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Amino Acids, Peptides, Polypeptides, and Proteins -
Chemical Structure
Reprinted from ScientificPsychic.com
with permission
DEFINITION: Amino acids are the basic organic
substances that constitute building blocks of enzymes, hormones, peptides, and
proteins, (i.e. body tissues.) Amino acids are defined by the -CH(NH2)COOH substructure. Nitrogen and two
hydrogens comprise the amino group, -NH2, and the acid entity is the
carboxyl group, -COOH. Amino acids link to each when
the carboxyl group of one molecule reacts with the amino group of another
molecule, creating a peptide bond -C(=O)NH- and
releasing a molecule of water (H2O). A peptide is a compound consisting of 2 or more amino
acids. Oligopeptides have 10 or fewer amino acids. Polypeptides
and proteins are chains of 10 or more amino acids, but peptides
consisting of more than 50 amino acids are classified as proteins.
See also: FATS/FATTY
ACIDS CARBOHYDRATES/SUGARS
In the animal kingdom, peptides and proteins regulate metabolism and provide
structural support. The cells and the organs of our body are controlled by
peptide hormones (see table below). Insufficient protein in the diet
may prevent the body from producing adequate levels of peptide hormones and
structural proteins to sustain normal bodily functions. Deficiency of good
quality protein in the diet may contribute to seemingly unrelated symptoms such
as sexual dysfunction, blood pressure problems, fatigue, obesity, diabetes,
frequent infections, digestive problems, and bone mass loss leading to
osteoporosis. Severe restriction of dietary protein causes kwashiorkor which is
a form of malnutrition characterized by loss of muscle mass, growth failure, and
decreased immunity.
Allergies are generally caused by the effect of foreign proteins on our body.
Proteins that are ingested are broken down into smaller peptides and amino acids
by digestive enzymes called "proteases". Allergies to foods may be caused by the
inability of the body to digest specific proteins. Cooking denatures
(inactivates) dietary proteins and facilitates their digestion. Allergies or
poisoning may also be caused by exposure to proteins that bypass the digestive
system by inhalation, absorption through mucous tissues, or injection by bites
or stings. Spider and snake venoms contain proteins that have a variety of
neurotoxic, proteolytic, and hemolytic effects.
Many structures of the body are formed from protein. Hair and nails are made
of keratins which are long protein chains containing a high percentage
(15%-17%) of the amino acid cysteine. Keratins are also components of animal
claws, horns, feathers, scales, and hooves. Collagen is the most common
protein in the body and comprises approximately 20-30% of all body proteins. It
is found in tendons, ligaments, and many tissues that serve structural or
mechanical functions. Collagen consists of amino acid sequences that coil into a
triple helical structure to form very strong fibers. Glycine and proline account
for about 50% of the amino acids in collagen. Gelatin is produced by
boiling collagen for a long time until it becomes water soluble and gummy. Tooth
enamel and bones consist of a protein matrix (mostly collagen) with dispersed
crystals of minerals such as apatite, which is a phosphate of calcium. Muscle
tissue consists of approximately 65% actin and myosin, which are
the contractile proteins that enable muscle movement.
Amino Acids
Naturally occurring amino acids, their abbreviations, and structural
formulas
*
Essential amino acids
Ala = alanine
CH3CH(NH2)COOH |
Arg = arginine
H2N-C(=NH)NHCH2CH2CH2CH(NH2)COOH
|
Asn = asparagine
H2N-C(=O)CH2CH(NH2)COOH
|
Asp = aspartic acid
HOOC-CH2CH(NH2)COOH
|
Cys = cysteine
HS-CH2CH(NH2)COOH |
Gln = glutamine
H2N-C(=O)CH2CH2CH(NH2)COOH
|
Glu = glutamic acid
HOOC-CH2CH2CH(NH2)COOH
|
Gly = glycine
H2N-CH2COOH |
His = histidine
*
 |
Ile = isoleucine
*
CH3CH2CH(CH3)CH(NH2)COOH
|
Leu = leucine
*
CH3CH(CH3)CH2CH(NH2)COOH
|
Lys = lysine
*
H2N-CH2CH2CH2CH2CH(NH2)COOH
|
Met = methionine
*
CH3-S-CH2CH2CH(NH2)COOH
|
Phe =
phenylalanine *
 |
Pro = proline
 |
Ser = serine
HOCH2CH(NH2)COOH |
Thr = threonine
*
CH3CH(OH)CH(NH2)COOH |
Trp = tryptophan
*
 |
Tyr = tyrosine
 |
Val = valine
*
CH3CH(CH3)CH(NH2)COOH
|
Arginine is synthesized by the body but at a rate that is insufficient to
meet growth needs. Methionine is required in large amounts to produce cysteine
if the latter amino acid is not adequately supplied in the diet. Similarly,
phenylalanine can be converted to tyrosine, but is required in large quantities
when the diet is deficient in tyrosine. Tyrosine is essential for people with
the disease phenylketonuria (PKU) whose metabolism cannot convert phenylalanine
to tyrosine. Isoleucine, leucine, and valine are sometimes called
"branched-chain amino acids" because their carbon chains are branched.
StereochemistryIn all twenty amino acids, except glycine, the carbon
atom with the amino group is attached to four different substituents. The
tetrahedral bond angles of carbon and the asymmetry of the attachments make it
possible for amino acids to have two non-superimposable structures, the L and R forms, which are
mirror images of each other. Only L-amino acids are found
in proteins. L-amino acids have the amino group to the left
when the carboxyl group is the top, as illustrated here. The wedge bonds are
above the display plane and the dotted bonds are below the display plane.
 |
| L-Alanine
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Formation of a peptide from two amino acids
This illustration shows the reaction of two amino acids, where R and
R' are any functional groups from the table above. The blue circle shows
the water (H2O) that is released, and the
red circle shows the resulting peptide bond (-C(=O)NH-).
Peptides and Proteins
Some Important Peptide Hormones
| Hormone |
Number of
amino acids |
Function |
| Insulin |
51 |
Lowers blood glucose level, promotes glucose storage as glycogen and
fat. Fasting decreases insulin production. |
| Glucagon |
29 |
Increases blood glucose level. Fasting increases glucagon production.
|
| Ghrelin |
28 |
Stimulates release of Growth Hormone, increases feeling of hunger.
|
| Leptin |
167 |
Its presence suppresses the feeling of hunger. Fasting decreases
leptin levels. |
| Growth Hormone |
191 |
Promotes amino acid uptake by cells and regulates development of the
body.
Growth hormone levels increase during fasting. |
| Prolactin |
198 |
Initiates and maintains lactation in mammals
|
| Human Placental Lactogen |
191 |
Produced by the placenta late in gestation
|
| Luteinizing Hormone |
204 |
Induces the secretion of testosterone |
| Follicle Stimulating Hormone |
204 |
Induces the secretion of testosterone and dihydrotestosterone
|
| Chorionic Gonadotropin |
237 |
Produced after implantation of an egg in the placenta
|
| Thyroid Stimulating Hormone |
201 |
Stimulates secretion of thyroxin and triiodothyronine
|
| Adrenocorticotropic Hormone |
39 |
Stimulates production of adrenal cortex steroids (cortisol and
costicosterone) |
| Vasopressin |
9 |
Increases the reabsorption rate of water in kidney tubule cells
(antidiuretic hormone) |
| Oxytocin |
9 |
Causes contraction of mammary gland cells to produce milk and
stimulation of uterine muscles during childbirth |
| Angiotensin II |
8 |
Regulates blood pressure through vasoconstriction
|
| Parathyroid Hormone |
84 |
Increases calcium ion levels in extracellular fluids
|
| Gastrin |
14 |
Regulates secretion of gastric acid and pepsin, a digestive enzyme
consisting of 326 amino acids |
Peptide hormones are produced by the endocrine glands (pituitary, thyroid,
pineal, adrenal, pancreas) or by various organs such as the kidney, stomach,
intestine, placenta, or liver. Peptide hormones can have complex, convoluted
structures with hundreds of amino acids. The following graphics illustrate the
chemical structure of human insulin and its three-dimensional shape. Insulin is
made of two amino acid sequences. The A-Chain has 21-amino acids, and the
B-Chain has 30-amino acids. The chains are linked together through the
sulfur atoms of cysteine (Cys). Peptide hormones are generally different for
every species, but they may have similarities. Human insulin is identical to pig
insulin, except that the last amino acid of the B-Chain for the pig is alanine
(Ala) instead of threonine (Thr).
Chemical Structure of Human Insulin
 |
 |
 |
Ribbon representation
shows shape of peptide links |
Stick representation
shows all the atoms |
Space-filling representation
shows external shape
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How are proteins created?The genetic code in DNA (deoxyribonucleic
acid) provides the instructions for building proteins. In the 1960s, Marshal
Nirenberg at the National Institutes of Health (NIH) deduced how DNA is mapped
into proteins. DNA consists of long molecular sequences containing four
nucleotide bases: Adenine (A), Cytosine (C), Guanine (G), and Thymine (T). Each
combination of three bases, a DNA codon, corresponds to one specific amino acid.
Since there are 64 different 3-base combinations and only 20 amino acids, some
combinations do not have unique mappings. The genetic code applies to the vast
majority of genes in animals, plants, and microorganisms. The same codons
correspond to the same amino acids and to the same START and STOP signals, but
in some rare cases one or two of the three STOP codons are assigned to an amino
acid instead.
| Nucleotide Bases |
 |
 |
 |
 |
| Adenine (A) |
Cytosine (C) |
Guanine (G) |
Thymine (T) |
Chemical Structure of DNADNA forms a double helix in which the
nucleotide bases are attached to deoxyribose units linked through phosphate
groups. The bases in the center of the DNA helix always occur in complementary
matched pairs, with cytosine linking to guanine and thymine linking to adenine
through hydrogen bonding (shown as dotted lines).
 |
 |
The nucleotide bases in the center of the DNA
helix are flanked by deoxyribose units linked by phosphate groups.
The
figure on the right represents oxygen as red, nitrogen as blue, and
phosphorus as olive green. |
Transcription of DNA to mRNAThe nucleotide sequence of DNA is not used
directly in protein synthesis. Instead, the DNA molecule is transcribed into
messenger ribonucleic acid (mRNA) which is then used for protein synthesis.
Transcription begins as the hydrogen bonds in the DNA double helix break and
each DNA nucleotide base links with a complementary matching base to build the
mRNA molecule. Guanine links with cytosine and cytosine with guanine. Thymine
links with adenine, but adenine, which would normally link to thymine, links
with Uracil (U) during transcription. As an example, the DNA sequence
GATACC is transcribed into the complementary mRNA sequence CUAUGG
which builds the amino acid sequence Leu-Trp. The table below shows the
correspondence of the amino acids and the mRNA codons.
 |
| Uracil (U) |
The Genetic Code
| Amino Acid |
Abb. |
SLC |
RNA codons |
| Alanine |
Ala |
A |
GCA GCC GCG GCU |
| Arginine |
Arg |
R |
AGA AGG CGA CGC CGG CGU |
| Asparagine |
Asn |
N |
AAC AAU |
| Aspartic acid |
Asp |
D |
GAC GAU |
| Cysteine |
Cys |
C |
UGC UGU |
| Glutamic acid |
Glu |
E |
GAA GAG |
| Glutamine |
Gln |
Q |
CAA CAG |
| Glycine |
Gly |
G |
GGA GGC GGG GGU |
| Histidine |
His |
H |
CAC CAU |
| Isoleucine |
Ile |
I |
AUA AUC AUU |
| Leucine |
Leu |
L |
CUA CUC CUG CUU UUA UUG |
| Lysine |
Lys |
K |
AAA AAG |
| Methionine* |
Met |
M |
AUG |
| Phenylalanine |
Phe |
F |
UUC UUU |
| Proline |
Pro |
P |
CCA CCC CCG CCU |
| Serine |
Ser |
S |
AGC AGU UCA UCC UCG UCU |
| Threonine |
Thr |
T |
ACA ACC ACG ACU |
| Tryptophan |
Trp |
W |
UGG |
| Tyrosine |
Tyr |
T |
UAC UAU |
| Valine |
Val |
V |
GUA GUC GUG GUU |
| Stop codons |
|
|
UAA UAG UGA |
SLC is the single-letter code used to
represent the amino acids in protein data bases.
Codon
letters: A = Adenine, C = Cytosine, G = Guanine, U =
Uracil
* AUG signals "start" of translation when it
occurs at the beginning of a
gene.
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Amino acid profiles of some proteinsThe following table shows
representative amino acid profiles of some common dietary protein supplements.
The percentages are composites of several commercial products.
Percentage (%) of amino acid
| Amino Acid |
egg
protein |
whey
protein |
soy
protein |
| alanine |
6.6 |
5.2 |
4.2 |
| arginine |
5.6 |
2.5 |
7.5 |
| aspartic acid |
8.9 |
10.9 |
11.5 |
| cysteine |
2.5 |
2.2 |
1.3 |
| glutamic acid |
13.5 |
16.8 |
19.0 |
| glycine |
3.6 |
2.2 |
4.1 |
| histidine |
2.2 |
2.0 |
2.6 |
| isoleucine |
6.0 |
6.0 |
4.8 |
| leucine |
8.5 |
9.5 |
8.1 |
| lysine |
6.2 |
8.8 |
6.2 |
| methionine |
3.6 |
1.9 |
1.3 |
| phenylalanine |
6.0 |
2.3 |
5.2 |
| proline |
3.8 |
6.6 |
5.1 |
| serine |
7.3 |
5.4 |
5.2 |
| threonine |
4.4 |
6.9 |
3.8 |
| tryptophan |
1.4 |
2.2 |
1.3 |
| tyrosine |
2.7 |
2.7 |
3.8 |
| valine |
7.0 |
6.0 |
5.0 |
Egg protein is considered to have one of the best amino acids profiles for
human nutrition. Plant proteins generally have lower content of some essential
amino acids such as lysine and methionine. Soy protein is one of the best plant
proteins, nevertheless, the most prominent difference in this chart is the
proportion of the sulfur-containing amino acids cysteine and methionine. Egg
protein has approximately twice as much cysteine and three times as much
methionine than is found in soy protein. Also, whey protein has half the amount
of arginine and phenylalanine than egg and soy proteins.
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