Amino acids are the monomers that make up proteins. Specifically, a protein is made up of one or more linear chains of amino acids, each of which is called a polypeptide. There are 20 types of amino acids commonly found in proteins. Amino acids share a basic structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and a hydrogen atom. Although the generalized amino acid shown above is shown with its amino and carboxyl groups neutral for simplicity, this is not actually the state in which an amino acid would typically be found. At physiological pH, the amino group is typically protonated and bears a positive charge, while the carboxyl group is typically deprotonated and bears a negative charge. Every amino acid also has another atom or group of atoms bonded to the central atom, known as the R group, which determines the identity of the amino acid. For instance, if the R group is a hydrogen atom, then the amino acid is glycine, while if it’s a methyl group, the amino acid is alanine. The twenty common amino acids are shown in the chart below, with their R groups highlighted in blue.

1. CHEMISTRY OF AMINO ACIDS AND
PROTEINS

2. WHAT IS BIOCHEMISTRY ?
 Biochemistry is the application of chemistry to
the study of biological processes at the cellular
and molecular level.
• It emerged as a distinct discipline around the
beginning of the 20th century when scientists
combined chemistry, physiology and biology to
investigate the chemistry of living systems by:
A. Studying the structure and behavior of the complex
molecules found in biological material and
B. the ways these molecules interact to form cells, tissues and
whole organism

3. AMINO ACIDS
 Amino acids are the fundamental building blocks of
proteins
 Amino acids contain a basic amino group and an acidic
carboxyl group
 Joined as amides between the NH2 of one amino acid
and the CO2H to the next amino acid in a peptide
 Chains with fewer than 50 units are called peptides
 Protein: large chains that have structural or catalytic
functions in biology

5. STRUCTURE

6.  In neutral (water) solution, the COOH is ionized and the NH2 is
protonated
 The resulting structures have “+” and “-” charges (a dipolar
ion, or zwitterion)
 They are like ionic salts in solution

7. TYPE OF SIDE-CHAINS
• Neutral: Fifteen of the twenty have neutral side chains
• Asp and Glu have a second COOH and are acidic
• Lys, Arg, His have additional basic amino groups side
chains (the N in tryptophan is a very weak base)
• Cys, Ser, Tyr (OH and SH) are weak acids that are good
nucleophiles

8. STERIC RELATIONSHIP OF THE
STEREOISOMERS

9. CHIRALITY OF AMINO ACIDS
 Glycine, 2-amino-acetic acid, is achiral
 In all the others, the  carbons of the amino acids are
centers of chirality
 The stereochemical reference for amino acids is the
Fischer projection of L-serine
 Proteins are derived exclusively from L-amino acids

10. ABBREVIATIONS, CODES AND
IDENTIFICATION OF AMINO ACIDS
Alanine A, Ala
Arginine R, Arg
Asparagine N, Asn
Aspartic acid D, Asp
Cysteine C, Cys
Glutamine Q, Gln
Glutamic Acid E, Glu
Glycine G, Gly
Histidine H, His
Isoleucine I, Ile
Leucine L, Leu
Lysine K, Lys
Methionine M, Met
Phenylalanine F, Phe
Proline P, Pro
Serine S, Ser
Threonine T, Thr
Tryptophan W, Trp
Tyrosine Y, Tyr
Valine V, Val

13. CLASSIFICATION OF AMINO ACIDS
Different ways can be adopted viz:
(i) the structure and chemical nature of a.as
(ii) nutritional requirement
(iii) metabolic fate

14. I. BASED ON R-GROUP

15. II. BASED ON NUTRITIONAL REQUIREMENT
A. Essential or indispensable amino acids:
• All 20 of the amino acids are necessary for protein
synthesis
• Humans can synthesize only 10 of the 20
• The other 10 must be obtained from food(Essential aas)
• These include: Arginine, Valine, Histidine, lsoleucine,
Leucine, Lysine, Methionine, Phenylalanine, Threonine,
Tryptophan.

16. B. Non-essential or dispensable amino acids:
 Can be synthesised in the body (10 a.as)
 These are-glycine, alanine, serine, cysteine, aspartate,
asparagine, glutamate, glutamine, tyrosine and proline

17. LIMITING AMINO ACID: THE ESSENTIAL AMINO ACID
FOUND IN SMALLEST QUANTITY IN A FOODSTUFF.
Protein source Limiting amino acid
Wheat lysine
Rice lysine and threonine
Maize lysine and tryptophan
Pulses methionine
Beef methionine and cysteine
Whey none
Milk none

18. III. BASED ON METABOLIC FATE:
• 1. Glycogenic amino acids: These amino acids can serve as precursors
for the formation of glucose or glycogen. e.g. alanine, aspartate,
glycine, methionine.
• 2. Ketogenic amino acids: Fat can be synthesized from these amino
acids. Two amino acids leucine and lysine are exclusively ketogenic
• 3. Glycogenic and ketogenic amino acids: The four amino acids
isoleucine, phenylalanine, tryptophan, tyrosine are precursors for
synthesis of glucose as well as fat.

19. UNCOMMON AMINO ACIDS (NON-STANDARD
AMINO ACIDS)
A. AMINO ACID DERIVATIVES IN PROTEINS:

20. B. NON-PROTEIN AMINO ACIDS
I. D-Amino acids : The vast majority of amino acids isolated
from animals and plants are of L-category.
 Certain D-amino acids are found in the antibiotics
(Actinomycin-D, Valinomycin, Gramicidin-S).
 D-serine and D-aspartate are found in brain tissue.
 D-Glutamic acid and D-alanine are present in bacterial cell
walls.
II. Non-α amino acids: e.gs given in table 4.2

22. USES OF AMINO ACIDS
 Aspartame (aspartyl-phenylalanine-methyl ester) is an artificial
sweetener.
 5-HTP (5-hydroxytryptophan) has been used to treat neurological
problems associated with PKU (phenylketonuria), as well as
depression.
 L-DOPA (L-dihydroxyphenylalanine) is a drug used to treat
Parkinsonism.
 Monosodium glutamate is a food additive to enhance flavor.

23. PROPERTIES OF AMINO ACIDS
PHYSICAL PROPERTIES:
 Solubility: most are soluble in water
 Melting point: above 200oC
 Taste: sweet (Gly, Ala, Val), tasteless (Leu) or bitter (Arg, Ile).
Monosodium glutamate (MSG; Ajinomoto) is used as a flavoring
agent in food industry, and Chinese foods to increase taste and flavor
 Optical properties: except glycine, all amino acids are
diastereomers due to the presence of alpha Carbon, others have two
stereogenic Carbons – Thr and Ile
 Amphoteric nature: Amino acids contain both acidic (-COOH)
and basic (-NH2) groups. They can donate a proton or accept a proton,
hence amino acids are regarded as Ampholytes, Zwitterion or dipolar
ion

24. NB: In strongly acidic pH (low pH), the amino acid is positively charged
(cation) while in strongly alkaline pH (high pH), it is negatively
charged( anion)
 Isoelectric pH (symbol pl): the pH at which a molecule exists
as a zwitterion or dipolar ion and carries no net charge. Thus,
the molecule is electrically neutral.

25. TITRATION CURVES REVEAL PKA OF WEAK ACIDS

26. TITRATION CURVES OF AMINO ACIDS

29. EFFECT OF CHEMICAL ENVIRONMENT ON PKA

30. CHEMICAL PROPERTIES
Mostly attributed to the –COOH and –NH2
(a) Reactions due to -COOH group
 Amino acids form salts (-COONa) with bases and esters
(-COOR') with alcohols
 Decarboxylation: Amino acids undergo decarboxylation
to produce corresponding amines

31.  Reaction with ammonia: The carboxyl group of dicarboxylic amino
acids reacts with NH3 to form amide
Aspartic acid + NH3 ------ Asparagine
Glutamic acid + NH3------Glutamine
Reactions due to -NH2 group
 The amino groups behave as bases and combine with acids (e.g. HCI) to form
salts (-NH3
+Cl-)
 Reaction with ninhydrin : The α-amino acids react with ninhydrin to form a
purple, blue or pink colour complex (Ruhemann's purple)

32. Amino acid + Ninhydrin ---------- Keto acid +
NH3+CO2+Hydrindantin
Hydrindantin+ NH3 + Ninhydrin ------- Ruhemann's purple

33.  Proline reacts with ninhydrin, but in a different way. While most
ninhydrin tests result in a purple color, the proline reaction is more
yellow due to substitution of the alpha amino group with alpha
imino group held in ring

35. COLOUR REACTIONS

36. COLOUR REACTIONS OF AMINO ACIDS : AMINO ACIDS CAN BE
IDENTIFIED BY SPECIFIC COLOUR REACTIONS E.G XANTHOPROTEIC TEST,
SAKAGUSHI TEST, ETC
A. SAKAGUCHI TEST

37. XANTHOPROTEIC TEST

38.  Transamination: Transfer of an amino group from an amino acid to a
keto acid to form a new amino acid and is a very important reaction in
amino acid metabolism
 Oxidative deamination : The amino acids undergo oxidative
deamination to liberate free ammonia.

39. Amino acids useful as drugs
Some non-standard amino acids that are used as drugs
include:
 D-Penicillamine (D-dimethylglycine), a metabolite of
penicillin, is employed in the chelation therapy of Wilson's
disease. This is possible since D-penicillamine can
effectively chelate copper.
 N-Acetylcysteine is used in treatment of cystic fibrosis,
and chronic renal insufficiency because of it antioxidant
activity.
 Gabapentin (γ-aminobutyrate linked to cyclohexane) is
used as an anticonvulsant.