Amino Acids and the Peptide Bonds

Amino Acids
Amino acids are organic compounds that combine to form proteins. An amino acid
is an organic compound containing an amino group and an acidic group, usually, but not
always, a carboxylic acid. This description fits a very large number of compounds, most
of which are non-physiological. In addition, many physiologically important amino acids
are not used in proteins. However, in biochemistry, the term “amino acid” generally refers
to one of the 20 types of monomeric units most commonly used to construct proteins.

General Structure
An amino acid contains both a carboxylic group and an amino group. Amino acids
that have an amino group bonded directly to the alpha-carbon are referred to as alpha
amino acids. The simplest representation of an alpha amino acid is shown below.

Every alpha amino acid has a carbon atom, called an alpha carbon, Cα; bonded
to a carboxylic acid, –COOH, group; an amino, –NH2, group; a hydrogen atom; and an
R group that is unique for every amino acid. If you notice in the structure above, Cα is a
chiral center, that is to say, this carbon atom is attached to four different groups. Chirality
refers to a molecule that has optical activity, so amino acids are optically active molecules.
The only exception is glycine, the simplest amino acid, in which R-H.

L and D Amino Acids

Every amino acid (except glycine) can occur in two isomeric forms, because of the
possibility of forming two different enantiomers (stereoisomers) around the central carbon
atom. By convention, these are called L- and D- forms, analogous to left-handed and
right-handed configurations.
 Only L- amino acids are manufactured in cells and incorporated into proteins.
Some D- amino acids are found in the cell walls of bacteria, but not in bacterial proteins.
Glycine, the simplest amino acid, has no enantiomers because it has two hydrogen atoms
attached to the central carbon atom. Only when all four attachments are different can
enantiomers occur.

Acid-Base Properties of Amino Acids

An amino Acid is a molecule that contains two functional groups, a basic amine group
and an acidic carboxylic acid group.
Amino acids are amphoteric; which means they can react either as an acid or as a base.
It can have several forms depending on the pH of a system. At low pH or acidic condition,
the amino group (-NH2) is protonated by the addition of a proton (H+) from the acid. While
at high pH or basic conditions, the carboxylic acid (-COOH) is deprotonated by the
removal of a proton.
Zwitterions is compound with no overall electrical charge, but
which contains separate parts which are positively and
negatively charge. In the zwitterion form, the function groups
have different charges yet doesn’t have a net charge.

Isoelectric point (pl), is the pH at which a particular molecule

carries no electrical charged or is electrically neutral in the static
mean.
In more acidic media (pH<pl), the concentration of ions increases while the concentration
of the zwitterion decreases.
In a more basic (pH>pl), the concentration of negative ions increases while the
concentration of the zwitterion decrease. And more than 98% of the amino acids is in
zwitterion form with the range of +-2 of the pl
Types of Amino Acids
A. Essential Amino Acids

Essential amino acids cannot be made by the body. As a result, they must
come from food. The nine amino acids humans cannot synthesize are
phenylalanine, valine, threonine, tryptophan, methionine, leucine, isoleucine,
lysine, and histidine.

B. Non-Essential Amino Acids

Nonessential means that our bodies produce an amino acid, even if we do

not get it from the food we eat. Nonessential amino acids include: alanine,
asparagine, aspartic acid, and glutamic acid.

C. Conditional Amino Acids

Conditional amino acids are usually not essential, except in times of illness
and stress. Conditional amino acids include: arginine, cysteine, glutamine,
tyrosine, glycine, ornithine, proline, and serine.

Classification of Amino Acids (Based on the nature of the R group)

Non-Polar / Hydrophobic Amino Acids
Non-polar amino acids contain hydrophobic side chains. These are the amino
acids alanine, valine, isoleucine, leucine, and methionine. Note that in each case, the side
chain consists of an aliphatic carbon chain. Although methionine has a thioether link prior
to the terminal methyl group, this sulfur has generally similar properties to a methylene
group.

An examination of the valine and isoleucine structures (above) reveals that these two
compounds have two substituents on their β-carbon. This means that residues contain
two chiral centers (a minor point), and, more importantly, that this amino acid have greater
steric hindrance, which allows these residues fewer possible conformations while forming
part of a protein structure. These amino acids are classed as β-branched to reflect their
more restricted conformational flexibility.

Three amino acids possess aromatic rings: phenylalanine, tyrosine, and tryptophan.

Phenylalanine is a non-polar amino acid; while tyrosine and tryptophan are

borderline cases. Tyrosine is not very soluble in water but contains a polar hydroxyl group
in the para position of the phenyl ring. Because, in proteins, the tyrosine hydroxyl is often
solvent-exposed, tyrosine is frequently listed as a polar amino acid. Tryptophan is also
borderline hydrophobic/polar, because the proton attached to the indole nitrogen can act
as a hydrogen bond donor to water or other hydrogen bond acceptors. However, the
majority of the large tryptophan side-chain is non-polar.

Polar / Hydrophilic Amino Acids

A. Neutral / Uncharged
Serine and Threonine contain hydroxyl
groups. A comparison of their structures reveals
that threonine is almost identical to serine except
for the substitution of a methyl group for one of
the serine β-carbon hydrogens. The hydroxyl
groups on serine and threonine are essentially
always protonated, and therefore uncharged.

Asparagine and Glutamine contain amide groups in their side chains. Amide
groups are polar and are capable of forming hydrogen bonds with water or with other
compounds. However, amide groups do not become charged at biologically relevant pH
values.

Cysteine is structurally similar to serine, with the substitution of a sulfur atom for the
serine hydroxyl oxygen. However, the sulfhydryl group has a pKa = ~8.4, which means
that means that, at pH 7.4, about 10% of free cysteine sulfhydryl groups are deprotonated,
and therefore negatively charged. Defining the polarity of cysteine is difficult; the ionized
cysteine is polar, while the protonated form is much less polar than serine. Cysteine also
has the ability to form covalent bonds called disulfide bonds between cysteine side
chains. These disulfide bonds can be formed between cysteine molecules, or between
cysteine side-chains from within proteins. Disulfide bonds are the most common form of
covalent bond between amino acid side-chains in proteins. Note, however, that disulfide
bonds are rarely observed in intracellular proteins.

B. Acidic / Negatively Charged

Aspartic acid and Glutamic acid are the only standard amino acids with carboxylic
acid groups in their side-chains. Although the side-chain pKa depends on the local
environment, these residues are generally negatively charged, because the pKa value of
the side-chain is ~4 for both of these compounds the pKa value is typically, lower for
aspartate than for glutamate by about 0.6 pH units, but this is heavily environment
dependent in proteins.
 C. Basic / Positively Charged
Lysine and Arginine are basic amino acids that are positively charged at
physiological pH. The side-chains of these compounds contain a primary amine (in lysine)
or a guanidine group (in arginine) that can be readily protonated.

Histidine can also be protonated and is frequently grouped with lysine and
arginine for this reason.The pKa of the histidine side-chain in proteins is heavily
environment dependent and varies considerably for different proteins. The histidine side-
chain is often capable of changing its protonation state as the environment surrounding
the protein alters, which means that histidine is frequently part of pH-depending switching
mechanisms. Histidine exists in two neutral forms, δ and ε, shown below.
These are generally equivalent structures, with the only difference being the
nitrogen that bears a proton, but they exhibit different geometric constraints on hydrogen
bonding properties.
Glycine and Proline (Neither Polar or Non – Polar)
The standard scheme for amino acids classification is based on an assessment of
the relative polarity of the side chain. Glycine and proline, however, do not fit into this
standard classification scheme for amino acid side-chains. Glycine has the smallest side-
chain (a hydrogen) and is the only non-chiral amino acid. Because it effectively lacks a
side-chain, glycine has much less steric hindrance than the other amino acids. In addition,
because it effectively lacks a side-chain, the glycine sidechain does not really have a
polar or non-polar character.

Proline is often referred to as an imino acid; unique among the standard amino
acids, the proline α-amino group is actually a secondary amine. Proline has a
conformationally restricted structure, with significantly fewer possible conformations of
the α-carbon bonds than the other amino acids. Although the proline side chain appears
to be non-polar, proline has a fairly high tendency to appear on the solvent-exposed
surface of proteins. Thus, although it appears to be non-polar, in a sense proline behaves
more like a polar amino acid.

Functions and Dietary Sources

Only twenty amino acids are most normally found as compounds of human
peptides and proteins. These naturally occurring amino acids are used by cells so as to
synthesize peptides and proteins. They are typically identified by this rather generic
formula: H2NCHRCOOH.

1. Alanine
Alanine is basically a non-essential amino acid sometimes found in high levels in its
free state in human plasma. This amino acid is synthesized by reductive amination of
pyruvate and participates in sugar and acid metabolism. It is also known for increasing
immunity and providing energy for brain and central nervous system, let alone the muscle
tissue. In addition, Alanine plays a central role in glucose-Alanine cycle taking place
between tissues and liver.
 Alanine helps your body convert the simple sugar called glucose into energy you need,
while eliminating excess toxins from your liver. As you know, amino acids are the building
blocks of proteins, thus becoming a key to building muscles, and Alanine is also there in
the list, helping protect cells from being damaged during intense physical activity.
Alanine is a non-essential amino acid, i.e. a healthy body can produce it for its own
needs. However, it may become an essential amino acid which means you would need a
dietary supplementation if your body is unable to manufacture it for some reasons. In
order to avoid this deficiency, individuals with low-protein diets or eating disorders, as well
as those who suffer from liver disease or diabetes, may need to take supplements of this
amino acid. To be healthy, human body requires Alanine to process the B vitamin.
Naturally, you can get this amino acid from such sources as meat, poultry, eggs, dairy
products, and fish. Vegetarians are recommended to eat protein-rich plant foods - for
example, avocado, as they also supply Alanine.

2. Arginine
It plays an important role in the cell division and in the immune functioning. In addition,
it helps healing wounds, release hormones, and remove ammonia from your body. This
amino acid is proved to be a precursor of nitric oxide, which, as you know, causes a blood
vessel relaxation. Therefore, through the nitric oxide (NO) it becomes a mediator in
different biological systems. In addition, Arginine is an intermediate in the urea cycle,
cleaved into ornithine and urea.
Arginine may be useful under many body conditions, including colds, high blood
pressure, migraines, congestive heart failure, and even erectile dysfunction, male
infertility and sexual dysfunction in women. Many people use Arginine in order to boost
up the immune system and to improve the athletic performance - this amino acid is known
for aiding in bodybuilding. The others use it to faster recover after surgery.
This amino acid is also known to be effective in relieving leg cramping and weakness,
both conditions caused by blocked arteries. Besides, Arginine can improve kidney
function in kidney transplant patients who take cyclosporine. That is why this amino acid
is known for promoting wound healing after surgery.
3. Asparagine
Asparagine is known for its key role in the biosynthesis of glycoproteins. In addition, it
is also essential for the synthesis of many other proteins. Human nervous system also
needs this amino acid to be able to maintain an equilibrium. Asparagine increases the
resistance to fatigue and improves the smooth functioning of the liver. So, Asparagine
benefits work best in the field of nervine health and liver protection.
 Currently, Asparagine is one of the twenty most common amino acids on our planet -
one of the principals and the most abundant that help to transport nitrogen. Besides, this
amino acid is required by human body cells for the protein production. It can be produced
in the liver and is recognized worldwide for its ability to help increase the resistance to
fatigue, thus improving athletic stamina.
This amino acid is an essential component of proteins involved in signaling, neuronal
development and transmission across nerve endings. It is also necessary for
transformation of amino acid from one form to another. In addition, Asparagine is known
for its key role in the biosynthesis of glycoproteins, as well as in the synthesis of many
other proteins.
The most common typical dietary sources of this amino acid include beef, chicken,
dairy products, seafood, and eggs. As for vegetarians, they may find helpful to consume
asparagus, soy, and whole grains to get more amino acid from them.

4. Aspartic Acid
This amino acid is non-essential and widely distributed in proteins, though it is proved
to play a major role in the energy cycle of your body. This amino acid is necessary for
stamina, brain and neural health. This, in turn, is believed to boost up the production of
chemicals necessary for proper mental functioning and is recognized as an important
element removing excess toxins from the cells, especially ammonia, that damages human
liver, brain, and nervous system.
Some time ago, Aspartic acid was found to be very important in the functioning of RNA
and DNA, as well as in the production of immunoglobulin and antibody synthesis.
Aspartate is believed to help your body promote a robust metabolism. From time to time
it is used to treat depression and fatigue. This amino acid plays a key role in the citric acid
cycle (also known as Krebs cycle), within which several other amino acids and
biochemicals are formed.
Moreover, this amino acid promotes a transportation of minerals to the cells, which
are essential to form healthy RNA and DNA, Aspartic acid is a non-essential amino acid,
so your healthy body can produce its own supply. Besides, it can also be found in such
food sources as dairy, beef, poultry, sugar cane and molasses
5. Cysteine
This amino acid provides resistance to the body against all harmful effects, because
it is responsible for building up white blood-cell activity. Cysteine is also necessary for the
proper functioning of the skin and helps your body recover from surgery.
Cysteine is also used to produce Glutathione and Taurine. Since Cysteine is a non-
essential amino acid, it can be produced by humans to satisfy their bodies' demands. If,
for some reasons, your body is unable to produce this amino acid, you can find it in lots
of high-protein foods like pork, chicken, eggs, milk, and cottage cheese. Vegetarians are
recommended to pay more attention to eating garlic, granola and onions.
This amino acid is proved to be beneficial in numerous ways. First of all, it is essential
for the detoxification and for the formation of skin. Besides, it participates in the recovery
of hair and nail tissue. Then, Cysteine is used in manufacturing antioxidants and in
protecting your brain and liver from damage made by alcohol and drugs consumption and
even by a cigarette smoke. Finally, this amino acid helps protect against harmful toxins
and damages caused by radiation.
According to various researches, other benefits of Cysteine include reducing the
effects of aging on the human body. Besides, this amino acid also helps promote building
muscles, healing of severe burns, and fat burning. The list of benefits is virtually endless,
including those like the effectiveness in treating bronchitis, angina and acute respiratory
distress, and the ability to help maintain optimal health and improve immune system
functioning.
6. Glutamic Acid
This amino acid is an excitatory neurotransmitter increasing the firing of neurons in
the human central nervous system. Moreover, Glutamic acid is recognized as a major
excitatory neurotransmitter in the human brain and in the spinal cord, transformed into
Glutamine or Gamma-Aminobutyric Acid. This amino acid is necessary for proper cell
functioning, but is considered as a non-essential amino acid, because human body is able
to produce it.
Being one of the few nutrients able to pass through the blood-brain barrier, this amino
acid appears to support brain function. In other words, Glutamic acid turned out to be
human brain's primary 'food'. When it reaches the brain, it utilizes all excess ammonia,
which is a toxic waste product of metabolism, by transforming it into the amino acid called
Glutamine. In fact, this conversion is the only way our brain employs in order to be
detoxified, indicating that not only is Glutamine not toxic, but it also has some essential
antioxidant properties.
7. Glutamine
Glutamine, also known as L-Glutamine, seems to be the most active amino acid
involved in lots of metabolic processes. For example, glutamine is converted to glucose
if your body needs more glucose as an energy source. Besides, it also participates in
maintaining of a normal blood glucose level and the proper pH range. In fact, glutamine
was recognized as the most abundant free amino acid found in the human muscles and
in plasma. A human body utilizes this amino acid at high rates for rapidly dividing cells,
like leucocytes, in order to supply them with an energy, i.e., to create the best conditions
for the nucleotide biosynthesis. In other words, glutamine is vital for the proper immune
function.
 8. Glycine
This amino acid is the first of all necessary ones for a healthy digestive system,
because it helps regulate the synthesis of the bile acid utilized to help you digest fats.
This amino acid is essential for the development and quality of human skeletal muscles,
tissues, and structural integrity, as well as for the synthesis of nucleic acids.
Glycine is a non-essential amino acid, implying that our bodies can produce it. Like
many other amino acids, this one is used to help create muscle tissues and convert
glucose into energy. In addition, it is also vital for maintaining healthy central nervous and
digestive systems.
Glycine is utilized in human body to help construct normal DNA and RNA strands,
which are basically a genetic material necessary for proper cellular function and
formation. This amino acid helps prevent the breakdown of muscles, because it can boost
your body's levels of creatine - a compound helping build muscle mass. Aside from the
muscles, high concentrations of this amino acid are also found in the skin and other
connective tissues.

9. Histidine
Histidine is usually referred to as a semi-essential amino acid, as adults are normally
able to produce an adequate amount of it. However, children may not. This amino acid is
also known for being a precursor of histamine a compound that is generally released by
the immune system cells in an allergic reaction.

10. Isoleucine
The primary function of Isoleucine in the body is to boost up the energy levels and to
assist the body in recovering from strenuous physical activity. Isoleucine is considered as
an essential amino acid which is found in lots of proteins. In other words, this amino acid
must be obtained through the diet in adequate quantities in order to meet the needs of
your body. Isoleucine participates in hemoglobin synthesis, as well as in the regulation of
blood sugar and energy levels.

11. Leucine
Leucine is considered a vital amino acid for the protein synthesis and various
metabolic functions - in other words, it is an essential amino acid, which helps in regulating
the blood-sugar levels, promotes the growth and the recovery of muscle and bone tissues,
as well as the production of the growth hormone.
 12. Lysine
Lysine is recognized as an amino acid necessary as a building block for all proteins in
your body. It plays a major role in calcium absorption, as well as in helping building muscle
protein. Besides, Lysine aids in recovering from surgery or traumas and helps your body
produce hormones, enzymes, and antibodies. This amino acid was also proved to
depress the central nervous system while having antiseizure properties. In addition, this
amino acid is proved to help the human body absorb calcium, while playing an essential
role in the formation of collagen.
13. Methionine
Methionine is a sulfur-containing proteinogenic amino acid, acting as an intermediate
in the biosynthesis of different phospholipids. Methionine is a supplier of sulfur
Normally, most people do not need to take the Methionine supplementation when in
good health. Naturally, you can get some of this amino acid from food like meat, fish, and
dairy products. As for vegans and people who follow the low-protein diet, they can obtain
it from whole grains.
14. Phenylalanine
Phenylalanine is a precursor of Tyrosine, combined with which it leads to the formation
of adrenaline. In turn, adrenaline is converted into a brain chemical utilized to produce
noradrenaline responsible for promoting mental alertness and memory, and for the
elevation of mood and for the suppression of appetite.
Phenylalanine is an essential amino acid, also acting as a building block for proteins,
indicating that, although your body requires this amino acid for health, it is unable to
produce it by itself.
15. Proline
Proline is an essential component of collagen, and therefore is vital for proper
functioning of joints and tendons. Besides, this amino acid helps maintain and strengthen
heart muscles. As for atherosclerosis, Proline prevents its appearance the following way:
every time your heart beats, your arteries expand and contract unless some fat is built up
onto the walls of the arteries, which condition is known as atherosclerosis. In this case,
Proline can help your artery be able to effectively stretch out and go back to its normal
size and shape. This ability of the amino acid is essential for maintaining the appropriate
pressure levels throughout the body.
16. Serine
Serine plays an important role in various biosynthetic pathways. In addition, it is the
precursor to a number of amino acids like Glycine and Cysteine. Besides, it also helps an
enzyme catalyze its reaction - the hydrolysis of peptide bonds in polypeptides and
proteins, which is basically a major function in the digestive process.
 17. Threonine
It helps in the synthesis of glycine and serine which, in their turn, assist in the
production of collagen, elastin, and muscle tissue. In addition, Threonine aids building
strong bones and tooth enamel and speeds up a wound healing process after trauma or
surgery by boosting up the immune system. Threonine works the following way: it
combines with aspartic acid and Methionine to jointly help liver digest fats and fatty acids.
18. Tryptophan
Tryptophan can be obtained from plant or animal sources and is widely used in
alternative medicine to help treat insomnia, anxiety, depression, and even PMS. Besides,
this amino acid is used for smoking cessation and for other conditions. It is known
worldwide for relieving minor PMS, for enhancing relaxation and sleep, for soothing
nerves and anxiety, and for reducing carbohydrate cravings. Tryptophan is also vital for
the production process of serotonin, which is a brain chemical involved in regulating
mood.
19. Tyrosine
Tyrosine represents a starting material for neurotransmitters. This amino acid also
increases plasma neurotransmitter levels, especially dopamine and noradrenalin, as well
as participates in the synthesis of enkephalins providing pain-relieving effects in the body.
The compounds are very important in terms of brain health, since they are responsible
for transmitting nerve impulses and preventing conditions like depression.
20. Valine
This amino acid aids preventing the breakdown of muscle, because it supplies the
muscles with an extra glucose responsible for the energy production during physical
activity. Valine is also a precursor in the penicillin biosynthetic pathway and is known for
inhibiting the transport of Tryptophan across the blood-brain barrier. Besides, it is also
proved to help alleviate disorders of the muscles, and to be an effective appetite
suppressant.
 Peptide Bond
 In 1902, Emil fischer proposed that protein were long chain of amino acid joined
together by amide bonds between the α-carboxyl group of one amino acid and the
α-amino group of another. For these amide bonds, Fischer proposed the special
name peptide bond.
 A peptide bond is an amide type of covalent chemical bond linking two consecutive
alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2
(nitrogen number two) of another along a peptide or protein chain.

Peptide Bond Formed by the α-carboxyl group of one amino acid and α-amino group

When two amino acids form a dipeptide through a peptide bond it is type of
condensation reaction. In this kind of condensation, two amino acids approach each
other, with the non-side chain (C1) carboxylic acid moiety of one coming near the non-
side chain (N2) amino moiety of the other. One loses a hydrogen and oxygen from its
carboxyl group (COOH) and the other loses a hydrogen from its amino group (NH2). This
reaction produces a molecule of water (H2O) and two amino acids joined by a peptide
bond (-CO-NH-). The two joined amino acids are called a dipeptide.
The formation of the peptide bond consumes energy, which, in organisms, is derived
from ATP. Peptides and proteins are chains of amino acids held together by peptide
bonds (and sometimes by a few isopeptide bonds). Organisms use enzymes to produce
nonribosomal peptides, and ribosomes to produce proteins via reactions that differ in
details from dehydration synthesis.

Degradation
A peptide bond can be broken by hydrolysis (the addition of water). In the presence
of water they will break down and release 8–16 kilojoule/mol (2–4 kcal/mol) of Gibbs
energy. This process is extremely slow, with the half life at 25 °C of between 350 and 600
years per bond.
In living organisms, the process is normally catalyzed by enzymes known as
peptidases or proteases, although there are reports of peptide bond hydrolysis caused by
conformational strain as the peptide/protein folds into the native structure. This non-
enzymatic process is thus not accelerated by transition state stabilization, but rather by
ground state destabilization.
Edman degradation, developed by Pehr Edman, is a method of sequencing
amino acids in a peptide. In this method, the amino-terminal residue is labeled and
cleaved from the peptide without disrupting the peptide bonds between other amino acid
residues.

Phenyl isothiocyanate is reacted with an uncharged N-terminal amino group, under

mildly alkaline conditions, to form a cyclical phenylthiocarbamoyl derivative. Then, under
acidic conditions, this derivative of the terminal amino acid is cleaved as a thiazolinone
derivative. The thiazolinone amino acid is then selectively extracted into an organic
solvent and treated with acid to form the more stable phenylthiohydantoin (PTH)- amino
acid derivative that can be identified by using chromatography or electrophoresis. This
procedure can then be repeated again to identify the next amino acid.
References:
www.phschool.com/science/biology_place/biocoach/bioprop/landd.html
www.aminoacidsguide.com/Ala.html
www.khanacademy.org/test-prep/mcat/biomolecules/amino-acids-and-
proteins1/a/chemistry-of-amino-acids-and-protein-structure
www.rose-hulman.edu/~brandt/Chem330/Amino_acids.pdf
https://www.healthline.com/nutrition/essential-amino-acids
Introduction to Organic Chemistry(3rd Ed.) jin xing,Singapore: Thomas & P oon