chemistry of amino acids and proteins for I AHS.pdf

This ppt contains chemistry of amino acids and proteins notes and Assignment questions for I year Allied Health sciences, RGUHS syllabus

1. P. Santosh Kumar

2. I BSc AHS- Objectives
•General structure of D and L amino acids
•Amino acids; Definition and classification of
amino acids with examples
•Peptides; definition & Biologically important
peptides
•Classification of proteins based on composition,
function and shape with examples
•Functions of amino acids and proteins

3. PROTEINS
•The word protein is derived from Greek word,
“proteios” which means primary.
•Out of the total dry body weight, 3/4
ths
are made up of
proteins.
Proteins mainly contain Carbon (C), Hydrogen (H),
Oxygen (O), & Nitrogen (N),
•Minor constituents - Sulfur (S), Phosphorus (P), Iron
(Fe), Iodine (I), Manganese (Mn) and Zinc (Zn)

4. Proteins are most abundant biological macromolecules
present in all cells and all parts of cells.
Proteins are great variety –
•Different kinds,
•Different sizes,
•Differ in their properties and
•Diversity of biological functions and activities.
•Abnormalities in protein structure will lead to molecular
diseases with alterations in metabolic functions.

5. Definition of proteins: Proteins are polymers of
L α -amino acids linked together by peptide bonds.
* The peptide bonds are shaded in yellow; the R groups are in red.

6. Functions of Proteins
1.Proteins are used for body building; all the major and
functional aspects of the body are carried out by protein
molecules
2.Muscle contraction – Actin, Myosin, Tropomyosin
3.Acts as structural compounds – keratin of hair and nails,
collagen in muscles, elastin of blood vessels
4.All enzymes are proteins except ribozyme Ex:
Hexokinase, Amylase
5.Acts as hormones – growth hormone, insulin, ACTH etc.
6.Protect of body from foreign compounds-
Immunoglobulins
7.Acts as transporters – Transferrin transport iron, Albumin
carries bilirubin, fatty acids etc..

7. 8.Storage proteins – Ferritin stores iron in liver and bone
marrow
9.Proteins required for vision- Rhodopsin and Iodopsin
present in retina of eye
10. Blood clotting (Haemostasis) requires proteins –
Fibrinogen, Prothrombin etc.
11.Acts as membrane proteins – Sodium potassium ATPase
Pump
12.Proteins acts as Buffers – Hemoglobin, Plasma proteins
13.Proteins required for respiration- Hemoglobin,
Myoglobin
14.Acts as receptors – Receptors of Insulin, Glucagon,
Steroid hormones
15.Acts as genetic proteins – Histones, transcription and
translation proteins

8. Definition: Amino acids are building blocks
(monomeric units) of proteins. They are a group of
organic compounds containing two functional groups –
amino (-NH
2) and carboxyl (-COOH).
Although about 300 amino acids occur in nature, only 20
of them are incorporated in human proteins during
translation, called as standard amino acids. Recently
Selenocysteine 21
st
amino acid and
Pyrrolysine 22
nd
amino acid identified.
Amino acids

9. General structure of  amino acids
All amino acids (except proline – imino acid) are α -amino
acids- the amino group is attached to the same carbon atom
to which the carboxyl group is attached.
Third valency position occupied by H atom, fourth valency
by occupied by side chain represented by R which is different
for each of the 20 amino acids found in proteins.

10. •The amino acids mostly exist in the ionized form in the
biological system.
-The amino group (-NH
3
+
) is basic while
-Carboxyl group (-COO
-
) is acidic in nature.
General structure
COOH

C NH
2

H
R
COO
-
C NH
3
+
H
R
Ionic form

11. Stereoisomerism in amino acids/General structure of
D&L amino acids
•Amino acids exhibits D-L stereoisomerism called
enatiomerism due to presence of asymmetric carbon
•The amino acids contains four distinct groups (COO
-
,
NH
3
+
, H, R) held by α-carbon. Thus all the amino acids
(except glycine where R = H) have optical isomers.
•If the NH
2 group is on the right side of α –carbon atom,
the amino acid is D-isomer, and if the NH
2 group is on
the left side the amino acid is L-isomer.
•D and L isomers are mirror images of each other.
H

CNH
2
R
COOH
L- amino acid
H
CCOOH
R
NH
2
D- amino acid

12. •In naturally only L –α amino acids occur in proteins.
Only few D- amino acids are found
ex:
−D- alanine & D- glutamate in the cell wall of gram
positive bacteria and
−D-serine and D-aspartate in brain tissue.

13. Optical isomerism:
•Optical isomers are stereoisomers, which have the
capacity to rotate the plane of polarized light to right or
left.
•If the light turn right then the amino acid is called as
dextrorotatory, denoted as (d) or (+) and
•if light turns left that amino acid called as
levorotatory, denoted as (l) or (-).
➢α-carbon atom of all amino acids (except glycine- no
asymmetric carbon) contain asymmetric carbon atoms
and exhibit optical activity.

14. Common amino acids/Standard amino acids
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20

15. Classification of Amino Acids
•There are different ways of classifying the amino acids
I.Based on the structure
II.Based on polarity
III.Based on charge
IV.Based on the nutritional requirement
V.Based on metabolic fate

16. Classification based on structure



2. Aromatic amino acids: Phenylalanine, Tyrosine
Tryptophan, Histidine
Proline
3. Heterocyclic amino acids
4. Imino acid :
5. Derived amino acids:
A. Mono Amino Mono Carboxylic Acids (neutral)
B. Mono Amino Di Carboxylic Acids (acidic):
C. Di Amino Mono Carboxylic Acids (Basic) :
a. Simple amino acids:
b. Branched Chain amino acids:
c. Hydroxy amino acids:
d. Sulphur containing amino acids:
e. Amino acids with amide group:
Glycine, Alanine
Valine, Leucine, Isoleucine
Serine, Threonine
1. Aliphatic amino acids
Cysteine, Methionine
Aspargine, Glutamine
Aspartic acid, Glutamic acid
Lysine, Arginine

17. 5.Derived amino acids:
a) Found in proteins –
- Hydroxy proline, hydroxy lysine (Collagen)
- Gamma carboxy glutamic acid (Clotting)
- Methylated and acetylated proteins (Ribosomal
proteins and histones)
b) Not found in proteins (Non-protein amino acids)
- Ornithine, citrulline – Urea cycle
- Homocysteine – Sulphur containing amino acid
c) Non-alpha amino acids
- GABA – Derived from glutamic acid
- Beta alanine (seen in Co-enzyme A)

18. Simple amino acids
COO
-
CH NH
3
+
H
COO
-
CH NH
3
+
CH
3
Glycine Alanine

19. Branched chain amino acids
COO
-
CH NH
3
+
COO
-
CH NH
3
+
Valine Leucine
CH CH
3
+
CH
3
+
CH CH
3

CH
2
CH
3
COO
-
CH NH
3
+
CH CH
3
+
CH
2
CH
3
Isoleucine

20. Hydroxyl amino acids
Serine Threonine
OHCH
CH
3
+
CH OH
COO
-
CH NH
3
+
COO
-
CH NH
3
+

21. Sulphur containing amino acids
COO
-
CH NH
3
+
COO
-
CH NH
3
+
Cysteine Methionine
S
CH
2
CH
2
CH
3
CH
2
SH

22. Amino acids with amide group
COO
-
CH NH
3
+
COO
-
CH NH
3
+
Aspargine Glutamine
CO –NH
2
CH
2
CH
2
CH
2
CO –NH
2

23. Mono amino dicarboxylic acids
COO
-
CH NH
3
+
COO
-
CH NH
3
+
Aspartic acid Glutamic acid
COO
–
CH
2
CH
2
CH
2
COO
–

24. Di basic mono carboxylic acids
COO
-
CH NH
3
+
Arginine
Lysine
CH
2
CH
2
CH
2
C = NH
2
+

NH
NH
2
Guanidium group
COO
-
α CH NH
3
+
β CH
2
γ CH
2
δ CH
2
ε CH
2
NH
3
+

25. Aromatic amino acids
Benzene group
Phenol group
NH
3
+CH
COO
-
NH
3
+CH
COO
-
Phenylalanine
Tyrosine
C
H
2
HO C
H
2

26. Imidazole groupIndole group
NH
3
+CH
COO
-
NH
3
+CH
COO
-
Tryptophan Histidine
N
CH
2
HN N
CH
2
Heterocyclic amino acids

27. Imino acid
Proline
NH
2
+
COO
-
Pyrrolidine group

28. 2. Non-Polar amino acids – they are hydrophobic in nature (neutral)
a) Polar but Uncharged (neutral) amino acids
b) Polar & negatively charged amino acids
Alanine, valine, leucine, isoleucine
Methionine,
Phenylalanine, tryptophan
proline
Glycine, Serine, threonine, Asparagine, glutamine
Cysteine, Tyrosine,
Lysine, arginine, histidine (Basic amino acids)
c)Polar and positively charged amino acids
Aspartic acid, glutamic acid (Acidic amino acids)
II. Based on polarity
1. Polar amino acids – they are hydrophilic in nature

29. 3) Neutral amino acids (15 amino acids)
1) Acidic amino acids (2 amino acids)
Glycine, Serine, threonine, Asparagine, glutamine, cysteine,
Tyrosine,
Alanine, valine, leucine, isoleucine
Methionine,
Phenylalanine, tryptophan
proline
Lysine, arginine, histidine
2) Basic amino acids (3 amino acids)
Aspartic acid, glutamic acid
III. Based on charge

30. IV. Based Nutritional requirements
1. Essential amino acids: Their carbon skeleton cannot be
synthesized by human beings and so preformed amino acids
are to be taken in food for normal growth.
E.g. Valine, Leucine, Isoleucine, Lysine, Methionine,
Phenylalanine, Threonine, Tryptophan and
2. Partially essential or semi essential amino acids: Growing
children, Pregnant & Lactating women these amino acids
not synthesized in sufficient quantities and require them in
food But they are not essential for the normal adults.
E.g. Histidine and Arginine
3. Non-essential amino acids: Their carbon skeleton can be
synthesized by the body and hence not required in the diet.
E.g. Glycine, alanine, serine, cysteine, tyrosine, aspartic acid,
glutamic acid, asparagine, glutamine, proline.

HAMnemonic: MATT VIL PHLy

31. V. Based on Metabolic fate
During the catabolism of amino acids, the amino groups are
removed from amino acids to form keto acids (carbon
skeleton of amino acids). These carbon chains are further
catabolized. Based on metabolic fate of these carbon
chains amino acids are classified into
1. Purely Ketogenic- can be converted to ketone bodies or
acetyl CoA or fat
e.g. Leucine – converted to ketone bodies

32. 2. Ketogenic and Glucogenic- after removal of amino group if
the carbon skeleton of amino acid splits into two parts, one
of which can be converted to glucose and the other part can
be converted to ketone bodies or fat
e.g. Lysine, Phenylalanine, Isoleucine, Tyrosine & Tryptophan
– enter the ketogenic and glucogenic pathway
3. Purely Glucogenic – can be converted into glucose
All the remaining 14 amino acids - Glycine, Alanine, Valine,
Serine, Threonine, Cysteine, Methionine, Glutamic acid,
Glutamine, Aspartic acid, Asparagine, Arginine, Histidine,
Proline – enter only into glucogenic pathway
Mnemonic: L PITT

33. Functions of amino acids
1.Amino acids are building blocks
of proteins
2.Histidine residues are important in
the buffering activity of proteins.
3.Non protein amino acids like
Ornithine, Citrulline,
Arginosuccinate acts as
intermediates of metabolism –
urea synthesis.

34. 4. Monosodium glutamate (ajinomoto) used as
flavouring agent in food industries.
Amino acid derivates:
5.Dopamine - derivative of tyrosine acts as
neurotransmitters
6.Histamine – synthesized from histidine, mediator of
allergic reactions

35. 7.Thyroxin from tyrosine is
important thyroid hormone
8.Cycloserine- a derivative of serine
an antituberculous drug
9.γ-carboxyglutamic acid (GABA)
found in plasma proteins involved
in blood clotting.

36. Amino acids useful as drugs:
10.D- Penicillamine (D-dimethylglycine) – chelates copper,
employed in the chelation therapy of Wilson’s disease
11.N-Acetylcysteine – used in cystic fibrosis, chronic renal
insufficiency, function as antioxidant
12.Gabapentin – (γ-aminobutyrate linked to cyclohexane) is
used as an anticunvulsant
13.Azaserine acts as anticancer drug

37. Functions of amino acids
1.Amino acids are building blocks of proteins
2.Histidine residues are important in the buffering activity of
proteins.
3.Non protein amino acids like Ornithine, Citrulline,
Arginosuccinate acts as intermediates of metabolism –
urea synthesis.
4.Monosodium glutamate (ajinomoto) used as flavouring
agent in food industries.
Amino acid derivates:
5.GABA – derivative of glutamic acid, Dopamine - derivative
of tyrosine acts as neurotransmitters
6.Histamine – synthesized from histidine, mediator of
allergic reactions

38. 7.Thyroxin from tyrosine is important thyroid hormone
8.Cycloserine- a derivative of serine an antituberculous drug
9.γ-carboxyglutamic acid found in plasma proteins involved in
blood clotting.
Amino acids useful as drugs:
10.D- Penicillamine (D-dimethylglycine) – chelates copper,
employed in the chelation therapy of Wilson’s disease
11.N-Acetylcysteine – used in cystic fibrosis, chronic renal
insufficiency, function as antioxidant
12.Gabapentin – (γ-aminobutyrate linked to cyclohexane) is
used as an anticunvulsant
13.Azaserine acts as anticancer drug

39. Peptide bond formation
•Amino acids held together
in proteins by covalent
peptide bonds or linkage.
Definition: Peptide bonds
(CO-NH bridge) are
anhydride (by losing water),
covalent bonds formed
between alpha carboxyl
group of an amino acid and
alpha amino group of
succeeding amino acid.

40. Salient features of peptide bonds
1.Peptide bond is a strong covalent, anhydride bond (i.e formed
by the loss of a water molecule)
2.Peptide bonds are amide linkages
3.Peptide bonds are Semi-rigid & partial double bond in nature,
4.All atoms –C,N,O and H are coplanar
5.Peptide bond generally exists in –trans configuration so no
freedom of rotation. (except peptide bond formed by proline, an
imino acid, which has –cis configuration).
6.Both –C=O and –NH groups of peptide bonds are polar and are
involved in hydrogen bond formation
7.During denaturation, peptide bonds are not affected, because
peptide bonds are strong covalent bonds.

41. Amino acids are linked by peptide bonds
•Dipeptide: 2 amino acids joined by -1 peptide bond.
•Tripeptide: 3 amino acids - 2 peptide bonds.
•Tetrapeptide: 4 amino acids - 3 peptide bonds.
•Pentapeptide and so on
•Oligopeptide: Few amino acids.
•Polypeptide: 10-50 amino acids.
Molecular weights generally below 10000.
•Proteins: More than 50 amino acids
Generally have high molecular weights.
Importance of peptide bonds:
Peptide bonds responsible for the polymerization of amino acids to
form peptides (oligopeptides, polypeptides) and proteins

42. Biological important peptides:
•Several peptides occur in the living organisms have
various biological functions.
•Generally the term ‘peptide’ applied when number of
constituent amino acids is less than 10.
1.Carnosine & Anserine: (dipeptides); β-Alanine &
Histidine, Anserine derivative of Carnosine, Both are
present in muscles
2.Glutathione (γ-glutamyl cysteinyl glycine):
powerful reducing agent and antioxidant.
3.TRH (Thyrotropin releasing hormone)
(Tripeptide): Secreted by hypothalamus, stimulates
the pituitary gland to secret TSH.
4.Enkephalins (Pentapeptide): Neurotransmitters
inhibit pain sensation

43. 5.Angiotensins: Angiotensin I (decapeptide), Angiotensin II
(octapeptide),
Angiotensin II – hypertensive action stimulates release of
Aldosterone
6.Nonapeptides
−Oxytocin: Posterior pituitary hormone, causes Uterine
contraction
−ADH (Vasopressin): Posterior pituitary hormone,
stimulates water reabsorption in kidneys and thus increase
blood pressure.
7.Bradykinin (Nonapeptide) and Kallidin (Decapeptide): :
Powerful vasodilator, Produced from plasma proteins by
snake venom enzymes
8.Glucagon (29): hyperglycaemic hormone secreted by
pancreas
9.Insulin (51): hypoglycaemic hormone secreted by pancreas
10.Gramicidin, Actinomycin, bacitracin : Antibiotics
11.Gastrin, Secretin: Gastrointestinal Hormones

44. Glutathione (γ-glutamyl cysteinyl glycine): GSH
•Tripeptide made up of γ-glutamic acid, cysteine and glycine.
Glutathione abbreviated as GSH because of sulfhydryl
group (SH) of cysteine is the active group of glutathione.
•It exists in 2 forms, reduced glutathione (GSH) and oxidized
glutathione (GS-SG).
•Reduced glutathione is biologically active and it is a
powerful reducing agent and antioxidant, required for
many reduction reactions.
(GSH)
(Reduced)
(GS-SH)
Oxidized)

45. Functions of glutathione:
1.Toxic amounts of peroxides and free radicals like H
2O
2 and
superoxides produced in the cells are scavenged by glutathione
peroxidase a selenium containing enzyme.
2.It maintains RBC membrane structure and integrity
3.GSH required for the intestinal absorption of iron by
converting Fe
3+
to Fe
2+

4.GSH required for the conversion of methemoglobin (Fe
3+
) to
Hemoglobin (Fe
2+
)
5.Act as coenzyme in maleyl acetoacetate isomerase
6.GSH protects the sulfhydryl; (SH) group of several enzymes
7.Glutathione involved in amino acids transport in the intestine
and kidney tubules via Meister cycle or γglutamyl cycle.
8.Glutathione involved in the detoxification of toxic compounds
like organophosphates and nitrocompounds and converted to
mercapturic acids.

46. Structure of proteins
Proteins have different levels of structural organization;
primary, secondary, tertiary and quaternary

47. Levels of organization of proteins
•Primary structure of protein:- Primary structure
denotes the number and sequence of amino acids in the
protein or polypeptide from N- terminal to C- terminal
and the location of disulfide bonds, if any.
53

48. •Secondary structure of protein:- Secondary structure
refer to the twisting and folding of the polypeptide
chain, formed by the interaction between amino acids,
which are about 3-4 amino acids apart in the linear
sequence in primary structure of amino acids.
54

49. •Tertiary structure of protein:- Denotes the overall
arrangement and inter relationship of the various
regions, or domains of a single polypeptide chain giving
the compact three dimensional structure of the whole
protein.
•It is formed when alpha helix and beta sheets are held
together by weak interactions.
Steric relationship of amino acids which are far apart
from each other in the linear sequence, but are close to
each other by non-covalent interactions of folding
55

50. •Quaternary structure of protein:- Quaternary
structure refers to the spatial arrangement and
aggregation of subunits (polypeptide chains) of an
oligomeric protein to form one functional protein.
56

51. Classification of Proteins
I. Based on Composition
II. Classification based on shape:
III. Classification based on Nutritional value:
IV. Classification of proteins based on biological functions:
I. Based on Composition
1. Simple proteins: they contain only amino acids no
additional groups.
Albumins: serum albumin, lactalbumin, egg albumin
Globulins: egg globulin, serum globulins, legumin of
peas
Protamines: Protamine zinc insulinate is a common
commercial preparation of insulin.
Prolamines: zein from corn, gliadin of wheat, hordein of
barley

52. Glutelins : Glutelin (wheat), Oryzenin (Rice)
Histones: Thymus histones
Globins: considered along with histones

53. Summary of Classification of proteins based on
composition

54. 2. Conjugated proteins: They are combinations of protein with a
non-protein part, called prosthetic group
Glycoproteins: proteins + carbohydrates ex: mucin (saliva)
ovomucoid egg white)
Lipoproteins: proteins loosely combined with lipid components.
Present in blood & cell membranes Ex: LDL, HDL
Nucleoproteins: proteins + nucleic acids ex: Histones
Chromoproteins: proteins with colored prosthetic groups e.g.
hemoglobin (heme –prosthetic group, globin- protein part)
flavoproteins,
Phosphoproteins: contain phosphorus, phosphoric acid is esterified
to the OH groups of serine & threonine residues of proteins, e.g.
casein of milk & vitellin of egg yolk
Metallo proteins: contain metal ions e.g. hemoglobin (iron),
cytochrome ( iron), tyrosinase (copper) & carbonic anhydrase (zinc)

55. Conjugated proteins & its prosthetic groups

56. 3. Derived proteins: Partially hydrolyzed products of simple
and conjugated proteins.
I.Primary derived proteins: denatured or coagulated or
fist hydrolyzed products of proteins
i. Coagulated proteins: denatured proteins by heat, acids,
alkalies etc.
Ex: cooked proteins, coagulated Albumin
ii. proteans: earliest products of protein hydrolysis by
enzymes dilute acids and alkalies etc..
Ex: fibrin from fibrinogen
iii. Meta proteins: second stage products of protein hydrolysis
by stronger acids or alkalies.
Ex: Acid alkali meta proteins
II. Secondary derived proteins: progressive hydrolytic
products of protein hydrolysis.
Ex: Proteoses & Peptones from albumin, peptides

57. II. Classification based on shape:
Globular: spherical or oval in shape, easily soluble ex:
hemoglobin, Albumin
Fibrous: The molecules are elongated or needle shaped,
resist digestion ex: keratin, collagen, elastin

58. III. Classification based on Nutritional value:
1. Complete proteins/nutritionally rich proteins / first
class proteins: have all the ten essential amino acids in the
required proportion by the human body to promote good
growth. Ex: egg albumin, milk casein.
2. Partially incomplete proteins: These proteins are
partially lacking one or more essential amino acids and
hence can promote moderate growth. e.g. wheat and rice
proteins (limiting Lysine, Threonine), pulses lack cysteine
and methionine’s.
3. Incomplete proteins: These proteins completely lack one
or more essential amino acids. Hence they do not promote
growth at all
Ex: Gelatin (lacks Tryptophan), zein (lacks Tryptophan,
Lysine)

59. IV. Classification of proteins based on biological
functions:
1. Structural proteins : Keratin of hair and nails,
collagen of bone.
2. Enzymes or catalytic proteins : Hexokinase, pepsin.
3. Transport proteins: Hemoglobin, serum albumin.
4. Hormonal proteins: Insulin, growth hormone.
5. Contractile proteins : Actin, myosin.
6. Storage proteins: Ovalbumin, glutelin.
7. Genetic proteins : Nucleoproteins.
8. Defence proteins : Snake venoms, immunoglobulins.
9. Receptor proteins for hormones, viruses
10.Membrane proteins: Na-K pump
11. Buffer proteins: Plasma proteins
12.Visual proteins: Rhodopsin, Iodopsin

60. Amino acid and protein chemistry Assignment questions
Long assays:
1.Define amino acids, Classify them with specific examples of each class.
2.Define proteins. Enumerate the functions. Discuss the classification of proteins
based on chemical nature and solubility.
Short assays:
3.Write the functions of amino acids
4.Define peptides. How are they formed? Discuss the functions of any three
biologically important peptides.
5.What are amino acids? Classify amino acids based on metabolic fate.
6.Essential amino acids
7.Describe the classification of protein based on nutritional importance.
8.Explain the classification proteins based on their function.
9.Explain the classification proteins based on composition and shape.
10.Enumerate the functions of glutathione, oxytocin and vasopressin
Short answers:
11.Write the general structure of D and L amino acids with diagram
12.Conjugated proteins

61. References:
•Vasudevan DM, Sreekumari S, Vaidyanathan K. Textbook of
biochemistry for medical students. Jaypee brothers Medical
publishers
•Satyanarayana U. Biochemistry. Elsevier Health Sciences