1. Amino acids
&
Proteins
Dr. Farhana Atia
Assistant Professor
Department of Biochemistry
Nilphamari Medical College, Nilphamari
Email: farhana.atia@gmail.com
2. Amino acids
• Amino acids are monomer unit of proteins &
polypeptides.
• 300 amino acids in nature
• Only 20 are biologically active & take part in
protein synthesis
3. Biomedical Importance
• Support infant growth & maintain health in
adult
• Perform a multitude of structural, hormonal &
catalytic functions essential for life
• Amino acids & their derivatives participates in
various intracellular function such as
– nerve transmission
– regulation of cell growth
– biosynthesis of porphyrin, purine, pyrimidine,
urea
4. • Short polymer of amino acid [polypeptides] perform
prominent role in neuro-endocrine system as
hormones, hormone releasing factor, neuro-
modulators or neurotransmitters.
• Genetic defect in metabolism of amino acids can
result in severe illness such as
– Phenyl ketonuria,
– Albinism,
– Maple syrup urine disease etc.
• Amino aciduria, another genetic disease result from
an impaired ability to transport specific amino acid
to cell
5. Structure
• Each amino acid [except proline]
has
– A carboxyl group
– An amino group
– A side chain (R)
Bonding to α carbon
• At physiologic pH (7.4) carboxyl
group is dissociated (COO⁻) &
amino group is protonated (NH₃⁺)
• Proline- side chain & α amino group
form a ring structure [imino group]
a
6. • In protein all carboxyl & amino groups are combined in
peptide linkage & not available for chemical reaction
except for hydrogen bond formation.
• So side chain (R) dictate role of amino acid in protein
• Based on side chain amino acid may be-
• Non polar
• Oily or lipid like property & promote hydrophobic
interaction that stabilize protein structure
• buried within the hydrophobic core of the protein.
• Polar
• Prefer to reside in an aqueous environment
• Generally found exposed on the surface of a protein.
7. Classification of amino acid
According to R group based on their polarity
1. Non polar & hydrophobic R group
2. Uncharged polar side chain/ neutral aa
3. Positively charged R group/ Basic aa
4. Negatively charged R group/ Acidic aa
8.
9. Essential amino acid
• Ten of 20 amino acid needed for synthesis of body
protein are essential
• They can not be synthesized in human at adequate rate
• So must be supplied in diet
• 8 are essential all the time
• Arginine & histidine: required only in period of rapid
tissue growth [childhood & recovery from illness]
10. Properties of amino acid
• The genetic code specify 20 α-amino acid
• Selenocysteine is referred to as 21st amino acid
• Only L- α-aa occur in protein (D-aa in microorganism)
• May have +ve/ -ve/ zero net charge
• Soluble in polar solvent (water, ethanol), insoluble in
non polar solvent (benzene, ether)
• Isoelectric point (pI): pH at which an amino acid is
electrically neutral (bears no net charge)
– Imp: amino acid may be precipitated at this pH
(separated)
11. • Zwitter ion: Dipolar form of a molecule which
contain same amount of +ve & -ve ion. At pI,
amino acid become zwitter ion
– COOH looses H⁺ [COO⁻], -NH₂ gains H⁺ [NH₃⁺]
Diprotonated form Deprotonated formDipolar form
12. Peptide bond
• Peptide bond is the amide
linkage that is formed
between two amino acids,
which results in (net) release
of a molecule of water (H2O)
• Bond formed between
carboxyl group of one amino
acid & amino group of
another
• Not broken by denaturation
13. Characteristics of peptide bond
• Partial double bond
• Rigid & coplanar
• Trans configuration
• Uncharged (neither accept or give off proton) but
polar
• Naming of peptides
– Left: N-terminal
– Right: C-terminal
– Read from NC terminal
14. Dipeptide: 1 bond between 2 amino acids
Tripeptide: 2 bonds between 3 amino acids
Polypeptide: long peptide chain containing large
number of amino acid
– Usually 3-100 amino acids
– Molecular wt <10,000
• Protein: Complex organic nitrogenous
compound composed of >100 amino acids
linked together by peptide bond
• High molecular weight > 10,000
15. Properties
• Colloid in nature
• Soluble in water, salt solution, dilute acid &
alkali
• Coagulates by weak & strong acid
• Each protein has an iso-electric pH & can be
precipitated
• Denatured by many kinds of physical &
chemical treatment
Proteins
16. Biomedical importance
• Physically & functionally complex macromolecule that
perform multiple critical roles
• Internal protein network (cytoskeleton) maintains
cellular shape & physical integrity
• Actin & myosin- contractile machinery of muscle
• Maintain colloidal osmotic pressure
• Hemoglobin transports O₂
• Circulating antibodies defend against foreign invaders
• Receptor enables cell to sense & responds to
hormones & other environmental cues
• Transport various molecule by forming complex (LP)
17. • Enzyme catalyze reaction
– Generate energy
– Synthesize & degrade biomolecules
– Replicate & transcribe genes
– Process mRNA
• Act as transporter/ carrier (ferritin)
• Proteins are subject to physical & functional
changes that mirror the life cycle of organism in
which they reside
• In molecular medicine, identification of biomarkers
(proteins) is related to specific physiologic state/
disease
20. Structure of protein
Proteins have different level of structural organization
1. Primary structure
2. Secondary structure
3. Tertiary structure
4. Quaternary structure
21. Primary structure
• Denotes the number &
sequence of amino acid
in protein
• Sequence is determined
by gene
• Maintained by covalent
bond of peptide linkage
• Determine biological
activity of protein
• Single amino acid
change have profound
effect
Insulin
22. Secondary structure
• Configurational relationship
between residues (3-4 aa) in
the linear sequence
• Preserved by non covalent
bond/ force
– Hydrogen bond
– Hydrophobic interaction
– Electrostatic bond
– Van der Waals force
1. α-helix
2. β-pleated sheet
23. Tertiary structure
• Denotes the overall
arrangement & inter
relationship of various
region/ domain of single
polypeptide chain
• Formed when α-helix & β-
sheet are held together by
weak interaction
• Domain: Functional & 3-
dimensional structural unit
of a polypeptide chain
• Maintained by non covalent
interaction
• Eg- immunoglobulins
24. Quaternary structure
• Results when 2/ more
polypeptide chain held
together by non covalent
force
• PP chain- structurally
identical/ totally
unrelated
• Each pp chain termed-
monomer/ subunit
• Dimer- CPK
• Tetramer- Hb, Ig, LDH
25. Denaturation
• Unfolding & disorganization or nonspecific
alteration in the secondary, tertiary &
quaternary structure of protein molecule
• Primary structure is not altered [no hydrolysis
of peptide bond]
• Results in
– ↓ solubility
– ↑ precipitability
– May lose biological activity
27. Denaturation
Denaturing agents are-
• Heat
• Organic solvent [Urea]
• Mechanical mixing
• Strong acid/ base
• Detergents
• Ions of heavy metal [Hg, Pb]
• X-ray, UV ray, high pressure
28. Renaturation: may/may not be possible
• Some protein can return to their functional
shape but
• Most protein is permanently disorganized
• Uremia Ig chains disrupt Dialysis (urea
removed) chain reassociate, function
regained
