‫جامعة الكوفة‬
University of Kufa
‫كليةة البةا الطيبة‬
College of Veterinary
‫قسم الفسلجة‬
Department of Physiology
‫الكيمياء الحياتية‬
Biochemistry
‫الم حلة األولى‬
First Stage
‫ األحماض األمينية‬:‫محاض ة بعنوان‬
Lecture about: Amino Acids
‫ نعمان عباد محمد‬.‫م‬.‫إعداد م‬
Directed by: Nu'man Abbadi Muhammad
2012
2012
-1-
:‫أهداف المحاض ة‬
:‫ينبغي أن يتعلم البالّا عن األحماض األمينية اآلتي‬
.‫ ت كيطها وأنواعها‬.1
.‫ النوع الغي شائع منها والذ حصل له تعديل بعد التخليق‬.2
.‫ الخواص الضوئية في المحاليل‬.3
.‫ القاعدية وخاصيتها كمحاليل منظمة‬-‫ الصفات الحامضية‬.4
.‫ أهميتها ودو ها الوظيفي‬.5
Aims of the Lecture:
The students should be learning about Amino acids:
1. The structures and types.
2. The modified & uncommon types.
3. Optical properties in solutions.
4. Acid-Base properties and Buffer characteristic.
5. The importance and functional role.
-2-
AMINO ACIDS
Proteins are the most abundant and functionally diverse molecules in living
systems. Virtually every life process depends on this class of molecules. For example;
 Enzymes and polypeptide hormones direct and regulate metabolism in the
body.
 Myosin, a contractile protein of muscle permits movement.
 In bone, the protein collagen forms a framework for the deposition of calcium
phosphate crystals.
 In the bloodstream, proteins, such as hemoglobin and plasma albumin, shuttle
molecules essential to life, whereas immunoglobulins fight infectious bacteria
and viruses.
In short, proteins display an incredible diversity of functions, yet all share the
common structural feature of being linear polymers of amino acids. This lecture
describes the properties of amino acids.
 STRUCTURE OF THE AMINO ACIDS
Of the over 300 naturally occurring amino acids, 20 constitute the monomer units
of proteins (These are the only amino acids that are coded for by DNA, the genetic
material in the cell). Each amino acid (except for proline) has a carboxyl group, an
amino group, and a distinctive side chain ("R-group") bonded to the α-carbon atom
as shown in figure (1).
Figure (1) General structure of the amino
acids found in proteins.
Figure (2) Peptide bonds.
At physiologic pH (approximately pH = 7.4), the carboxyl group is dissociated,
forming the negatively charged carboxylate ion (-COO-) and the amino group is
protonated (-NH3+) proteins, almost all of these carboxyl and amino groups are
combined in peptide linkage as shown in figure (2) and, in general, are not available
for chemical reaction except for hydrogen bond formation. Thus, it is the nature of the
side chains that ultimately dictates the role an amino acid plays in a protein. It is,
therefore, useful to classify the amino acids according to the properties of their side is,
whether they:
A. Amino acids with nonpolar side chains:
These amino acids has a nonpolar side chain that does not bind or give off protons
or participate in hydrogen or ionic bonds see figure (3), so that they have "oily" or
lipid-like a property that promotes hydrophobic interactions.
1. Location of nonpolar amino acids in proteins: Their side chains tend to
cluster together in the interior of the protein in solutions result from the
hydrophobicity of the nonpolar R-group, which act like droplets of oil in an aqueous
-3-
environment, thus they fill up the interior of the folded protein and help give it its
stable three-dimensional shape.
Figure (3) the 20 common amino acids of proteins.
2. Proline: The side chain of proline and its α-amino group form a ring structure, and
thus it contains an imino group, rather than an amino group see figure (3). The
unique geometry of proline contributes to the formation of the fibrous structure of
collagen, and often interrupts the α-helices found in globular proteins.
B. Aromatic R Groups:
Phenylalanine, tyrosine, and tryptophan, with their aromatic side chains, are
relatively nonpolar (hydrophobic). All can participate in hydrophobic interactions.
The hydroxyl group of tyrosine can form hydrogen bonds, and it is an important
functional group in some enzymes. Tyrosine and tryptophan are significantly more
polar than phenylalanine, because of the tyrosine hydroxyl group and the nitrogen of
the tryptophan indole ring. Tryptophan and tyrosine, and to a much lesser extent
phenylalanine, absorb ultraviolet light. This accounts for the characteristic strong
absorbance of light by most proteins at a wavelength of 280 nm, a property exploited
by researchers in the characterization of proteins.
-4-
C. Amino acids with uncharged polar side chains:
The R groups of these amino acids are more soluble in water, or more
hydrophilic, than those of the nonpolar amino acids, because they contain functional
groups that form hydrogen bonds with water. This class of amino acids includes
serine, threonine, cysteine, asparagine, and glutamine. The polarity of serine and
threonine is contributed by their hydroxyl groups; that of cysteine by its sulfhydryl
group; and that of asparagine and glutamine by their amide groups.
1. Disulfide bond: The side chain of cysteine contains a sulfhydryl group (-SH),
which is an important component of the active site of many enzymes. The -SH groups
of two cysteines can become oxidized to form a dimmer cystine, which contains a
covalent cross-link called a disulfide bond (-S-S-) see figure (4).
2. Side chains as sites of attachment for other compounds: Serine and threonine
contain a polar hydroxyl group that can serve as a site of attachment for structures
such as a phosphate group (the side chain of serine is an important component of the
active site of many enzymes). In addition, the amide group of asparagine, as well as
the hydroxyl group of serine or threonine, can serve as a site of attachment for
oligosaccharide chains in glycoproteins.
Figure (4) Disulfide bonds
between Cysteine residues
D. Positively Charged (Basic) R Groups:
The most hydrophilic R groups are those that are either positively or negatively
charged. The amino acids in which the R groups have significant positive charge at
pH 7.0 are lysine, which has a second primary amino group at the ε position on its
aliphatic chain; arginine, which has a positively charged guanidino group; and
histidine, which has an imidazole group. Histidine is the only common amino acid
having an ionizable side chain with a pKa near neutrality. In many enzyme-catalyzed
reactions, a histidine residue facilitates the reaction by serving as a proton
donor/acceptor.
E. Amino acids with acidic side chains:
The amino acids aspartic and glutamic acid are proton donors. At neutral pH, the
side chains of these amino acids are fully ionized, containing a negatively charged
carboxylate group (-COO-). They are called aspartate or glutmate to emphasize that
these amino acids are negatively charged at physiologic pH, see Figure (3).
 Uncommon Amino Acids
Several amino acids occur only rarely in proteins (Figure 4.4). These include
hydroxylysine and hydroxyproline, which are found mainly in the collagen and
gelatin proteins, and thyroxin and 3,3`,5-triiodothyronine, iodinated amino acids
that are found only in thyroglobulin, a protein produced by the thyroid gland. The γ-5-
Carboxyglutamic acid is found in several proteins involved in blood clotting. Certain
proteins involved in cell growth and regulation are reversibly phosphorylated on the (OH) groups of serine, threonine, and tyrosine residues. Finally, N-methylarginine
and N-acetyllysine are found in histone proteins associated with chromosomes.
 Optical properties of amino acids
The α-carbon of each amino acid is attached to four different chemical groups and
is, therefore, a chiral or optically active carbon atom. Glycine is the exception because
its α-carbon has two hydrogen substituents and, therefore, is optically inactive, (amino
acids that have an asymmetric center at the α-carbon can exist in two forms,
designated D and L, that are mirror images of each other see figure -5- The two forms
in each pair are termed stereoisomers, optical isomers, or enantiomers). All amino
acids found in proteins are of the L-configuration. However, D-amino acids are found
in some antibiotics and in bacterial cell walls.
Figure (6) L- and D-amino acids.
 ACIDIC AND BASIC PROPERTIES OF AMINO ACIDS
Amino acids in aqueous solution contain weakly acidic α-carboxyl groups and
weakly basic α-amino groups. In addition, each of the acidic and basic amino acids
contains an ionizable group in its side chain. Thus, both free amino acids and some
amino acids combined in peptide linkages can act as buffers. The quantitative
relationship between the concentration of a weak acid (HA) and its conjugate base (A) is described by the Henderson-Hasselbalch equation.
A. Derivation of the equation
In general, a weak acid (HA), called the conjugate acid, dissociates into a hydrogen
ion and an anionic component (A-), called the conjugate base. The name of an
undissociated acid usually ends in “ic acid” (e.g., acetoacetic acid) and the name of
the dissociated anionic component ends in “ate” (e.g., acetoacetate). The tendency of
the acid (HA) to dissociate and donate a hydrogen ion to solution is denoted by its Ka,
the equilibrium constant for dissociation of a weak acid (Equation 1). The higher the
Ka, the greater is to dissociate a proton. For the reaction (HA
A- + H+ )
[H+] [A-]
Ka = ───── ------ (1)
[HA]
By solving for the [H+] in the above equation, taking the logarithm of both sides
of the equation, multiplying both sides of the equation by -1 , and substituting pH = log [H+] and pKa = -log [Ka] we obtain the Henderson-Hasselbalch equation:
-6-
[A-]
pH = pKa + log ─── ------ (2) (Henderson-Hasselbalch equation)
[HA]
If the pKa for a weak acid is known, this equation can be used to calculate the ratio
of the unprotonated to the protonated form at any pH. From this equation, you can see
that a weak acid is 50% dissociated at a pH equal to its pKa. Most of the metabolic
carboxylic acids have pKa-values between 2 and 5, depending on the other groups on
the molecule. The pKa reflects the strength of an acid. Acids with a pKa of 2 are
stronger acids than those with a pKa of 5 because, at any pH, a greater proportion is
dissociated.
 Buffers
A buffer is a solution that resists change in pH following the addition of an
acid or base. A buffer can be created by mixing a weak acid (HA) with its
conjugate base (A-). If an acid such as HCl is added to such a solution, A- can
neutralize it, in the process being converted to HA. If a base is added, acid can
neutralizes it, in the process being converted to A-. 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, (the amounts of HA and A- are equal, the pH is equal to the pKa). As
shown in Figure 1.9, a solution containing acetic acid (HA = CH3-COOH) and
acetate (A- = CH3-COO-) with a pKa of 4.8 resists a change in pH from pH 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. At pH values
greater than the pKa, the deprotonated base form (CH3-COO-) is the predominant
species in solution).
Figure (7) the titration curve
for acetic acid.
-7-
 Titration curve of an amino acid
When an amino acid is dissolved in water, it exists in solution as the dipolar ion,
or zwitterion (German for “hybrid ion”). A zwitterion can act as either an acid
(proton donor) or a base (proton acceptor):
Substances having this dual nature are amphoteric and are often called
ampholytes (from “amphoteric electrolytes”). A simple monoamino monocarboxylic
α- amino acid, has two groups, the carboxyl group and the amino group, that can yield
or accept protons as shown in figure (8).
Figure (8) Ionic form of
glycine in acidic, neutral
and basic solutions
1. Dissociation of the carboxyl group: The titration curve of an amino acid can be
analyzed in the same way as described for acetic acid. Consider Glycine, for
example, which contains both an α-carboxyl and an α-amino group. At a low
(acidic) pH, both of these groups are protonated (as shown in Figure 8). As the pH
of the solution is raised, the -COOH group of form 1 can dissociate by donating a
proton to the medium. The release of a proton results in the formation of the
carboxylate group,-COO-. This structure is shown as form 2, which is the dipolar
form of the molecule (This form, also called a zwitterion, is the isoelectric form
of glycine that has an overall charge of zero).
2. Application of the Henderson-Hasselbalch equation: 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 glycine in the
same way as described for acetic acid.
[H+] [Form2]
K1 = ─────────
[Form1]
Where form1 is the fully protonated form of glycine and Form 2 is the isoelectric
form of glycine (see Figure 8). This equation can be rearranged and converted to its
logarithmic form to yield:
[Form2]
pH = pK + log ─────
[Form1]
-8-
3. Dissociation of the amino group: The second titratable group of glycine is the
amino (-NH3+) group which is a much weaker acid than the (-COOH) group and,
therefore, has a much smaller dissociation constant, K2, (Its pKa is therefore
larger). Release of a proton from the protonated amino group of form 2 results in
the fully deprotonated form of glycine, form 3 (see Figure 8).
4. pKs of glycine: The sequential dissociation of protons from the carboxyl and
amino groups of glycine is summarized in Figure (8). Each titratable group has a
pKa that is numerically equal to the pH at which exactly one half of the protons
have been removed from that group. The pKa for the most acidic group (-COOH)
is pK1, whereas the pKa for the next most acidic group (-NH3+) is pK2.
5. Titration curve of glycine: By applying the Henderson-Hasselbalch equation to
each dissociable acidic group, it is possible to calculate the complete titration
curve of a weak acid. Figure (9) shows the change in pH that occurs during the
addition of base to the fully protonated form of glycine (form 1) to produce the
completely deprotonated molecule (Form 3). Note the following:
Figure (9) Titration curve of
glycine
a. Buffer pairs: 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.
b. When pH = pK: When the pH is equal to pK1 (2.34), equal amounts of forms 1
and 2 of glycine exist in solution. When the pH is equal to pK2 (9.6), equal amounts
of forms 2 and 3 are present in solution.
c. Isoelectric point: At neutral pH, glycine exists predominantly as the dipolar form 2
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,
in which the sum of the positive charges equals the sum of the negative charges. For
-9-
an amino acid, such as glycine, that has 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
= [2.34 + 9.6]/2 = 5.97, see Figure 8). The pI is thus midway between pK1 (2.34) and
pK2 (9.6). It corresponds to the pH at which Form 2 (with a net charge of zero)
predominates, and at which there are also equal amounts of Form 1 (net charge of +1)
and Form 3 (net charge of -1).
6. Net charge of amino acids at neutral pH: At physiologic pH, all 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 defined as amphoteric, and
are referred to as ampholytes (amphoteric electrolytes).
 Other applications of the Henderson-Hasselbalch equation:
The Henderson-Hasselbalch equation can be used to calculate how the pH of a
physiologic solution responds to changes in the concentration of weak acid and/or its
corresponding "salt" form. For example, in the bicarbonate buffer system, the
Henderson-Hasselbalch equation predicts how shifts in [HCO3 -] and pCO2 influence
pH (Figure 10-A).
Figure (10) The Henderson-Hasselbalch equation is used to predict: (A) Change in pH
as [HCO3 -] and pCO2 are altered, (B) the ionic form of drugs.
- 10 -
The equation is also useful for calculating the abundance of ionic forms of acidic
and basic drugs. For example, most drugs are either weak acids or weak bases (Figure
10-B). Acidic drugs (HA) release a proton (H+) causing a charged anion (A-) to form
(HA
A- + H+ ). Weak bases (BH+) can also release a H+ . However, the
protonated form of basic drugs is usually charged, and the loss of a proton produces
the uncharged base (B) as follow (BH+
B + H+ ).
A drug passes through membranes more readily if it is uncharged. Thus, for a
weak acid, the uncharged HA can permeate through membranes and A- cannot. For a
weak base, such as morphine, the uncharged form, B, penetrates through the cell
membrane and BH+ does not. Therefore, the effective concentration of the permeable
form of each drug at its absorption site is determined by the relative concentrations of
the charged and uncharged forms. The ratio between the two forms is, in turn,
determined by the pH at the site of absorption, and by the strength of the weak acid or
base, which is represented by the pKa of the ionizable group. The HendersonHasselbalch equation is useful in determining how much drug is found on either side
of a membrane that separates two compartments that differ in pH, for example, the
stomach (pH 1.0-1.5) and blood plasma (pH 7.4).
 Summery
■ The 20 amino acids commonly found as residues in proteins contain an α-carboxyl
group, an α-amino group, and a distinctive R group substituted on the α-carbon atom.
The α-carbon atom of all amino acids except glycine is asymmetric, and thus amino
acids can exist in at least two stereoisomeric forms. Only the L stereoisomers are
found in proteins.
■ Other less common amino acids also occur, either as constituents of proteins
(through modification of common amino acid residues after protein synthesis) or as
free metabolites.
■ Amino acids are classified into five types on the basis of the polarity and charge (at
pH 7) of their R groups.
■ Amino acids vary in their acid-base properties and have characteristic titration
curves. Monoamino monocarboxylic amino acids (with nonionizable R groups) are
diprotic acids (+H3NCH(R)COOH) at low pH and exist in several different ionic
forms as the pH is increased. Amino acids with ionizable R groups have additional
ionic species, depending on the pH of the medium and the pKa of the R group.
 References
1. Lippincott Biochemistry Forth Edition (2010).
2. Lehninger Principles of Biochemistry, Fourth Edition (2006).
3. Robert K. Murray, MD, PhD. ‘Harper’s Illustrated Biochemistry’. TwentyEighth Edition. 2009.
4. Marks' Essential Medical Biochemistry, 2nd Edition Copyright 2007
Lippincott Williams & Wilkins.
- 11 -
‫الخالصة‬
‫ِ‬
‫البروتين تحتوي على مجموعة‬
‫‪ ‬هنالك (‪ )20‬حامض أميني تمثل الوحدات البنائية في‬
‫ذرة‬
‫كاربوكسيل ومجموعة أمين‪ ،‬و مجموعة هيدروكاربونية جميعها متصل على ّ‬
‫الكربون ألفا‪.‬وتكون ذرة الكربون ألفا غير متَ ِ‬
‫ناظرةُ في ُك ّل األحماض األمينية ماعدا‬
‫ّ‬
‫ُ‬
‫ِ‬
‫جد على األقل بشكلين فراغيين‬
‫َن تَتوا َ‬
‫الجاليسين ‪ ،‬ومثل هذه األحماض أألمينيه ُي ْمك ُن أ ْ‬
‫احدهما صورة مرآتيه لآلخر ويعرفان باليميني واليساري‪ .‬فقط الشكل اليساري يدخل في‬
‫ِ‬
‫البروتين‪.‬‬
‫تركيب‬
‫‪ ‬أحماض أمينيه أخرى ‪ ،‬توجد بشكل نادر في بعض البروتينات حيث يتم تعديلها بعد‬
‫حر‪.‬‬
‫تصنيع البروتين‪ .‬أَو توجد كمركب أيضي ّ‬
‫اع على أساس قطبية وشحنة المجموعة‬
‫ف إلى خمسة أنو ِ‬
‫‪ ‬األحماض األمينية تُ ّ‬
‫صن ُ‬
‫ذرة الكربون ألفا (في المحاليل المتعادلة)‪.‬‬
‫الهيدروكاربونية المتصلة ب ّ‬
‫ِ‬
‫قاعدية وَلها منحنيات تسحيح‬
‫تفاوت األحماض األمينية في خصائص الحامضية‪ ِِ -‬ال‬
‫‪ ‬تَ ُ‬
‫ممي ِزة‪ .‬األحماض األمينية أحادية الكاربوكسيل واألمين (المجموعة الهيدروكاربونية‬
‫ِ‬
‫ذرة الكربون ألفا ِ‬
‫امض ثنائية البروتون في المحاليل‬
‫غير قابلة‬
‫للتأين) هي حو َ‬
‫المتصلة ب ّ‬
‫إن‬
‫منخفضة الحامضية‪ ,‬وتتغير إلى أشكال أيونية مختلفة بازدياد قاعدية الوسط‪ّ .‬‬
‫األحماض األمينية التي تمتلك مجموعة هيدروكاربونية قابلة للتأ ِ‬
‫ين يكون َلها مركبات‬
‫ِ‬
‫الوسط وثابت التحلل للمجموعة الهيدروكاربونية‪.‬‬
‫أيونية إضافية‪ ،‬اعتمادا على حامضية‬
‫‪- 12 -‬‬