Proteins and Aminoacids

Proteins and amino acids
Lecture 4,5&6
Noor Ullah
B.Sc MLT, M.Phil Biochemistry/ Mol. Biology
PhD Scholar Biochemistry
Lecturer MLT, KMU IPMS
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”.
• Proteins are the most abundant organic molecules of the living system
• They occur in every part of the cell and constitute about 50% of the cellular dry
weight
• Proteins form the fundamental basis of structure and function of life
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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 S and P are also present. Few proteins contain other elements
such as I, Cu, Mn, Zn and Fe, 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.
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

Abbreviations and symbols for the commonly occurring amino
acids

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 exclusively 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.

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 hereunder.
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.

Non-standard amino acids
3. Gamma-carboxyglutamic acid is found in certain plasma proteins involved in

blood clotting.
4. Cystine is formed by combination of two cysteines. Cystine is also considered

as derived amino acid.
B. Non-protein amino acids: These amino acids, although never found in proteins,
perform several biologically important functions.
• They may be either alpha-or non-alpha-amino acids.

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.

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.

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, pregnancy and lactating women.

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.
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

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.

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.

Biologically active Amino Acids
• In addition to their primary function as components of protein, amino acids have several other
biological roles.
1. Several α-amino acids or their derivatives act as chemical messengers- glycine, glutamate, γ-
amino butyric acid (GABA, a derivative of glutamate), and serotonin and melatonin (derivatives of
tryptophan) are neurotransmitters
• Thyroxine (a tyrosine derivative produced in the thyroid gland of animals) is a hormone
2. Amino acids are precursors of a variety of complex nitrogen-containing molecules- the

nitrogenous base components of nucleotides and the nucleic acids, heme and chlorophyll
3. Several standard and nonstandard amino acids act as metabolic intermediates. For example,
arginine, citrulline, and ornithine are components of the urea cycle- the principal mechanism for
the disposal of nitrogenous waste
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

1. Based on shape and size
a) Fibrous proteins
• When the axial ratio of length: width of a protein molecule is more than 10, it is
called a fibrous protein. Examples: α-keratin from hair, collagen.
b) Globular protein
• When the axial ratio of length: width of a protein molecule is less than 10, it is
called as globular protein. Examples: Myoglobin, hemoglobin, ribonuclease, etc.

• Fibrous proteins have structural roles whereas globular proteins
are functional (active in a cell’s metabolism)
In globular proteins the hydrophobic R groups are folded into the core of the
molecule, away from the surrounding water molecules, this makes them
soluble. In fibrous proteins the hydrophobic R groups are exposed and
therefore the molecule is insoluble.

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, cytochromes.
d) Structural proteins: Proteins of skin, cartilage, nail.
e) Enzymes: Proteins acting as enzymes.
f) Hormones: Proteins acting as hormones.

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.

A. Simple Proteins
• Major subclasses of simple proteins are as follows:
a) Protamines- Salmine, sardinine
b) Histones- chromosomal nucleoproteins and globin of haemoglobin.
c) Albumins- Legumelin in legumes, leucosin in cereals, Ovalbumin in egg,
lactalbumin in milk
d) Globulins- Alpha-1- globulins- for example, alpha 1 antitrypsin (AAT), AFP.
Alpha-2- globulins- for example, Haptoglobin, Ceruloplasmin. Beta globulin-
Transferrin and lipoproteins
e) Gliadins- Wheat
f) Keratins- These are characteristic constituents of chidermal tissue such as
horn, hair, nails, wool, hoofs and feathers.

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, silk and reptilian scales.
g) Collagen: A protein found in connective tissue and bone as long, thin, partially
crystalline substance.
h) Elastins: These are the proteins present in yellow elastic fiber of the connective
tissue, ligaments and tendons.

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)
such as hyaluronic acid and the chondroitin sulphate. 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%)
and carbohydrate is bound much more firmly in the glycoproteins than the mucoprotein-
immunoglobulins
B. Conjugated Proteins
d) Chromoproteins: These are proteins that contain colored substance as the
prosthetic group- Hemoglobins and cytochromes
e) Metalloproteins: As the name indicates, they contain a metal ion as their

prosthetic group. Examples: Ferritin: Contains Fe, Carbonic Anhydrase:
Contains Zn, Ceruloplasmin: Contains Cu.

C. Derived Proteins
• This class of proteins are derived from simple or compound proteins by

denaturation or hydrolysis.
• (a) Primary derived proteins: Denatured or coagulated proteins. 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
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 (with molecular weights ranging from
several thousand to several million Daltons)
• 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.

Peptide Linkage

• 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.

• Molecules with low molecular weights, typically consisting of fewer than 50

amino acids, are called peptides
• The term protein describes molecules that consist of one or more polypeptide
chains
• Proteins may have thousands of amino acid residues

Selected Biologically Important Peptides
• The tripeptide glutathione (γ-glutamyl-l-cysteinyl glycine) is a singularly
important peptide
• Found in almost all organisms, glutathione (GSH) is involved in protein and DNA
synthesis, drug and environmental toxin metabolism, amino acid transport etc.
• Glutathione functions as a reducing agent- protects cells from the destructive

effects of oxidation by reacting with substances such as peroxides (R–O–O–R),
by-products of O2 metabolism

• In red blood cells, hydrogen peroxide (H2O2) oxidizes the iron of hemoglobin to
its ferric form (Fe3+)- Forming Methemoglobin, which is incapable of binding O2
• Glutathione protects against the formation of methemoglobin by reducing H2O2

in a reaction catalyzed by the enzyme glutathione peroxidase
• In the oxidized product GSSG, two tripeptides are linked by a disulfide bond:

• Because of the high GSH:GSSG ratio (100/1) normally present in cells,
glutathione is an important intracellular antioxidant
• The abbreviation GSH is used because the reducing component of the molecule
is the —SH group of the cysteine residue

• Thyrotropin releasing hormone (TRH): It is a tripeptide of hypothalamus
• TRH stimulates pituitary gland to release thyrotropic hormone
• Oxytocin: It is a hormone secreted by posterior pituitary gland and contains 9

amino acids (nonapeptide)
• Oxytocin, the signal molecule that stimulates the ejection of milk by mammary
glands during lactation and stimulates the contraction of uterine muscle during
childbirth, is also associated with trust and empathy and has modulating roles in
certain social behaviors

• Examples of these behaviors include bonding between mating pairs, mothers and
babies, and members of an in-group
• Both oxytocin and vasopressin signaling deficits have been linked to social
impairment in children
• Vasopressin (antidiuretic hormone, ADH): ADH is a nonapeptide produced by

posterior pituitary gland
• It regulates a wide variety of functions, including water balance, appetite, body

temperature, and sleep

• In response to low blood pressure or a high blood Na+ concentration,
osmoreceptors in the hypothalamus trigger vasopressin secretion
• Vasopressin stimulates water reabsorption in the kidneys by initiating a signal

transduction mechanism that inserts aquaporins into kidney tubule membrane
• Vasopressin also has roles in parenting behavior and social bonding
• High levels in males are associated with increased aggressive behavior

• Angiotensins: Angiotensin-I is a decapeptide which is converted to angiotensin II (8
amino acids)
• The later has more hypertensive effect
• Angiotensin II also stimulates the release of aldosterone from adrenal gland
• Bradykinin and kallidin: Nona and decapeptides
• Both are powerful vasodilators
• They are produced from plasma proteins by snake venom enzymes
• Peptide antibiotics: Gramicidin, bacitracin, tyrocidin and actinomycin are peptide in

nature
• Aspartame: It is a dipeptide (aspartyl-phenylalanine methyl ester), produced by a

combination of aspartic acid and phenylalanine
• Aspartame is about 200 times sweeter than sucrose, and is used as a low-
calorie artificial sweetener in soft drink industry
• Gastrointestinal hormones: Gastrin, secretin etc. are the gastrointestinal

peptides which serve as hormones

Levels of Protein Structure
1. Primary structure
2. Secondary structure
3. Tertiary structure
• These are used to organize the folding within a single polypeptide.
4. Quaternary structure arises when two or more polypeptides join to form a
protein.

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.

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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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)

α-Helix
• α-Helical structure- Pauling and Corey
(1951)
• α-Helix is the most common and spiral

structure of protein
• It has a rigid arrangement of

polypeptide chain

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. α-Helix is a stable conformation formed spontaneously with the lowest energy.

Salient features of α-Helical structure
6. The right handed α-helix is more stable than left handed helix (a right handed
helix turns in the direction that the fingers of right hand curl when its thumb
points in the direction the helix rises)
7. Certain amino acids (particularly proline) disrupt the α –helix
8. Large number of acidic (Asp, Glu) or basic (Lys, Arg, His) amino acids also
interfere with α-helix structure

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)

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)
• β-Pleated sheet may be formed either by separate polypeptide chains (H-bonds

are interchain) or a single polypeptide chain folding back on to itself (H-bonds are
intrachain)
• 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

Structure of β-pleated sheet (A) Hydrogen bonds between
polypeptide chains (B) Parallel β-sheet (C) Antiparallel β-sheet.

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.

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.

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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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, salts of heavy metals (Pb, Hg), urea, salicylate,
detergents (e.g. sodium dodecyl sulfate)
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. The viscosity of denatured protein (solution) increases while its surface tension
decreases.
6. Denatured protein is more easily digested. This is due to increased exposure of

peptide bonds to enzymes.
Characteristics of denaturation
• Cooking causes protein denaturation and, therefore, cooked food (protein) is more
easily digested.
• Further, denaturation of dietary protein by gastric HCl enhances protein digestion by

pepsin.
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.

Coagulation
• The term ‘coagulum’ refers to a semi-solid viscous precipitate of protein.
• Irreversible denaturation results in coagulation.
• Coagulation is optimum and requires lowest temperature at isoelectric pH.
• Albumins and globulins (to a lesser extent) are coagulable proteins.
• Heat coagulation test is commonly used to detect the presence of albumin in

urine.

Functions of proteins
Function Description Key examples

There are thousands of different enzymes to catalyze specific chemical
Catalysis 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.
Tubulin is the subunit of microtubules that give animals cells their shape and
Cytoskeletons pull on chromosomes during mitosis.
Fibrous proteins give tensile strength needed in skin, tendons, ligaments and
Tensile strengthening 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.

Functions of proteins

Biomedical/ clinical concepts
1. Proteins are the most abundant organic molecules of life. They perform static
(structural) and dynamic functions in the living cells.
2. The dynamic functions of proteins are highly diversified such as enzymes,
hormones, clotting factors, immunoglobulins, storage proteins and membrane
receptors.
3. Half of the amino acids (about 10) that occur in proteins must be consumed by
humans in the diet, hence they are essential.
4. A protein is said to be complete (or first class) protein if all the essential amino
acids are present in the required proportion by the human body e.g. egg albumin.
5. Cooking results in protein denaturation exposing more peptide bonds for easy
digestion.
6. Monosodium glutamate (MSG) is used as a flavoring agent in foods to increase
taste and flavor.
7. In some individuals intolerant to MSG, Chinese restaurant syndrome (brief and
reversible flu-like symptoms) is observed.

Proteins and Aminoacids

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Proteins and amino acids

• Proteins form the fundamental basis of structure and function of life

03/20/2024 Khyber Medical University Institute of Paramedical Sciences 2

• In addition to C, H, and O, proteins also contain N.

• The nitrogen content is around 16% of the molecular weight of proteins.

R is called a side chain and can be a hydrogen, aliphatic, aromatic or

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• Two amino acids leucine and lysine are exclusively ketogenic.

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3. Gamma-carboxyglutamic acid is found in certain plasma proteins involved in

4. Cystine is formed by combination of two cysteines. Cystine is also considered

• They may be either alpha-or non-alpha-amino acids.

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• Certain D-amino acids are also found in the antibiotics (actinomycin-D,

• 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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4. Monosodium glutamate (MSG) is used as a flavoring agent in food industry, and

• In some individuals intolerant to MSG, Chinese restaurant syndrome (brief and

• All the amino acids except

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• Isoelectric pH (pI) is defined as the pH at which a molecule exists as a zwitterion or

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• Thyroxine (a tyrosine derivative produced in the thyroid gland of animals) is a hormone

2. Amino acids are precursors of a variety of complex nitrogen-containing molecules- the

• 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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a) Defense proteins: Immunoglobulins involved in defense mechanisms.

b) Contractile proteins: Proteins of skeletal muscle involved in muscle contraction

c) Respiratory proteins: Involved in the function of respiration, like hemoglobin,

d) Structural proteins: Proteins of skin, cartilage, nail.

e) Enzymes: Proteins acting as enzymes.

f) Hormones: Proteins acting as hormones.

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B. Conjugated proteins: These are proteins which in addition to amino acids in

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• β-keratins are deficient in cysteine and, rich in glycine and alanine.

• They are present in spider’s web, silk and reptilian scales.

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a) Nucleoproteins-The nucleoproteins are compounds made up of simple basic proteins such

e) Metalloproteins: As the name indicates, they contain a metal ion as their

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• This class of proteins are derived from simple or compound proteins by

• Examples: Protein products obtained by the enzymatic digestion of proteins.

• Peptides are chains of Amino Acids.

• In a peptide, polypeptide, or protein, the amino-terminal end is placed on the

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• Molecules with low molecular weights, typically consisting of fewer than 50

• Proteins may have thousands of amino acid residues