Chemistry

 41     Course  Pack  1:  Amino  Acids  

 
PROTEINS

LECTURE 2: AMINO ACIDS: STRUCTURE AND PROPERTIES

Topic Learning Outcomes: At the end of this topic, you should be able
to:
1. Demonstrate knowledge of the structure, chemistry and reactivity of amino
acids.
2. Relate the structure of amino acids to their biological roles.
3. Recognize protein from non-protein amino acids.

Introduction

Amino acids make up the most abundant organic constituent of cells,

which are the proteins. Amino acids form the repeating units of these
biopolymers that are biosynthesized through the formation of peptide bonds.
Thus the structure, and biological functions of proteins are dependent on the
amino acids comprising these proteins. Knowing the structure and properties of
amino acids, therefore is key to understanding protein structure and biological
functions. This section will also tell you about other amino acids and their roles
in biological systems.

Amino acids

Amino acids are organic compounds containing both a carboxyl and an amino
group. It is the repeating unit of proteins, which is made up of 20 common
protein amino acids arranged in various orders and proportions. These common
protein amino acids are coded for by the genetic code. However there are
numerous other amino acids, produced by metabolism in cells.

What are common protein amino acids? The structural features of these
common amino acids are the following:
1. A central carbon atom bonded to 4 substituents
2. A carboxyl functional group as a substituent to the central carbon atom
3. An amino group as another substituent to the central carbon
4. An acidic hydrogen as the 3rd substituent to the central carbon
5. A variable side chain denoted simply as R also attached to the central
carbon.

The carboxyl, amino and acidic hydrogen are the common substituents to the
central carbon that is sp3 hybridized. It means simply that these substituents are
found in all protein amino acids. The substituent R is variable for all protein
amino acids found in nature. The sp3 hybridization of the central carbon atom

  1  
Chemistry  41     Course  Pack  1:  Amino  Acids  
 
results in bond angles that are 109o from each other, forming a tetrahedral
configuration.

Of the 20 common protein amino acids, 19 have the α-structure shown below
(Fig. 1.1a) while one, proline (Fig. 1.1b) is an imino acid that has a structure
where the central carbon is part of the pyrrolidone ring.

a) b)
source: https://study.com/academy/lesson/proline-structure-lesson-quiz.html

Fig. 2.1a. Structure of an α-amino acid. Fig. 1.1b. The Imino acid, proline

Structural features of amino acids and associated properties

Amino acids have properties associated with its structural features.

Properties due to the central carbon atom

1. Central carbon
1.1. Asymmetry
Except for glycine, the central carbon of the 19 common protein
amino acid is an asymmetric carbon or a chiral center. This carbon is sp3
hybridized with 4 bonds attached to 4 different substituents. Thus,
because of this asymmetry, it can have two different arrangements in
space called mirror images or enantiomers. Fig. 2.2 shows the
enantiomers of amino acids denoted D and L and the reference compound
glyceraldehyde.

  2  
Chemistry  41     Course  Pack  1:  Amino  Acids  
 
Figs. 2.2 The reference compound, glyceraldehyde and the structure showing the spatial
arrangements of the enantiomers of amino acids denoted, D and L. The reference substituent is
the position of the hydroxyl group in glyceraldehyde corresponding to the position of the amino
group in amino acids.

Mirror image isomers, also called enantiomers, have identical

physical properties except for their arrangements in space. Naturally
occurring amino acids are in the L configuration. It is this spatial
arrangement that is recognized by enzymes and naturally occurring
biological systems. When the spatial arrangement is changed to the D
configuration, the ability of specific groups to fit and/or bind properly with
sites in biologically active molecules, e.g. enzymes, is disrupted (Fig. 1.3).
Proteins that have protective functions such as immunoglobulins contain
J-proteins that have D-amino acids. Similarly, natural antibiotics, e.g.
bacitracin also contain D-amino acids so that these peptides and proteins
are unrecognizable to hydrolytic enzymes of microorganisms.

adapted from: https://wou.edu/chemistry/files/2019/07/table-of-pka-values.jpg

Fig. 2.3. Specificity of binding of D and L amino acids

1.2. Optical activity

Asymmetry or the difference in the spatial arrangements of the

substituents of amino acids attached to the chiral carbon determines the
ability of the molecule to rotate plane-polarized light. The difference in
rotation is due to the difference in the mass of the substituents and the
polarizability of the nucleophilic electron pairs in the substituents of the
molecules. The size and degree of polarizability determines the rotation of
plane-polarized light, i.e. if rotation is clockwise, the molecule is
designated (d) or (+), meaning it is dextrorotatory; if rotation is counter-
clockwise, the molecule is levoratory and designated (l) or (-). Fig. 2.4.

  3  
Chemistry  41     Course  Pack  1:  Amino  Acids  
 

Source:
https://chem.libretexts.org/Bookshelves/Biological_Chemistry/Supplemental_Mod
ules_(Biological_Chemistry)/Proteins/Amino_Acids/Properties_of_Amino_Acids/
Stereochemistry_of_Amino_Acids
Fig. 2.4. Rotation of plane-polarized light due to the different in the spatial configuration of D and
L amino acids.

Note that optical activity, while dependent on spatial configuration,

is not the same as the latter. A D-amino acid can rotate plane-polarized
light in the counterclockwise direction and designated (l), i.e. the amino
acid is D (l)-amino acid. An example of this is D(l)-alanine.

Properties due to the substituents of the central carbon atom

2. α-carboxyl group

2.1. Acidity
The carboxyl group is the acidic functional group of organic
compounds. This group is acidic because it contains two electronegative
oxygen atoms that make the carbonyl atom to which these oxygen atoms
are attached partially positive. Of the two oxygen atoms, one is sp2
hybridized, while the other which is bonded to hydrogen is sp3 hybridized.
By orbital electronegativity, the sp2-hybridized oxygen is more
electronegative hence the electron density is drawn toward it increasing
the δ-positivity of the carbonyl carbon. To relieve this, the OH bond
increases polarization of electrons towards the carbonyl carbon
weakening the bond. In a polar environment such as water, that provides
the “pull”, the proton dissociates. Dissociation of the acidic proton is also
favored by the stability of the resulting carboxylate anion. This stability is
the result of electron delocalization of the negative charges over several
atoms (Fig. 2.5).

  4  
Chemistry  41     Course  Pack  1:  Amino  Acids  
 

Fig. 2.5. Resonance stabilization of the carboxylate anion

The pKa value of the carboxyl functional group is below 7.0, thus at
physiological pH, the carboxyl functional group is ionized. pKa values refer
to the negative logarithm of the dissociation constant, Ka or the logarithm
of 1/Ka, For the carboxyl functional group, the range of pKa values for the
different amino acids is 1.7-2.6. It is a weaker acid than HCl and the like
but a stronger acid than -NH3+.

3. α-amino group
3.1. Basicity
The amino group is the basic functional group of amino acids. Amino
groups are basic due to the presence of a lone pair in nitrogen that
increases electron density in this atom. Amino acids contain the amino
functional group hence are also basic; some amino acids also have an
amino group in R. At physiological pH, the amino group is positively
charged upon protonation resulting in the formation of a conjugate weak
acid, -NH3+. The range of pKa values of –NH3+ for the amino acids are
above 7.0, hence this is a weaker acid than the carboxyl group.

4. α-hydrogen

4.1. Acidity
Amino acids also possess an acidic α-hydrogen that is responsible
for some of the chemical reactivities of amino acids. The acidity of the α-
hydrogen is due to inductive effect on the α-carbon by a δ-positive
carbonyl carbon. The carbonyl carbon is δ-positive hence by inductive
effect the α-carbon is also δ-positive. This results in a polar C-H bond with
the hydrogen loosely held and therefore weakly acidic. The increased
polarity of the C-H bond due to this structural effect weakens this bond
facilitating the release of a proton to a receiver or a strong nucleophile in a
highly polar environment. Dissociation of the proton leaves a paired
electron that can delocalize during Schiff’s base formation or form

  5  
Chemistry  41     Course  Pack  1:  Amino  Acids  
 
condensation products.

5. Variable side chain, R

5.1. Polarity
The 4th substituent is the variable side chain of amino acids
denoted simply as “R”. Some side chains are made up of hydrocarbons
only or contains heteroatoms that are centrally located in the molecule and
are therefore non-polar; others contain atoms that can H-bond with water
and are polar, while other R groups are either acidic, i.e. it contains the
carboxyl functional group or are basic, i.e. it contains the amino functional
group. The R group is essentially the determinant of the classification of
amino acids based on the polarity of this group.

The polarity of the side chain, R, determines the solubility of the

amino acids. Some contains hydrocarbons and are non polar with
variable van der waals radii. Still others contain electronegative
heteroatorns that are often attached to a hydrogen atom or a less
electronegative atom, making them polar. Some R groups also exhibit
acidic or basic properties because of the presence of the carboxyl and
amino functional group, respectively. In protein molecules, these R groups
jut out of the planar structure of the peptide bond and are therefore
responsible for many of the intermolecular forces of attraction or non-
covalent interactions that shape protein structures. These intermolecular
forces include H-bonding, hydrophobic interactions, and ionic bonds or
salt bridges.

On the basis of the structure and properties of the R groups, amino

acids are classified into a) nonpolar, b) polar, uncharged and c) polar,
charged amino acids. The last two classifications were made based on its
form at the physiological pH, which is 6.7-7.4. Polar uncharged amino
acids contain R groups that do not ionize at physiological pH hence are
uncharged. Charged amino acids are those containing R group that are
either negatively or positively charged at physiological pH. Amino acids
containing the carboxyl group in R are negatively charged while those with
amino groups are positively charged at physiological pH. Table 2.1 gives
the classification of the amino acids based on the polarity of R, the names,
abbreviations, and structure of R.

5.2. Acidity and basicity

R groups containing carboxyl functional groups adds to the acidity
of the amino acid while R groups containing the amino functional group
are classified as basic amino acids. Table 2.1 also lists the pKa values of
the ionizable protons of the acidic functional groups of the 20 commonly
occurring protein amino acids.

  6  
 Chemistry  41   The 20 biological
  amino
Course  Pacids
ack  1:  Amino  Acids  
 
The 20 biological amino acids
Aliphatic nonpolar side chains: Aliphatic polar side ch
The 20 biological amino acids
The 20 biological
Table 2.1. The 20 common
Aliphatic amino
protein amino
nonpolar acids
sideacids.
chains: Aliphatic polar side ch

Amino Acid Structure of R 3- 1- pK1 pK2 pK3

Aliphatic nonpolar side chains: Aliphatic
letter polar side chains:
ogical amino acids Aliphatic nonpolar side chains:
abbrev abbrev
letter
Aliphatic polar side chains:
The 20
Non-polar biological
Glycine
Gly
amino acids
Alanine
Ala
Proline
Pro
Serine
Ser
T
T
de chains:
Alanine G
Aliphatic polar side chains:
Ala
A A 2.34
P 9.69 S T
Glycine Alanine Proline Serine T
Gly Ala Pro Ser T
Aliphatic nonpolar side G
chains: A Aliphatic
P polar side chains:
S T
Glycine
Gly The 20 biological
ValineAlanine
Ala
Glycine Alanineamino acids
Proline
Pro
Serine
Val
Ser
Proline
V Threonine
2.32
Thr
Serine
9.62
Threonine
G A
Gly PAla ProS T Ser Thr
G A P S T

Alanine Aliphatic nonpolar side chains:

Proline Serine Threonine Aliphatic polar side chains:
Ala
Leucine
Pro Ser
Leu
Thr
L 2.36 9.68
A P Glycine SAlanine T Proline Serine Threonine
Asparagine G
Valine Isoleucine Leucine
Gly Ala Pro Ser Thr
Asn G
Val Ile Leu
G A P S TN Q
V I L
Valine Isoleucine Leucine Asparagine G
Val Ile Leu Asn G
V N Q
Isoleucine Aromatic side chains: IIle I 2.36 L
9.68 Sulfur containing side
Valine Isoleucine
Glycine Leucine
Alanine Asparagine
Proline Glutamine
Serine Threonine
Val GlyIle
Valine Ala Leu
Isoleucine Pro Asn
Leucine
Gln
Asparagine
Ser ThrGlutamine
V G I Val Aromatic
AIleL side chains:
P N Leu
Q
SAsn Sulfur containing
T Gln side
V I L N Q

Aromatic
Isoleucineside chains: Sulfur
Phe containing
F side chains:
Leucine Asparagine Glutamine
Phenylalanine 1.83 9.13
Ile Aromatic
Leu side chains: Asn Gln Sulfur containing side chains:
I L Valine NIsoleucine Q Leucine Asparagine Glutamine
Val Ile Leu Asn Gln
V I L N Q
s: Sulfur containing side chains:
Aromatic side chains:
Phenylalanine Tryptophan Sulfur containing sideMethionine
Tyrosine chains:
Phe Trp
Methionine
Valine Isoleucine Met
Leucine M 2.28Tyr 9.21
Asparagine Met
Glutamine
Val IleF
Phenylalanine
W
LeuTryptophan Asn Y
Tyrosine
Gln M
Methionine
V I Phe L Trp N Q
Tyr Met
Basic
F side chains: W Y Acidic
M side chains:
Phenylalanine Tryptophan Tyrosine Methionine Cysteine
Phe
Aromatic
Trp
side chains: Tyr Met
SulfurCys
containing side chains:
F
Phenylalanine Basic side chains:
Tryptophan Tyrosine Methionine Acidic side chains:
Cysteine
Phe W Y
Trp MTyr C
Met Cys
F W Y M C
The 20 biological amino
Tryptophan
acids
Basic side chains:Tryptophan
Tyrosine
Methionine
Trp side chains:
Acidic
Cysteine
W 2.38 9.39
Trp Basic side chains:
Tyr Met Cys Acidic side chains:
W Phenylalanine
Y M Tryptophan C Tyrosine Methionine Cysteine
Phe Trp Tyr Met Cys
Aliphatic nonpolar side
F chains: W Aliphatic
Y polar side chains:
M C
Acidic side chains:
Basic side chains:
Proline Pro P Acidic side
1.99 chains:
10.60
Phenylalanine Tryptophan
Lysine Tyrosine
Histidine Methionine
Arginine Cysteine
Glutamic acid As
Phe Trp Lys Tyr His Met Arg CysGlu As
F W K Y H M R C E D
Lysine Polar, unchargedHistidine Arginine Glutamic acid As
Glycine Alanine Proline
Lys Serine
His Threonine
Arg Glu As
Gly Basic side
Ala chains: Pro
K HSer AcidicThrside
R chains: E D
G A Acidic and basic groups are shown
PArginine S in their ionizedT form. ©2007 Peter A. Doucette
Lysine Histidine Glutamic acid Aspartic acid
Lys His
Lysine Arg
Histidine GluArginine Asp
Glutamic acid Aspartic acid
K   H
Lys R and basic groups E
Acidic
His areArg D form. ©2007 Peter A.
shown in their ionized
Glu Asp
7  
Doucette
K H R E D

Acidic and basic groups areArginine

Histidine shown in their ionized form. ©2007
Glutamic acid Peter A.Aspartic
Doucetteacid
 The 20 biological amino acids
mino
ide
acids
Proline
chains:
Pro
Serine
Chemistry  
Ser 41  
Threonine
Aliphatic
Thr
polar side chains:
  Course  Pack  1:  Amino  Acids  
P S T
  Aliphatic nonpolar side chains: Aliphatic polar side cha
Serine
Aliphatic polar side chains: Ser S 2.21 9.15
Valine Isoleucine Leucine Asparagine Glutamine
Val Ile Leu Asn Gln
V I L N Q
Alanine Threonine
Proline Serine Thr
Threonine T 2.63 10.43
ogical amino acids
Ala Pro Ser Thr
Aromatic
A side chains: P S Sulfur
T containing side chains:
Glycine Alanine Proline Serine Th
Gly Ala Pro Ser Th
Leucine
Proline Asparagine
TyrosineSerine Glutamine
GThreonine Tyr
A Y 2.20
P 9.11 10.07S T
Leu AsnSer Gln
de chains:
Pro
N Aliphatic
Q
Thr polar side chains:
LP S T

no acids Sulfur containing side chains:

Isoleucine Leucine Asparagine Glutamine

Ile Aliphatic
Leu Asn
polar side chains: Gln
Alanine
Phenylalanine
I Ala
Cysteine
Proline
Tryptophan
L
Serine
N Tyrosine Cys
Threonine
QMethionine C 1.71
Cysteine10.78 8.33
Pro Ser Thr Asparagine Gl
Phe Trp Tyr
Valine Met
Isoleucine Cys
Leucine
A P S T Asn Gl
F W Y
Val M
Ile CLeu
VGlutamine N Q
s: Leucine Asparagine Sulfur containing sideI chains: L
Leu Asn Gln
Basic side chains:Asparagine Acidic
AsN side chains:
N 2.02 8.80
L N Q
Aromatic side chains: Sulfur containing side c
Tyrosine
Proline Methionine
Serine Cysteine
Threonine
Tyr
Pro
Sulfur
Met
Ser
containing side chains:
Cys
Thr
PY MS TC

Glutamine
Acidic side chains: GlN Q 2.17 9.13
Isoleucine
Ile
Leucine
Leu
The
Asn 20 biological
Asparagine Glutamine
Gln amino acids
I L N Q
Tryptophan Tyrosine Methionine Cysteine
Trp Tyr Met Cys
: W Y
Aliphatic
Sulfur
M
nonpolar
containing side
side chains:
chains:
C
Aliphatic polar side cha
Phenylalanine Tryptophan Tyrosine Methionine C
Lysine Histidine Phe Arginine Glutamic
Trp acid Aspartic
Tyr acid Met C
Lys His Acidic
F Argside chains: Glu
W AspY M C
Leucine
K Tyrosine Glycine
Asparagine
HMethionine
Glutamine
RCysteine E Gly G 2.34
D 9.60
Leu Asn Gln
Tyr Met Cys
L Y N Q
M Basic Cside chains: Acidic side chains:
Acidic and basic groups are shown in their ionized form. ©2007 Peter A. Doucette
Acidiccontaining
side chains:
Charged
Sulfur side chains:
Glycine Alanine Proline Serine Th
Arginine Lysine
Glutamic acid Aspartic
Gly acid Lys
Ala K 2.18
Pro 8.95 10.53 Ser Th
Arg Glu AspG A P S T
R E D

Tryptophan Tyrosine Methionine Cysteine

Trp
nized Tyr
form. ©2007 Peter A. Doucette Met Cys
W Y M C

Histidine Arginine Acidic side

Glutamic chains:
acid Aspartic acid
His Arg Glu Asp
H Arginine
R E D Arg R 2.17 9.04 12.48
Lysine Histidine Arginine Glutamic acid Asp
Tyrosine Methionine Cysteine
Lys His Arg GluAsparagine Asp
G
Valine Isoleucine Leucine
Tyr
s are shown Met ©2007 Peter A. Doucette
in their ionized form. Cys
KVal H RLeu E Asn DG
Ile
Y Arginine MGlutamic acid C
Aspartic acid N Q
V I L
Arg Glu Asp
R E D
Acidic side chains: Acidic and basic groups are shown in their ionized form. ©2007 Peter A. Doucette
Aromatic side chains: Sulfur containing side
onized form. ©2007 Peter A. Doucette

  8  
Histidine Arginine Glutamic acid Aspartic acid
His Arg Glu Asp
 L N Q
he Trp Tyr Met Cys
W Y M C
Sulfur containing side chains:
asic side chains: Chemistry  41   Acidic
  side chains:Course  Pack  1:  Amino  Acids  
Asparagine Glutamine
Isoleucine   Leucine
Asn Gln
Ile Leu
I L N Q
Phenylalanine Tryptophan Tyrosine Methionine Cysteine
Phe Trp Tyr Met Cys
: F Sulfur
W containing side chains:
Y M C

Basic side chains: Acidic side chains:

Tyrosine Methionine Cysteine

Tyr Met Cys
Y M C
Lysine Histidine
Histidine Arginine His acid
Glutamic H 1.82acid
Aspartic 9.17 6.00
Lys His Arg Glu Asp
K Acidic
H side chains: R E D

Tryptophan
Acidic Tyrosine
and basic groups are shown Methionine
in their ionized form. Cysteine
©2007 Peter A. Doucette
Trp Tyr Met Cys
W Aspartic
Y acid M C Asp D 2.09 9.82 3.86
Lysine Acidic side chains:
Histidine Arginine Glutamic acid Aspartic acid
Lys His Arg Glu Asp
K H R E D

Glutamic acid Glu E 2.19 9.67 4.25

Acidic and basic groups are shown in their ionized form. ©2007 Peter A. Doucette

Arginine Glutamic acid Aspartic acid

Arg Glu Asp
R E D

ed form. ©2007 Peter A. Doucette

*pKa values from: https://wou.edu/chemistry/files/2019/07/table-of-pka-
Histidine
values.jpg
Arginine Glutamic acid Aspartic acid
His Arg Glu Asp
H Note: R some biochemists E and authors also
D classify amino acids in accordance
with the organic classification of the R groups. Thus, the amino acids are
grouped
are shown in their ionized as 1)Peter
form. ©2007 aliphatic, 2) aromatic, 3) hydroxyl-containing, 4) thiol-containing
A. Doucette
groups, 4) cyclic, 5) carboxyl-containing, 6) amine-containing and 7) amide-
containing.

Acidity and Basicity of R

The pKa values of the ionizing groups of amino acids can be obtained by
pH titration, i.e, by adding small amounts of standard base, which will neutralize
the H+ released. The pH of the resulting solution will increase. A titration curve
is a plot of the pH values of the solution and the amount of OH- added. The
concentration of the OH- used is usually in the range 0.1-0.5 M.

By convention, pK1 refers to the dissociation of the acidic proton of the –

COOH functional group while pK2 is the ionization of the –NH3+ proton. At the pH
lower than the pK1 value, the –COOH functional group is electrically neutral, i.e.
the acidic proton do not dissociate. Similarly, at pH lower than the pK2 value, the
amino group is protonated and assumes the form of the conjugate acid, -NH3+ of
the weak base, -NH2. These pKa values determine the ease of ionization of the

  9  
The pKa values for any polyprotic acid always get progressively higher, because it
becomes increasingly difficult to stabilize the additional electron density that results
from each successive proton donation. H3PO4 is a strong acid because the (single)
Chemistry  
negative 41   on its conjugate base H2PO4-  can be delocalized
charge Course  
overPtwo
ack  oxygen
1:  Amino  Acids  
atoms.
 
protons of acidic forms of the functional groups and therefore its form in solution
H2PO4- is substantially less acidic, because proton donation now results in the
at a particular pH. It is also useful for separating amino acids in an electric field.
formation of an additional negative charge: a –2 charge is inherently higher in energy
than a –1
Atcharge because
that pH, of negative-negative
the acidic electrostatic
form of the amino group isrepulsion.
positivelyThe third Thus,
charged.
deprotonation, resulting in formation of a third negative charge, has an
for amino acids in solution at pH lower than pK1, most amino acids contain even higher two
pK a. We will have more to say about the acidity of phosphate
ionizing protons, one each from the carboxyl and –NH3+ groups. groups in chapter 9, acid
The amino
when we study the reactions of phosphate groups on biomolecules.
therefore is also a weak polyprotic acid of the form H A. Hence, the titration 2
curve will also show at least two inflection points or plateaus. These are points in
Exercise
the graph 7.29: In a pH
where buffer at physiological
= pKa pH, what
and [A-] = [HA]. form(s)
In these of phosphoric
points, note thatacid
pH values
predominate? What is the average
do not vary significantly netaddition
even with charge? of small amount of acids (moving to
the left) or base (moving to the right from the point where pH = pKa. This is also
the point when amino acids, acting as buffers in biological systems will have its
Free amino buffering
maximum acids are polyprotic,
capacity. with
The pKa values
plateau of approximately
gives the range of 2pH
forvalues
the carboxylic
at which
acid group and 9-10 for the ammonium group. Alanine, for example, has the
the buffer will still have a maximum buffering capacity, i.e. at pH = pKa ± 1.0. acid
constants pKa1 = 2.3 and pKa2 = 9.9.

CH3 pKa = 2.3 CH3 CH3

pKa = 9.9
OH O O
H3N H3N H2N
O O O
cation at low pH zwitterion at pH 7 anion at high pH
fig 56
The Henderson-Hasselbalch equation tells us that alanine is almost fully protonated and
positively charged when dissolved in a solution that is buffered to pH 0.5. At pH 7,
alanine has lost one proton from the carboxylic acid group, and thus is a zwitterion (it
has both a negative and a positive formal charge). At pH levels above 12, the
ammonium group is fully deprotonated, and alanine has a negative overall charge.

Organic Chemistry With a Biological Emphasis 370

Tim Soderberg

Source: Soderberg T. “Organic Chemistry with a Biological Emphasis”

Fig. 2.6 shows the forms of alanine, a nonpolar amino acid at different pH of the solution, and the
titration curve resulting from the neutralization of the ionizable protons.

The pKR values of amino acids provide the hint on which R groups
contribute to the acidity of the peptide and protein comprising the amino acids.
For amino acids with ionizable protons in R such as the acidic, basic and some
polar uncharged amino acids, the amino acid also assumes the form of a weak
acid of the form H3A. For example, aspartic acid has the following pKa values:
pK1 = 2.1; pK2 = 9.8 and pKR = 3.9.

  10  
Chemistry  41     Course  Pack  1:  Amino  Acids  
 

Source: https://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/proteins.htm

Fig. 2.7. The titration curve of aspartic acid, an acidic amino acid

It could be observed that the amino acids with more than two ionizable
protons have three inflection points at which points, pKa = pH. All amino acids
with ionizable protons In R, including polar, uncharged amino acids with acidic
protons in R, such as tyrosine and cysteine have similar titration curves.

Like other weak acids with ionizable protons, amino acids will exist in
different forms at different pH values. At pH lower than pK1, all amino acids will
be positively charged. An amino acid that is nonpolar or have no ionizable
protons in R will have the general formula H2A. As pH is increased, the carboxyl
proton, being the more acidic proton, ionizes and the amino acid will become
zwitterionic, i.e. it has both positive and negative charges but is electrically
neutral or its net charge is zero (Fig. 2.8). The net charge of the amino acid is
the algebraic sum of all positive and negative charges at the pH indicated. As pH
is increased further, the proton from the amino, which has the higher pKa value
since the amino group is a weaker acid, will then dissociate and the amino acid
becomes negatively charged. At pH = pKa, there is an equilibrium concentration
between the weak acid and its conjugate base. The ratio of these forms can be
determined using the Henderson-Hasselbalch equation. The forms of the amino
acid with the general formula H3A (acidic, basic, some polar uncharged amino
acids such as cysteine and tyrosine) will likewise change depending on the pH.

The pH at which the amino acid exists primarily in the zwitterionic form is
the isoelectric pH or pI of the amino acid. It is computed as the average of the
algebraic sum of the pKa values before and after the zwitterionic form. When the
pH = pI value of the amino acid, the amino acid, being electrically neutral, will not
move in an electric field. The pI of the different amino acids is also variable.

The figures below show the zwitterion form an amino acid that has no

  11  
Chemistry  41     Course  Pack  1:  Amino  Acids  
 
ionizable proton in R. For these groups of amino acids, the structure at
physiological pH is shown on the left.

Source: https://2012books.lardbucket.org/books/introduction-to-chemistry-
general-organic-and-biological/index.html
Fig. 2.8. The ionic state of a zwitterion.

The right drawing is incorrect since the carboxyl group will only be
protonated at a very low pH at which pH the amino group is protonated. Even
when the carboxyl group is deprotonated, ionization of this proton occurs at pH
ranges of 1.8-2.4 for amino acids. At this pH, the amino group is still protonated
since it is a strong base. Its conjugate acid therefore is weak and dissociates
only at pH ranges of 9-10.4.

Thus amino acids in solution assume its form as protons are ionized in a
solution at a particular pH. These forms change charges from positive to zero to
negative as pH of the solution increases. The form with a net charge of zero
occurs predominantly at the pH equal to the pI of the amino acid. At this pH, the
amino acid will not move in an electric field. Fig. 2.9 shows the predominant
forms of 2 nonpolar amino acids, an acidic and basic amino acid at pH of 6.0.
The pI value is also provided and is variable for the amino acids. The
predominant form of an amino acid at pH lower than the pI value of that amino
acid is positively charged while the predominant form at pH higher than the pI
value is negatively charge.

Fig. 2.9. The ionic forms of

the amino acids, arginine,
alanine, aspartic acid and
isoleucine in solution at
various pH values; a) alanine,
b) cysteine, c) aspartic acid
and d) lysine  

  12  
Chemistry  41     Course  Pack  1:  Amino  Acids  
 

Exercise 2.1. At what pH will you be able to separate the amino acids val, his and arg?

When amino acids are linked as a result of the formation of the peptide
bond, it is the ionizable proton in the R group that will contribute to the acidity and
basicity, as well as the form of the peptide in solution.

Other properties

Molecular size

Amino acids have molecular weights raging from 57 to 186 daltons (1

dalton is equivalent to 1 amu). If we take the average weight to be about 110
daltons, a proteIn with a molecular weight of 22.000 daltons (or 22 kDa) contain
approximately 220 amino acids residues.

Hydrophobicity

Hydrophobicity is the most important characteristics of the R groups of

amino acids that drives protein folding. When a protein folds, exposed
hydrophobic side chains get buried and expels water which cannot interact with
these side chains. Protein structure, folding and stability increases the entropy of
water. This is called the hydrophobic effect. Table 2.2. gives the hydrophobicity
values of the amino acids.

Table 2.2. The hydrophobicity values of the amino acids (https://www.web-

books.com/MoBio/Free/Ch2A2.htm)

Non-polar AA 1-letter H* Polar, uncharged 1-letter H*

Amino Acid abbrev value Amino Acid abbrev value
Alanine A 1.8 Serine S -0.8
Valine V 4.2 Threonine T -0.7
Leucine L 3.8 Tyrosine Y -1.3
Isoleucine I 4.5 Cysteine C 2.5
Phenylalanine F 2.8 Asparagine N -3.5
Methionine M 1.9 Glutamine N -3.5
Tryptophan W -0.9 Glycine G -0.4
Proline P -1.6
Charged, acidic 1-letter H* Charged, basic 1-letter H*
Amino Acid abbrev value Amino Acid abbrev value
Aspartic acid D -3.5 Histidine H -3.2
Glutamic acid E -3.5 Lysine K -3.9
Arginine R -4.5
*H value = relative hydrophobicity scale; the higher the value is, the more hydrophobic the R
group is and the amino acid is buried in the protein in aqueous solutions; a negative value means
that the amino acid is hydrophilic and are found outside the protein structure in aqueous solution.

  13  
Chemistry  41     Course  Pack  1:  Amino  Acids  
 
Properties unique to structure of some amino acids:

 Bridge formation by the side chain of cysteines

 rigidity of the pyrrolidone rings of prolines which causes helices to break

 flexibility of glycines which causes polypeptides to turn.

Reactivities

The reactions that amino acids undergo are primarily due to the carboxyl group,
the amino group, the a-hydrogen and functional groups in R. These are the
same reactions as organic compounds with the same functional groups, e.g.
carboxyl groups are acidic and can undergo substitution reactions. Amino
groups are basic and are nucleophiles in substitution or addition reactions. The
R groups of amino acids contain substituted and unsubstituted arenes, thiols,
hydroxyls, amides, amino, and carboxylic groups. These functional groups
participate in various reactions including oxidation-reduction reactions
transforming them into intermediates and products essential for structural stability
and cellular metabolism. Some of these reactions are shown in Figs. 2.10, 2.11,
2.12.

Oxidation of thiol groups

Fig. 2.10. Oxidation of thiol groups leading to the formation of disulfide bonds between proximal
cysteines.

Source: https://2012books.lardbucket.org/books/introduction-to-chemistry-
general-organic-and-biological/s21-amino-acids-proteins-and-enzym.html#gob-
ch18_t01

  14  
Chemistry  41     Course  Pack  1:  Amino  Acids  
 
The ninhydrin reaction:

Paper Chromatography
Source: https://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/proteins.htm

Fig. 2.11. The ninhydrin reaction is a substitution reaction involving the a-amino group of amino
acids and the reagent, 2,2-Dihydroxy-1H-indene-1,3(2H)-dione. The product is a purple colored
compound often referred to as Ruhemann’s purple. (https://byjus.com/chemistry/ninhydrin-test/)

Acylation of the amino groups

Source: https://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/proteins.htm

Fig. 2.12. The acylation reaction of amino acids

Non-protein amino acids

Other than the 20 common protein amino acids there are a number of
amino acids occurring in nature. Many of these have functions such as the role
of hydroxyproline in maintaining the stability of quaternary structures of collagen,
β-alanine is found in microbial cell wall while ornithine, homoserine and
homocysteine are intermediates of metabolism. Interestingly, 2 amino acids,
selenocysteine (Sec/U) and pyrrolysine (Pyl/O) are non protein amino acids that
are regulators of the genetic mechanism; these are incorporated at the stop

  15  
Chemistry  41     Course  Pack  1:  Amino  Acids  
 
codon, UGA and UAG, respectively.

Fig. 2.13. Some non-protein amino acids.

See also: https://www.slideshare.net/mprasadnaidu/non-protein-aminoacids

In summary, you have been introduced to the following

1. The general structural features of amino acids and their properties

2. The structure, unique properties and reactivities of the 20 common protein
amino acids, which are crucial to the structure and functions of proteins,
which they comprise.
3. The acidity and basicity properties of amino acids and their forms at
varying pH of the solution.
4. The structure and function of some non-protein amino acids that are
essential for the genetic regulation, protection of important structures,
metabolic processes, and structural stability as well.

Additional references:

Schmitz,  A.  chapter  18  from  the  book  Introduction  to  Chemistry:  General,  Organic,  
and  Biological  (v.  1.0).    

https://biochem.oregonstate.edu/content/biochemistry-­‐free-­‐and-­‐easy  

https://microbenotes.com/amino-acids-properties-structure-classification-and-
functions/

  16