The document provides a comprehensive overview of amino acids and proteins, detailing their structures, classifications, and roles in biological functions. It explains the general structure of amino acids, their polarity and charge, as well as how they contribute to protein structures at various levels. Additionally, it emphasizes the distinction between essential and non-essential amino acids and their significance in human nutrition.

2. Chemistry of amino acids and
proteins

3. Amino acids
Definition of an amino acid
It is an organic acid in which one hydrogen
atom is replaced by an amino group (NH2).The
amino group is usually attached to the - carbon
atom (the carbon atom next to the - COOH group).

4. H

R -αC - COOH

NH 2
General structure of amino acids
N.B.
R is the side chain and may be represented by H, CH3, CH3-
CH2, or CH3-CH2-….

5. General structure of amino acids
- Each amino acid (except proline) has a carboxyl
group, an amino group, and a distinctive side chain
“R-group” bonded to the  -carbon atom.
- Proline's side chain and the α-amino group form a
rigid, five-membered ring structure. So, proline is
a secondary (rather than a primary) amino group.
It is frequently referred to as an imino acid.

6. Primary and secondary amino groups
2
(imino group)
Amino acid
R
R-group
Proline (imino acid)
α α

7. Ionization of amino acids
- At physiologic pH (approximately pH 7.4), the
carboxyl group is dissociated, forming the
negatively charged carboxylate ion (–COO-), and
the amino group is protonated forming the
positively charged ammonium ion (-NH3
+).
- So, amino acids are referred to as amphoteric
electrolytes (ampholytes) and can act as buffers i.e.
they act as an acids in alkaline medium and as
bases in acidic medium.

8. H

H2N -αC - COOH

R
Ionization of amino acids
H

+H3N -αC – COO

R
At physiological pH (7.4)
H+
Carboxylate
ion
Ammonium
ion Ampholyte

9. Optical properties of amino acids
• The -carbon of all amino acids (except glycine)
is attached to four different chemical groups, so
it is a chiral or optically active carbon atom.
• Glycine is optically inactive because its -
carbon has two hydrogen atoms.

10. All amino acids except glycine are optically
active
COOH COOH
H2N α C H H2N α C H
R CH3
Any amino acid Alanine
(Optically active, shows
D and L isomers)
chiral (asymmetric)
carbon atom

11. Glycine is optically inactive
H H
H2N α C COOH H2N α C COOH
R H
Any amino acid Glycine
(Optically inactive)
Achiral (symmetric)
carbon atom

12. D- and L- isomers (enantiomers, mirror image
isomers) of amino acids

13. D- and L- isomers (enantiomers, mirror image
isomers) of amino acids
COOH COOH
H2N α C H H α C NH2
R R
L - amino acid D - amino acid
Amino
group

14. • All amino acids found in proteins are of the
L- configuration.
• However, D-amino acids are found in some
antibiotics and in plant and bacterial cell walls.

15. Classification of amino acids
A. According to the charge and polarity of their side
chains
• Amino acids with non polar side chains
• Amino acids with polar side chains
B. According to the biological value
• Essential amino acids
• Non-essential amino acids
C. Chemical classification

16. Non polar and polar side chains
.
+ +
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Nonpolar
Negatively
charged
(acidic)
Uncharged
Polar
Positively
charged
(basic)
Net
Charge =
0
Net
Charge =
0
Net
Charge =
2+
Net
Charge =
2-

17. Amino acids with non polar side chains
- The side chains of these amino acids have an even
distribution of electrons.
- Non polar side chains does not bind or give off
protons or participate in hydrogen or ionic bonds.
- Non polar side chains are “oily” or lipid-like, a
property that promotes hydrophobic interactions.

18. Amino acids with non polar side chains

19. Amino acids with polar side chains
- The side chain has an uneven distribution of
electrons and can form hydrogen bonds with water.
- They are classified into:
A. amino acids with uncharged polar side chains.
B. amino acids with acidic side chains.
C. amino acids with basic side chains.

20. Amino acids with uncharged polar side chains
- These amino acids have zero net charge at neutral
pH.
- They include:
A. serine, threonine, and tyrosine; each contains a
polar hydroxyl group that can participate in
hydrogen bond formation.
B. cysteine; it contains a polar sulfhydryl (-SH)
group that can participate in hydrogen bond
formation.

21. C. asparagine and glutamine; each contains a
carbonyl group and an amide group, both of
which can also participate in hydrogen bonds.

22. Amino acids with uncharged polar side chains

23. Amino acids with acidic polar side chains
- They include aspartic acid and glutamic acid.
- At neutral pH, the side chains of these amino acids
are fully ionized, containing a negatively charged
carboxylate group (- COO-). Therefore, they are
called aspartate and glutamate.

24. COO-
I
CH2
I
CH.NH3
+
I
COO-
Aspartate
COO-
I
CH2
I
CH2
I
CH.NH3
+
I
COO-
Glutamate
Amino acids with acidic polar side chains

25. Amino acids with basic polar side chains
- They include lysine and arginine.
- At physiologic pH, the side chains of these 2 amino
acids are fully ionized and positively charged.
- In contrast, histidine is weakly basic, and the free
amino acid is largely uncharged at physiologic pH.

26. CH2-CH2-CH2-CH2-CH.COO-
I I
NH3
+ NH3
+
Lysine
CH2-CH2-CH2-CH.COO-
I I
NH NH3
+
I
HN=C-NH3
+
Arginine
Amino acids with basic polar side chains

27. CH2 - CH-COO-
I
NH3
+
NH
N
Histidine

28. Location of nonpolar amino acids in soluble
and membrane proteins
• In proteins found in aqueous solutions (a polar
environment), nonpolar R-groups of amino acids
cluster together in the interior of the protein and
help give it its three-dimensional shape.
• However, for proteins that are located in a
hydrophobic environment, such as a membrane,
the nonpolar R-groups are found on the outside
surface of the protein, interacting with the lipid
environment

29. Location of nonpolar amino acids in soluble and
membrane proteins

30. Classification of amino acids according to their
biological value
A. Essential amino acids
- They can not be synthesized by the human body
so it is essential to take them in diet.
- They involve the following 9 amino acids;
1. Threonine Hydroxy amino acid
2. methionine. Sulfur-containing amino acid
3. valine
4. leucine Branched amino acids
5. Isoleucine
6. Lysine
7. Histidine
8. Phenylalanine Aromatic amino acid
9. Tryptophan Heterocyclic amino acid
Basic amino acids

31. How to remember the essential amino acid?
I Left Home To Make
Isoleucine Leucine Histidine Tryptophan Methionine
Visit Throught London Philipin Argantin
Valine Threonine Lysine Phenylalanine Arginine

32. B. Non essential amino acids
- They can be synthesized by the human body so it is not
essential to take them in diet.
- They involve the following 10 amino acids;
1. Glycine 2. Alanine
3. Serine 4. Cysteine
5. Tyrosine 6. proline
7. Aspartate 8. Glutamate
9. Asparagine 10. Glutamine

33. N.B.
Arginine is essential under some conditions.

34. Sulfur containing
•Cysteine
•Methionine
Chemical classification of amino acids
Neutral Acidic
•Aspartic
•Glutamic
Basic
•Arginine
•Lysine
Aliphatic Aromatic
•Phynylalanine
•Tyrosine
Heterocyclic
•Tryptophan
•Proline
•Histidine
With a straight
hydrocarbon chainsi
•Glycine
•Alanine
•Valine
•Leucine
•Isoleucine
Hydroxyl containing
•Serine
•Threonine
With an amide group
•Asparagine
•Glutamine

35. Abbreviations and symbols for the
commonly occurring amino acids
• Three-letter abbreviation
• One-letter symbol

36. Abbreviations and symbols for the commonly
occurring amino acids

37. Beware!!

38. ‫عليكم‬ ‫السالم‬
‫بركاته‬ ‫و‬ ‫هللا‬ ‫رحمة‬ ‫و‬

39. 39
Levels of Proteins Structure
There are four levels of protein structure
1.
Primary Structure.
2.
Secondary Structure.
3.
Tertiary Structure.
4.
Quaternary Structure.

40. 40
Primary Structure
- It refers to the number and sequence of amino
acids in a polypeptide chain.
- It is stabilized by peptide bonds.
- It gives rise to a straight chain.
aa1 aa2 aa3 aa4 aa5 aa6
Peptide Bonds
Amino Acids (aa)

41. 41
Different Proteins Having Different Primary
Structures
Gly Ala Asp Met Ser
Gly Asp
Ala Met Asp
Gly Ser
Gly Asp Met Asp
Asp
Asp
Ser

42. 42
Secondary Structure
•
It refers to folding of a primary structure into a
spiral (called α helix) and pleats (called β
pleated sheets) held together by hydrogen
bonds.
•
There are 2 forms of the Secondary Structure.
Alpha Helix
Beta Pleated Sheet
Hydrogen Bonds

43. Secondary structure

44. 44
Tertiary Structure
•
It the bending and folding of the secondary
structure into a more complex 3- dimentional
arrangement.
•
It is stabilized by hydrogen bonds, ionic bonds,
or disulfide bridges (S-S).
Alpha Helix
Beta pleated sheet

45. Tertiary structure

46. Examples of Bonds in Protein Molecule

47. 47
Quaternary Structure
•
It refers to the non-covalent association of
several polypeptide chains each called a subunit
in the protein molecule.
•
It is present in proteins that are composed of
more than one polypeptide chain.
•
Examples
1. Enzymes.
2. Hemoglobin; composed of 4 polypeptide
chains
or subunits; 2 α chains and 2 β chains.
3. Collagen: composed of 3 polypeptide chains or
subunits.
Subunit

48. Quaternary Structure

49. II. STRUCTURE OF THE AMINO ACIDS
• Amino acids that described in nature are more
than 300 different amino acids BUT, only 20 are
constituents of mammalian proteins.
• These 20 A.A. are the only A.A. coded for by DNA
(the genetic material in the cell).
• Each amino acid (except proline) has a carboxyl
group, an amino group, and a distinctive side
chain “R-group” bonded to the  -carbon atom.

50. ‫عليكم‬ ‫السالم‬
‫بركاته‬ ‫و‬ ‫هللا‬ ‫رحمة‬ ‫و‬

51. H H
 
H2N- αC – COOH H2N- αC - COOH
R1 R2
H2O

52. H H
 
H2N-αC – CO HN- αC - COOH
R1 R2
peptide bond
Dipeptide

53. Proteins
O R H O R H O R
H2N-CH-C N-CH-C N-CH-C N-CH-C N-CH-C N-CH-COOH
R H O R H O R H
Peptide bonds

54. Peptides
They are composed of amino acids linked together
by peptide bonds.
O R H O R H O R
H2N-CH-C N-CH-C N-CH-C N-CH-C N-CH-C N-CH-COOH
R H O R H O R H
Peptide bonds

55. Sulfur containing
•Cysteine
•Methionine
Chemical Classification of Amino Acids
Neutral Acidic
•Aspartic
•Glutamic
Basic
•Arginine
•Histidine
Aliphatic Aromatic
•Phynylalanine
•Tyrosine
Heterocyclic
•Tryptophan
•Proline
•Histidine
With a hydrocarbon
side chain
•Glycine
•Alanine
•Valine
•Leucine
•Isoleucine
Hydroxyl containing
•Serine
•Threonine
With an amide group
•Asparagine
•Glutamine

56. H-CH-COOH
I
NH2
Glycine
Aliphatic with a straight or branched side chain
CH3-CH-COOH
I
NH2
Alanine
CH-CH-COOH
I
NH2
Valine
CH3
CH3
CH-CH2-CH-COOH
I
NH2
Leucine
CH3
CH3
CH-CH-COOH
I
NH2
Isoleucine
CH3-CH2
CH3
CH2-CH2-COOH
I
NH2
-Alanine

57. Aliphatic with Hydroxyl-Containing Side Chain
CH3-CH-COOH
I I
OH NH2
Serine
CH3-CH-CH-COOH
I I
OH NH2
Threonine
CH2-CH2-CH-COOH
I I
OH NH2
Homoserine

58. Aliphatic with Sulphur-Containing Side Chain
CH3-CH-COOH
I I
SH NH2
Cysteine
CH2-CH2-CH-COOH
I I
S-CH3 NH2
Methionine
HOOC – CH – CH2 CH3 – CH –
COOH
I I I I
NH2 S S NH2
Cystine CH2-CH2-CH-COOH
I I
SH NH2
Homocysteine

59. Phenylalanine
CH2 CH-COOH
I
NH2
Tyrosine
CH2 CH-COOH
I
NH2
I
OH
Amino Acids with Aromatic Side Chain

60. Tryptophan
CH2 CH-COOH
I
NH2
N
H
COOH
N
H
Proline
Histidine
CH2 CH-COOH
I
NH2
NH
N
HO
COOH
N
H
Hydroxyproline
Heterocyclic Amino Acids

61. COOH
I
CH2
I
CH.NH2
I
COOH
Aspartic acid
CO-NH2
I
CH2
I
CH.NH2
I
COOH
Asparagine
COOH
I
CH2
I
CH2
I
CH.NH2
I
COOH
Glutamic acid
CO-NH2
I
CH2
I
CH2
I
CH.NH2
I
COOH
Glutamine
Acidic Amino Acids and their Amides

62. CH2-CH2-CH2-CH2-CH.COOH
I I
NH2 NH2
Lysine
CH2-CH2-CH2-CH.COOH
I I
NH NH2
I
HN=C-NH2
Arginine
CH2-CH-CH2-CH2-CH.COOH
I I I
NH2 OH NH2
5-Hydroxylysine
CH2-CH2-CH2-CH.COOH
I I
NH2 NH2
Ornithine
Basic Amino Acids

63. Classification of Amino acids according to
Their Biological value
A. Essential amino acids;
-They can not be synthesized by the human body
so it is essential to take them in diet.
- They involve the following 8 amino acids;
1. Threonine Hydroxy amino acid
2. methionine. Sulfur-containing amino
acid
3. valine
4. leucine Branched amino acids
5. Isoleucine
6. Lysine Basic amino acids
7. Phenylalanine Aromatic amino acid
8. tryptophan Heterocyclic amino acid

64. B. Non essential amino acids
-They can be synthesizes by the human body so
it is not essential to take them in diet.
-They involve the following 12 amino acids;
1. Glycine 2. Alanine
3. Serine 4. Cysteine
5. Arginine 6. Histidine
7. Tyrosine 8.proline
9. Aspartate 10. Glutamate
11. Asparagine 12. Glutamine
NB
Arginine and Histidine are essential under some
conditions

65. Classification of Peptides
• Dipeptides;
- Composed of 2 amino acids linked
together by one peptide bond.
• Oligopeptides;
- Composed of 3-10 amino acids linked
together by peptide bonds
- Include tripeptide (3 amino acids linked
together by 2 peptide bonds),
tetrapeptide (4 amino acids linked
together by 3 peptide bonds),
pentapeptide (5 amino acids linked
together by 4 peptide bonds), and so on.

66. Classification of Peptides
• Polypeptides;
- Composed of 11-100 amino acids
linked together by peptide bonds.
• Proteins;
- composed of > 100 amino acids linked
together by peptide bonds.

67. Amino acids of proteins
- Amino acids present in proteins are of the L-type
i.e. the amino (H2N-) group is present on the left
side of the vertical formula.
- There are more than 300 different amino acids in
nature.
- Only 20 amino acids are constituents of
mammalian proteins. These 20 amino
acids are the only amino acids coded for
by DNA.

68. N.B.
- Amino acids that described in nature are
more than 300 different amino acids.
- Only 20 amino acids are constituents of
mammalian proteins. These 20 amino
acids are the only amino acids coded for
by DNA.
- Each amino acid (except proline) has a
carboxyl group, an amino group, and a
distinctive side chain “R-group” bonded to
the  -carbon atom.

69. Proteins
Definition
• The name proteins is derived from the Greek
word proteis, meaning first rank of importance,
because scientist suspected that proteins might
be the most important of all biologic substances
• They are polymers of L-amino acids linked
together by peptide bonds.

70. Structural function e.g.
- Proteins of cell membrane, cytoplasm, cell organells, receptors
- Collagen, elastin, keratin, rhodopsin
BIOMEDICAL IMPORTANCE OF PROTEINS
Importance
of
Proteins
Transport Functions
e.g.
Albumin, Hb, transferrin
and lipoproteins
Metabolic
Regulation
e.g.
enzymes and
protein hormones
Contraction
e.g.
actin and myosin
Protection
e.g.
Immunoglobulins
Blood
Clotting
e.g.
Fibrinogen
prothrombin.

71. Proline
- Proline differs from other amino acids in that it's
side chain and α-amino group form a rigid, five-
membered ring structure. So, proline has a
secondary (rather than a primary) amino group.
It is frequently referred to as an imino acid.

72. • Polar amino acids
The side chain has an uneven distribution of
electrons.

73. Sulfur containing
•Cysteine
•Methionine
Chemical classification of amino acids
Neutral Acidic
•Aspartic
•Glutamic
•Asparagine
•Glutamine
Basic
•Arginin
e
•Lysine
Aliphatic Aromatic
•Phynylalanin
e
•Tyrosine
Heterocyclic
•Tryuptophan
•Proline
•Histidine
With a hydrocarbon
side chain
•Glycine
•Alanine
•Valine
•Leucine
•Isoleucine
Hydroxyl
containing
•Serine
•Threonine

74. cannot be manufactured by the
body
How to remember the essential amino acid?
I Left Home To Make
Isoleucine Leucine Histidine Tryptophan Methionine
Visit Throught London Philipin Argantin
Valine Threonine Lysine Phenylalanine Arginine

75. Alanine Glutamic Acid Lysine
Threonine
Arginine Glutamine Methionine Tryptophan
Aspartic Acid Glycine Phenylalanine
Tyrosine
Asparagine Histidine Proline Valine
Cysteine-Cystine Isoleucine Serine
9 Essential amino acids
cannot be manufactured by the body
11 Non-essential amino acids (+ selenocystein)
can be manufactured by the body with proper nutrition.
20 amino acids:

76. cannot be manufactured by the
body
How to remember the essential amino acid?
I Left Home To Make
Isoleucine Leucine Histidine Tryptophan Methionine
Visit Throught London Philipin Argantin
Valine Threonine Lysine Phenylalanine Arginine

77. Amino acids with uncharged polar side chains

78. Amino acids with acidic polar side chain

79. Amino acids with basic polar side chains

80. Abbreviations and symbols for the commonly
occurring amino acids
GLu
ASP