Proteins are composed of amino acids and play important structural and functional roles in the body. There are 20 standard amino acids that are used to build proteins through peptide bonds between amino and carboxyl groups. Proteins have primary, secondary, tertiary, and sometimes quaternary structures that determine their shape and function. Their structures are stabilized through hydrogen bonds, disulfide bridges, and other weak interactions. Denaturation disrupts these structures and causes proteins to lose their native 3D shapes and biological functions.

1. PROTEINS ANDAMINO ACIDS
BY
HAIDER ALI
JIBRAN INSTITUTE OF HEALTH SCIENCES
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2. PROTEINS
• Proteins are nitrogenous “macromolecules” composed of many amino acids.
• The term protein is derived from Greek word “Proteios” , which means
“primary”, or “holding first place”.
• They are named so because proteins are the most important of biological
substances and are fundamental structural components of the body.
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3. COMPOSITION OF PROTEINS
• In addition to C, H, and O, proteins also contain N.
• The nitrogen content is around 16% of the molecular weight of proteins.
• Small amounts of Sulfur and Phosphorous are also present. Few proteins contain other elements such as
Iodine, Copper , Manganese, Zn and Iron, etc.
• Protein molecules are very large molecules made up of small units called Amino acids.
• More than 300 hundred amino acids have been described but only 20 amino acids have been found to be
present in mammalian tissues and take part in protein synthesis.
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4. AMINO ACIDS
R is called a side chain and can be a hydrogen, aliphatic, aromatic or
heterocyclic group. Each amino acid has an amino group –NH2, a
carboxylic acid group -COOH and a hydrogen atom each attached to
carbon

5. ABBREVIATIONS AND SYMBOLS FOR THE COMMONLY OCCURRING AMINO ACIDS
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7. OH! TIE SERIES THREADS
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12. AMINO ACID CLASSIFICATION BASED ON THEIR METABOLIC FATE
• The carbon skeleton of amino acids can serve as a precursor for the synthesis of glucose
(glycogenic) or fat (ketogenic) or both.
• Glycogenic amino acids: These amino acids can serve as precursors for the formation of
glucose or glycogen. e.g. alanine, aspartate, glycine, methionine etc.
• Ketogenic amino acids: Fat can be synthesized from these amino acids.
• Two amino acids leucine and lysine are totally ketogenic.
• Glycogenic and ketogenic amino acids: The four amino acids isoleucine, phenyl-alanine,
tryptophan, tyrosine are precursors for synthesis of glucose as well as fat.
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13. NON-STANDARD AMINO ACIDS
A. Amino acid derivatives in proteins: The 20 standard amino acids can be
incorporated into proteins due to the presence of universal genetic code.
• Some of these amino acids undergo specific modification after the protein
synthesis occurs.
• These derivatives of amino acids are very important for protein structure and
functions. Selected examples are given here under.
1. Collagen—the most abundant protein in mammals—contains 4-hydroxyproline
and 5-hydroxylysine.
2. Histones—the proteins found in association with DNA—contain many
methylated, phosphorylated or acetylated amino acids.
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14. NON-STANDARD AMINO ACIDS
3. Gamma-carboxyglutamic acid is found in certain plasma proteins involved in blood
clotting.
B. Non-protein amino acids: These amino acids, although never found in proteins,
perform several biologically important functions.
example:
Ornithine
Citrulline ============ Conversion of Ammonia to urea by the help of Urea cycle
Arginosuccinic acid
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15. D-AMINO ACIDS
• Most amino acids isolated from animals and plants are of L-category.
• Certain D-amino acids are also found in the antibiotics (actinomycin-D,
valinomycin, gramicidin-S).
• D-serine and D-aspartate are found in brain tissue.
• D-Glutamic acid and D-alanine are present in bacterial cell walls.
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16. NUTRITIONAL CLASSIFICATION OF AMINO ACIDS
• Nutritionally, amino acids are of three types:
A. Essential
B. Non-essential
C. Semi-essential amino acids
1. Essential amino acids: These are the ones which are not synthesized by the
body and must be taken in diet. They include valine, leucine, isoleucine,
phenylalanine, threonine, tryptophan, methionine and lysine. For
remembering the following formula is used—MATT VIL PHLY.
2. Non-essential amino acids: They can be synthesized by the body and may not
be the requisite components of the diet.
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17. SEMI-ESSENTIAL AMINO ACIDS
3. Semi-essential amino acids: These are growth promoting factors since they are
not synthesized in sufficient quantity during growth.
• They include arginine and histidine (Ah): They become essential in growing
children.
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19. PROPERTIES OF AMINO ACIDS
1. Solubility: Most of the amino acids are usually soluble in water and insoluble in
organic solvents.
2. Melting points: Amino acids generally melt at higher temperatures, often above
200°C.
3. Taste: Amino acids may be sweet (Gly, Ala, Val), tasteless (Leu) or bitter (Arg, Ile)
4. Monosodium glutamate (MSG) is used as a flavoring agent in food industry, and
Chinese foods to increase taste and flavor. In some individuals intolerant to MSG,
Chinese restaurant syndrome (brief and reversible flu-like symptoms) is observed.
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20. OPTICAL PROPERTIES
• All the amino acids except
glycine possess optical
isomers due to the presence
of asymmetric carbon atom.
• Some amino acids also have
a second asymmetric carbon
e.g. isoleucine, threonine.
• The structure of L- and D-
amino acids in comparison
with glyceraldehyde has
been given
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21. AMINO ACIDS AS AMPHOLYTES
• Amino acids contain both acidic (COOH) and basic (NH2) groups and can donate a
proton or accept a proton, are regarded as ampholytes.
• Zwitterion or dipolar ion: The name zwitter is derived from the German word
which means hybrid.
• Zwitter ion (or dipolar ion) is a hybrid molecule containing positive and
negative ionic groups.
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22. ZWITTER ION
• The amino acids rarely exist in a neutral form with free carboxylic (COOH) and
free amino ( NH2) groups.
• In strongly acidic pH (low pH), the amino acid is positively charged (cation)
while in strongly alkaline pH (high pH), it is negatively charged (anion).
• Each amino acid has a characteristic pH (e.g. leucine, pH 6.0) at which it carries
both positive and negative charges and exists as zwitterion (Fig.4.2).
• Isoelectric pH (pI) is defined as the pH at which a molecule exists as a zwitterion
or dipolar ion and carries no net charge. Thus, the molecule is electrically
neutral. 22

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24. CLASSIFICATION OF PROTEINS
• Proteins are classified:
1. On the basis of shape and size
2. On the basis of functional properties
3. On the basis of solubility and physical properties
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25. 1. On the basis of shape and size
• Fibrous proteins have structural roles whereas globular proteins
are functional (active in a cell’s metabolism)
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26. 2. BASED ON FUNCTIONAL PROPERTIES
a) Defense proteins: Immunoglobulins involved in defense mechanisms.
b) Contractile proteins: Proteins of skeletal muscle involved in muscle contraction
and relaxation.
c) Respiratory proteins: Involved in the function of respiration, like hemoglobin,
myoglobin.
d) Structural proteins: Proteins of skin, cartilage, nail.
e) Enzymes: Proteins acting as enzymes.
f) Hormones: Proteins acting as hormones.
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27. 3. BASED ON SOLUBILITY AND PHYSICAL PROPERTIES
A. Simple proteins: These are proteins which on complete hydrolysis yield only
amino acids.
B. Conjugated proteins: These are proteins which in addition to amino acids in
their structure, contain a non-protein group called prosthetic group
C. Derived proteins: These are the proteins formed from native protein by the
action of heat, physical forces or chemical factors.
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28. A. SIMPLE PROTEINS
• Major subclasses of simple proteins are as follows:
a) Protamine and Salmine= is the specific antagonist that neutralizes heparin-
induced anticoagulation.
b) Histones- chromosomal nucleoproteins.
c) Albumins- legumes, Ovalbumin in egg, lactalbumin in milk
d) Globulins- Alpha-1- globulins- for example, alpha 1 antitrypsin (AAT)(lungs
protective), AFP (marker of liver cancer).Beta globulin- Transferrin and
lipoproteins
e) Gliadins- Wheat
f) Keratins- These are characteristic constituents of horn, hair, nails, wool, hoofs
and feathers.
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29. A. SIMPLE PROTEINS
• Human hair has a higher content of cysteine than that of other species and is
called α-keratin.
• β-keratins are deficient in cysteine and, rich in glycine and alanine.
• They are present in spider’s web.
g) Collagen: A protein found in connective tissue and bone.
h) Elastins: These are the proteins present in elastic fiber of the connective tissue,
ligaments and tendons.
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30. B. CONJUGATED PROTEINS
• Conjugated proteins are simple proteins combined with a non-protein group called prosthetic group.
• Protein part is called apo protein, and entire molecule is called holoprotein.
a) Nucleoproteins-The nucleoproteins are compounds made up of simple basic proteins such histone with
Nucleic Acids as the prosthetic group- DNA, RNA
b) Mucoproteins- Mucoproteins are the simple proteins combined with mucopolysaccharides (MPS).
Several gonadotropic hormones such as FSH, LH and HCG are mucoproteins.
c) Glycoproteins- These proteins carry a small amount of carbohydrates as prosthetic group ( <4%).
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31. B. CONJUGATED PROTEINS
d) Chromoproteins: These are proteins that contain colored substance as the
prosthetic group- Hemoglobins.
e) Metalloproteins: As the name indicates, they contain a metal ion as their
prosthetic group. Examples:
Ferritin: Contains Iron,
Carbonic Anhydrase: Contains Zn,
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32. C. DERIVED PROTEINS
• This class of proteins are derived from simple or compound proteins by
denaturation or hydrolysis.
• (a) Primary derived proteins: Denatured but the peptide bonds remain intact.
• Heat, X-ray, UV rays, vigorous shaking, acid, alkali can cause denaturation.
• (b) Secondary derived proteins: These are the proteins formed by the
progressive hydrolysis of proteins at their peptide linkages.
• Examples: Protein products obtained by the enzymatic digestion of proteins.
Proteoses, Peptones and Peptides
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33. PEPTIDE LINKAGE AND PEPTIDES
• Peptides are chains of Amino Acids.
• Polypeptides range in size from small to very large, consisting of two or three to
thousands of linked amino acid residues.
• The –COOH group of one amino is joined to the –NH2 group of another by a
covalent bond called as peptide bond.
• In a peptide, polypeptide, or protein, the amino-terminal end is placed on the
left, the carboxyl-terminal end on the right and the sequence is read left to right,
beginning with the amino-terminal end.
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34. PEPTIDE LINKAGE
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35. PEPTIDE LINKAGE AND PEPTIDES
• Three amino acids can be joined by two peptide bonds to form a tripeptide;
similarly, four amino acids can be linked to form a tetrapeptide, five to form a
pentapeptide, and so forth.
• When a few amino acids are joined in this fashion, the structure is called an
oligopeptide. When many amino acids are joined, the product is called a
polypeptide.
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36. PEPTIDE LINKAGE AND PEPTIDES
• Proteins may have thousands of amino acid residues.
• The terms “protein” and “polypeptide” are sometimes used interchangeably
but molecules having molecular weights below 10,000 are referred to as
polypeptides and those having higher molecular weights called proteins.
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37. LEVELS OF PROTEIN STRUCTURE
1. Primary structure
2. Secondary structure
3. Tertiary structure
4. Quaternary structure arises when two or more polypeptides join to form a
protein.
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38. PRIMARY STRUCTURE
• The primary structure of a protein is its
unique sequence of amino acids.
• Lysozyme, an enzyme that attacks
bacteria, consists on a polypeptide chain
of 129 amino acids.
• The precise primary structure of a
protein is determined by inherited
genetic information.
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39. PRIMARY STRUCTURE
• Even a slight change in primary structure can affect a protein’s conformation and ability to function.
• In individuals with sickle cell disease, abnormal hemoglobins develops because of a single amino acid
substitution.
• These abnormal hemoglobins crystallize, deforming the red blood cells and leading to clogs in tiny blood vessels.
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41. SECONDARY STRUCTURE
• The secondary structure of a protein
results from hydrogen bonds at regular
intervals along the polypeptide
backbone.
• Typical shapes that develop from
secondary structure are coils (an alpha
helix) or folds (beta pleated
sheets)
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42. Α-HELIX
• α-Helical structure- Pauling and Corey
(1951)
• α-Helix is the most common and
coiled structure of protein
• It has a rigid arrangement of
polypeptide chain
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43. SALIENT FEATURES OF Α-HELICAL STRUCTURE
1. The α-helix is a tightly packed coiled structure with amino acid side chains extending outward from the
central axis
2. The α-helix is stabilized by extensive hydrogen bonding
• It is formed between H atom attached to peptide N, and O atom attached to peptide C
• The hydrogen bonds are individually weak but collectively, they are strong enough to stabilize the helix
3. All the peptide bonds, except the first and last in a polypeptide chain, participate in hydrogen bonding
4. Each turn of α-helix contains 3.6 amino acids and travels a distance of 0.54 nm. The spacing of each
amino acid is 0.15 nm.
5. Certain amino acids (particularly proline) disrupt the α –helix
6. Large number of acidic (Asp, Glu) or basic (Lys, Arg, His) amino acids also interfere with α-helix
structure
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44. Β-PLEATED SHEET
• β-Pleated sheets (or simply β-sheets) are composed of two or more segments of
fully extended peptide chains
• In the β-sheets, the hydrogen bonds are formed between the neighboring
segments of polypeptide chain(s)
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45. PARALLEL AND ANTI-PARALLEL Β-SHEETS
• The polypeptide chains in the β-sheets may be arranged either in parallel (the
same direction) or anti-parallel (opposite direction)
• Many proteins contain β-pleated sheets
• As such, the α-helix and β-sheet are commonly found in the same protein
structure
• In the globular proteins, β-sheets form the core structure
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Structure of β-pleated sheet (A) Hydrogen bonds between polypeptide
chains (B) Parallel β-sheet (C) Antiparallel β-sheet.

47. TERTIARY STRUCTURE
• Tertiary structure is determined by a
variety of interactions among R groups
and between R groups and the
polypeptide backbone.
• These interactions include hydrogen
bonds among polar and/or charged
areas, ionic bonds between charged
R groups, and hydrophobic interactions
and van der Waals
interactions among hydrophobic R
groups.
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48. TERTIARY STRUCTURE
• While these three interactions are
relatively weak, disulfide bridges, strong
covalent bonds that form between the
sulfhydryl groups (SH) of cysteine
monomers, stabilize the structure.
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49. QUATERNARY STRUCTURE
• Quaternary structure results from the
aggregation of two or more polypeptide
subunits.
• Collagen is a fibrous protein of three
polypeptides that are supercoiled like a rope.
• This provides the structural strength for their
role in connective tissue.
• Hemoglobin is a globular protein with two
copies of two kinds of polypeptides.
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51. DENATURATION OF PROTEINS
• The phenomenon of disorganization of native protein structure is known as
denaturation.
• Denaturation results in the loss of secondary, tertiary and quaternary structure
of proteins.
• This involves a change in physical, chemical and biological properties of protein
molecules.
• Physical agents (Heat, vigorous shaking, X-rays and UV radiations)
• Chemical agents (Acids, alkalis)
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Khyber Medical University Institute of Paramedical Sciences 52

53. CHARACTERISTICS OF DENATURATION
1. The native helical structure of protein is lost
2. The primary structure of a protein with peptide linkages remains intact i.e.,
peptide bonds are not hydrolyzed.
3. The protein loses its biological activity.
4. Denatured protein becomes insoluble in the solvent in which it was originally
soluble.
5. Denatured protein is more easily digested. This is due to increased exposure of
peptide bonds to enzymes.
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54. CHARACTERISTICS OF DENATURATION
• Cooking causes protein denaturation and, therefore, cooked food (protein) is
more easily digested.
7. Denaturation is usually irreversible. For instance, omelet can be prepared from
an egg (protein-albumin) but the reversal is not possible.
8. Careful denaturation is sometimes reversible (known as renaturation).
• Hemoglobin undergoes denaturation in the presence of salicylate.
• By removal of salicylate, hemoglobin is renatured.
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55. COAGULATION
• The term ‘coagulum’ refers to a semi-solid viscous precipitate of protein.
• Irreversible denaturation results in coagulation.
• Albumins and globulins (to a lesser extent) are coagulable proteins.
• Heat coagulation test is commonly used to detect the presence of albumin in
urine.
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56. FUNCTIONS OF PROTEINS
Function Description Key examples
Catalysis
There are thousands of different enzymes to catalyze specific chemical
reactions within the cell or outside it.
Rubisco
Muscle contraction
Actin and myosin together cause the muscle contractions used in locomotion
and transport around the body.
Cytoskeletons
Tubulin is the subunit of microtubules that give animals cells their shape.
Tensile strengthening
Fibrous proteins give tensile strength needed in skin, tendons, ligaments and
blood vessel walls.
collagen
Blood clotting
Plasma proteins act as clotting factors that cause blood to turn from a liquid
to a gel in wounds.
Transport of nutrients
and gases
Proteins in blood help transport oxygen, carbon dioxide, iron and lipids.
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