form as time goes on.
 At the beginning at OH-, at the midpoint (1/2 equivalent), you come to pKa=4.76,
which is also the pH. At the point 50% un-dissociated, 50% and dissociated acid.
 Add one equivalent OH-, and finish the titration and all the acid is dissociated.
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The region of one pH down, and one pH up of the pKa is called the buffer
region. This region is where the Henderson-Hasselbach log factor is in control.
As you add more OH-, there less and less deviation from the flat line of pH. This
is buffering, one pH until below and one pH until above, the curve does not
change much.
pH will remain constant two pH units.
The carboxyl group is titrated to undissociated from. *Look at top figure*. Go from 0%
undissociated to 100% dissociated (carboxyl group).
Slide 20- Example of Henderson-Hasselbach equation slide
We have a solution of acetic acid, and add .1 equivalent , so that means if we had 1M
then we’re adding 1/10M ; same if it is in millimolar.
Relationship : If 1/10 dissociated, then 9/10 is undissociated
With 0.1 eq OH¯ added:
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pH = pKa + log ([0.1] / [0.9])
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pH = 4.76 + (-0.95)
pH = 3.81
Slide 21- Several Titration Curve Slide
Titrate imidazole group which is a side chain of hystidine (sp?) the amino acid. It has a
rather unusual structure (ring), it can get a proton or it can lose a proton and rise to
electrons while you titrate.
We can also titrate the ammonium ion that can be titrated to ammonia.
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The acetic acid goes to carboxyl group going to dissociated carboxyl group at pK
4.6.
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The imidazole group has a pKa 6.99. The imidazole protonated group is much
weaker acid than acetic acid because the pKa is higher.
o The inverse relationship between pKa and acidity. The higher Ka the
lower the pKa.
o If we titrate this group, we have a buffering region around pH of 7 which
is in range of physiological pH.
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The side chain of hystidine like other proteins is help to maintain the pH of
circulation at 7-7.5.
o The weakest acid is the ammonium group at pKa 9.25. It is titrated all the
way through.We have a buffer group at that level too.
Variety of agents that can be used as buffer. Physiologically we don’t use all those as
buffers, you would be messed up if you used all of them.
Slide 22- Phosphoric Acid Buffer
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Phosphoric acid is has one of those single important element - phosphate.
In physiological terms, the phosphate is very important. Biologically,
hydroxapatite (calcium phosphate) has phosphate is which is in teeth (mineral
portion) and the skeletal system. It is also in energy because of ATP (triphosphate).
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It can also be used in a buffer.
Phosphoric acid is H3PO4.
It has three ionization potentials because of the three protons that can be
deprotonated (donated).
If we start the titration of phosphoric acid, the first pKa is 2.15. go through that,
after one equiv of OH-, we have converted H3PO4 to H2PO4-.
At the midpoint we have H3PO4 and H2PO4-. The pKa is 2.15, it is very acidic
molecule (low pKa).
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Next titration we are going from H2PO4- to HPO4 (-2). We are going to titrate
another proton off. The pKa is 7.2 now.
o The second proton leaving, leaves much more slowly. H2PO4- is much
weaker than phosphoric acid.
 The proton leaving an uncharged molecule is easier than leaving a
charged molecule. The negativity charged molecule gives the
positively charged proton a difficult time escaping. It is a weaker
acid (H2PO4-)
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The buffering region between H2PO4- and HPO4(-2), that region is for
intracellular systems. The cells (brain, liver, every cell) are buffered internally by
this system. Therefore, the system is essentially is using one common system.
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Last buffer system, it’s even a weaker acid with a pKa of 12.4. A buffering
system is up to pH of 12.-12.5.
Useful buffering system in the body.
Slide 23 Buffer System Slide
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Buffer- It’s ability to maintain a constant pH over a large addition over the
opposite type of molecule mainly sodium hydroxide.
For instance, an acid and it’s dissociate anion, if we add OH-, then titrate the
proton off to make water. We are going to get the anion.
If we have the anion and we add acid, we are going to protonate the anion and go
back to the acid. It’s a circular arrangement.
You can add OH- (base) or add H+(acid) and come back to the orginal molecules.
This is what a buffer does.
Slide 24- Why is it important?
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For example, we have enzymes like pepsin that have maximum proteolytic
activity at about pH of 2.5-3.
Fumarase that is in the carboxylic acid which functions as best around 7.5.
Lysozyme is for degredation of bacterial walls which functions in the lysosomes
that has best function at pH of 5. The pH can change the ionic characteristics. The
pH has to be optimal for the enzymes to work properly.
Slide 25- Anserine
Some compounds like Anserine can be used to form buffers. It’s a polypeptide of balanyl and histidine. You can recognize this tomorrow. This molecule can buffer at the
three areas. It can buffer at the amine group, carboxyl group, and the imidazole group.
Slide 26- Next Slide
Just an example of substances of buffer.
HEPEs is favorite for biochemist because of it’s pKa of 7.4 It’s right around the
physicological pH.
Slide 27- What is it looks like.
Slide 28- Carbonic Acid
Last buffer system. It’s in the extracellular system for circulation. It is involved with
carbonic acid. The difficulty is that it’s not a closed system like in a cell. The carbon
dioxide leaves through the lungs and enters through the lungs. The carbon dioxide
combines with water to make carbonic acid. It can dissociate into proton and the anion.
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Proton and anion leave though renal acitivity. Proton can go to the GI tract (b/c
it’s acid of stomach pH=2.) The protons usually come from this dissociation.
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The ability to make bicarbonate and lose happens both ways. Carbonic acid is
almost non-existent in this system.
What matters is the ratio b/w carbon dioxide (acid) and the biocarbonate (base).
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Slide 29 Normal concentration
pH = pKa + log ([HCO3-]/[CO2])
Normal:
7.4 = 6.1 + log (24 mM/1.2 mM)
24M to 1M ratio is 24:1 dissociated acid to carbon dioxide value of 1.3 add to 6.1 and
then get 7.4. this is normal concentration.
Carbon dioxide is produced in great quantities when we use energy.
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If we metabolize too much carbon dioxide in running, you don’t go into acidosis
because we pant (hyperventilation). The nature is maintaining the pH by panting.
If you don’t pant, then you will go into acidosis (pH of entire body changes ,
hallucinate, and die).
Hypoventilate- you don’t lose carbon dioxide properly. You will have the same
situation. If you don’t get rid of it so you can get acidosis.