Introduction to protein , Structure of Amino acid, Asymmetric carbon, Nomenclature of amino acid, Classification of amino acid, Properties & functions of amino acids, Definition of protein, Peptide bond

1. Amino Acids and Proteins
Part: 1
Dr. Ifat Ara Begum
Associate Professor
Department of Biochemistry
Dhaka Medical College, Dhaka
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Dr Ifat, Dept of Biochemistry, DMC

2. Learning Objectives
 Mention some introductory facts about protein
 Define amino acid
 Describe the structure of an amino acid
 Understand the properties of amino acid
 List the functions of amino acid
 Define protein
 Define peptide bond
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Dr Ifat, Dept of Biochemistry, DMC

3. Introduction to Protein
 Large biomolecules
 Macromolecules that are made up of
one or more chain (s) of amino acids
 The sequence of amino acids is
determined by DNA
 Are found in every cell in the body
 Are involved in most of the body’s
functions and life processes
A representation of the 3-D
structure of the protein myoglobin
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4. Biomolecule, also called biological molecule, any of numerous
substances that are produced by cells and living organisms.
The four major types of biomolecules
are carbohydrates, lipids, nucleic acids, and proteins
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Dr Ifat, Dept of Biochemistry, DMC

5. • Greek word, “PROTEIOS” , means “Primary” or
“Holding the first place”.
• Swedish chemist Berzelius suggested the name.
• The first protein to be sequenced was Insulin by
Frederick Sanger in 1949
He won the noble prize for this achievement in 1958
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7. Definition & Structure of Amino Acid
 Amino group containing carboxylic acid
 Each amino acid has a central carbon atom
(Asymmetric α carbon)
to which four (04) diff groups or atoms are
attached:
 A basic amino ( -NH2 ) group
 An acidic carboxyl ( -COOH) group
 A hydrogen (H) atom
 A “R” group or side chain that is unique to each
amino acid
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Dr Ifat, Dept of Biochemistry, DMC

8. Amino (NH2 )
group
- Basic
- Has a pKa between 9 and 10
-At body pH (7.4), it exist as protonated form (NH3
+) by accepting proton
- It is metabolized to proton (H+)
Carboxyl
(COOH) group
- Acidic
- Has a pKa that is usually close to 2
-At body pH (7.4), it exist as deprotonated form (COO-) by donating proton
- It is metabolized to HCO3
- ion
Hydrogen (H)
atom
-
R group or side
chain
-Amino acids differ from each other with respect to this side chain
- Its nature determines the properties and functions in protein.
- Example: H, CH3, CH3-CH2 etc
- It may be polar / non polar, acidic / basic
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The pKa of a group is the pH value at which the concentration of the
protonated group equals that of the unprotonated group.
In total, there are 20 amino acids in human body from where all body
proteins are constructed. So they are called “Primary Amino Acid” or
“Standard Amino Acid”

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13. Remember:
The acidic properties of COOH group
&
the basic properties NH2 group
make the amino acid molecule “Amphoteric”
The carboxyl group is able to
donate proton
and
the amino group is able to accept
proton
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Dr Ifat, Dept of Biochemistry, DMC

14.  A carbon atom that is attached to four
different types of atoms or groups of atoms.
 Amino acids have the chiral carbon atom
adjacent to the carboxyl group (COO-).
Exception: Glycine
Asymmetric Carbon / Chiral carbon
Glycine: The smallest amino acid, which has
symmetric α carbon atom. Here, R is replaced by
another H atom
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15.  As all body amino acids (except
glycine) have asymmetric α
carbon,
they can produce optical stereo
isomers (space isomer) with
optical activity
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Dr Ifat, Dept of Biochemistry, DMC
α Carbon: Carbon atom next to
carboxyl group

16.  Mirror image pairs of amino acids
are designated as L (levo) & D
(dextro)
L- α amino acids: Amino group is attached directly with the
α carbon and placed on left side with respect to spatial
configuration
 Body proteins are assembled from
L- α amino acids
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18.  Conventionally, by the first three
letters of their name.
e.g. Alanine (Ala)
Nomenclature of Amino Acids
Exception:
Glutamine (Gln)
Asparagine (Asn)
Isoleucine (Ile)
Tryptophan (Trp)
Remember: “GAIT”
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20. A) Based on structure of side chain (R) & their reaction in
solution
Three types of Amino Acids
Acidic AA Basic AA Neutral AA
Aliphatic AA Aromatic AA Imino AA
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21. Types Synonym No. of
Amino group
No. of
carboxyl group
Charge at
normal body
pH
Example
Acidic
amino Acid
Mono amino
di - carboxylic
acid
01 02 Negatively
charged
Aspartic acid (Asp)
Glutamic acid (Glu)
Basic amino
Acid
Di - amino
mono
carboxylic acid
02 01 Positively
charged
Histidine (His),
Arginine (Arg),
Lysine (Lys)
Neutral
amino Acid
Mono amino
mono
carboxylic acid
01 01 No net charge Rest 15 amino acids
grouped under three
types again
(e.g. Ala, Tyr, Trp,
Cys, Met etc)
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22. Neutral
amino acid
Aliphatic amino acid Aromatic amino acid Imino acid
Sulphur containing: Cysteine,
Methionine Example:
Phenyl alanine,
Tyrosine
Tryptophan
- It contains Imino group
(-NH) ,
not amino group (NH2 )
- Example: Proline
Branched chain: Valine,
Leucine, Isoleucine
Hydroxyl group containing:
Serine, Threonine
Amide group containing:
Asparagine, Glutamine
Simple structure: Glycine,
Alanine
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23. B) Based on polarity of side chain (R)
Two types of Amino Acids
Polar AA /
Hydrophilic AA
Non polar AA /
Hydrophobic AA
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Dr Ifat, Dept of Biochemistry, DMC

24. Polar / Hydrophilic AA:
 They have hydrophilic side
chain (R)
 Example:
- Acidic AA
- Basic AA
- Some of the neutral AA like
Gly, Ser, Thr, Tyr, Cys, Gln,
Asn
Total 12 in numbers
Non polar / Hydrophobic AA:
 They have hydrophobic side
chain (R)
 Example:
Rest of the neutral AA like
Met, Val, Leu, Ile, Ala, Trp,
Pro, Phe
Total 08 in numbers
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25. C) Nutritional Classification of Amino Acids
Three types of Amino Acids
Essential AA /
Indispensable
AA
Semi
essential
AA
Non essential AA /
Dispensable AA
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26. Points Essential AA /
Indispensable AA
Semi essential AA Non essential AA /
Dispensable AA
Definition Amino acids which are not
produced in body ,
therefore essentially be
supplied in diet
Amino acids which are produced in body
in a limited rate , therefore essentially be
supplied in diet when their requirement
in body is high (like during growth in
children, not essential for adult)
Amino acids which are
produced in body in
sufficient amount , so, not
essential in diet.
Source Mainly from animal
protein- meat, fish, egg,
milk etc
- -
Total no. 08 02 -
Example Met, Trp, Thr, Val, Phe,
Ile, Leu, Lys
(Remember, MTV PILL)
Arg, His Asp, Glu, Cys, Ser, Gly,
Ala, Asn, Gln, Tyr, Pro
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27. Within the body,
Tyrosine and Cystine are synthesized from the
EAA Phenylalanine & Methionine respectively.
So, Tyr & Cys may become EAA if the dietary
supply of Phe & Met is reduced or absent.
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28. D) Metabolic Classification of Amino Acids
Three types of Amino Acids
Absolute
Glucogenic AA
/ Glycogenic
AA
Absolute
Ketogenic AA
Both Glucogenic
& Ketogenic AA
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29. Points Absolute Glucogenic AA /
Glycogenic AA
Absolute Ketogenic AA Both Glucogenic &
Ketogenic AA
Definition Amino acids having carbon
skeleton that possess metabolic
potential to produce glucose
Amino acids having carbon
skeleton that possess metabolic
potential to produce ketone bodies
Amino acids having carbon
skeleton that possess
metabolic potential to
produce both glucose &
ketone bodies
What
happens
really?
They initially produce
precursors of glucose (e.g.
pyruvate or intermediates of
TCA cycle)
from which later on, glucose is
produced
They initially produce precursors
of ketone bodies (acetyl CoA or
aceto acetyl CoA)
from which later on, ketone body
is produced
They initially produce acetyl
CoA or aceto acetyl CoA
along with pyruvate or TCA
cycle intermediates
and then produce ketone
body or glucose
Example Gly, Ala, Glu, Gln, Val etc Leu, Lys Phe, Tyr, Trp, Ile
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30. E) Combined Nutritional & Metabolic Classification
Metabolic Type Nutritional type
Essential Non essential
Absolute Glucogenic His, Met, Thr, Val, Arg Ala, Asp, Asn, Cys, Glu, Gln,
Gly, Pro, Ser
Both Glucogenic &
Ketogenic
Phe, Trp, Ile Tyr
Absolute Ketogenic Leu, Lys -
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32. Physical Properties
 Colorless
 Crystalline
 Water soluble
 High melting point (>200
degree C)
 Stereoisomerism (D-L
isomers, optical isomers)
 Optical activity
Chemical Properties
 Act as ampholytes (i.e. behave both as acid &
base)
 Acts as buffer and have definite iso-electric pH
 Undergo decarboxylation to form corresponding
amines
 Purple colour reaction with ninhydrine
 Forms
 Salts with acid or base
 Esters with alcohol.
 Carbamino compounds with CO2
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34. 1. Act as building blocks of
- Peptides (2-10 AAs )
- Polypeptides (10 - 100 AAs )
&
- Proteins (>100 AAs )
2. Supports gluconeogenesis in fasting &
starvation.
3. Synthesis of specialized products. e.g.
neurotransmitters, hormones, purine,
pyrimidine, heme, etc.
4. Directly acts as neurotransmitter (Gly, Glu,
Asp)
5. Detoxification of toxic substances in liver by
Gly, Cys etc
6. Acts as metabolic fuel meeting up 10% of body energy need
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36. Definition of protein
 Macromolecular polymer of amino acids
linked together by peptide bond.
 Minimum molecular weight: 5000-8000
 Number of amino acid: >100
 Elementary Composition: C, O, N, H, S in different
percentages
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39. Definition
 It is a covalent bond
that connects adjacent amino acids
to form
peptide, polypeptide & protein
 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
Formation
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40. Characteristics of peptide bond
 Covalent bond, i.e. sharing of electron pair.
 Shows partial double bond character
 Rigid, planer & do not rotate.
 It is not broken by denaturing agents
but
is broken by proteolytic enzymes
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