Proteins

Description
Proteins are polymers of amino acids, with each
amino acid residue joined to its neighbor by a
specific type of covalent bond called a peptide
bond.

Proteins are the most abundant biological

macromolecules, occurring in all cells and all
parts of cells.

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Proteins
Description
Proteins are made up of 20 amino acids
linked by peptide bonds.

Polypeptide backbone is the repeating

sequence of the N-C-C-N-C-C…

The side chain R group is not part of the

linear amino acid link.

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Proteins
Functions of Proteins
Enzymes – many proteins function as enzymes, biochemical catalysts.
Enzymes catalyze nearly all reactions that occur in living systems.
Transport – some proteins bind other molecules together and transport
substances such as hemoglobin. Other proteins serve as pores and
channels in membranes, allowing for the passage of small, charged
molecules.
Support – proteins such as tubulin, actin, collagen provide support and
shape to cells and hence to tissues and organs.
Hormones – some proteins are hormones, which regulate biochemical
activities in target cells or tissues like insulin, oxytocin, HGH, etc.; other
proteins serve as receptors for hormones.

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Proteins
Functions of Proteins
Functions continued…
Regulation – control in the expression of genes
Receptors – proteins on the cell surface can act as receptors for various
ligands and as modifiers of cell-cell interactions.
Protection – antibodies defending vertebrates against bacterial and viral
infections; toxins produced by bacteria can kill larger organisms.

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Proteins
Chemistry of amino acids
Amino acids are compounds that contain both an amino group and a
carboxyl group.
α-amino acid has an amino group attached to the carbon adjacent to the
carboxyl group.
R-group gives identity to the amino acid.

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Proteins
Chemistry of amino acids
With the exception of glycine, all protein-derived amino acids have at least
one stereocenter.
Amino acids are chiral, hence optically active.
The vast majority of α-amino acids have the L-configuration at the α-carbon
(Proline is usually D).

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Proteins
Chemistry of amino acids
Amino acids are capable of behaving as both an acid and a base, since they have both a proton donor and a proton acceptor.

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Proteins
Classification of Amino Acids
Classification based on R Groups
1. Aliphatic: G, I, L, V, A
2. Cyclic: P
3. Aromatic: W, Y, F
4. Sulfur-containing: M, C
5. Alcoholic : S, T, Y
6. Carboxyl: D, E
7. Amine: K, R, H
8. Amide: Q, N

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Proteins
Classification of Amino Acids
Classification based on R Groups
1. Aliphatic: G, I, L, V, A
2. Cyclic: P
3. Aromatic: W, Y, F
4. Sulfur-containing: M, C
5. Alcoholic : S, T, Y
6. Carboxyl: D, E
7. Amine: K, R, H Glycine is smallest amino acid; not chiral.
8. Amide: Q, N

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Proteins
Classification of Amino Acids
Classification based on R Groups
1. Aliphatic: G, I, L, V, A
2. Cyclic: P
3. Aromatic: W, Y, F
4. Sulfur-containing: M, C
5. Alcoholic : S, T, Y
Proline differs from the other 19 amino acids
6. Carboxyl: D, E because its three-carbon side chain is bonded to the
7. Amine: K, R, H nitrogen of its α-amino group as well as to the α-
carbon creating a cylic molecule.
8. Amide: Q, N Pyrrolidine ring – cyclic structure in proline
Proline is a secondary amino acid.
Technically an imino acid.

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Proteins
Classification of Amino Acids
Classification based on R Groups
1. Aliphatic: G, I, L, V, A
2. Cyclic: P
3. Aromatic: W, Y, F
4. Sulfur-containing: M, C
5. Alcoholic : S, T, Y
6. Carboxyl: D, E
7. Amine: K, R, H
8. Amide: Q, N
The side chain of tryptophan contains a bicyclic
indole group.

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Proteins
Classification of Amino Acids
Classification based on R Groups
1. Aliphatic: G, I, L, V, A
2. Cyclic: P
3. Aromatic: W, Y, F
4. Sulfur-containing: M, C
5. Alcoholic : S, T, Y
6. Carboxyl: D, E
7. Amine: K, R, H
8. Amide: Q, N

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Proteins
Classification of Amino Acids
Classification based on R Groups
1. Aliphatic: G, I, L, V, A
2. Cyclic: P
3. Aromatic: W, Y, F
4. Sulfur-containing: M, C
5. Alcoholic : S, T, Y
6. Carboxyl: D, E
7. Amine: K, R, H
8. Amide: Q, N

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Proteins
Classification of Amino Acids
Classification based on R Groups
1. Aliphatic: G, I, L, V, A
2. Cyclic: P
3. Aromatic: W, Y, F
4. Sulfur-containing: M, C
5. Alcoholic : S, T, Y
6. Carboxyl: D, E
7. Amine: K, R, H
8. Amide: Q, N

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Proteins
Classification of Amino Acids
Classification based on R Groups
1. Aliphatic: G, I, L, V, A
2. Cyclic: P
3. Aromatic: W, Y, F
4. Sulfur-containing: M, C
5. Alcoholic : S, T, Y
6. Carboxyl: D, E
7. Amine: K, R, H
8. Amide: Q, N
The side chain of histidine contains an imidazole
ring substituent

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Proteins
Classification of Amino Acids
Classification based on R Groups
1. Aliphatic: G, I, L, V, A
2. Cyclic: P
3. Aromatic: W, Y, F
4. Sulfur-containing: M, C
5. Alcoholic : S, T, Y
6. Carboxyl: D, E
7. Amine: K, R, H
8. Amide: Q, N
Monosodium glutamate – used in food as flavor
enhancer

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Proteins
Classification of Amino Acids
Classification based on polarity

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Proteins
Essential and Non-Essential Amino Acids
Essential amino acids:
• Histidine, isoleucine, leucine, lysine, methionine, phenylalanine,
threonine, tryptophan and valine.
Non-essential amino acids:
• Alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid,
glutamine, glycine, proline, serine, tyrosine
• Citrulline, cystine, gamma-aminobutyric acid, ornithine and taurine

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Proteins
Uses of Amino Acids
Alanine – Aids in the metabolism of glucose.
Arginine – Arginine retards growth of tumors and cancer by enhancing
immune function. It increases the size and activity of the thymus gland,
which manufactures T-lymphocytes (T cells), crucial components of the
immune system. It also aids in the detoxification of the liver by
neutralizing ammonia.
Asparagine – needed to maintain the balance of the nervous system; it
prevents you from being overly nervous or overly calm.
Aspartic acid – increases stamina. Chronic fatigue may result from low
levels of aspartic acid, because this leads to lowered cellular energy.

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Proteins
Uses of Amino Acids
Carnitine – It helps to transport fatty acids which are burned within cells for
the generation of metabolic energy. This prevents fatty buildup in the
heart, liver and other tissues. Thus, carnitine increases the use of fat as
an energy source.
Cysteine – helps to detoxify harmful toxins and protect the body from
radiation damage. It is one of the best free radical destroyers, and works
best with selenium and Vitamin E. Cysteine is also a precursor to
glutathione.

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Proteins
Uses of amino acids
Gamma-amino butyric acid (GABA) – an amino acid that acts as a
neurotransmitter in the central nervous system. It is essential for brain
metabolism, aiding in the proper brain function. GABA is formed in the
body from another amino acid, glutamic acid. Its function is to decrease
neuron activity and inhibit nerve cells from over firing.
Glutamic acid – is an excitatory neurotransmitter that increases the firing of
neurons in the CNS. Glutamic acid can detoxify ammonia by picking up
nitrogen atoms, in the process creating another amino acid, glutamine.
The conversion of glutamic acid into glutamine is the only means by
which ammonia in the brain can be detoxified.

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Proteins
Uses of amino acids
Glutamine – is the most abundant free amino acid found in the muscles of
the body. Because it can readily pass the blood-brain barrier, it is known
as brain fuel. Glutamine is unique among the amino acids in that each
molecule contains not one nitrogen atom but two. Thus, its creation
helps to clear ammonia from the tissues, especially brain tissue, and it
can transfer nitrogen from one place to another.
Glutathione – made up of 3 amino acids cysteine, glutamic acid and
glycine. Glutathione is a powerful antioxidant that is produced in the
liver. The largest stores of glutathione are found in the liver, where it
detoxifies harmful compounds so that they can be excreted through the
bile.

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Proteins
Uses of amino acids
Glycine - retards muscle degeneration by supplying additional creatine, a
compound that is present in muscle tissue and is utilized in the
construction of DNA and RNA. Glycine is essential for the synthesis of
nucleic acids, bile acids, and other nonessential amino acids in the
body.
Histidine - is an essential amino acid that is significant in the growth and
repair of tissues. It is important for the maintenance of the myelin
sheaths that protect nerve cells, and is needed for the production of
both red and white blood cells. Histidine also protects the body from
radiation damage, aids in removing heavy metals from the system, and
may help in the prevention of AIDS.

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Proteins
Uses of amino acids
Histamine, an important immune system chemical, is derived from histidine.
Histamine aids in sexual arousal. Because the availability of histidine
influences histamine production, taking supplemental histidine—
together with vitamins B3 (niacin) and B6 (pyridoxine), which are
required for the transformation from histidine to histamine—may help
improve sexual functioning and pleasure.
Isoleucine - one of the essential amino acids, is needed for haemoglobin
formation and also stabilizes and regulates blood sugar and energy
levels. It is metabolized in muscle tissue. It is one of the three branched-
chain amino acids. These amino acids are valuable for athletes because
they enhance energy, increase endurance, and aid in the healing and
repair of muscle tissue.
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Proteins
Uses of amino acids
Leucine – is an essential amino acid and one of the branched-chain amino
acids (the others are isoleucine and valine). These works together to
protect muscle and act as fuel. They promote the healing of bones, skin,
and muscle tissue, and are recommended for those recovering from
surgery. Leucine also lowers elevated blood sugar levels, and aids in
increasing growth hormone production.
Lysine is an essential amino acid that is a necessary building block for all
protein. It is needed for proper growth and bone development in children;
it helps calcium absorption and maintains a proper nitrogen balance in
adults. This amino acid aids in the production of antibodies, hormones,
and enzymes, and helps in collagen formation and tissue repair.

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Proteins
Uses of amino acids
Methionine is an essential amino acid that assists in the breakdown of fats,
thus helping to prevent a build-up of fat in the liver and arteries that
might obstruct blood flow to the brain, heart, and kidneys. The synthesis
of the amino acids cysteine and taurine may depend on the availability
of methionine.
Ornithine helps to prompt the release of growth hormone, which promotes
the metabolism of excess body fat. This effect is enhanced if ornithine is
combined with arginine and carnitine. Ornithine is necessary for proper
immune system and liver function.

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Proteins
Classification and Occurrence of Proteins
Phenylalanine – is an essential amino acid. Once in the body, it can be
converted into another amino acid, tyrosine, which in turn is used to
synthesize two key neurotransmitters that promote alertness: dopamine
and epinephrine (andrenaline).
Proline – Proline improves skin texture by aiding in the production of
collagen and reducing the loss of collagen through the aging process. It
also helps in the healing of cartilage and the strengthening of joints,
tendons, and heart muscle. It works with vitamin C to promote healthy
connective tissue.

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Proteins
Uses of amino acids
Serine – is needed for the proper metabolism of fats and fatty acids, the growth
of muscle, and the maintenance of a healthy immune system. It aids in the
production of immunoglobulin and antibodies. Serine can be synthesized
from glycine in the body.
Taurine - High concentrations of taurine are found in the heart muscle, white
blood cells, skeletal muscle, and central nervous system. It is a building
block of all the other amino acids as well as a key component of bile, which
is needed for the digestion of fats, the absorption of fat-soluble vitamins, and
the control of serum cholesterol levels.
Threonine - Threonine is an essential amino acid that helps to maintain the
proper protein balance in the body. It is important for the formation of
collagen and elastin.

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Proteins
Uses of amino acids
Tryptophan - Tryptophan is an essential amino acid that is necessary for
the production of vitamin B3 (niacin). It is used by the brain to produce
serotonin, a necessary neurotransmitter that transfers nerve impulses
from one cell to another and is responsible for normal sleep. A sufficient
amount of vitamin B6 (pyridoxine) is necessary for the formation of
tryptophan, which, in turn, is required for the formation of serotonin.
Tyrosine – acts as a mood elevator; a lack of adequate amounts of tyrosine
leads to a deficiency of norepinephrine in the brain, which in turn can
result in depression.

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Proteins
Uses of amino acids
Valine - an essential amino acid, has a stimulant effect. It is needed for
muscle metabolism, tissue repair, and the maintenance of a proper
nitrogen balance in the body. Valine is found in high concentrations in
muscle tissue.

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Proteins
Classification and Occurrence of Proteins
Three basic classes according to shape and solubility
1. Fibrous – simple, regular linear structures; often serve structural roles
in cells; typically insoluble in water
2. Globular – roughly spherical in shape; the polypeptide chain is
compactly folded so that the hydrophobic amino acid side chains are in
the interior of the molecule and the hydrophilic are outside; usually very
soluble in aqueous solutions.
3. Membrane – found in association with the various membrane systems
of cells; characteristically have fewer hydrophilic amino acids than
cytosolic proteins

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Proteins
Four Levels of Organization of Proteins
The architecture of protein molecules is quite complex. Nevertheless, this
complexity can be resolved by defining the various levels of structural
organization.
Primary Structure – the amino acid sequence
Secondary Structure – helical and pleated segments that results through
hydrogen-bonding interactions between amino acid residues
Tertiary Structure – when the polypeptide chains of protein molecules bend
and fold in order to assume a more compact three-dimensional shape
Quaternary Structure – when two or more polypeptide chains of
characteristic tertiary structure interact

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Proteins
Four Levels of Organization of Proteins
Anti-parallel pleated sheats

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Proteins
Four Levels of Organization of Proteins
Keratin – predominant constituent of claws, fingernails, hair and horns in animals.

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Proteins
Four Levels of Organization of Proteins
Spider web silks are composite of α-helices and β-sheets

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Proteins
Four Levels of Organization of Proteins
Collagen’s triple helix
Collagen is a rigid, inextensible fibrous protein
that is a principal constituent of connective
tissue in animals, including tendons,
cartilage, bones, teeth, skin and blood
vessels.

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Proteins
Four Levels of Organization of Proteins
Tertiary and Quaternary Structures

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Proteins
Non-covalent Interactions
These are weak forces that stabilize the higher levels of protein structure.
1. Hydrogen bonds
2. Hydrophobic interactions
3. Electrostatic bonds
4. Van der Waals forces

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Proteins
Denaturation of proteins
Denaturation is the process of unfolding the protein.

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Proteins
Digestion of proteins

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