1

Essential Biochemistry
Third Edition
Charlotte W. Pratt | Kathleen Cornely

Lecture Notes for

Chapter 2
Aqueous Chemistry

(Free) Protons Dont Exist

n Hydrogen

ions or protons combine with H2O to

form hydronium ions (H3O+)
n Probably

n Proton
n H+

delocalized

jumping

relayed through network of water molecules

n Mobility greater than simple diffusion
n Like crowd surfing

The pH Scale
nIonization
n H2O

of water

H+ + OH-

n[H2O]

!"H + #$!"OH #$
K=
[ H 2 O]

(55.5 M) >> [H+] or [OH-]

n Define

KW, ionization constant of water

K W = K [ H 2 O] = !"H + #$!"OH #$

The pH Scale

K W = 10 14 M = "#H + $%"#OH $% = (10 7 M ) (10 7 M )

If [H+] is > 10-7 M, then [OH-] must be <10-7 M

Pure water

pH Scale

nConcentrations
nLets

of H+ and OH- on very small scale

convert to positive whole integers

pH = log "#H + $%
npH

= power of hydrogen (etymology uncertain)

pH Scale

nWhat

happens if [H+] increases

above 10-7 M?
n Will

the number in the exponent get

larger or smaller?
n So, as solution gets more acidic, pH
decreases

Acid-Base Chemistry
nUsing

Brnsted-Lowry definition of acids &

bases
nAcid
n HCl

nBase

= proton donating
+ H2O H3O+ + Cl-

= proton accepting

n NaOH

+ H3O+ Na+ + 2H2O

Acid-Base Chemistry
nMost

biological acids/bases are not strong

n CH3COOH

+ H2O CH3COO- + H3O+

"#CH 3COO $%"#H 3O+ $%

K=
[CH 3COOH ] [ H 2O]
n Ka

Much larger

= acid dissociation constant

"#CH 3COO $%"#H + $%
K a = K [ H 2 O] =
[CH 3COOH ]

Acid-Base Chemistry
n Ka

still a small numberlets do the whole integer

thing again

pK = pK a = log K a
n The

more acidic the compound, the larger the value

of Ka
n The
n As

larger the value of Ka, the smaller the value of pK

pK , acid strength

n Greater

tendency to donate H+

10

Henderson-Hasselbalch
nHow

are pH and pK related?

nConsider
n HA

the dissociation of a weak acid:

= acid; A- = conjugate base

HA A + H +
nExpression

for Ka:

"#A $%"#H + $%
Ka =
[ HA]

+ Henderson-Hasselbalch
nRearrange:

nTake

!"H + #$ = K a [ HA ]
!"A #$

11

"#A $%"#H + $%
Ka =
[ HA]

the (-) log of both sides

nDifferent

form:

HA ]
[
+$
"
log #H % = log K a log
"#A $%

"#A $%
pH=pK + log
[ HA]

12

Henderson-Hasselbalch
"#A $% Conjugate base
pH=pK + log
[ HA] Acid
nWhat
npH
nSo

Different forms
of same group

happens when [A-] = [HA]?

= pK

the pK is the pH at which of the groups

are deprotonated (ionized)

13

Henderson-Hasselbalch
"#A $%
pH=pK + log
[ HA]
nMany

groups on biological molecules can

donate or accept H+
n Act

as acids and bases

n E.g. NH2/NH3+ and COO-/COOH on amino
acids

14

Polyprotic acids ionize more than

once and have multiple pKs
nH3PO4
nH2PO4-

= phosphoric acid

pK1 = 2.15

= monobasic

pK2 = 6.82

nHPO42- =
nPO43-

H3PO4

pK3 = 12.38

dibasic

= tribasic
pK1

H2PO4+
H+

pK2

HPO42+
H+

pK3

PO43+
H+

15

Determining Protonation State

n When

pH = pK, [HA] = [A-]; group is protonated

n When

pH < pK:

"#A $%
pH - pK = log
[ HA]

"#A $%
If pH < pK, then pH - pK = (-) = log
[ HA]
"#A $%
< 1 and [HA] > "#A $%
[ HA]
n So

if pH < pK, the group is more protonated

16

Determining Protonation State

n When

pH = pK, [HA] = [A-]

n When

pH > pK:

"#A $%
pH - pK = log
[ HA]

"#A $%
If pH > pK, then pH - pK = (+) = log
[ HA]
"#A $%
> 1 and "#A $% > [HA]
[ HA]
n So

if pH > pK, the group is more deprotonated

17

Aqueous Buffers
n When

you add a strong acid to water, all of the acid

contributes to pH
n HCl

H+ + Cl-

n When

you mix a strong acid with a weak acid

(conjugate base), the pH change is less
n HCl

+ A- HA + Cln The conjugate base of the weak acid can accept some
of the H+
n Acid neutralized

18

Aqueous Buffers

nSame

thing goes for strong base + weak acid

n NaOH

+ HA Na+ + A- + H2O
n Weak acid donates H+ to some of the OHn Base neutralized
nBuffers

resist pH changes

n Buffers: acid

(HA) + conjugate base (A-)

19

Buffering Capacity
n Titration
n Rapid
n More

curve for acetic acid

change in pH at the start and end points

gradual change in-between

n Best

buffering capacity in
flat area of curve
n ~1

pH unit on either side of

midpoint (pK)

+ Convenient Rule of Thumb

pH (range) = pK 1

20

10
n This

means [A] = 10 [HA]

0.1
n This

means [A] = 1/10 [HA] or [HA] = 10 [A-]

Buffers tend to resist changes in pH when [HA] and [A]

differ by no more than a factor of 10.

21

Maintaining pH in Blood
n Normal

internal pH is 6.9-7.4

n Metabolic
n How

n CO2

reactions generate acid

can the pH be adjusted?

(g) in blood forms carbonic acid (H2CO3):

n CO2

+ H2O H2CO3 H+ + HCO3pK ~3.6

22

Maintaining pH in Blood
n CO2

(g) in blood forms carbonic acid (H2CO3):

n CO2

+ H2O H2CO3 H+ + HCO3n Occurs spontaneously, but carbonic anhydrase helps

n Lungs expel CO2 (g), pulls equilibrium away from low pH
n Law of mass action
n Changes in lung function adjust blood pH in min or hours
n What

about a more long term way of adjusting pH?

23

Maintaining pH Homeostasis

n Kidneys

play major role in buffering metabolic acids

Filter HCO3- from bloodstream into kidney filtrate

n Need way to reclaim HCO3- for buffering acids inside the
kidney cell
n

1) Antiporter moves H+ out of cell and Na+ in (ion

exchanger)
From
bloodstream

2) H+ combines with HCO3- to

form CO2
n

CO2 diffuses across membrane

24

Maintaining pH Homeostasis
3) Converted back to HCO3- to
neutralize acids in the cell
n (H+ pumped out)

Metabolites are in
constant motion
From
bloodstream

25

Maintaining pH Homeostasis
n How

do you replenish bicarbonate in the bloodstream?

n Metabolic
n Use

processes generate CO2

carbonic anhydrase to regenerate H+ + HCO3-

n Pump

H+ out into filtrate (urine) and HCO3- into blood