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Amino Acid Chemistry

2

Dr. Amber Zaidi

Assistant Professor
MBBS, MPhil, PhD Scholar
Department of Biochemistry
NUST School of Health Sciences
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Learning Objectives NUST SCHOOL OF
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• Describe a Zwitter ion and its significance

• Describe the functions of amino acids

• Discuss Amino Acids as Buffers

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Zwitter Ion NUST SCHOOL OF
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• A zwitterion is an ion that contains two functional groups.

• An ion possessing both positive and negative electrical
charges.
• Therefore, zwitterions are mostly electrically neutral (the net
formal charge is usually zero).
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Functions of Amino Acids NUST SCHOOL OF
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1. Enzymes and Hormones

2. Contractile proteins
3. Bone Protein
4. Blood stream proteins
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Isomeric forms of Amino Acid NUST SCHOOL OF
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• The amino acids form two stereoisomers that are mirror

images of each other.
• The structures are much like our left and right hands.
• These mirror images are termed enantiomers
All amino acids except for glycine are “stereoisomers”
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Acidic and Basic Properties NUST SCHOOL OF
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• Amino acids in an aqueous solution contain weakly acidic α-

carboxyl groups and weakly basic α-amino groups
• Each of the acidic and basic amino acids contains an ionizable
group in its side chain

• Thus amino acids can act as Buffers

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A. pH NUST SCHOOL OF
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• The concentration of protons ([H+]) in aqueous solution is

expressed as pH.
• pH = log 1/ [H+] or –log [H+]

• The larger the Ka, the stronger the acid, because most of the
HA has dissociated into H+ and A−.
• Conversely, the smaller the Ka, the less acid has dissociated
and, therefore, the weaker the acid.
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Henderson–Hasselbalch equation NUST SCHOOL OF
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• This equation demonstrates the quantitative relationship

between the pH of the solution and concentration of a weak
acid (HA) and its conjugate base (A−)
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Buffer NUST SCHOOL OF
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• A buffer is a solution that resists a change in pH following the

addition of an acid or base and can be created by mixing a
weak acid (HA) with its conjugate base (A−)
• If an acid is added to a buffer, A− can neutralize it, being
converted to HA in the process.
• If a base is added, HA can likewise neutralize it, being
converted to A− in the process.
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Maximum Buffering Capacity NUST SCHOOL OF
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• Maximum buffering capacity occurs at a pH equal to the pKa,

but a conjugate acid–base pair can still serve as an effective
buffer when the pH of a solution is within approximately ±1 pH
unit of the pKa.
• If the amounts of HA and A− are equal, the pH is equal to the
pKa.
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Example NUST SCHOOL OF
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• A solution containing acetic acid (HA = CH3 – COOH) and

acetate (A− = CH3 – COO−)
• A pKa of 4.8 resists a change in pH from 3.8 to 5.8, with
maximum buffering at pH 4.8.
• At pH values less than the pKa, the protonated acid form (CH3
– COOH) is the predominant species in solution. At pH greater
than the pKa, the deprotonated base form (CH3– COO−) is the
predominant species.
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Dissociation of Alanine NUST SCHOOL OF
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• The dissociation constant of the carboxyl group of an amino

acid is called K1, rather than Ka, because the molecule contains
a second titratable group.
• The Henderson– Hasselbalch equation can be used to analyze
the dissociation of the carboxyl group of alanine:
• K1 = [H+ ] [II] / [I]
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• where I is the fully protonated form of alanine and II is the

isoelectric form of alanine
• This equation can be rearranged and converted to its
logarithmic form to yield

• pH = pK1 + log [II] / [I]

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Amino group dissociation NUST SCHOOL OF
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• The second titratable group of alanine is the amino (−NH3+)

group.
• Because this is a much weaker acid than the –COOH group, it
has a much smaller dissociation constant, K2.
• (Note: Its pKa is, therefore, larger)
• Release of a H+ from the protonated amino group of form II
results in the fully deprotonated form of alanine, form III.
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pKs and sequential dissociation NUST SCHOOL OF
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• The sequential dissociation of H+ from the carboxyl and amino

groups is summarized in Figure using alanine as an example.

• Each titratable group has a pKa that is numerically equal to the

pH at which exactly one half of the H+ have been removed
from that group.
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• The pKa for the most acidic group (−COOH) is pK1, whereas the
pKa for the next most acidic group (−NH3 +) is pK2.
• The pKa of the α-carboxyl group of amino acids is ∼2, whereas the
pKa of the α-amino group is ∼9.
• By applying the Henderson–Hasselbalch equation to each
dissociable acid group, it is possible to calculate the complete
titration curve of a weak acid.
• Figure shows the change in pH that occurs during the addition of
base to the fully protonated form of alanine (I) to produce the fully
deprotonated form (III)
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a. Buffer pairs NUST SCHOOL OF
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The –COOH/–COO− pair can serve as a buffer in the pH region

around pK1, and the –NH3 +/–NH2 pair can buffer in the region
around pK2.
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b. When pH=pK NUST SCHOOL OF
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• When the pH is equal to pK1 (2.3), equal amounts of forms I

and II of alanine exist in solution.

• When the pH is equal to pK2 (9.1), equal amounts of forms II

and III are present in solution.
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c. Isoelectric point pI NUST SCHOOL OF
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• At neutral pH, alanine exists predominantly as the dipolar

form II in which the amino and carboxyl groups are ionized,
but the net charge is zero.

• The isoelectric point (pI) is the pH at which an amino acid is

electrically neutral, that is, when the sum of the positive
charges equals the sum of the negative charges.
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Isoelectric point of Alanine NUST SCHOOL OF
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• For Alanine, with only two dissociable hydrogens (one from

the α-carboxyl and one from the α-amino group), the pI is the
average of pK1 and pK2 (pI = [2.3 + 9.1]/2 = 5.7)

• The pI is, thus, midway between pK1 (2.3) and pK2 (9.1).
• pI corresponds to the pH at which the form II (with a net
charge of zero) predominates and at which there are also equal
amounts of forms I (net charge of +1) and III (net charge of −1).
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d. Net charge at neutral pH NUST SCHOOL OF
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• At physiologic pH, amino acids have a negatively charged

group (−COO−) and a positively charged group(−NH3+), both
attached to the α-carbon.

• Glutamate, aspartate, histidine, arginine, and lysine have

additional potentially charged groups in their side chains.
• Substances such as amino acids that can act either as an acid or
a base are described as Amphoteric.
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buffer system
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• The pH within our blood is maintained in the slightly alkaline

range of 7.35 to 7.45 by the bicarbonate buffer system.
• Most proteins function optimally at this physiologic pH and their
amino acid constituents exist in the chemical form;
• Exceptions include
1. Some digestive enzymes that function at acidic pH of the stomach
between pH 1.5 and 3.5.
2. Lysosomal enzymes also function at an acidic pH range between
pH 4.5 and 5.0.
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• Maintaining arterial pH at 7.40 ± 0.5 is important for health;

normally the bicarbonate buffer system is able to keep pH
within the acceptable range

• The need for a buffering system can be appreciated by

considering that organic acids (e.g., lactic acid) are generated
during metabolism and that glucose and fatty acid oxidation
generate CO2, the anhydrous form of H2CO3 (carbonic acid).
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Bicarbonate Buffer system NUST SCHOOL OF
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• The bicarbonate ion concentration, [HCO3 −], and the carbon

dioxide concentration [CO2] influence the pH of the blood.
• The relatively water-insoluble CO2 is converted by the enzyme
carbonic anhydrase to the water-soluble HCO3 −
(bicarbonate), which is carried through the blood to the lungs
where dissolved CO2 is exhaled.
• Therefore, lungs regulate the loss and retention of CO2 by
altering the breathing rate.
• Kidneys retain or excrete bicarbonate, H+, ammonia, and
other acids/bases that may appear in the blood.
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E. Blood gases and pH NUST SCHOOL OF
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• As a consequence of certain disease processes or poisons,

blood pH can become abnormal.

• Acidemia is defined as an arterial pH <7.35 and

• Alkalemia is defined as an arterial pH >7.45.
• In the bicarbonate buffer system, CO2 is an acid and
bicarbonate is a base.
 Changes in breathing can impact the acid–base
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balance
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• Acidosis may develop in human body due to

1. Hypoventilation
2. Generation of excess metabolic acids (e.g., lactic acid)
3. Ketoacidosis that can accompany type 1 diabetes mellitus

• Alkalosis may develop

• Loss of excess acid through vomiting
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Are compensations 100%? NUST SCHOOL OF
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• Neither renal compensation nor compensation by breathing

rate changes (respiratory compensation) will bring pH back
toward normal physiologic range if excess metabolic acids have
been generated.

• “It should be noted that neither the lungs nor the kidneys can
fully compensate or overcompensate for pH imbalances”
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Reference Book NUST SCHOOL OF
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Lippincott Illustrated
Reviews
8th edition

Chapter 1

Amino Acids and the role of

pH
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