Proteins
Course Contents
• General chemistry of amino acids
• Composition
• Amphoteric nature
• Dipeptides
• Structure of Proteins
• o Primary
• o Secondary
• o Tertiary
• Quaternary
• Functions of Proteins
• Biological importance of Proteins
• Classification of Proteins on the basis of
• o Solubility
• o Composition
• o Biological functions
• Properties of Proteins
• o Colloidal nature
• o Denaturation of Protein
• After the completion of this unit students will be able to:
• 1. Discuss the general structure of amino acids.
• 2. Discuss the following
• - Essential and non essential amino acid.
• - Polar and non polar amino acid
• - Zwitter ion
• 3. Describe classification of proteins according to solubility, composition,
• function and shape.
• 4. Explain the significance of protein denaturation.
• 5. Discuss the structure of dipeptides and tripeptides.
• 6. Describe the primary, secondary, tertiary and quaternary structure of protein.
Amino Acids
• Amino acids are the structural units that make up proteins.
• They join together to form short polymer chains called peptides or
longer chains called either polypeptides or proteins.
• These polymers are linear and unbranched, with each amino acid within
the chain attached to two neighboring amino acids.
• The process of making proteins is called translation
Importance
• Building blocks of proteins
• As a source of energy: CO2+Urea
• Gluconeogenesis: glucose formation.
• Flavor enhancer: glutamic acid
• Artificial sweetener: Aspartame
• 5-hydroxytryptopan: Depression treatment
Amino Acids
• Amino acids: structural units of proteins.
• When joined together: peptides or Proteins.
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Date: October 25, 2015
• Linear and unbranched
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Date: October 25, 2015
Structure
Amino acid (Building blocks of proteins)
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Date: October 25, 2015
Naming the carbon atoms in amino acids
Amino Acids: Atom Naming
• Organic nomenclature: start from one end
• Biochemical designation: start from
-carbon and go down the R-group
Alpha, Beta and Gamma amino acids
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Essential and non essential amino acids
Lysine: K
Essential Tryptophan: W
Amino acids Threonine: T
Valine: V
KW TV FILM
Phenylalanine: F
Isoleucine: I
Leucine: L
Methionine: M
Nonessential
Alanine
Asparagine
Aspartic acid
Cysteine
Glutamic acid
Glutamine
Glycine
Proline
Selenocysteine
Serine
Tyrosine
Arginine
Histidine
Ornithine
Taurine
Structures of Amino Acids
Amino acids differ in the R group
Glycine
Gly
G
R: H
Alanine
Ala
A
R: CH3
A: means one CH3 only
Serine
Ser
S
Cysteine
Cys
C
Meth thio nine Methionine
Methyl Thio Isnain:2(CH2) Met
M
Phenylalanine
Phe
F
Phenyl
Alanine
Tyrosine
Tyr
Tyr osine
Y
Aey tair-e-lahoti
Tryptophan
Trp
W
Histidine
His
H
Valine
Val
V
Threonine
Thr
T
Leucine
Leu
L
Yo: means one CH2
Isoleucine
Ile
I
Isomer of leucine: One methyl group drops one step down
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Date: October 25, 2015
Aspartic acid
Asp
Asp: Starts with A
D
A: One: One Carbon
Glutamic acid
Glu
E
Glu: Two: Two carbons
Asparagine
Asn
N
Asp: From Aspartic acid
Ine: For amine: NH2 instead of OH in
COOH
Glutamine
Gln
Q
Glut: From Glutamic acid
Ine: For amine: NH2 instead of OH in
COOH
Lysine
Lys
K
4 carbons with one amino group
Arginine
Arg
R
Proline
Pro
P
All above mentioned amino acids show
chirality except glycine
• What is chirality?
Chirality
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Date: October 25, 2015
Most -Amino Acids are Chiral
• The -carbon has always
four substituents and is
tetrahedral
• All (except proline) have an
acidic carboxyl group, a basic
amino group, and an alpha
hydrogen connected to the -
carbon
• Each amino acid has an
unique fourth substituent R
• In glycine, the fourth
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Date: 2014
substituent is also hydrogen
Classification
Amino Acids: Classification
Common amino acids can be placed in five
basic groups depending on their R substituents:
• Nonpolar, aliphatic (7)
• Aromatic (3)
• Polar, uncharged (5)
• Positively charged (3)
• Negatively charged (2)
Aliphatic Amino Acids
Aromatic Amino Acids
Charged Amino Acids
Polar Amino Acids
Special Amino Acids
Peptides and peptide bond formation
Zwitterions
Isoelectric point
• The isoelectric point (pI) is the pH value at which the molecule
carries no electrical charge or the negative and positive
charges are equal. The PH at which amino acids are present in
zwitterion form.
Peptides and Peptide bonds
“Peptides” are small condensation
products of amino acids
They are “small” compared to proteins
(di, tri, tetra… oligo-)
Importance and functions
Proteins
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Proteins
• 1: Biochemical compounds: Polymers of amino acids
• 2: Composition: one or more polypeptides (amino acids)
• 3: Structure: folded into a globular or fibrous form
• 4: Function: It carries out several biological functions.
Importance and Functions of Proteins
Importance or Functions of proteins
• 1. cell structure: cytoskeleton (mircrofilamints, microtubules)
• 2. contractile machinery of muscle: Actin Myosin
• 3. Oxygen transport: Hemoglobin
• 4. Search for foreign invaders: Antibodies
• 5. Reaction catalysis: Enzymes
• 6. Sensing and responding: Receptors
• 7. Many other functions previously explained in amino acids section
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Date: 2014
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Date: 2014
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Types or Classes of Proteins
Type: 1
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Types according to composition
• Simple proteins (Only polypeptide chains)
e.g. Albumin, glubulin, glutinin, prolamin
• Conjugated proteins (Polypeptide chain + other molecules)
e.g. nucleoproteins, glycoprotein
• Derived proteins (obtained from simple proteins by the action of enzymes
and chemical agents)
e.g. Peptides i.e. proteoses (by water) and peptones (by enzymes)
Classification on solubility
• Proteins can be broadly classified into three groups, based on their
shape and solubility.
• Fibrous proteins: rod like structure. not soluble in water. Collagen.
• Globular proteins: spherical. soluble in aqueous solution.
Myoglobin.
• Membrane proteins: in association with lipid membranes. not
soluble in aqueous solution. Rhodopsin.
continued
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Levels of Protein Structures
Levels of protein structure
Primary Structure
• Sequence of the amino acids
Secondary structure
• Folding of short polypeptide units into geometrically ordered units
• The secondary protein structure is the specific local geometric shape
caused by intramolecular and intermolecular hydrogen bonding of
amide groups.
Types of secondary structures
• Alpha Helix: In the alpha helix, the polypeptide chain is coiled tightly
in the fashion of a spring.
• Beta Sheets: Beta sheets consist of beta strands connected laterally
by at least two or three backbone hydrogen bonds, forming a
generally twisted, pleated sheet. A beta strand (also β strand) is a
stretch of polypeptide chain typically 3 to 10 amino acids long with
backbone in an almost fully extended conformation.
Beta sheet and its types
Antiparallel
Parallel
Tertiary Structure
Tertiary structure
• The three dimensional assembly of secondary structure into a
functional unit.
Quaternary structure
More than one polypeptide chains
Fibrous and Globular Proteins
Fibrous proteins
• Scleroproteins: fibrous proteins,
• Examples: Keratin, collagen, elastin, and fibroin are all scleroproteins.
• The roles of such proteins include protection and support, forming
connective tissue, tendons, bone matrices, and muscle fiber.
Keratin
Collagen
Elastin
• Shape: long protein filaments: rods or wires.
• Function: structural and storage
• Solubility: inert and water-insoluble.
• Occurrence: occurs as an aggregate due to hydrophobic side chains
that protrude from the molecule.
• has limited residues with repeats
• The structures often feature cross-links between chains (e.g., cys-cys
disulfide bonds between keratin chains).
• Does not denature as easily as globular proteins.
Globular Proteins
Globular proteins
• Globular proteins: spheroproteins
• Globular proteins are spherical ("globe-like")
• somewhat water-soluble
• they actually form colloids in water
• The term globin can refer more specifically to proteins including the
globin fold
Continued
• The molecule's apolar (hydrophobic) amino acids are bounded
towards the molecule's interior
• whereas polar (hydrophilic) amino acids are bound outwards,
allowing dipole-dipole interactions with the solvent, which explains
the molecule's solubility.
• folding in a different way can effect function of globular proteins
• Less stable as compared to fibrous proteins
Assignments
Biological significance of proteins
Physical Properties of proteins
Chemical properties of proteins
Colloidal nature of proteins
Denaturation of proteins
Thank You
