Amino acids are the building blocks of proteins. There are 20 standard amino acids that make up the proteins in living organisms. Amino acids contain an amino group and a carboxyl group, and can be joined together via peptide bonds to form polypeptide chains. Proteins have complex structures with four levels of organization - primary, secondary, tertiary, and quaternary structure. The primary structure is the linear sequence of amino acids in the polypeptide chain. Secondary structures include alpha helices and beta sheets formed from regular patterns of hydrogen bonds between amino acids in the chain.

1. Amino Acids and Proteins
Naval Kishor Yadav
Asst Prof,
Department of Biochemistry
Manipal College of Medical Sciences

2. Proteins
Protein: Greek word: proteios – holding the first place
Proteins are diverse and abundant class of biomolecules
that constitute > 50% of the dry weight of the cells
Final product of information pathway
DNA RNA Proteins
Virtually has central role in all aspect of cell structure and
function
Proteins are polymers of L-α-amino acids

3. ~ 300 amino acids occur in nature
Only 20 – known as standard amino acids
Universal nature of the genetic code available for
the incorporation of only 20 amino acids
20 amino acids are commonly found in the proteins
and are joined together by peptide bonds from
carboxyl group to amino group

4. • Berzelius (Swedish chemist) suggested the
name proteins to the group of organic
compounds that are utmost importance to life.
• Mulder (Dutch chemist) in 1838 used the term
proteins for the high molecular wt, nitrogen-
rich and most abundant substances present in
animals and plants.
Historical background

5. Biomedical importance
Disease states Altered structure and function
of proteins
1. Hemoglobinopathies
a. Sickle cell anemia:
HbS, Mutation β6 Glu Val
b. Thalassemia: Insufficient production of either α
or β chain of hemoglobin
α-Thalassemia
β-Thalassemia
2. Marfan Syndrome:
Single amino acid change in an elastic connective
tissue protein-fibrilin

6. Biomedical importance
3. Cystic fibrosis: Single amino acid deletion in the
cystic fibrosis transmembrane regulatory (CFTR)
proteins
4. Prion Diseases: significant alterations in secondary
and tertiary structures of proteins
a. Creutzfeldt-Jakob Disease (Human)
b. Scrapie (Sheep)
c. Bovine spongiform Encephalopathy
(Mad Cow Disease)

7. Amino acid
Amino acids: Group of organic compounds
containing 2 functional groups:
amino (-NH2) and
carboxyl (-COOH)
Amino group- Basic
Carboxyl- Acidic

8. Amino acids provide the monomer unit to
the synthesis of long polypeptide chain of
proteins
Amino acids and their derivatives participate
in diverse cellular functions, such as
neurotransmitters, synthesis of heme, purine
and pyrimidines, and urea

9. Functions of amino acids
Amino Acids
Amino Acids

10. General structure of amino acids
Alpha- amino acids: Both the amino groups and
the carboxyl groups are attached to the same
carbon atom.
R-C-COOH R-C-COO-
(General structure) (Exists as ion)
Where R is different for each of the 20 amino acids
H
NH3+
H
NH2
Amino acids mostly exist in the ionized form in the
biological system

12. Each amino acid is assigned a 3 letter abbreviation
and 1 letter symbol: For eg;
Glycine: Gly/ G
Alanine: Ala/ A
Valine: Val/V
Leucine Leu/L
Asparagine: Asn/N

13. Classification of amino acids
Based on;
1) Structure
2) Polarity
3) Nutritional requirement
4) Metabolic fate

14. Amino acid classification based on structure

17. Classification of amino acids based
on polarity
Non-polar amino acids (hydrobhobic amino acids)
Polar amino acids with no charge on “R” group
Polar amino acids with positive “R” group
Polar amino acids with negative “R” group

18. Nutritional classification of amino
acids
Essential amino acids:
– Cannot be synthesized by the body and need to be supplied
through the diet
– Includes (10 amino acids) : Arginine, Valine, Histidine,
Isoleucine, Leucine, Lysine, Methionine, Phenylalanine,
Threonine, Tryptophan
(Pnemonics: MTV ATP HILL)
Semi-essential amino acids: Arginine and histidine
can be synthesized by adults and not by growing children
Non essential amino acids:
– Body can synthesize the remaining 10 amino acids to
sustain the biological demands

19. Classification of amino acids on
basis of metabolic fate
Carbon skeleton of amino acids can serve as precursor for the
synthesis of glucose or fats or both, hence classified as:
Glycogenic amino acids
Alanine, Aspartate, Glycine, Methionine, Serine, Cysteine,
Asparagine, Glutamate, Glutamine, Proline, Histidine, Arginine,
Methionine, Threonine and Valine
Ketogenic amino acids:
Leucine, Lysine
Glycogenic and ketogenic amino acids:
Isoleucine, Phenylalanine, Tryptophan, Tyrosine

20. Properties of amino acids

21. Physical Properties
1) Solubility: most amino acids are soluble in water and
insoluble in organic solvents
2) Melting points: generally have higher m.p >200oC
3) Taste: Sweet ( Gly, Ala) tasteless (Leu) bitter (Arg)
4) Optical properties: all amino acids except Glycine possess
optical isomers due to the presence of asymmetric
carbon atom
5) Ampholytic property: due to the presence of both -NH2
and –COOH groups, they can donate or accept proton

22. Optical isomers of amino acids
Asymmetric carbon atom ( carbon atom attached to
4 different groups) exhibit optical isomerism.
Except glycine all amino acids posseses four distinct
groups ( R, H, COO-, NH2+)
Thus all amino acids except glycine have optical
isomers

24. The structure of L- and D- amino acids are written based
on the configuration of L- and D- Glyceraldehyde as
shown

25. Ampholytic property
When an amino acid is dissolved in water, it exists
in ionic form
Zwitterion (German: zwitter=hybrid) is a hybrid
molecule contianing equal no. of positive and
negative charges.
It thus bears zero net charge

26. A zwitterion can act as either an acid (proton donor)
or a base (proton acceptor):
Substances having this dual nature are amphoteric and
are often called ampholytes.

27. Isoelectric pH (pI)
The pH at which the molecule has an equal number of +ve
and -ve charges and thus is electrically neutral.
For simple amino acids such as alanine, the pI is an average
of the pKa's of the carboxyl (2.34) and amino (9.69) groups.
For polyfunctional amino acids, pI is also the pH midway
between the pKa values on either side of the isoionic
species.

28. Fig: Existence of amino acids as cations,
anions and zwitterions

29. Chemical properties
General reactions of amino acids are due to
the presence of two functional groups
namely;
– carboxyl (-COOH) and
– amino (-NH2)

30. Reactions due to (-COOH) group
1) Amino acids form salts (-COONa) with bases and
esters (-COOR’) with alcohols
2) Decarboxylation : amino acids undergo
decarboxylation to form amines
3) Reactions with ammonia: the carboxyl group of
dicarboxylic acids react with ammonia to form amide
– E.g; Aspartic acid + NH3 Asparagine
– Glutamic acid +NH3 Glutamine

31. Reactions due to –NH2 group
1) The amino groups behave as bases and combine with acids
(e.g HCL) to form salts (-NH3
+Cl- )
2) Reaction with ninhydrin: The α- amino acids react with
ninhydrin to form a purple, blue or pink colour complex (
Ruhemann’s purple )
Ninhydrin reaction is effectively used for quantative
determination of amino acids. A common application of this test
is the visualization of amino acids in paper chromatography
(Proline and hydroxyproline give yellow colour with ninhydrin)
2

32. 3) Colour reactions of amino acids
4) Transamination
5) Deamination

33. Non Standard Amino Acids
Besides 20 standard amino acids present in protein
structure, there are several other amino acids
which are biologically imp. these include;
1) Amino acid derivatives found in proteins e.g;
collagen, histones, cystine
2) Non-protein amino acids performing specialized
functions : e.g; ornithine, citrulline, creatinine,
Gamma amino butyric acid
3) D-amino acids: found in antibiotics (actinomycin-D,
Valinomycin)

34. Peptides, Polypeptides and Proteins
Peptides are chains of amino acids (AAs)
Three AAs can be joined by two peptide bonds to form a
tripeptide
Similarly, AAs can be linked to form tetra-, pentapeptides and so
forth
When few AAs are joined this way, the structure is called an
oligopeptide
When many AAs are joined, the product is called a polypeptide
Proteins are polypeptides that may have thousands of AA
residues

35. Structure of proteins
Structure of proteins is rather
complex and can be studied under
four organizations:
Primary structure- denotes the
sequence of amino acids in
protein
Secondary structure- denotes
the spatial regular arrangement
of amino acids near to each
other in linear sequence
Tertiary structure- denotes the
random 3-D structure of a
functional protein
Quaternary structure- denotes
the spatial arrangement of
polypeptide chains (subunits) in
some proteins
:

36. Primary structure
Largely responsible for the function of protein
Majority of the genetic disease are mainly due to
abnormality in AA sequence (1o structure)
Primary structure determines the physical and
chemical properties of proteins

37. H
H H H H H H
O O O H H O H H O
N C C N N
C C C C
H CH3
CH2
OH
N-terminus
N C C
CH2
C
O
OH
CH2
N C C
CH
CH3
H3C
CH2
OH
H H O
N C C
H H O
N C C
H H O
N C C
CH2
SH
OH
C-terminus
Many amino acids joined together = Polypeptide chain

38. Peptide bonds
AAs are joined together covalently by peptide linkage
which is amide linkage between the carboxyl group of one
amino acid and the α-amino group of other
The peptide bonds are not broken by high conditions like
heat that denature proteins
Figure:

39. Characteristics of Peptide bond
Exists in resonating form
Shows partial double bond
character
Shorter than the normal C-N
bonds
No free rotation around the bond
(a) (b)
Fig: (a) resonance structures of the peptide bond, (b) peptide units within a polypeptide
Rigid and planar
Trans configuration
Uncharged but polar

41. Naming of peptides
For naming of amino acids, suffixes- ine (glucine), an
(tryptophan), ate (glutmate) are changed to –yl with
the exception of C-terminal amino acid
Eg. Glutamyl-Seryl-Lysyl-Valyl- Alanine
Peptide chains are written with the free amino (N-
terminal residue) at the left and the free carboxyl end
(C-terminal residue) at the right
AA sequence is read from the N-terminal end to the C-
terminal end.

42. Three-letter abbreviations linked by straight lines
represent an unambiguous primary structure.
Glu-Ala-Lys-Gly-Tyr-Ala
Lines are omitted for single-letter abbreviations.
E A K G Y A

43. Secondary structure of proteins
Spatial confirmation of polypeptide chain by
twisting and folding
2 types of secondary structure are mainly
known
i. α-helix
ii. β-sheet
iii. Bend/ loop

44. α-helix
Has spiral structure
Spiral structure consists of tightly packed
coiled polypeptide backbone core with AA
side chains extending outward from central
axis
Stabilized by H-bonding
Each turn of α-helix consist 3.6 AAs and
travels a distance of 0.54 nm

45. α-helix
Fig:
Fig:

46. • For example, the keratins are a family of closely
related, fibrous proteins whose structure is nearly
entirely α-helical

47. β-sheet
Another form of 2o structure in
which all of the peptide bonds
are involved in H-bonding
Composed of two or more
peptide chains or segments of
polypeptide chains
β-sheets can be arranged either
in parallel or anti-parallel to
each other

48. hydrogen bonding patterns in
an antiparallel beta sheet
hydrogen bonding patterns in
a parallel beta sheet

49. Bend / Loop
• Polypeptide chains can fold upon
themselves forming a bend or a
loop
• Usually 4 a.a. are required to
form the turn
• H-bond between the 1st and 4th
amino acid in the turn
• Bends are usually on the surface
of globular proteins
• Proline residues frequently
found in bends/loops

50. Tertiary structure
Compact 3-D arrangement of protein structure
formed by bending and folding of polypeptide chain
A compact structure with hydrophobic side chains
held interior and hydrophilic parts are on the
surface of protein molecule
Interactions between the AA’s side chains guide the
folding of polypeptide to form compact structure

51. The 3o structure is stabilized by
disulfide linkages,
H-bonds,
electrostatic bond and
hydrophobic interactions

52. Quaternary structure
Many proteins contain a single polypeptide (monomers),
but some may consist of two or more polypeptide chains
The arrangements of such subunits is known as
quaternary structure of proteins and the protein is said to
be oligomeric protein. Subunits (monomers) can be
identical or different i.e; The protein is homopolymeric or
heteropolymeric
Subunits are held together by non covalent bonds, H-
bonds, hydrophobic bonds and ionic bonds. E.g
hemoglobin

53. Hemoglobin consisting 2α and 2β- subunits, is an example of
quaternary structure of protein

54. Denaturation
The phenomenon of disorganisation of native
protein structure
Results in loss of secondary, tertiary, quatenary
structure

55. Agents of denaturation
Physical agents:
Heat, violent shaking, x-rays, UV radiation
Chemical agents:
Acids, Alkalies, Organic Solvents, Salts of heavy
metals

56. Features of denaturation
The native helical structure of protein is lost.
The primary structure of a protein remains intact.
Loses its biological activity.
Insoluble in solvents.
Viscosity of denatured proteins increases while its
surface tension decreases.

57. More easily digestible.
It is usually irreversible.
They cannot be crystallized.
Increase in ionizable groups due to loss of
hydrogen and disulfide bonds.

58. Classification of proteins
Can be classified in several ways:
1) Functional classification of proteins
2) Classification based on chemical nature
3) Nutritional classification of proteins

59. Functional classification of proteins
1) Structural proteins
keratin of hairs and nails, collagen of bone
2) Catalytic proteins
enzymes
3) Transport proteins
hemoglobins, Lipoprotein, albumin, transferrin
4) Hormonal proteins
insulin
5) Contractile proteins
actin, myosin

60. 6) Genetic proteins
nucleoproteins
6) Defence proteins
Immunoglobulins
7) Receptor proteins
receptor for hormones

61. Classification based on chemical nature
and solubility
Broadly classified into 3 major groups
Simple proteins: composed only of amino acid residues.
A. Globular proteins e.g albumin, globulins, histones,
B. Fibrous proteins e.g. Collagen, elastin. Keratins
Conjugated proteins: contains non-protein moieties
(prosthetic groups), besides amino acids. E.g;
metalloproteins (eg; ceruloplasmin),
chromoproteins (eg; hemoglobin),
nucleoproteins etc

62. Derived proteins: denatured or degraded
products of simple and conjugated proteins
• E.g coagulated proteins (by heat, acids,
alkali,) peptones, polypeptides, etc

63. Nutritional classification of
proteins
Classified into 3 categories;
Complete proteins: contain all essential 10
amino acids, e.g. Milk casein, egg albumin
Partially complete proteins: partially lack one
or more of essential amino acids, e.g wheat
and rice proteins (partially lacks Lys, Thr)
Incomplete proteins: completely lack one or
more essential amino acids. Hence can’t
promote growth at all, e.g. Gelatin (lacks Trp)

64. Elemental composition of protein (%)
Carbon 50-55 %
Oxygen 19-24 %
Nitrogen 13-19 %
Hydrogen 6-7.3 %
Sulphur 0-4 %
Other elements: P, Fe, Cu, Mg, Zn

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