ABDULLAH_AMINO_ACID_PRESENTATION_1[1].pptx

IONIC BEHAVIOR OF AMINO
ACID AND PROTEIN
SUBMITTED BY:- MD. ABDULLAH (M.Sc BIOCHEMISTRY/2ND SEMESTER)
JAMIA MILLIA ISLAMIA
‫الرحیم‬ ‫ن‬ ٰ‫الرحم‬ ‫ہللا‬ ‫بسم‬

CONTENT
INTRODUCTION
ACID BASE BUFFER
RELATION B/W PH & PKA
ZWITTERION &AMINO ACID CHARGE GIVEN pH
&pKa
CLASSIFICATION OF AMINO ACID
TITRARATION OF GLYCINE
CONCLUSION

INTRODUCTION
Amino acids are the building
blocks of proteins, and they
exhibit interesting ionic behavior
due to the presence of two
functional groups with opposing
properties:
An amino group (NH2), which is
basic and can accept a proton
(H+)
A carboxyl group (COOH), which is
acidic and can donate a proton
(H+)
At their isoelectric point (pI),
amino acids exist in a zwitterionic
form. A zwitterion ion is a
molecule that carries both a
positive and a negative charge but
is overall electrically neutral.

Here's a breakdown of the ionic behavior of amino acids:
In acidic solutions (pH < pI): The carboxyl group tends to donate its proton, becoming a negatively charged carboxylate
group (COO-). The amino group remains protonated (NH3+). The amino acid becomes positively charged.
In basic solutions (pH > pI): The amino group tends to lose its proton, becoming a neutral amine group (NH2). The
carboxyl group remains deprotonated (COO-). The amino acid becomes negatively charged.
At the isoelectric point (pH = pI): The amino acid exists in its zwitterionic form, with both the amino group protonated
(NH3+) and the carboxyl group deprotonated (COO-). The molecule is overall neutral because the positive and negative
charges balance each other.
This amphoteric behavior of amino acids (acting as both an acid and a base) is essential for their proper function in biological
systems. The charge on the amino acid side chain can influence protein folding, protein-protein interactions, and enzyme
activity.

LOW PH
α-carboxylic group is
protonated(-COOH) and
uncharged
α- amino group is protonated(-NH3+)
and positively charged
PH 7
deprotonated(-COO-)
α- amino group is protonated(-NH3+)
HIGH PH
deprotonated(-COO-) and
negatively charged
α- amino group is deprotonated (-
NH2) and uncharged

ACID BASE BUFFER
• ACIDS AND BASES ARE COMMON REAGENTS IN PHARMACEUTICAL PROCESSES.
• IN DIFFERENT ANALYTICAL TECHNIQUES INVOLVING ACID-BASE REACTION VIZ ACID BASE
TITRATION.
• SETTING PH
• AS THERAPEUTIC AGENTS
• AS BUFFER SOLUTION
• MAKING DRUGS SOLUBLE.

CONTD….,
• ACIDS ARE THE SUBSTANCES HAVING SOUR TASTE, AND PH BELOW 7 . THEY CAN TURN BLUE
LITMUS PAPER RED.
• BASES ARE THE SUBSTANCES HAVING BITTER TASTE AND PH ABOVE 7 . THEY CAN TURN RED
LITMUS PAPER BLUE
 TO EXPLAIN THE PROPERTIES OF ACIDS AND BASES, DIFFERENT CONCEPTS HAVE BEEN GIVEN
VIZ.
• ARRHENIUS CONCEPT (1887)
• BRONSTED LOWRY CONCEPT (1923)
• LEWIS CONCEPT (1923)

ARRHENIU
S
CONCEP
T (1887)
• In 1887 by Swante
Arrhenius.
• Theory of lonization
• Acids and bases are
defined based on the ions
formed during aqueous
dissolution.

Cont….
Substances which gives H+ ion dissolution in water
are called acids. whereas,
substances which gives OH- dissolution in water are
called bases.
Eg.
Acids:- HCl, CH3COOH
Bases :- NaOH, КОН
HCl ..............》H+ + Cl-
NaOH............》OH- + NA+
Acids and Bases when react with each other produce
salt and water.
HCl + NaOH.........》NaCl + H2O

Cont….
 Limitations:
 Based on aqueous solution and not the
substance.
 Nature in the absence of water/now
aqueous solvents can not be explained.
 Can't explain Basic nature of
substances lacking (OH- ions) like NH3,
Na2CO3, etc and
 Acidic nature of substances lacking (H+
ions) like CO2, SO2, AlCl3 etc.

Bronsted
lowry
Concept
(1923)
• In 1923 by Danish chemist JN
Bronsted and British chemist
TM Lowry independently.
• More generalized concept
applied to both aqueous and
non aqueous solutions

Cont….
Substances which donate proton
are acid. whereas,
substances which accept proton
are bases
HA + H2O........》A- + H3O+
B + H2O............》BH+ + OH-
Eg
HCI.............》H+ + Cl-
CH3COOH..........》CH3COO- + H+
NH3 + H+..........》 NH4
+
OH+ + H+ ..........》H2O

Cont….
Conjugated Acid-Base Pairs:
HA + H2O………….>> A- + H3O
ACID BASE C.BASE
C.ACID
B + H2O…………..>> BH- + OH-
BASE ACID C.ACID
C.BASE

Cont….
Limitations:
Limited to the concept of proton transfer.
Acids lacking protons can not be explained.
Eg. CaCl2, SO2, etc.
Acid-base reactions in which no proton
transfer take place can not be explained.
Eg
S02 + S02........》SO+2
+ SO3
-2
Acid1+ Base2 ......>> Base1 + Acid2
Can not explain acid-base reaction taking
place in non-protonic solvents

Lewis
Concept
(1923)
• In 1923 by Lewis.
• Electron pair Donor-acceptor theory
• Based on transfer of Electron pair in
terms of chemical structure.

Cont….
• Any species that can accept an
electron pair is regarded as
Acid. Whereas,
• Any species that can donate an
electron pair is called Base.
Eg.
• Acids: H+, Na+, NH4, H3BO3, BF3
etc.
• Bases: NH3, H2O, OH-, CI-, CN-,
NaOH etc.

Cont….
• Limitations
• Can not explain relative
strength of acids and bases.
• Explains acids and bases based
on electron transfer which is
very rapid. Hence all the acids
and bases should react very
fast. But many lewis acids and
bases react very slowly,

STRENGTH
S OF ACIDS
AND
BASES•
Reactivity α Strength
Strength = ease of proton
donation/acceptance
HA + H2O...........》H3O+ + A-
Equilibrium constant (Degree of
dissociation)
Keq = [H30+] [A-]/[HA][H2O]
lonization constant Ka= Keq X [H2O]
Ka = [H3O][A-]/[HA]
Ka varies directly with acid strength ie.
Ka>1 for strong acids & K<1 for weak
acids.

STRENGTH
S OF ACIDS
AND
BASES•
Acid strength can also be expressed in terms of
H+ ion concentrations. in aqueous solution, conc,
of proton is generally considered to be
concentration of H3O+ concentration
Pure water ionize to a small degree as:
2H2O H3O+ + OH-
H2O H+ + OH-
lonization product of water,
Kw=[H3O+] [OH-] or [H+] [OH-] = 1×10-14
(At 25°c constant value)
Since in pure water, concentration of both the ions
is equal each will have value of [H+] or
[H30+]=[OH-]=1X10-7

Cont…•
If an acid is added, [H+] increases and becomes
greater than [OH-], Similarly if a base is added, [OH-
] increases and becomes greater than [H+]. But still
they are related by expression
[H3O+] [OH-]=10-14
Hence, value of Kw remains constant , Thus
In neutral solution [H+] = [OH-]
In acidic solution [H+] > [OH-]
In basic solution [H+]<[OH-]
Eg. If acid is added to an aqueous solution to such
an extent that [H+] 1x10-3M, than corresponding
[OH-] will become [OH-]=1×10-11M.

Cont…•
• In order to express the concentration of H+ ions
in mare convenient way, a Danish chemist
Sorenson introduced a more practical and
compact concept of expressing acidity termed as
pH
• pH is negative logarithm (to the base of 10) of
the Hydrogen ion concentration.
pH= -log[H+]= log1/[H+]
In pure waters,
[H+]= 10-7
Therefore,
pH= -log[10-7]= -log1/10-7= -log1 + log
107 = 7
• pOH can also be expressed likewise.

RELATION B/W
pH & pOH WITH
[H+]
• Change in pH by 1 unit represents 10 fold change in
[H+].
• As the relationship is exponential, values of pH and
[H+] do not vary linearly between unit changes in [H+].
pH
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
pOH
14
13
12
11
10
9
8
7
6
5
4
3
2
1
0
[H+]moles/lit.
1.0
0.1
0.01
0.001
0.0001
0.00001
0.000001
0.0000001
0.00000001
0.000000001
0.0000000001
0.00000000001
0.000000000001
0.000000000000
1
0.000000000000
01
[H+]g eq./lit.
1*100
1*10-1
1*10-2
1*10-3
1*10-4
1*10-5
1*10-6
1*10-7
1*10-8
1*10-9
1*10-10
1*10-11
1*10-12
1*10-13
1*10-14
[H+]moles/lit. pH
0.0001 4.0
0.00009 1.04
0.00008 4.09
0.00007 4.15
0.00006 4.22
0.00005 4.30
0.00004 4.39
0.00003 4.52
0.00002 4.69
0.00001 5.00

BUFFER SOLUTION
• LETS TAKE THE EXAMPLE OF NACl SOLUTION AND AMMONIUM
ACETATE SOLUTION. BOTH WILL HAVE pH OF 7.0.
• WHEN WE ADD 1 Ml OF 0.1N HCI TO 1 LIT, SOLUTION OF NACl, pH
CHANGES FROM 7 TO 4 AS
• INITIAL [H+] =107
• THEREFORE, PH = 7
• FINAL[H+]=0.1/1000=1/10000=10-4
• WHEN WE ADD 1 Ml OF 0.1 N HCl TO 1 LIT, SOLUTION OF
AMMONIUM ACETATE, pH DOESN'T CHANGE SIGNIFICANTLY.

BUFFER SOLUTION
• LETS TAKE THE EXAMPLE OF NACL SOLUTION AND AMMONIUM
ACETATE SOLUTION. BOTH WILL HAVE PH OF 7.0.
• WHEN WE ADD 1 ML OF 0.1N NAOH TO 1 LIT, SOLUTION OF
NACL, PH CHANGES FROM 7 TO 10 AS
• INITIAL [H+] =107
• FINAL[OH-]=0.1/1000=1/10000=10-4
• THEREFORE [H+]=KW/10-4=10-14/10-4=10-10
• THEREFORE, PH = -LOG10-10=10
• WHEN WE ADD 1 ML OF 0.1 N NAOH TO 1 LIT, SOLUTION OF
AMMONIUM ACETATE, PH DOESN'T CHANGE SIGNIFICANTLY.

BUFFER
SOLUTION
• THE SOLUTION THAT RESISTS CHANGE IN PH ON
ADDITION OF ACID OR BASE IS KNOWN AS BUFFER
SOLUTION
• A BUFFER SOLUTION HAS A RESERVED PH OR A FAIRLY
CONSTANT PH EVEN WHEN SMALL AMOUNT OF ACID
OR ALKALI IN ADDED TO IT.
• BUFFER SYSTEMS ARE PAIRS OF RELATED CHEMICAL
COMPOUNDS CAPABLE OF RESISTING CHANGE IN PH
OF A SOLUTION CAUSED BY THE ADDITION OF SMALL
AMOUNTS OF ACID OR BASE.

BUFFER
SOLUTION
• BUFFER ACTION: THE PROPERTY BY VIRTUE OF WHICH A
SOLUTION RESISTS THE CHANGE IN PH, IN RESPONSE TO
ADDITION OF ACID/BASE.
• BUFFER SOLUTIONS: SOLUTIONS ABLE TO RESIST THE CHANGE IN
PH VALUES ON ADDITION OF ACID/BASE
 CLASSIFIED BROADLY INTO:
• ACIDIC BUFFER SOLUTION: WEAK ACID + ITS SALT WITH STRONG
BASE.
Eg. ACETIC ACID + SODIUM ACETATE (CH3COOH + CH3COONA)
• ALKALINE BUFFER SOLUTION: WEAK BASE + ITS SALT WITH
STRONG ACID.
Eg: AMMONIUM HYDROXIDE + AMMONIUM CHLORIDE (NH4OH +
NH4Cl)
• NEUTRAL BUFFER SOLUTION: SALT OF WEAK ACID & WEAK BASE.
Eg. AMMONIUM ACETATE (CH3COONH4)

BUFFER ACTION
• SOLUTION OF ACETIC ACID AND SODIUM ACETATE MIXTURE
• CH3COOH.........》 CH3COO- + H+ (PARTLY IONIZED)
• CH3COONA..........》CH3COO- + NA+ (FULLY IONIZED)
• AS SODIUM ACETATE IS FULLY IONIZED, THE ACETATE IONS SUPPRESS THE LONIZATION OF ACETIC ACID DUE TO
COMMON ION EFFECT AND THUS THE MIXTURE CONTAINS MORE UNIONIZED ACETIC ACID AND ALSO MORE ACETATE
IONS THAN IN ACETIC ACID ALONE.
• WHEN AN ACID IS ADDED TO THE SOLUTION H+ IONS FROM THIS SOLUTIONS REACT WITH ACETATE IONS TO FROM
THE WEAKLY DISSOCIATED/NEARLY UNIONIZED ACETIC ACID.
• CH3COO- + H+ ...........》 CH3COOH
• THUS (H+) DOESN'T CHANGE.

BUFFER ACTION
• SOLUTION OF ACETIC ACID AND SODIUM ACETATE MIXTURE
• CH3COOH.........》 CH3COO- + H+ (PARTLY IONIZED)
• CH3COONA..........》CH3COO- + NA+ (FULLY IONIZED)
• AS SODIUM ACETATE IS FULLY IONIZED, THE ACETATE IONS SUPPRESS THE LONIZATION OF ACETIC ACID DUE TO
COMMON ION EFFECT AND THUS THE MIXTURE CONTAINS MORE UNIONIZED ACETIC ACID AND ALSO MORE ACETATE
IONS THAN IN ACETIC ACID ALONE.
• WHEN AN BASE IS ADDED TO THE SOLUTION OH- IONS FROM THIS SOLUTIONS REACT WITH ACETATE IONS TO FROM
WATER AND ACETATE IONS.
• CH3COOH + OH- ...........》 CH3COO- + H2O
• THUS PH DOESN'T CHANGE.
• THUS ADDITION OF SMALL AMOUNT OF ACID OR ALKALI DOESN'T ALTER THE PH OF THE SOLUTION TO ANY
APPRECIABLE EXTENT.

BUFFER CAPACITY
• IT'S THE QUANTITATIVE MEASURE OF THE RESISTANCE TO CHANGE IN PH, A BUFFER
SOLUTION HAS.
• "MOLES OF STRONG ACID OR BASE REQUIRED TO CHANGE THE PH OF 1000 ML OF BUFFER
SOLUTION BY ONE UNIT“.
• GREATER IS THE BUFFER CAPACITY, BETTER IS THE BUFFER AS IT CAN ACCOMMODATE MORE
ACID OR BASE WITHOUT ALTERING THE PH SIGNIFICANTLY
Β = 2.3 Ka [H+][C]/(Ka + [H+])2
WHERE,
Β=BUFFER CAPACITY
[H+]=HYDROGEN ION CONCENTRATION OF BUFFER
[C]=BUFFER CONCENTRATION
• FROM ABOVE EQUATION, BUFFER CAPACITY Α BUFFER CONCENTRATION.

BUFFER
EQUATIO
NS
• PH OF ACIDIC BUFFER SOLUTION AND MAXIMUM
BUFFER ACTION:
• [H+] OBTAINED FROM DISSOCIATION OF WEAK ACID
AND HA,
HA <<…………..>> H+ + A-
Ka = [[H+][A-]/[HA],OR
[H+] = Ka[HA]/[A-]
-log[H+] = -log Ka [HA]/[A-]
pH= pKa + log[A-]/[HA]
pH = pKa + log [CONJUGATE BASE]/[ACID]
• IT IS CALLED HENDERSON-HASSELBACH EQUATION
FOR ACIDIC BUFFER. USING IT ONE CAN CALCULATE
THE PH OF A BUFFER SOLUTION OF KNOWN CONC. OR
ONE CAN MAKE BUFFER SOLUTION OF KNOWN PH .

BUFFER
EQUATIO
NS
• pH = pKa+ log[CONJUGATE BASE]/ACID
• MAXIMUM BUFFER ACTION CAN BE OBTAINED WHEN
CONC. OF ACID AND CONJUGATE BASE ARE EQUAL:
pH = pKa + log 1= PKA+0
pH=PKa
• IF CONC. OF ACID IS 10 TIMES THE CONC. OF
CONJUGATE BASE,
pH= pKa+ log1/10= pKa-1
• IF CONC. OF CONJUGATE BASE IS 10 TIMES THE
CONC. OF ACID,
pH= pKa + log 10/1
pH= pKa + 1

BUFFER
EQUATIO
NS
• TO MAKE A BUFFER SOLUTION OF SPECIFIC PH ANY
ACID CAN BE EMPLOYED HAVING PKA VALUES IN
THE RANGE OF PKA-1 TO PKA + 1.
• MAXIMUM BUFFER ACTION IS ACHIEVED IN HALF
NEUTRALIZED ACID
• IE, AT EQUILIBRIUM (CONJUGATE BASE) = (ACID)
• EG. PKA OF ACETIC ACID AT 25° C IS 4.75. WE CAN
USE MIXTURE OF ACETIC ACID AND SODIUM
ACETATE TO MAKE BUFFER SOLUTION OF PH IN THE
RANGE OF 3.75-5.75

BUFFER
EQUATIO
NS
• pH OF ALKALINE BUFFER SOLUTION AND MAXIMUM BUFFER
ACTION:
• [OH-] OBTAINED FROM DISSOCIATION OF WEAK BASE BOH,
BOH《.............》B+ + OH-
Kb= [B+][OH-]/[BOH]
[OH-]= Kb.[BOH]/[B+]
-log[OH-]= -log Kb[BOH]/[B+]
pOH= pKb + log [B+]/[BOH]pOH = pKb + log [CONJUGATE
ACID]/[BASE]
NOW, PH= 14 – POH
pH= 14- (pKb + log[CONJUGATE ACID]/[BASE])
• THIS IS CALLED AS HENDERSON-HASSELBACH EQUATION.
• IN CASE OF BASIC BUFFER ,MOST OF THE CONJUGATE ACID
FORMED IS FORM SALT OF WEAK BASE AND STRONG ACID
.HENCE THE TERM CONJUGATE ACID CAN BE REPLACED BY
SALT. HENCE,
pH = 14 - (pKb + log[SALT]/[BASE])

BUFFERS IN PHARMACEUTICAL SYSTEM
• BUFFERS ARE VERY FREQUENTLY USED IN PHARMACEUTICAL PREPARATIONS AS WELL AS PROCESSES.
• SOLID DOSAGE FORMS:
• IN SOLD DOSAGE FORMS SUCH AS TABLETS, CAPSULES, AND POWDERS BUFFERS ARE USED TO CONTROL
THE ENVIRONMENT AROUND THE SOLID PARTICLES AND ASSURES THE ABSORPTION OF THE DRUGS WHICH
WAS OTHERWISE DISSOLUTION RATE LIMITED.
• REDUCE THE GASTRIC IMITATION CAUSED BY ACIDIC DRUGS.
• REDUCING TOXICITY.
• SEMISOLID DOSAGE FORMS:
• SEMISOLID DOSAGE FORMS UNDERGO PH CHANGE ON LONG TIME STORAGE LEADING TO INSTABILITY.
BUFFERS LIKE CITRIC ACID BUFFER, PHOSPHORIC ACID BUFFERS ARE INCORPORATED TO MAINTAIN
STABILITY.

BUFFERS IN PHARMACEUTICAL SYSTEM
• BUFFERS ARE VERY FREQUENTLY USED IN PHARMACEUTICAL PREPARATIONS AS WELL AS PROCESSES.
• PARENTERAL PREPARATIONS:
• PH BELOW 3 CAUSES PAIN WHEREAS PH ABOVE 10 CAUSES TISSUE NECROSIS. SO BUFFERS ARE USED
TO MAINTAIN PH NEAR 7.4 (PH OF BLOOD) EG. PHTHALATE, CITRATE, GLUTAMATE, ACETATE ETC.
PH OPTIMIZATION HELPS IN OPTIMUM SOLUBILITY, STABILITY & REDUCED IRRITANCY.
• OPHTHALMIC PRODUCTS:
• CHANGE IN PH CAN AFFECT STABILITY AS WELL AS SOLUBILITY.

DESIRED CHARACTERISTICS OF BUFFERS
• SHOULD NOT FORM COMPLEXES WITH ACTIVE INGREDIENTS.
• SHOULD NOT PRECIPITATE IN REDOX REACTIONS.
• SHOULD NOT ALTER THE SOLUBILITY OF OTHER INGREDIENTS.
• SHOULD NOT UNDERGO ACID-BASE REACTION OTHER THAN REQUIRED AS A PART OF THE
BUFFER FUNCTIONS.
• SHOULD BE SAFE
• SHOULD NOT INTERFERE IN THE PHARMACOLOGICAL ACTIONS OF THE ACTIVE INGREDIENTS.
• SHOULD NOT MADE UP OF VOLATILE SUBSTANCES.
• SHOULD NOT PROMOTE MICROBIAL GROWTH.

BUFFER
A BUFFER IS AN AQUEOUS SOLUTION THAT RESISTS CHANGES IN PH WHEN SMALL
AMOUNTS OF ACID OR BASE ARE ADDED. IT ACTS LIKE A CHEMICAL SHIELD TO MAINTAIN A
RELATIVELY CONSTANT PH LEVEL.
Components:
Buffers are
typically made of
two key
components:
A weak acid: This
can donate a proton
(H+) when needed.
Its conjugate base:
This can accept a
proton (H+) when
needed.
Working
Mechanism:
Buffers work by
responding to
changes in pH:
If acid is added: The
conjugate base in
the buffer can accept
the extra protons,
minimizing the
overall pH change.
If base is added: The weak acid in the
buffer can donate protons to neutralize
the added base, again minimizing the
pH change.
Importance:
Buffers are
essential for
many biological
processes
because
enzymes,
proteins, and
other molecules
often have a
specific pH range
at which they
function
optimally.
Fluctuations in
pH can disrupt
these processes
and harm the
cell.
Examples: Some
common
biological
buffers include:
Bicarbonate
buffer
system: This
is crucial for
regulating
blood pH.
Phosphate buffer system: This is
found in both cells and body
fluids.
Overall, buffers play a
vital role in maintaining
the delicate pH balance
within living organisms,
ensuring the proper
functioning of various
biochemical reactions.

CLASSIFICATI
ON OF
AMINO ACID
BASED ON STRUCTURE & CHEMICAL
NATURE
o Aliphatic side chain
o Side chain with OH group
o Side chain with ‘S’
o Side chain with Acidic group
o Side chain with Basic group
o Aeromatic amino acid
o Imino acid.
BASED ON METABOLIC FATE
o Glucogenic
o Ketogenic
o Both
BASED ON POLARITY
o Hydrophilic (Polar)
o Hydrophobic (Non-Polar)
NUTRITIONAL CLASSIFICATION
o Essential
o Non Essential
o Semi Essential

AMIN
O
ACID
HYDROPHOBIC
R=ALKYL
GLYCINE
ALANINE
VALINE
LEUCINE
ISOLEUCINE
METHEOINE
PROLINE
R=AROMATIC
PHENYLALANI
NE
TRYPTOPHAN
HYDROPHILIC
R=NEUTRA
L
TYROSINE
SERINE
THEREONINE
CYSTEIN
GLUTAMINE
ASPARGINE
R=ACIDIC
ASPARTIC
ACID
GLUTAMIC
ACID
R=BASIC
LYSINE
ARGININE
HISTIDINE

STANDARD AMINO ACID
THREE LETTER (1 LETTER
SYMBOL)
GLYCINE Gly (G)
ALANINE Ala (A)
VALINE Val (V)
LEUCINE Leu (l)
ISOLEUCINE Ile (I)
SERINE Ser (S)
THRIONONE Thr (T)
CYSTEINE Cys (C)
METHIONINE Met (M)
ASPARTIC ACID Asp (P)
ASPARGINE Asn (N)
GLUTAMIC ACID Glu (E)
LYSINE Lys (K)
ARGININE Arg (R)
HISTIDINE His (H)
PHENYLALANINE Phe (F)
TYROSINE Tyr (Y)
TRYPTOPHAN Trp (W)
PROLINE Pro (P)
GLUTAMINE Gln (Q)

NON POLAR ALIPHATIC SIDE
CHAIN
Amino acids with
non-polar aliphatic
side chains are a
group of amino
acids characterized
by their
hydrophobic and
non-polar
properties. These
amino acids
include:
Alanine (Ala) : It is
a simple amino
acid with a methyl
group as its side
chain.
Valine (Val): It has
an isopropyl group
as its side chain,
contributing to its
non-polar nature.
Leucine (Leu) : It
contains an
isobutyl group as
its side chain.
Isoleucine (Ile): It is
similar to leucine
but has one carbon
atom less in its
side chain.
Methionine (Met):
Although it contains a
sulfur atom in its side
chain, it is often
considered aliphatic
due to its non-
reactive nature.
These amino acids are hydrophobic, meaning they tend to be
located within the interior of proteins, away from the aqueous
cellular environment. Their hydrophobicity increases as the
number of carbon atoms on the hydrocarbon chain increases.
They play a crucial role in protein structure by promoting the
folding of the protein into its native conformation.

NON-POLAR AROMATIC R GROUP AMINO ACIDS
Among the 20 standard amino acids, three are classified as non-polar aromatic:
Phenylalanine
Tryptophan
Tyrosine
These amino acids have aromatic side chains that include an aromatic ring and are non-polar, meaning they do not
have a charge. They participate in hydrophobic interactions, which are stronger than those of aliphatic R groups due to
the stacking of the aromatic rings.
These non-polar aromatic amino acids play crucial roles in protein structure and function. They contribute to the
three-dimensional structure of proteins and often stabilize their folded structures. Aromatic residues are
predominantly found within the cores of globular proteins, although they often comprise key portions of protein-
protein or protein-ligand interaction interfaces on the protein surface.
In addition to their role in protein structure, these aromatic amino acids often serve as precursors to important biochemicals:
Phenylalanine is the precursor to tyrosine.
Tryptophan is the precursor to 5-hydroxytryptophan, serotonin, tryptamine, auxin, and melatonin.
Tyrosine is the precursor to L-DOPA, dopamine, norepinephrine (noradrenaline), epinephrine (adrenaline), and the thyroid hormone
thyroxine. It is also a precursor to octopamine and melanin in numerous organisms

POLAR
UNCHARGED
AMINO ACIDS
ARE A GROUP
OF AMINO
ACIDS
characterized
by their
polarity and
lack of
charge. They
are
hydrophilic,
meaning they
can form
hydrogen
bonds with
SERINE AND
THREONINE:
these amino
acids
contain
aliphatic
hydroxyl
groups (an
oxygen
atom
bonded to a
hydrogen
atom,
represented
as ―OH).
TYROSINE:
tyrosine
possesses a
hydroxyl
group in the
aromatic
ring,
making it a
phenol
derivative.
ASPARAGINE
AND
GLUTAMINE:
both contain
amide R
groups. The
carbonyl
group can
function as
a hydrogen
bond
acceptor,
and the
amino
group (NH2)
CYSTEINE:
cysteine
contains a
thiol group
that is
responsible
for creating
disulfide
bridges.
These amino
acids play
crucial roles
in protein
structure and
function, and
their side
chains can
participate in
various
chemical
reactions. For
instance, the
hydroxyl
groups in
serine,
threonine,

✅ UNCHARGED
HYDROPHILIC AMINO
ACID & THEIR
DISTINGUISHING
FEATURES
🛑 Cysteine (Cys)
👉Forms disulfide bonds👉sensitive to
oxidation👉component of glutathione,
an important antioxidant in RBCs👉
deficient in glucose-6-phosphate
dehydrogenase (G6PD) deficiency
🛑 Serine (Ser)
👉Single-carbon
donor👉
phosphorylated by
kinases
🛑 Threonine (Thr)
👉
Phosphorylate
d by kinases
🛑 Tyrosine (Tyr)
👉Precursor of catecholamines, melanin
and thyroid hormones👉phosphorylated by
kinases👉aromatic side chains (increased in
hepatic coma)👉must be supplied in
phenylketonuria (PKU)👉signal transduction
(tyrosine kinase)
🛑 Asparagine (Asn)
👉Insufficiently
synthesized by
neoplastic cells👉
asparaginase used for
treatment of leukemia
🛑 Glutamine (Gln)
👉Most abundant amino acid👉major carrier of nitrogen👉
nitrogen donor in synthesis of purines and pyrimidines👉
NH3 detoxification in brain and liver👉amino group carrier
from skeletal muscle to other tissues in fasting state👉fuel
for kidney, intestine & cells in immune system in fasting
state

Polar positive amino acids are a subset of the polar amino acids. They are characterized by their positively charged
side chains. These side chains are weak bases and are fully or partly protonated in normal biological conditions, pH
7.0-7.41. The positive charge dominates over any hydrophobic effect, making these amino acids very polar.
The polar positive amino acids include:
Arginine (Arg): It is involved in protein synthesis.
Lysine (Lys): It plays a vital role in building muscle, maintaining body tissues, and supporting the body’s immune
system.
Histidine (His): It is used in the biosynthesis of proteins.
These amino acids are attracted to water and participate in hydrogen bonding with the highly polar water
molecules. Due to this water-loving characteristic, these amino acids are generally located on the surface of
proteins, in contact with the aqueous cell environment.

• ✅ CHARGED HYDROPHILIC AMINO ACID & THEIR DISTINGUISHING FEATURES ✅
• 🛑LYSINE (LYS)
• 👉BASIC👉POSITIVE CHARGE AT PH 7👉KETOGENIC👉ABUNDANT IN HISTONES👉HYDROXYLATION IN
COLLAGEN AIDED BY ASCORBIC ACID👉BINDING SITE FOR CROSS-BRIDGES BETWEEN TROPOCOLLAGEN
MOLECULES IN COLLAGEN
• 🛑ARGININE (ARG)
• 👉BASIC👉POSITIVE CHARGE AT PH 7👉ESSENTIAL FOR GROWTH IN CHILDREN👉ABUNDANT IN HISTONES
• 🛑HISTIDINE (HIS)
• 👉BASIC👉POSITIVE CHARGE AT PH 7👉EFFECTIVE PHYSIOLOGIC BUFFER👉RESIDUE IN HEMOGLOBIN
COORDINATED TO HEME FE²+👉ESSENTIAL FOR GROWTH IN CHILDREN👉ZERO CHARGE AT PH 7.40

Polar negative amino acids, also known as acidic amino acids, are characterized by their
negatively charged side chains. These side chains contain carboxylate groups, which are
normally deprotonated at physiological pH (7.0-7.4), making these amino acids very polar.
The polar negative amino acids include:
Aspartate (Asp): Its side chain is -CH2-COO–.
Glutamate (Glu): Its side chain is -CH2-CH2-COO–.
These amino acids are attracted to water and participate in hydrogen bonding with the highly
polar water molecules. Due to this water-loving characteristic, these amino acids are generally
located on the surface of proteins, in contact with the aqueous cell environment. The negative
charge allows them to participate in ionic interactions and form electrostatic bonds with
positively charged amino acids or other molecules in biological systems.

• ✅ CHARGED HYDROPHILIC AMINO ACID & THEIR DISTINGUISHING
FEATURES
🛑Aspartate
(Asp)
👉Acidic
👉strong
negative
charge at pH
7
👉forms
oxaloacetate
by
transaminati
on
👉important
for binding
properties of
albumin
🛑Glutamate
(Glu)
👉Acidic
👉strong
negative
charge at
pH 7
👉forms
alpha-
ketoglutar
ate by
transamin
ation
👉
important
for
binding
properties
of

PVT. TIMHALL
P PHENYLALANINE
V VALINE
T TRYPTOPHAN
T THREONINE
I ISOLEUCINE
M METHEIONINE
H HISTIDINE
A ARGININE
L LYSINE
L LEUCINE
There will be…
No HISsy fits
No ARGuing &
No Lying
In the BASIC Training
Hall
BASIC Training
HaLL
BASIC Amino Acids
Histidine
Arginine
Lysine
BRANCHed Chain Amino
Acids
L eucine
I soleucine
V aline
I LIVe for this
BRANCH of the
military
ESSENTIAL AMINO
ACIDS
SOMEMNEMONICFORAMINOACID

ZWITTERIO
N AND
AMINO
ACID
CHARGE
GIVEN pH
AND pKa

Acid: Donate H+
Bases:- Accept H+
pH= Acidic sin logs H+
pH = Basic sin logs
OH-
pH vs pKa
pH < pKa = Protonated
pH > pKa = De Protonated
pH =pKa = Buffer zone

Acid: Donate H+
Bases:- Accept H+
pH = Basic sin logs
OH-
pH vs pKa
pH =pKa = Buffer Zone

Acid: Donate H+
Bases:- Accept H+
pH = Basic sin logs
OH-
pH vs pKa
pH =pKa = Buffer Zone
If we raise the ph we’ll pass the pka to a value of 13, pH
is higher
than the pka, that means the pH the solution has a
stronger
desire for that proton ,methyl ammonium will give up its
proton to
give me the form CH3 NH2 because we took away the
third hydrogen

THE ISOELECTRIC POINT (PI) IS A FUNDAMENTAL CONCEPT IN BIOCHEMISTRY AND
PROTEIN CHEMISTRY. IT REPRESENTS THE PH AT WHICH A PROTEIN OR AMINO ACID
MOLECULE CARRIES AN EQUAL POSITIVE AND NEGATIVE CHARGE. LET’S DELVE INTO THE
DETAILS AND EXPLORE SOME EXAMPLES:
 DEFINITION OF ISOELECTRIC POINT (PI):
1. THE ISOELECTRIC POINT IS THE INTERMEDIATE PH AT WHICH AN AMINO ACID OR PROTEIN
SHOWS NO TENDENCY TO MIGRATE TOWARDS ANY OF THE ELECTRODES WHEN PLACED IN AN
ELECTRIC FIELD.
2. DIFFERENT AMINO ACIDS HAVE VARYING SIDE CHAINS (ACIDIC, BASIC, OR NEUTRAL), WHICH
AFFECT THEIR OVERALL CHARGE PROPERTIES, RESULTING IN DIFFERENT PI VALUES.
ISOELECTRIC POINT = PI


FORMULA FOR ISOELECTRIC POINT:
THE FORMULA TO CALCULATE THE ISOELECTRIC POINT IS: [ PI = FRAC{{PKA + PKB}}{2} ] WHERE:
1. (PI) REPRESENTS THE ISOELECTRIC POINT.
2. (PKA) IS THE NEGATIVE LOGARITHM VALUE (BASE 10) OF THE ACID DISSOCIATION CONSTANT ((KA)).
3. (PKB) IS THE NEGATIVE LOGARITHM VALUE (BASE 10) OF THE BASE DISSOCIATION CONSTANT ((KB)).
ISOELECTRIC POINT = PI
+1 -1
+1 + (-1) =
0

Titration curves are obtained when the ph of given volume of a sample solution
varies after successive addition of acid or alkali. The curves are usually plots of ph
against the volume of titrant added or more correctly against the number of
equivalents added per mole of the sample. This curve empirically defines several
characteristics
 The precise number of each characteristic depends on the nature of the acid
being titrated:
1) The number of ionizing groups,
2) the pka of the ionizing group(s)
3) the buffer region(s).
Titration curve

• Amino acids are weak polyprotic acids. They are present as zwitter ions at neutral ph and
are amphoteric molecules that can be titrated with both acid and alkali. All of the amino acids
have an acidic group (COOH) and a basic group (NH2) attached to the α carbon, and also they
contain ionizable groups that act as weak acids or bases, giving off or taking on protons
when the ph is altered.
• Glycine is a diprotic amino acid which means that it has two dissociable Protons, one on the α amino
group and the other on the carboxyl group. In the case of Glycine, the R group does not contribute a
dissociable Proton.
The dissociation of proton proceeds in a certain order which depends on the acidity of
the proton: the one which is most acidic and having a lower pka will dissociate first. So,
the H+ on the α-cooh group (pka1) will dissociate before that on the α-nh3 group
(pka2).

The ISOELECTRIC POINT
(PI) of an amino acid
represents the pH at which
it exists as a zwitterion,
with equal concentrations
of positively charged and
negatively charged forms.
Here are the pI values for
some common amino
acids:

ABDULLAH_AMINO_ACID_PRESENTATION_1[1].pptx

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