This document discusses amino acids and proteins. It defines that amino acids are the monomer units that make up proteins and polypeptides. There are 300 amino acids found in nature but only 20 are used in protein synthesis. Proteins perform important structural, catalytic and regulatory functions in the body. The structure of proteins involves four levels: primary, secondary, tertiary and quaternary. Denaturation involves the unfolding of protein structure through physical or chemical means.

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

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 NC 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

19. Based on biological function

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

26. Denaturation
• Denatured protein has more exposed site for
enzyme action
• Cooking denatured easy digestion

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