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Chemistry ofChemistry of
ProteinProtein
Dr Ifat Ara Begum
Associate Professor
Dept of Biochemistry
Dhaka Medical College
Dhaka
1
What is protein?What is protein?
 Macromolecular polymer of Amino
Acids linked together by peptide bonds.
 Minimum molecular weight : 5000-
8000
 Number of amino acids usually : >100
2
3
What is Amino acid?What is Amino acid?
Central asymmetric
alpha carbon 4
Amino group containing carboxylic acid
Asymmetric carbon/ ChiralAsymmetric carbon/ Chiral
carboncarbon
 A carbon atom that is attached to four
different types of atoms or groups of atoms.
 Amino acids having an asymmetric α carbon
can produce optical isomers with optical activity,
Exception: Glycine
Alpha CarbonAlpha Carbon
 Carbon adjacent to the COOH group
 Amino acid having an amino group directly
bonded to the α carbon : α-amino acid.
R/ Radical groupR/ Radical group
 A distinct hydrocarbon side chain, like
CH3, CH3-CH2 etc
 Amino acids differ from each other
only with respect to this hydrocarbon
side chain
 The nature of side chain determines
their properties and functions in
protein
7
 Exception: Glycine does not have R
group
Here R is replaced by another H atom.
(Symmetric α–carbon)
8
RememberRemember
 The acidic properties of COOH & the
basic properties of NH2 groups make
the AA molecule “Amphoteric”
 Primary amino acid is L- α type:
The amino group is usually placed on
left side of the α carbon
Nomenclature of Amino AcidNomenclature of Amino Acid
 By the first three letters of their name.
e.g. Serine (ser)
 Exception:
Tryptophan (Trp),
Isoleucine (Ile)
Asparagine (Asn)
Glutamine (Gln).
11
12
Classification
of Amino Acid
Based on polarity of side chain,Based on polarity of side chain,
their structure & reactiontheir structure & reaction inin
solutionsolution
13
Types of
amino acid
Characteristic Example
Non polar
(Hydrophobic) Neutral
Ala, Val, Leu, Ile,
Pro, Phe, Trp, Met
Polar
(Hydrophilic)
Neutral: Non
charged
Gly, Ser, Thr, Cys,
Tyr, Asn, Gln
Acidic: Negatively
charged
Aspartic acid
Glutamic acid
Basic: Positively
charged
His, Arg, Lys
Nutritional classification of AminoNutritional classification of Amino
AcidAcid
Metabolic classification of Amino AcidMetabolic classification of Amino Acid
Properties of Amino AcidProperties of Amino Acid
 Crystalline
 Stereoisomerism (D-L isomers, optical
isomers)
 Optical activity
 Iso electric pH
 Act as:
• Ampholytes : Amphoteric
• Buffer
16
Isoelectric pH of Amino acidIsoelectric pH of Amino acid
17
 The pH at which an AA exists as Zwitterion
ZwitterionZwitterion
18
 Formerly called dipolar ion
 A molecule with two or more functional
groups, of which at least one has a (+) ve
and one has a (-) ve electrical charge 
and the net charge of the entire molecule is
zero
Functions of Amino AcidFunctions of Amino Acid
 Building block of peptides /
polypeptides / proteins
 Supports gluconeogenesis in fasting &
starvation.
 Synthesis of specialized products. e.g.
NTs, hormones, purine, pyrimidine,
heme, etc.
 Metabolic fuel to provide energy
19
What is peptide bond?What is peptide bond?
 It is a covalent bond
that connects
adjacent amino acids
to form peptide, polypeptide & protein.
21
How it is formed?How it is formed?
 It is formed by joining
the –COOH group of one amino acid
&
the –NH2 group of another amino
acid
with
removal of one molecule of water.
22
23
CharacteristicsCharacteristics
 Covalent bond, i.e. sharing of electron
pair.
 Not broken by denaturing agent
 Broken by proteolytic enzymes
24
25
Classification
of Proteins
26
Based on size,
shape &
solubility
Functional
classification
Nutritional
classification
3 types:
1)Simple
protein:
Fibrous /
globular
protein
2)Conjugated
protein
3)Derived
protein
8 types:
1. Structural
protein
2. Contractile
protein
3. Catalytic protein
4. Gene regulatory
protein
5. Hormonal
protein
6. Protective
protein
7. Receptor protein
8. Transport
3 types:
1. Complete
protein
2. Incomplet
e protein
3. Partially
incomplete
protein
27
28
Denaturation of proteinDenaturation of protein
The unfolding and disorganization
of
protein’s secondary, tertiary &
quaternary structures,
which is not accompanied by hydrolysis
of peptide bond.
29
30
Denaturation
Usually
Irreversible
(e.g. Boiled
egg)
Reversible
(Under ideal
condition.
e.g.
Ribonuclease
at high urea
conc. )
Denaturing agent:
 Heat
 Organic solvents
 Mechanical mixing
 Strong acid/base
 Detergents
 Ions of heavy metals, e.g. lead,
mercury etc.
Changes in protein following denaturationChanges in protein following denaturation
 Physical change:
 Increased
viscosity
Decreased
diffusibility
 Chemical change:
 Increased chance
of precipitation
 Decreased
solubility
 Biological change :
 Loss of function
Increased digestibility by
proteolytic enzymes
Functions of proteinFunctions of protein
34
35

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Chemistry of protein

  • 1. Chemistry ofChemistry of ProteinProtein Dr Ifat Ara Begum Associate Professor Dept of Biochemistry Dhaka Medical College Dhaka 1
  • 2. What is protein?What is protein?  Macromolecular polymer of Amino Acids linked together by peptide bonds.  Minimum molecular weight : 5000- 8000  Number of amino acids usually : >100 2
  • 3. 3
  • 4. What is Amino acid?What is Amino acid? Central asymmetric alpha carbon 4 Amino group containing carboxylic acid
  • 5. Asymmetric carbon/ ChiralAsymmetric carbon/ Chiral carboncarbon  A carbon atom that is attached to four different types of atoms or groups of atoms.  Amino acids having an asymmetric α carbon can produce optical isomers with optical activity, Exception: Glycine
  • 6. Alpha CarbonAlpha Carbon  Carbon adjacent to the COOH group  Amino acid having an amino group directly bonded to the α carbon : α-amino acid.
  • 7. R/ Radical groupR/ Radical group  A distinct hydrocarbon side chain, like CH3, CH3-CH2 etc  Amino acids differ from each other only with respect to this hydrocarbon side chain  The nature of side chain determines their properties and functions in protein 7
  • 8.  Exception: Glycine does not have R group Here R is replaced by another H atom. (Symmetric α–carbon) 8
  • 9. RememberRemember  The acidic properties of COOH & the basic properties of NH2 groups make the AA molecule “Amphoteric”  Primary amino acid is L- α type: The amino group is usually placed on left side of the α carbon
  • 10.
  • 11. Nomenclature of Amino AcidNomenclature of Amino Acid  By the first three letters of their name. e.g. Serine (ser)  Exception: Tryptophan (Trp), Isoleucine (Ile) Asparagine (Asn) Glutamine (Gln). 11
  • 13. Based on polarity of side chain,Based on polarity of side chain, their structure & reactiontheir structure & reaction inin solutionsolution 13 Types of amino acid Characteristic Example Non polar (Hydrophobic) Neutral Ala, Val, Leu, Ile, Pro, Phe, Trp, Met Polar (Hydrophilic) Neutral: Non charged Gly, Ser, Thr, Cys, Tyr, Asn, Gln Acidic: Negatively charged Aspartic acid Glutamic acid Basic: Positively charged His, Arg, Lys
  • 14. Nutritional classification of AminoNutritional classification of Amino AcidAcid
  • 15. Metabolic classification of Amino AcidMetabolic classification of Amino Acid
  • 16. Properties of Amino AcidProperties of Amino Acid  Crystalline  Stereoisomerism (D-L isomers, optical isomers)  Optical activity  Iso electric pH  Act as: • Ampholytes : Amphoteric • Buffer 16
  • 17. Isoelectric pH of Amino acidIsoelectric pH of Amino acid 17  The pH at which an AA exists as Zwitterion
  • 18. ZwitterionZwitterion 18  Formerly called dipolar ion  A molecule with two or more functional groups, of which at least one has a (+) ve and one has a (-) ve electrical charge  and the net charge of the entire molecule is zero
  • 19. Functions of Amino AcidFunctions of Amino Acid  Building block of peptides / polypeptides / proteins  Supports gluconeogenesis in fasting & starvation.  Synthesis of specialized products. e.g. NTs, hormones, purine, pyrimidine, heme, etc.  Metabolic fuel to provide energy 19
  • 20.
  • 21. What is peptide bond?What is peptide bond?  It is a covalent bond that connects adjacent amino acids to form peptide, polypeptide & protein. 21
  • 22. How it is formed?How it is formed?  It is formed by joining the –COOH group of one amino acid & the –NH2 group of another amino acid with removal of one molecule of water. 22
  • 23. 23
  • 24. CharacteristicsCharacteristics  Covalent bond, i.e. sharing of electron pair.  Not broken by denaturing agent  Broken by proteolytic enzymes 24
  • 26. 26 Based on size, shape & solubility Functional classification Nutritional classification 3 types: 1)Simple protein: Fibrous / globular protein 2)Conjugated protein 3)Derived protein 8 types: 1. Structural protein 2. Contractile protein 3. Catalytic protein 4. Gene regulatory protein 5. Hormonal protein 6. Protective protein 7. Receptor protein 8. Transport 3 types: 1. Complete protein 2. Incomplet e protein 3. Partially incomplete protein
  • 27. 27
  • 28. 28
  • 29. Denaturation of proteinDenaturation of protein The unfolding and disorganization of protein’s secondary, tertiary & quaternary structures, which is not accompanied by hydrolysis of peptide bond. 29
  • 30. 30
  • 32. Denaturing agent:  Heat  Organic solvents  Mechanical mixing  Strong acid/base  Detergents  Ions of heavy metals, e.g. lead, mercury etc.
  • 33. Changes in protein following denaturationChanges in protein following denaturation  Physical change:  Increased viscosity Decreased diffusibility  Chemical change:  Increased chance of precipitation  Decreased solubility  Biological change :  Loss of function Increased digestibility by proteolytic enzymes
  • 35. 35