MS-1 FUND 1: 10:10-11:00
Tuesday, August 21, 2012
Dr. Elgavish
Abbreviations:
1) H + Ion (Slide 4)
Biochemical Principles
Transcriber:
Editor:
Page 1 of 4 a) Water Molecule b) Slide 4 is depicting two water molecules with a covalent bond between the oxygen atom and the hydrogen atom (2x) and a hydrogen bond between the two water molecules. c) The hydrogen bond is weaker than the covalent bond. This is related to the distance of the bonds.
The stronger the bond, the shorter the distance. i) Hydrogen bond distance = 0.177 nm ii) Covalent bond distance = 0.0965 nm d) Slide 5 shows the electronegativity of oxygen in the water molecule.
i) There is a scale of electronegativity among all atoms
(1) Ex. Chlorine, bromine, and nitrogen are more electronegative than hydrogen.
e) When there is a chemical bond between a high electronegative atom like oxygen and a low electronegative atom like hydrogen there is a gradient of negative charge between the two poles i) There is a partial negative charge on the oxygen and a partial positive charge on the hydrogens ii) This relationship causes the entire molecule to be electroneutral f) When a water molecule interacts with another water molecule, the two opposite poles interact and create the hydrogen bond shown on slide 4.
g) Slide 5 shows the result of the full dissociation of a water molecule. There is a complete separation of the very low electronegative hydrogen atom, which proceeds to become a fully positive charged entity
(the hydrogen ion ) i) Its counterpart is the hydroxyl ion which is fully negatively charged h) Slide 6 depicts the Hydronium ion i) A hydronium ion is formed when a positively charged hydrogen ion binds to an electroneutral water molecule. This ionic bond is formed with the partial negatively charged oxygen.
(1) The molecule retains negative and positive poles
(a) In a 3d representation, the positive pole is on the side with the hydrogens, and the negative pole with the oxygen.
ii) In bulk water, a network of three water molecules could bind to a hydronium ion through three hydrogen bonds
2) Slide 8 just shows different examples hydrogen donors and hydrogen acceptors a) Molecules in which there is a hydrogen bound to an oxygen or nitrogen will typically be hydrogen donors, and will typically create a hydrogen bond with oxygen or nitrogen acceptors.
3) pH (slide 9) a) Acid and Base (several definitions but we will focus on the simplest) b) Acid releases a hydrogen ion c) Base receives and binds to a hydrogen ion d) Both an acid and a base can dissociate i) A stronger acid dissociates easier than a weaker acid. The same is true for a strong base relative to a weak base
(1) Ex. HCl: strong acid; easily dissociates hydrogen from the chlorine
(2) Ex. Acetic Acid: relatively weak acid; the acetate ion hangs onto the hydrogen ion more strongly than in the case of the strong acid
(3) Ex. Sodium Hydroxide (NaOH): strong base; Ammonium Hydroxide (NH4OH) ii) A strong bond between the H ion and its anion creates a weak acid e) pH Scale i) Sorensen (Denmark) created the pH scale for being able to conveniently write small numerical concentrations
A service sponsored by:
The University of Alabama Medical Alumni Association http://www.alabamamedicalalumni.org/

MS-1 FUND 1: 10:10-11:00
Tuesday, August 21, 2012
Dr. Elgavish
Abbreviations:
Biochemical Principles ii) pH = -log
10
[H + ]
(1) Ex. If [H + ] = 1 x 10 -7 M, pH = 7 f) The smaller the pH, the higher the acidity g) Slide 10 shows the pH scale coupled with the pOH scale i) pH + pOH = 14
Transcriber:
Editor:
Page 2 of 4 h) Slide 12 shows the pH of some household examples: i) Most Basic to Most Acidic on pH scale
(1) 1 M NaOH (14 pH), Household bleach (~13), household ammonia (~12), Solution of baking soda (NaHCO
3
) (~9), Seawater, egg white (~8), Human blood, tears (~7.2), Milk, saliva (~6.5),
Black coffee (~5), Beer (~4.3), Tomato juice (~4), Red wine (~3.8), Cola, vinegar (~3), Lemon juice (~2), Gastric juice (~1.5), 1 M HCl (0)
(2) Neutral pH (7) is called the neutral pH because it is directly in the middle of the range (0-14) ii) GERD - gastroesophageal reflux disease: a problem with the valve-like structure that connects your stomach with your esophagus. The valve is supposed to be closed, except for when food passes. In
GERD, however, it is slightly opened and this allows the very acidic gastric juices to go up into the esophagus and cause damage.
(1) Developed drugs called PPIs (proton pump inhibitors) : when they are taken, they raise the normal pH of the stomach, 1.4, up to pH 4 (i.e. lowering the acidity); therefore, the gastric juices do not do as much harm to the esophagus.
4) Dissociation of Weak Electrolytes (Slide 13) a) Consider a generalized weak acid, HA. The A is the anion part after the dissociation, and the H is the hydrogen ion. The acid dissociation reaction is: i) HA

H + + A ii) And the equilibrium constant (the extent of the dissociation, or the amount/concentration of the HA that dissociates) is… iii) K a
= [H + ] [A ] / [HA]
(1) The square brackets denote equilibrium concentrations
(2) Therefore, K a is the product of the concentration of H
+
ions that dissociated multiplied by the concentration of Anions that dissociated, and this is divided by the concentration of the nondissociated weak acid
5) The Henderson-Hasselbach Equation a) For any acid HA, the relationship between the pK a
, the concentrations existing at equilibrium, and the solution pH is derived by: i) K a
= [H+] [A-] / [HA]
(1) Taking the –log of both sides we obtain:
(a) –log K a
= -log H + + (-log ([A ] / [HA]))

(i) pK a
= pH - log([A
-
] / [HA])
1.
and rearranging it to: ii) pH= pK a
+ log([A ]/[HA]) (note the resemblance to the ΔG equation which is presented in another lecture)
(1) pK a is used for the relatively small numbers. Similar to pH.
(a) ex. K a
= 10
-5
translates to a pK a
= 5
6) Consider the Dissociation of Acetic Acid (slides 15-17) a) Three examples b) First Example i) Assume 0.1 eq base (10 % of the amount of acetic acid) has been added to a fully protonated solution of acetic acid. None of the acetic acid has dissociated.
A service sponsored by:
The University of Alabama Medical Alumni Association http://www.alabamamedicalalumni.org/

MS-1 FUND 1: 10:10-11:00
Tuesday, August 21, 2012
Dr. Elgavish
Abbreviations:
Biochemical Principles ii) The Henderson-Hasselbach equation can be used to calculate the pH of the solution: iii) With 0.1 eq OH added: iv) pH= pK a
+ log([A ]/[HA]) v) pH = pK a
+ log
10
([0.1]/[0.9])
Transcriber:
Editor:
Page 3 of 4 vi) pH = 4.76 + (-0.95) vii) pH = 3.81
(1) Each acid or base has a unique pK a
, therefore the pK a of acetic acid is 4.76.
(2) The ratio of ([A-]/ [HA]) is ([0.1]/[0.9]) because after the base interacted with the acetic acid, it took away some of the hydrogen from acetic acid. Also, the sum of this ratio always has to equal
1. (0.1 + 0.9 = 1) c) Second Example i) What happens if exactly 0.5 eq of base is added to a solution of the fully protonated acetic acid? ii) pH= pK a
+ log([A ]/[HA]) iii) pH = pK a
+ log
10
([0.5]/[0.5]) iv) pH = 4.76 + 0 v) pH = 4.76 = pK a
(1) pK a
is the pH which is exactly in the middle of the dissociation scale (when half of it is dissociated and half of it is not).
(2) When more base is added to the solution, it becomes more basic or higher pH. d) Third Example i) What is the pH if 0.9 eq of base is added to a solution of the fully protonated acid? ii) pH= pK a
+ log([A ]/[HA]) iii) pH = pK a
+ log
10
([0.9]/[0.1]) iv) pH = 4.76 + 0.95 v) pH = 5.71
7) Slide 18 shows a graphical summary of the three examples a) Graph 1. As the equivalents of OH
- increase, the relative abundance (concentration) of un-dissociated acetic acid goes down. Complementarily, the concentration of the dissociated acetic acid (acetate) goes up. Also, at any one time the sum of the two equals 1. b) Graph 2. The titration curve is relatively flat at a pH around the pKa; the curve is relatively flat at ± 1 pH unit of the pKa. This becomes important in buffers.
8) Slide 19 shows that there can be more than one dissociable hydrogen atoms attached to an acid. a) Monoprotic : only has one dissociable hydrogen i) Ex. Acetic acid, ammonium b) Diprotic : 2 dissociable hydrogens i) Carbonic acid, Glycine c) Triprotic : 3 dissociable hydrogens i) Phosphoric acid, Dihydrogen phosphate, Monohydrogen phosphate d) When there are multiple dissociable hydrogens, there are multiple pKas associated with the molecule ( one for each particular hydrogen)
(1) Ex. Diprotic acids have two pKas e) Also, the second pKa is always weaker than the first (i.e. higher number) and so forth and so on.
9) Slide 20 shows the acid dissociation constants and pKa values for some weak electrolytes
10) Buffers (Slide 21) a) Buffers are solutions that resist changes in pH as acid and base are added b) Most buffers consist of a weak acid and its conjugate base
A service sponsored by:
The University of Alabama Medical Alumni Association http://www.alabamamedicalalumni.org/

MS-1 FUND 1: 10:10-11:00
Tuesday, August 21, 2012
Dr. Elgavish
Abbreviations:
Biochemical Principles Page 4 of 4 c) Note in the slide 18 you can see how the plot of pH versus base added is flat near the pKa *key to how buffers work*
Transcriber:
Editor: d) Buffers can only be used reliably within one pH unit of their pKa
11) Slide 23 shows the example of acetic acid with the purple box representing its buffering ability. The next lecture begins with slide 24.
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The University of Alabama Medical Alumni Association http://www.alabamamedicalalumni.org/