The document discusses amino acids and proteins. It begins by listing the learning objectives, which include describing the 20 common amino acids, their structure and classification, as well as the structure and functions of peptides and proteins. It then defines amino acids as the building blocks of proteins, notes that 20 are commonly found in mammalian proteins, and describes their basic structure with an amino group, carboxyl group, hydrogen, and side chain. The document further classifies amino acids based on their chemical, nutritional, and metabolic properties and functions. It also explains how amino acids polymerize to form peptides and proteins, and the levels of structure in proteins from primary to quaternary.

1. 1
BY : Kumsa. K (BSc., MSc.)
Email: kumsa26@gmail.com/kumsa.kene@ju.edu.et

2.  After learn this chapter you will be able to:
 List the elements of the 20 AA
 Describe the function of AA
 Classify the amino acids
 Explain peptides and proteins
 Elaborate primary, secondary, tertiary, and quaternary
structure of proteins
Learning Objectives
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3. 3
 Amino acids are compounds containing C, H, O, and N
 They are the building units of proteins
 Although more than 300 different amino acids have been
described in nature, only 20 are commonly found as
constituents of mammalian proteins.
 These are the only amino acids that are coded for by DNA , the
genetic material in the cell - known as protogenic amino acids,
 whereas, those that do not occur in proteins are called as non-
protogenic amino acids
Amino acids

4.  Structure of amino acids
 Each amino acid has 4 different groups attached to α- carbon,
a central carbon
 These 4 groups are :
- Amino group (NH2),
- Carboxyl group (COOH),
- Hydrogen atom (H),
- Side Chain (R)
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5. Abbreviations and Codes of AAs
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
In addition to 20 L-amino acids that take part in protein
synthesis, recently two more new amino acids described.
They are:
Selenocysteine - 21st amino acids
Pyrrolysine - 22nd amino acid
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6.  Polymerized to form proteins
 Stabilize 3-D structure of proteins
by forming H and disulfide bonds
 Presence of specific AAs at the active site of enzymes is vital
for catalytic activity
 Some AAs Glucogenic.
 Cys and met are sources of S in the body
 C skeleton and N of AAs used for:-the synthesis of purine and
pyrimidine bases
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Functions of amino acids

7.  Gly and met help in the detoxification mechanisms
 Met can act as a methyl group donor
• in methylation reactions
 Certain AAs give rise to biologically important derivatives:
Glycine is a precursor for
– Heme of hemoglobin
– Creatine that acts as the mediator of energy in
muscles
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Functions of amino acids

8. Tyrosine is the precursor for
– A number of hormones
» Thyroxine, triiodothyronine, epinephrine and nor-
epinephrine
– Skin pigment melanin
Tryptophan can give rise to
– vitamin niacin
– the neurotransmitter, Serotonin.
Histidine can be converted to
– the mediator of allergic reactions i.e. histamine
Functions…(Cont’d)
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9.  Precursors for Production of Nitrogen-containing
Compounds like:-
Heme
Nucleotides
Amines
Nucleotide Coenzymes
Glutathione
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Functions…(Cont’d)

10. Classification of Amino Acids
AAs can be classified by one of the three methods:
 Chemical Classification
 Biological or Nutritional Classification
 Metabolic Classification
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11. I. Chemical Classification
 Based on the properties of their R groups, AAs can be
classified into five classes:
»Aliphatic, Nonpolar R groups
»Aromatic R groups
»Polar, uncharged R groups
»Positively charged R groups
»Negatively charged R groups
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12. A) Non polar, aliphatic amino acids
 R is hydrophobic group which can not enter in H bond
formation
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13. B) Aromatic R Groups
 Also Hydrophobic
 hydroxyl group of
tyrosine can form
H- bond
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14. C) Polar amino acids
 R contains polar hydrophilic group so can forms H bond with H2O
 In those amino acids, R may contain:-
 OH group : as in serine, threonine and tyrosine
 SH group : as in cysteine
 Amide group: as in glutamine and aspargine
 NH2 group or nitrogen (basic AAs): as lysine, arginine and
histidine
 COOH group (acidic AAs): as aspartic and glutamic acid
 Polar AAs can be uncharged, positively charged and negatively
charged
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15. Polar, Uncharged
R Groups
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16. 16

17. 17
 Nutritionally, AAs can be classified as
1) Nonessential Amino Acids
--body can synthesize for itself
--more than 1/2 of AAs are nonessential
2) Essential Amino Acids
--body cannot make for itself
--there are nine AAs
--must be supplied in foods
3) Conditionally Essential Amino Acids
--an AA normally nonessential but must be supplied in diet in
special circumstances
II- Nutritional classification

18. Essential amino acids
• Arginine
• Histidine
• Isoleucine
• Leucine
• Lysine
• Methionine
• Phenylalanine
• Threonine
• Tryptophan
• Valine
Non-Essential amino acids
 Alanine
 Asparagine
 Aspartic Acid
 Cysteine
 Glutamic Acid
 Glutamine
 Glycine
 Proline
 Serine
 Tyrosine
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19. Summary of essential and semiessential amino acids:
Villa HM = Ten Thousands Pound
V= valine i= isoleucine l= lysine l= leucine
A = arginine* H= histidine* M= methionine
T= tryptophan Th= threonine P= phenyl alanine
*= Histidine & arginine are semi essential. They are essential
only for infants growth,
but not for old children or adults where in adults histidine
requirement is obtained by intestinal flora & arginine by urea
cycle.
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20. III- Metabolic classification
according to metabolic products of amino acids, they may be:
1- Ketogenic amino acids
• which give ketone bodies
• Lysine and Leucine are the only pure ketogenic amino acids
3- Glucogenic amino acids
• Which give glucose
• Include the rest of amino acids
2- Mixed ketogenic and glucogenic amino acids
• give both ketone bodies and glucose
• These are: isoleucine, phenyl alanine, tyrosine and
tryptophan
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21. 21
Amino Acids
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22. 22
 20 amino acids are commonly found in protein.
 These 20 amino acids are linked together through “peptide
bond” forming peptides and proteins
 Peptide Bond Formation between
 the α-carboxyl group of one amino acid and
 the α-amino group of a second amino acid to form a
peptide
 The chains containing less than 50 amino acids are called
“peptides”, while those containing greater than 50 amino acids
are called “proteins”.
Peptides and Proteins

23. Cont…….
23
The pentapeptide Ser-Gly-Tyr-Ala-Leu
Formation of a peptide bond by condensation

24. 24
 The product formed when two amino acids are joined is called a
dipeptide
 linkage of three amino acid, a tripeptide, with four amino
acids a tetrapeptide and so on
 If the peptide contains 2-10 amino acid residues it is called an
Oligopeptide
 Ordinarily, a peptide with more than ten residues is termed a
Polypeptide
 Proteins may have thousands of amino acid residues
… Cont’d

25. Examples on Peptides:
1- Dipeptide ( two amino acids joined by one peptide bond):
Example: Aspartame which acts as sweetening agent being used in
replacement of cane sugar. It is composed of aspartic acid and
phenylalanine.
2- Tripeptides ( 3 amino acids linked by two peptide bonds).
Example: Glutathione (GSH) which is formed from 3 amino acids:
glutamic acid, cysteine and glycine. Glutathione important for:-
 protects against hemolysis of RBC by breaking H2O2 which causes
cell damage.
 It also participates in a detoxication, eicosanoid synthesis and
transport of AAs across cell membranes. 25

26. 3- octapeptides: (8 amino acids)
Examples: Two hormones; oxytocine and vasopressin (ADH).
Oxytocin : posterior pituitary hormone ,induces uterine
contraction , octapeptide.
4-polypeptides: 10- 50 amino acids: e.g. Insulin hormone and
glucagon
Insulin : formed from 2 polypeptide chains connected by 2
disulfide linkages; one is 30 and the other is 21 AA residues.
Glucagon: 29 residues, a pancreatic hormone, opposing the action
of insulin.
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27. PROTEINS
The most abundant biological macromolecules,
occurring in all cells & all parts of cells
formed of  C, O, H & N
» also may contain  S, P, non-protein organic
groups & metal ions
Polymers of genetically coded 20 AAs linked together by peptide
linkages
occur in great variety thousands of different kinds,
exhibit enormous diversity of biological function
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28. 28
Functions of Proteins
 Structural: main structural component in bone, muscles, cytoskeleton &
cell membrane
 Nutritional: provide the body with essential AAs, N & S
 Catalytic: almost all metabolic enzymes are proteins in nature
 Endocrine: most of hormones and all receptors are protein in nature
 Defence: play an important role in the body’s defensive mechanisms
 Membrane Transport: proteins in the membranes act as channels or
transporters
 Transport Role: carry lipids, hormones, minerals
 Gene Regulation: control cellular activities through control of gene
expression:

29.  Structural
 Movement
 Transport
 Storage
 Hormone
 Protection
 Enzymes
Collagen; bones, tendons, cartilage
Keratin; hair, skin, wool, nails, feathers
Myosin & Actin; muscle contractions
Hemoglobin; transports O2
Lipoproteins; transports lipids
Casein; in milk. Albumin; in eggs
Insulin; regulates blood glucose
Growth hormone; regulates growth
Immunoglobulins; stimulate immunity
Snake venom; plant toxins;
Sucrase; catalyzes sucrose hydrolysis
Pepsin; catalyzes protein hydrolysis
Functions of Proteins
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30. According to their composition, proteins can be classified as
1. Simple protein:- Containing only amino acids upon hydrolysis,
such as Egg Albumin; present in egg, milk and blood
2. Conjugated protein:-On hydrolysis, give protein part and non
protein part, E.g Phosphoproteins, lipoproteins,
Metalloproteins, Glycoproteins, Nucleoproteins
3. Derived proteins:- Produced from hydrolysis of simple
proteins
e.g. - Gelatin: from hydrolysis of collagen
- Peptone: from hydrolysis of albumin
Classification of proteins
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31. I- Simple proteins:-
1, Albumin and globulins: present in egg, milk and blood and they
are proteins of high biological value i.e. contain all essential amino
acids and easily digested.
Types of globulins:
α1 globulin: e.g. antitrypsin:
α2 globulin: e.g. hepatoglobin: protein that binds hemoglobin to
prevent its excretion by the kidney
β-globulin: e.g. transferrin: protein that transport iron
γ-globulins: Immunoglobulins (antibodies):responsible for
immunity.
2, Globins (Histones): They are basic proteins rich in histidine
amino acid. They are present in :
a - combined with DNA
b - combined with heme to form hemoglobin of RBCs.
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32. 3, Scleroproteins: They are structural proteins, not digested
include: keratin, collagen and elastin.
a) α-keratin: protein found in hair, nails, enamel of teeth and outer
layer of skin.
b) collagens: protein of connective tissues found in bone, teeth,
cartilage, tendons, skin and blood vessels. They form about 30% of
total body proteins.
Scurvy: disease due to deficiency of vitamin C which is important
synthesis of collagen. Thus, synthesis of collagen is decreased
leading to abnormal bone development, bleeding, loosing of teeth
and swollen gum.
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33. c) Elastin: present in walls of large blood vessels (such as aorta).
• It is very important in lungs, elastic ligaments, skin, cartilage,
• It is elastic fiber that can be stretched to several times as its normal
length,
Emphysema: is a chronic obstructive lung disease (obstruction of air
ways) resulting from deficiency of α1-antitrypsin particularly in
cigarette smokers.
Role of α1-antitrypsin: Elastin is a lung protein. Smoke stimulate
enzyme called elastase to be secreted form neutrophils (in lung).
Elastase cause destruction of elastin of lung.
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34.  α1-antitrypsin is an enzyme (secreted from liver) and inhibit
elastase and prevent destruction of elastin.
 So deficiency of α1-antitrypsin especially in smokers leads to
degradation and destruction of lung lead to loss of elasticity of
lung, this disease called emphysema.
II. Conjugated proteins
i.e. On hydrolysis, give protein part and non protein part and
subclassified into:
1- Phosphoproteins: Phosphorus is attached to OH group of serine
or threonine. e.g. Casein of milk and vitellin of yolk.
34

35. Classes of Conjugated Proteins
35

36. 2- Lipoproteins:
These are proteins conjugated with lipids.
Functions: a- help lipids to transport in blood
b- Enter in cell membrane structure helping lipid
soluble substances to pass through cell membranes.
3- Glycoproteins:
proteins conjugated with sugar (carbohydrate)
e.g. – Mucin
- Some hormones such as erythropoietin.
- present in cell membrane structure
- blood groups.
4- Nucleoproteins: These are basic proteins ( e.g. histones)
conjugated with nucleic acid (DNA or RNA).
e.g. a- chromosomes: are proteins conjugated with DNA
b- Ribosomes: are proteins conjugated with RNA
36

37. 5- Metalloproteins: These are proteins conjugated with metal like
iron, copper, zinc, ……
a- Iron-containing proteins: Iron may present in heme such as in
- hemoglobin (Hb)
- myoglobin ( protein of skeletal muscles and cardiac muscle),
- cytochromes,
- catalase, peroxidases (destroy H2O2)
- tryptophan pyrrolase (desrtroy indole ring of tryptophan).
Iron may be present in free state ( not in heme) as in:
- Ferritin: Main store of iron in the body. ferritin is present in liver,
spleen and bone marrow.
- Hemosidrin: another iron store.
- Transferrin: is the iron carrier protein in plasma.
37

38.  There are four levels of organization of protein
structure:
»Primary structure
»Secondary structure
»Tertiary structure
»Quaternary structure
38
Structural Organization of Proteins

39. Primary Structure of proteins
 is the linear sequence of aminoacids in the
polypeptide chain
 The precise primary structure of a protein is
determined by inherited genetic information
 At one end is an amino acid with a free amino
group (N-terminus) and at the other is an
amino acid with a free carboxyl group (C-
terminus)
 The bond is only peptide bond.
 E.g. Lysozyme, an enzyme that attacks
bacteria, consists of a polypeptide chain of
129 amino acids.
39

40. Secondary Structure of proteins
 It is the way that the chain of amino acids folds itself due to
intramolecular hydrogen bonding
 Results from hydrogen bond formation between hydrogen of –
NH group of peptide bond, and carbonyl oxygen of another
peptide bond
 Other regions of the polypeptide chain form
»Non regular non repetitive secondary structures, such
as coils, loops, & turns
40

41. According to H-bonding there are two main forms of
secondary structure:
α-helix:
•a spiral structure resulting from hydrogen bonding between
one peptide bond and the fourth one
α-Helix 
41

42. β-sheets:
•two or more polypeptides, or segments of the same peptide
chain
are linked together by hydrogen bond between:
- Hydrogen of NH- of one chain, and
- carbonyl oxygen (C=O) of adjacent chain (or segment)
42
b- sheet 

43. Tertiary structure is determined by variety of interactions
- among R groups and
- between R groups and the polypeptide backbone
 There are four bonds in tertiary structure.
 They include:-
I) Covalent bonding,
II) Hydrogen bonding
III) Salt bridges (ionic bonds) formed between NH2 and COOH
IV ) Hydrophobic interactions among hydrophobic R groups
43
Tertiary Structure Proteins

44. Tertiary Structure Proteins
44

45. 45
Quaternary Structure of proteins
 results from the aggregation (combination) of two or more
polypeptide subunits held together by non-covalent interaction
like H-bonds, ionic or hydrophobic interactions.
 In general, most proteins consist of more than one polypeptide
chain, are referred to as;
»dimeric, trimeric, or multimeric (oligomeric) proteins
Examples on protein having quaternary structure:
 Collagen is a fibrous protein of three polypeptides (trimeric) that
are supercoiled like a rope.
 This provides the structural strength for their role in connective
tissue.
– Hemoglobin is a globular protein with four polypeptide
chains (tetrameric)
– Insulin : two polypeptide chains (dimeric)

46. quaternary structure of an
enzyme having 4 interwoven
aminoacids strands
46

47. Summary of Protein Structure
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48. 6/8/2022
By Abebe D. 49