Water Is Present in a Great Huge Amount

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

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.

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.

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

Long chain of methylene groups make up the hydrophobic tale.

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.

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

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 responsibleforfoldingof 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 acquiredspherical concentrated figure b/c of hydrophobic tails wanted to get away. Folding globular protein is controlled by water.

Assembly of quaternary structures

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

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.

Covalent bonds like Carbons-Carbon single bonds require 368 kJ/mol. Double bonds requires greater bonds energy to break 682 kJ/mol.

The non-covalent dissociations are important in biochemistry.

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.

Ion-ion interaction is a lot stronger than H-bonding. It is 40-100 kJ/mol.

Van Der wall

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.
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.

Kinetic Bond Energies

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.

However, No movement (agitation) or energy utilization will occur if it a perfect crystal in absolute zero temperature.

Slide 14- Acid Base Equilibria

Water’s role as achemical. 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.

Take two molecules of water together, one is an acid (give a proton ) and donate it to another water.
The product of these water molecules ionizing gives a hydronium ion and hydroxide ion.
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.
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.
Because:

So the pH = -log [hydronium or hydrogen concentration]

Molecules interact with water and do things to water.

Slide 15-Conjugate Acid- Base Systems.

There are many organic acids (acetic acid, proponic acid ect).

This acid(1), the reason it is an acid is because it is in presence of water. The water molecule is a base (1).

The acid gives up the proton to the water making an anion, and hydronium ion.
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

Equilibrium constant is the product of the products over the reactants of the equation on the previous slide.
The denominator is the dissociated acid and water, the numerator the dissociate acid and water (as H+).
You can take the water out of this constant because it is present in huge amounts.
Then you get a new factor Ka which is dissociation constant of the acid.

The amount of anion generated by the acid when it dissociates multiplied by the proton divided by the concentration of the original acid.

Kd = [A-] [H+][HA] [H2O]
Let Ka = Kd [H2O]
Ka = [A-] [H+] [HA]

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 ).
The higher the Ka, the higher the acidity.
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+.

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.

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:

•pH = pKa + log ([0.1] / [0.9])

•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.

The acetic acid goes to carboxyl group going to dissociated carboxyl group at pK 4.6.

The imidazole group has a pKa 6.99. The imidazole protonated group is much weaker acid than acetic acid because the pKa is higher.
The inverse relationship between pKa and acidity. The higher Ka the lower the pKa.
If we titrate this group, we have a buffering region around pH of 7 which is in range of physiological pH.

The side chain of hystidine like other proteins is help to maintain the pH of circulation at 7-7.5.
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

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 inenergy because of ATP (tri-phosphate).

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).

Next titration we are going from H2PO4- to HPO4 (-2). We are going to titrate another proton off. The pKa is 7.2 now.

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-)

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.

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

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?

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 b-alanyl 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 ina 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.

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.

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).

Slide 29 Normal concentration