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Amino Acids and Peptides

Concept 3.1: Amino Acids Are Three-Dimensional
Introduction
We have many amino acids:
➔ only 20 are usually found in proteins.
➔ The general structure of amino acids includes an amino group and a carboxyl group, both of which
are bonded to the alpha carbon (the one next to the carboxyl group).

The alpha-carbon is also bonded to:

1- Amino group: —NH2 functional group
2- Carboxyl group: —COOH functional group that disassociates to give the
carboxylate anion, —COO–, and a hydrogen ion.
3- The side chain group or R group
Side chain group: Portion of an amino acid that determines its identity.
4- Hydrogen.

Stereochemistry of Amino Acids

Overlook:
➔ the most important properties of these compounds is their three-dimensional shape, or
stereochemistry.
➔ Every object has a mirror image.
➔ The chiral carbon causes a mirror image compounds.
➔ Chiral carbon means that we this carbon has 4 different groups attached to it.
➔ Stereoisomers: molecules that differ from each other only in their configuration (three-dimensional
shape); also called optical isomers.

Details related to Amino Acids.

➔ occurs in all amino acids except glycine.
➔ Glycine has two hydrogen atoms bonded to the -carbon; in other words, the side
chain (R group) of glycine is hydrogen. Glycine is not chiral (or, alternatively, is
achiral) because of this symmetry.

➔ Two stereoisomers of amino acids are designated as L- and D-amino acids based
on similarity to glyceraldehyde.

➔ The terminology comes from the Latin words laevus and dexter, meaning “left” and “right,”
respectively, which comes from the ability of optically active compounds to rotate polarized light to
the left or the right.

➔ Amino acids are tetrahedral structures

Concept 3.2: Structures and Properties of Amino

Introduction
Why are amino acid side chains so important?
➔ The R groups make Amino Acids different.
➔ the side chain of the simplest amino acid, glycine, is a hydrogen atom, and in this case alone two
hydrogen atoms are bonded to the alpha-carbon.

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➔ Side-chain carbon atoms are designated with letters of the Greek alphabet, counting from the -
carbon. These carbon atoms are, in turn, the beta -, Gamma-, delta-, and Epsilon ε-carbons.
➔ a terminal carbon atom is referred to as the omega carbon, from the name of the last letter of the
Greek alphabet.

Classification of the Amino Acids:

What is the main groups of Amino Acids?
1- The first of these is the polar or nonpolar nature of the side chain.
2- The second depends on the presence of an acidic or basic group in the side chain.

A- Nonpolar Amino Acids.

➔ One group of amino acids has nonpolar
side chains.
➔ This group consists of glycine, alanine,
valine, leucine, isoleucine, proline,
phenylalanine, tryptophan, and
methionine.

➔ In several members of this group—

namely alanine, valine, leucine, and
isoleucine—each side chain is an aliphatic
hydrocarbon group.

➔ Proline has an aliphatic cyclic structure;

proline is often called an Imino acid. It is
the only amino acid whose side chain
loops back onto its own backbone

➔ In phenylalanine, the hydrocarbon group

is aromatic, (it contains a cyclic group
similar to a benzene ring).

➔ In tryptophan, the side chain contains an

indole ring, which is also aromatic.

➔ In methionine, the side chain contains a sulfur atom in addition to aliphatic hydrocarbon
groupings.

➔ Leucine has an extra methylene group (-CH2-) than

Valine.

B- Polar-Neutral Amino Acids

➔ Group of amino acids that has polar side chains that are
electrically neutral at neutral pH.
➔ This group includes serine, threonine, tyrosine, cysteine,
glutamine, and asparagine.
➔ In serine and threonine, the polar group is a hydroxyl
(-OH) bonded to aliphatic hydrocarbon groups,

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➔ The hydroxyl group in tyrosine is bonded to an aromatic hydrocarbon group, which eventually
loses a proton at higher pH. (The hydroxyl group in tyrosine is a phenol, which is a stronger acid
than an aliphatic alcohol). As a result, the side chain of tyrosine can lose a proton in a titration,

➔ cysteine, the polar side chain consists of a thiol group (S—H), which can react with other cysteine
thiol groups to form disulfide (—S—S—) bridges in proteins in an oxidation reaction So, The thiol
group can also lose a proton.

➔ The amino acids glutamine and asparagine have amide groups, which are derived from carboxyl
groups, in their side chains. Amide bonds do not ionize in the range of pH usually encountered in
biochemistry.

➔ Glutamine and asparagine can be considered derivatives of the Group 3 amino acids, glutamic acid
and aspartic acid, respectively; those two amino acids have carboxyl groups in their side chains.

C- acidic Amino Acids

➔ Amino Acids have carboxyl groups in
their side chains in addition to the one
present in all amino acids.
➔ Include glutamic acid and aspartic acid.

➔ Carboxyl group can lose a proton,

forming carboxylate anions.

➔ The side chain of each of these two amino acids is negatively charged at neutral pH.

D- Basic Amino Acids

➔ They have basic side chains, and the side chain in
all three is positively charged at or near neutral
pH.
➔ They are Three amino acids—histidine, lysine,
and arginine.

➔ In lysine, the side-chain amino group is attached

to an aliphatic hydrocarbon tail.

➔ In arginine, the side-chain basic group, the

guanidino group, is more complex in structure than the amino group, but it is also bonded to an
aliphatic hydrocarbon tail.

➔ In free histidine, the pKa of the side-chain imidazole group is 6.0, which is not far from
physiological pH.

➔ Both Lys and Arg have long side chains with a positively charged amine group.

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E- Uncommon Amino Acids
➔ Derived from the common amino acids
➔ They are produced by modification of the parent amino acid after the protein is synthesized by the
organism in a process called posttranslational modification.

➔ Hydroxyproline and hydroxylysine differ from the parent amino acids in that they have hydroxyl
groups on their side chains.

➔ they are found only in a few connective-tissue proteins, such as collagen.

➔ Thyroxine differs from tyrosine in that it has an extra iodine-containing aromatic group on the side
chain.

➔ Thyroxine is formed by posttranslational modification of tyrosine residues in the protein

thyroglobulin. Thyroxine is then released as a hormone by proteolysis of thyroglobulin.

Properties of Amino Acids

Acidity: alpha–COOH Groups and alpha—NH3+ Groups
➔ Average pKa of an alph–carboxyl group is 2.19, which makes it a considerably stronger acid than
acetic acid (pKa 4.76)
➔ Greater acidity is due to the electron-withdrawing inductive effect of the –NH3+ group
➔ Compared with a value of 10.76 for a 2° alkylammonium ion, average value of pKa for an alpha–
NH3+ group is 9.47.

Basicity: alpha–NH3+ groups

➔ Guanidine group - Side chain of arginine is a considerably stronger base than an aliphatic amine
➔ Basicity of the guanidino group is attributed to the large resonance stabilization of the protonated
form relative to the neutral form
➔ Imidazole group - Side-chain imidazole group of histidine is a heterocyclic aromatic amine

Question: pKa of the side-chain imidazole group of histidine is 6.0, What is the ratio of
uncharged to charged side chains at pH 7.0?
Solution
Ratio is 10:1 because the pH is one unit higher than the pKa

Names and Abbreviations of the Common Amino Acids

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Concept 3.3: Amino Acids Can Act as Both Acids and Bases
In a free amino acid, the carboxyl group and amino group of the general structure are charged at
neutral pH—the carboxylate portion negatively and the amino group positively.

Amino acids without charged groups on their side chains exist in neutral solution as zwitterions with no
net charge. A zwitterion has equal +ve & -ve charges; in solution, it is electrically neutral.

Note: Neutral amino acids do not exist in the form NH2-CHR-COOH (i.e., without charged groups)

Titration of Amino Acids

What happens when we titrate an amino acid?
When an amino acid is titrated, its titration curve indicates the reaction of each functional group with a
hydrogen ion.

In alanine as an example
➔ the carboxyl and amino groups are the two
titratable groups.

➔ At very low pH, alanine has a protonated

(and thus uncharged) carboxyl group and a
positively charged amino group that is also
protonated.

➔ Under these conditions, the alanine has a

net positive charge of 1.

➔ As base is added, the carboxyl group loses its proton to become a

negatively charged carboxylate group, and the pH of the solution
increases. Alanine now has no net charge. See figure above

➔ As the pH increases still further with the addition of more base,

the protonated amino group (a weak acid) loses its proton, and the
alanine molecule now has a negative charge of 1. The titration
curve of alanine is that of a diprotic acid, see figure.

Another example in histidine

➔ the imidazole side chain also contributes a titratable group. At very low pH values, the histidine
molecule has a net positive charge of 2 because both the imidazole and amino groups have positive
charges.

➔ As base is added and the pH increases, the carboxyl group loses a proton to become a carboxylate as
before, and the histidine now has a positive charge of 1. See figure below

➔ As still more base is added, the charged imidazole group

loses its proton, and this is the point at which the histidine
has no net charge.

➔ At still higher values of pH, the amino group loses its

proton, as was the case with alanine, and the histidine
molecule now has a negative charge of 1. The titration curve
of histidine is that of a triprotic acid, see figure.

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Like the acids the titratable groups of each of the amino acids have characteristic pKa values:
➔ The pKa values of -carboxyl groups are fairly low, around 2.
➔ The pKa values of amino groups are much higher, with values ranging from 9 to 10.5.
➔ The pKa values of side-chain groups, including side-chain carboxyl and amino groups, depend on the
groups’ chemical nature.

The following table lists the pKa values of the titratable groups of the amino acids.

How do we classify amino acids?

classification of an amino acid as acidic or basic
depends on:
1- the pKa of the side chain
2- chemical nature of the group.

➔ Histidine, lysine, and arginine are considered

basic amino acids because each of their side
chains has a nitrogen-containing group that can
exist in either a protonated or deprotonated form

Note: although histidine has a pKa in the acidic

range it is considered as a basic.

➔ Aspartic acid and glutamic acid are considered

acidic because each has a carboxylic acid side
chain with a low pKa value.

These groups can still be titrated after the amino acid is incorporated into a peptide or protein, but the
pKa of the titratable group on the side chain is not necessarily the same in a protein as it is in a free
amino acid. In fact, it can be very different. For example, a pKa of 9 has been reported for an aspartate
side chain in the protein thioredoxin.
‫ ممكن‬،‫بالبوتي‬
‫األمين حر مش شط تكون نفسها ر‬
‫ي‬ ‫ للسايد تشاين لما يكون الحمض‬pKa ‫بيحكيل أنه ال‬
‫ي‬ ‫كل القصة وما فيها‬
‫ زي لما يكون حر‬3.86 ‫ مش‬9 ‫ه‬‫ للسايد تشاين تبعها ي‬pKa‫ومعطين مثال الثيوريدوكسن "بروتي" فيه حمض االسبارتك و‬
‫ي‬ ‫تختلف‬

The fact that amino acids, peptides, and proteins have different pKa values gives rise to the possibility
that they can have different charges at a given pH.

➔ Alanine and histidine, for example, both have net charges of -1 at high pH (above 10); the only
charged group is the carboxylate anion.
➔ At lower pH (around 5) alanine is a zwitterion with no net charge, but histidine has a net charge of 1
at this pH because the imidazole (amino) group is protonated.

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This property is useful in electrophoresis, a common method for separating molecules in an electric
field. This method is extremely useful in determining the important properties of proteins and nucleic
acids

Amino Acid Isoelectric Point/ pH

➔ It is the pH at which a molecule has no net charge, symbolled as pI.
➔ At its isoelectric pH, a molecule will not migrate in an electric field. This property can be put to use
in separation methods.
➔ The pI of an amino acid can be calculated by the following equation:

Most of the amino acids have only two pKa values, so this equation is easily used to calculate the pI.
While For the acidic and basic amino acids, however, we must be sure to average the correct pKa values.

How to know which pKa value shall I use to calculate pI in case of acidic or basic amino acid?
The easiest way, not only for acidic or basic even for a polypeptide chain. Steps:
1- Start with a fully protonated amino acid or polypeptide chain and write its charge
2- Organize the pKa value from the lowest to the highest pKa value
3- Then start lowering charge by 1 (as we lose H+ when increasing pH)
4- Number of arrows should be equal to number of pKa values, each arrow represents a pKa value
5- Now write pKa values from lowest to highest from left to right
6- Take the pKa values before and after isoelectric point then apply the equation

Example: what is the pI of arginine?

Simply arginine is a basic amino acid→ 2 amine group → at low pH it has a net charge of +2
It has a 3 pKa values, pKa of -amino = 9.04. pKa of -COOH =2.17/ pKa of R group= 12.48
‫ر‬
12.48 ‫ واخبا‬9.04 ‫ بعدين‬2.17 ‫والبتيب تبعهم تصاعديا رح يكون‬
Now charges as 2.17 9.04 12.48 pKa values
+2 → +1 → 0 → -1
so the pKa values before and after the point are Isoelectric point
9.04 & 12.48 and they are the proper pKa to calculate pI
Now, pI=(9.04+12.48)/2=10.76. so at pH =10.76 the arginine will have a net charge equal to ZERO
‫تبع‬ ‫ر‬
‫ لكل التايببل قروبز بالمركب ي‬pKa‫ وبعدين برتب قيم ال‬،pH ‫اش بشوف شحنة المركب عند اقل‬ ‫ انه انا اول ي‬،‫مخترص القصة‬
‫وف‬ ‫ر‬
‫) ي‬pKa‫ بعدد قيم ال‬1 ‫ منها لحد ما يخلصوا التايببل قروبز (يع ين بنقص‬1 ‫ بعدين بجيب شحنة المركب وببلش انقص‬،‫تصاعديا‬
pI‫ وهيك بطلع ال‬2 ‫ بجمعهم وبقسمهم ع‬،‫ قبل الصفر وا يل بعد‬pKa‫ رفبوح ماخذ قيمة ال‬pKa ‫بمثل قيمة‬‫ي‬ ‫النهاية كل سهم‬

Question: Which of the following amino acids has a net charge of +2 at low pH? Which has a net
charge of -2 at high pH? Aspartic acid, alanine, arginine, glutamic acid, leucine, lysine.
Answer:
Arginine and lysine have net charges of +2 at low pH because of their basic side chains; aspartic acid
and glutamic acid have net charges of -2 at high pH because of their carboxylic acid side chains. Alanine
and leucine do not fall into either category because they do not have titratable side chains.

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Concept 3.4: The Peptide Bond
Individual amino acids can be linked by forming covalent
bonds. The bond is formed between the -carboxyl group
of one amino acid and the -amino group of the next one.
Water is eliminated in the process, and the linked amino
acid residues remain after water is eliminated (see figure).
this bond is called peptide bond.

What are Peptides?

compounds formed by linking small numbers of amino
acids, ranging from two to several dozen.

In a protein, many amino acids (usually more than a

hundred) are linked by peptide bonds to form
a polypeptide chain (see the second figure).

Another name for a compound formed by the reaction

between an amino group and a carboxyl group is an
amide.

The carbon–nitrogen bond formed when two amino

acids are linked in a peptide bond is usually written as a single bond, with one pair of electrons shared
between the two atoms.

With a simple shift in the position of a pair of electrons, it is quite possible to write this bond as a
double bond. This shifting of electrons is well known in organic chemistry and results in resonance
structures, structures that differ from one another only in the positioning of electrons.

The positions of double and single bonds in one resonance structure are different from their positions in
another resonance structure of the same compound.

No single resonance structure actually represents the

bonding in the compound; instead all resonance
structures contribute to the bonding situation.

The peptide bond can be written as a resonance hybrid

of two structures (see figure), one with a single bond
between the carbon and nitrogen and the other with a
double bond between the carbon and nitrogen.

Characteristics of peptide bond

1- It has partial double bond character→the peptide group that forms the link between the two amino
acids is planar.
2- stronger than an ordinary single bond because of this resonance stabilization.

This structural feature has important implications for the three-dimensional conformations of peptides
and proteins. There is free rotation around the bonds between the --carbon of a given amino acid
residue and the amino nitrogen and carbonyl carbon of that residue, but there is no significant rotation
around the peptide bond. This stereochemical constraint plays an important role in determining how
the protein backbone can fold.

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Few definitions already mentioned
➔ Residues: portions of monomer units included in polymers after splitting out water between the linked
monomers
➔ peptide bond: an amide bond between amino acids in a protein
➔ peptides: molecules formed by linking two to several dozen amino acids by amide bonds
➔ polypeptide chain: the backbone of a protein; it is formed by linking amino acids by peptide (amide) bonds
➔ resonance structures: structural formulas that differ from each other only in the position of electrons

Concept 3.5: Small Peptides with Physiological Activity

proteins and peptides play a number of biochemical roles.

What are some biological functions of small peptides?

One of the most important of these roles is that of hormones. Also, other classes of compounds,
particularly steroids, can be hormones. The notoriety of steroid hormones in doping scandals in sports
can obscure the fact that peptides also can be hormones. We can take a quick look at peptide hormones
now to prepare the way for later discussions.

Some important peptide hormones have cyclic structures. Two

well-known examples with many structural features in common are
oxytocin and vasopressin (see figure).

In each, there is an -S-S- bond responsible for the cyclic structure.

Each of these peptides contains nine amino acid residues, each has
an amide group (rather than a free carboxyl group)

at the C-terminal end, and each has a disulfide link between

cysteine residues at positions 1 and 6.

The difference between these two peptides is that oxytocin has an

isoleucine residue at position 3 and a leucine residue at position 8,
and vasopressin has a phenylalanine residue at position 3 and an
arginine residue at position 8.

Both of these peptides have considerable physiological importance

as hormones

Biochemical Connections
Physiology- Peptide Hormones—Small Molecules with Big Effects
Both oxytocin and vasopressin are peptide hormones.

Oxytocin induces labor in pregnant women and controls contraction of uterine muscle. During
pregnancy, the number of receptors for oxytocin in the uterine wall increases. At term, the number of
receptors for oxytocin is great enough to cause contraction of the smooth muscle of the uterus in the
presence of small amounts of oxytocin produced by the body toward the end of pregnancy.

The fetus moves toward the cervix of the uterus because of the strength and frequency of the uterine
contractions. The cervix stretches, sending nerve impulses to the hypothalamus. When the impulses
reach this part of the brain, positive feedback leads to the release of still more oxytocin by the posterior
pituitary gland.

The presence of more oxytocin leads to stronger contractions of the uterus so that the fetus is forced
through the cervix and the baby is born.

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Oxytocin also plays a role in stimulating the flow of milk in a nursing mother (‫)األم المرضعة‬. The process
of suckling sends nerve signals to the hypothalamus of the mother’s brain. Oxytocin is released and
carried by the blood to the mammary glands. Th presence of oxytocin causes the smooth muscle in the
mammary glands to contract, forcing out the milk that is in them. As suckling continues, more hormone
is released, producing still more milk.

On the other hand, Vasopressin plays a role in the control of blood pressure by regulating contraction
of smooth muscle of the blood vessels. Like oxytocin, vasopressin is released by the action of the
hypothalamus on the posterior pituitary and is transported by the blood to specific receptors.

Vasopressin stimulates reabsorption of water by the kidneys, thus having an antidiuretic effect. More
water is retained, and the blood pressure increases.

Although the relationships between oxytocin, childbirth, and lactation and that between vasopressin
and blood pressure have been known for decades, recently even more interesting effects of these simple
peptides have been discovered.

In mammals, including humans, both are neuropeptides that affect behavior, especially social
interactions. Abnormal social behaviors, such as pathological trusting found in Williams–Beuren
syndrome, social isolation in depression, and diminished social cognition in autism negatively affect the
lives of those who suffer from these diseases.

Until recently, sorting out the myriad (‫ )ال تعد وال تحص‬effects of neurochemistry on actual behavior was
too daunting.

Neuropeptides, including oxytocin and vasopressin, have moved to the front of the hormones thought to
be involved in social behaviors. These peptides affect personality, trust, altruism, social bonding, and
our ability to recognize and understand the facial expressions and feelings of others.

In many species, including humans, oxytocin influences female social and sexual behaviors, including
intercourse, maternal attachment, and pair bonding.

In males, vasopressin influences erection, ejaculation, aggression, territoriality, and pair bonding.

There is not a hard and fast split between these two peptides in the sense that one is a female
neuropeptide and the other is a male one. Both peptides have behavioral roles in both genders.

Studies can involve many techniques. In nonhuman mammals, manipulation of hormone levels or
hormone receptor levels can allow the study of behavioral effects. For example, in rats, infusion of
oxytocin into the brain stimulates maternal behavior in virgin rats that would normally ignore or attack
pups.

Manipulations that blocked oxytocin receptors in the rat brain reduced maternal behaviors,
such as mother–infant bonding. Only 3% to 5% of mammals are socially monogamous or even have a
distinct preference for a mate.

Administration of oxytocin has been shown to introduce pair bonding and mate preference in mammals
not traditionally monogamous, whereas blockage of oxytocin receptors has the opposite effect in those
monogamous species studied.

In male prairie voles (‫الباري‬

‫)فأر ر‬, administration of vasopressin increases monogamy-related behaviors,
such as paternal care, mate guarding, and selective mate preference.

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The study has gone to the genetic level where scientists have isolated specific genes for vasopressin
receptors and subsequently have been able to correlate behavior to variations in these genes. Of course,
with humans we cannot just inject peptides into brains and block receptors so easily.

Other techniques have to be employed. One of those involved nasal inhalation of these neuropeptides.

But how to check actual behavior in a controlled setting?

One way used a game involving economic gains and losses by individuals and teams. Participants were
playing a game and making decisions that would better their results and those of their team,
but what was really being tested was how their behaviors changed when they inhaled the peptides.

Several conclusions were drawn—oxytocin tends to create trust between humans. Those who inhaled
oxytocin were more likely to make decisions during the game that benefited others, especially in their
team.
In males, the hormone was a double-edged sword, however. It did tend to stimulate trust and altruistic
behaviors but only toward the males’ specific group that they identified with. It tended to make the
same males less trusting of outsiders. Even when there was a betrayal by a partner during the game,
those who inhaled oxytocin were more likely to be forgiving and not punish the offender in the next
round. Those who did not inhale the oxytocin were more likely to seek revenge in the next round.

One in 68 children in the United States can be characterized as having one of the autism spectrum
disorders (ASDs), yet, at present, no drugs exist to treat the debilitating social defects found.

Oxytocin has been the focus of much research in the last few years and is seen as one of the more
hopeful prospects for a treatment.

In individuals with ASD, nasal inhalation of oxytocin has, in some studies, shown temporary
improvements in social cognition, empathy, and reciprocity.

Unfortunately, results are still inconclusive because other studies show no effects.

Despite the lack of clarity, oxytocin can be found sold on the Internet as “liquid trust,” where it is
marketed as a romance enhancer, perhaps the first “love potion” actually based on some science. And
just this year, man’s best friend was thrown into the equation.

Studies show that humans and dogs release oxytocin when they gaze into each other’s eyes, perhaps
accounting for why many humans form bonds with their animals that seem as strong as those with
other humans .

The same studies noted that this may have been the departure between wolves and domestic dogs,
as wolves do not display this behavior and have much less interest in staring lovingly into a human’s
eyes.

Although much research is still needed, the results to date also bring up some interesting ethical
questions. Would it be fair, for example, for a salesman to wear a cologne that gave off oxytocin right
before he tried to sell you encyclopedias? Would it give males an unfair advantage in the dating and
mating game if they wore the same cologne?

One thing is clear, however—oxytocin and vasopressin are much more than nine simple amino acids

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