2. Amino Acids
2
• Amino acid:Amino acid: a compound that contains an amino group, a
carboxyl group and a side-chain that is specific to each
amino acid.
• -Amino acid-Amino acid:: an amino acid in which the amino group
is on the carbon adjacent to the carboxyl group
• The are 20 common α-amino acids used by the ribosomes
to make proteins. These 20 have L chirality at the α-
carbon.
3. • The building blocks of proteins
• 20 amino acids are naturally incorporated into polypeptides
and are called proteinogenic or standard amino acids. These 20
are encoded by universal genetic code.
• 10 standard amino acids (Lys, Met, His, Leu, Ile, Thr, , Try, Phe,
Val & Arg) are called "essential" for humans because they
cannot be created from other compounds by the human body,
and so must be taken in as food.
• From these building blocks different organisms can make such
widely diverse products as enzymes, hormones, antibodies,
antibiotics, and a myriad of other substances having distinct
biological activities.
• Also used as single molecules in biochemical pathways
Chemistry of Amino Acids R side chain
|
H2N— C —COOH
|
H
3
4. Chemistry of Amino Acids
• Two functional groups:
–carboxylic acid group
–amino group on the alpha (α) carbon
• Have different side groups (R)
–Properties dictate behavior of AAs
5. Stereochemistry of AAs
• All amino acids (except glycine) are optically active (chiral)
2 forms of enantiomers/stereoisomers
• d = dextrorotatory ,dextro means right
• l = levorotatory, levo means left
• D, L = relative to glyceraldehyde
5
6. Amino acids join together via peptide bonds
Two amino acids can react with loss of a water molecule to form a
covalent bond.
6
• Chain of amino acids = peptide or protein
Amide linkage is planar
NH and CO are anti
7. Classification of Amino Acids
Classification based on side-chain structure:
– Non-polar amino acids.
– Polar, uncharged amino acids.
– Acidic amino acids.
– Basic amino acids.
Other side chain structural classifications:
– Aromatic, cyclic, hydroxyl, and thiol amino acids.
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8. Nonpolar side chains (predominant form at pH 7.0)
H-
CH3 -
CH3 CH2 CH( CH3 ) -
( CH3 ) 2CHCH2 -
CH3 SCH2 CH2 -
N
H
( CH3 ) 2CH
glycine (gly, G)
alanine (ala, A)
valine (val, V)
leucine (leu, L)
isoleucine (ile, I)
methionine (met, M)
phenylalanine (phe, F)
tryptophan (trp, W)
N
H H
+
proline (Pro, P)
Classification of Amino Acids
8
R
=
Polar side chains (predominant form at pH 7.0)
asparagine (asn, N)
glutamine (glu, G)
serine (ser, S)
threonine (thr, T)
H2 NCCH2-
O
H2 NCCH2CH2 -
O
HOCH2 -
CH3 CH-
OH
H-
CH3 -
CH3 CH2 CH( CH3 ) -
( CH3 ) 2CHCH2 -
CH3 SCH2 CH2 -
( CH3 ) 2CH
alanine (ala, A)
valine (val, V)
leucine (leu, L)
isoleucine (ile, I)
methionine (met, M)
CH3 CH2 CH( CH3 ) -
( CH3 ) 2CHCH2 -
CH3 SCH2 CH2 -
N
H
( CH3 ) 2CH
leucine (leu, L)
isoleucine (ile, I)
methionine (met, M)
N
H H
+
proline (Pro, P)
9. Acidic side chains (predominant form at pH 7.0)
aspartic acid (asp, D) glutamic acid (glu, E)
cysteine (cys, C) tyrosine (tyr, Y)
-
OCCH2 -
HSCH2-
-
OCCH2 CH2 -
HO CH2 -
O O
Classification of Amino Acids
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Basic side chains (predominant form at pH 7.0)
arginine (arg, R) histidine (his, H)
lysine (lys, K)
H2 NCNHCH2 CH2 CH2 -
NH2
+
H3 NCH2 CH2CH2CH2-
N
N
H
CH2 -
+
10. Essential Amino Acids
• An essential amino acid is an amino acid that cannot be
synthesized itself by the organism (usually referring to
humans), and therefore must be supplied in the diet.
• 10 amino acids are essential amino acid
• They are - arg, his, ile, leu, lys, met, phe, thr, trp, val
• Must obtain from the diet
• An adequate diet must contain these essential amino acids.
Typically, they are supplied by meat and dairy products
• Essential amino acids help the body function and regulate
neurotransmitters, chemicals in the brain that control mood
and behavior.
• A lack of essential amino acids can cause emotional or
physical difficulties and lead to health disorder
13. • Although α-amino acids are commonly written in the unionized form, they
are more properly written in the zwitterion (internal salt) form (Germ.
Zwitter means hybrid)
• Both the –NH2 and the –COOH groups in an amino acid undergo ionization
in water.
• At physiological pH (7.4), a zwitterion forms
– Both + and – charges
– Overall neutral
– Amphoteric
• Amino group is protonated
• Carboxyl group is deprotonated
• Soluble in polar solvents due to ionic character
Zwitterions
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15. Reactions of amino acids
1- Reactions due to COOH group:
- Salt formation with alkalis, ester formation with alcohols, amide
formation with amines and decarboxylation
2- Reactions due to NH2 group: Deamination & reaction with ninhydrin
Ninhydrin reagent reacts with amino group of amino acid yielding
colored product. The intensity of blue color indicates quantity of
amino acids present.
• Ninhydrine can react with imino acids as proline and hydroxy
proline but gives yellow color
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R CO2
H3N H H3C O CH3
O O
base R CO2H
HN H
O
H3C
HOCH2CH3
H+R CO2CH2CH3
H2N H
Amino acids will undergo reactions characteristic of the amino
(amide formation) and carboxylic acid (ester formation) groups.
16. Detecting Amino Acids
Ninhydrin is the classical reagent for
detecting amino acids.
Reaction requires 2-5 min at 100o
C and
is sensitive at the nanomole level.
Ruhemann’s Purple
570 nm
OH
O
O
OH
NH2-CH-COOH
CH3
+
O
O
O
O
NCO2
CH3
CHO
+ +2
Note: The product from Pro is
Yellow and absorbs at 440 nm. 16
17. Peptides and Proteins
•20 amino acids are commonly found in protein.
•These 20 amino acids are linked together through “peptide
bond forming peptides and proteins.
•The chains containing less than 50 amino acids are called
“peptides”, while those containing greater than 50 amino
acids are called “proteins”.
Peptide bond formation: Peptide bondPeptide bond is theis the amide bond
between the -carboxyl group of one amino acid and the -
amino group of another
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19. Peptides and Proteins
Peptide: a short polymer of amino acids joined by peptide bonds;
they are classified by the number of amino acids in the chain
– dipeptide: a molecule containing two amino acids joined by a
peptide bond
– tripeptide: a molecule containing three amino acids joined by
peptide bonds
– 12-20 residues (Each unit/AA) – oligopeptide.
– polypeptide: a macromolecule containing many amino acids
Linear polymers (no branches)
AA monomers linked head to tail through formation of peptide
bonds
– protein: a biological macromolecule of molecular weight 5000
g/mol or greater, consisting of one or more polypeptide chains
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20. The Amide Bond
H2N R'+R COOH R
O
H
N
R
-H20
• Basic amide synthesis is the reaction of a carboxylic
acid and an amine with the loss of water.
• Some of the main properties of the amide bond is it’s
low basicity, which is useful in purification, and it’s
stability, due to resonance.
• Since the free electrons of the N atom are tied up in forming
partial (≈ 40%) double bond, N atom can not accept a proton (H+
).
• This N also has a partial positive charge which will repel protons
and prevent them from binding to the nitrogen (thus no
ionization).
R C
O
NH2
δ−
δ+
21. 21
•The synthesis of a specific dipeptide such as Ala-Gly from
alanine and glycine is complicated because both amino
acids have two functional groups.
•As a result, four products—namely, Ala-Ala, Ala-Gly, Gly-
Gly and Gly-Ala—are possible.
Peptide Synthesis
22. 22
The method can be applied to synthesis of tripeptides and
even larger peptides.
Peptide Synthesis
23. Analysis of the amino acid sequence
• Determine number of polypeptide chains (subunits)
• Determine number of disulfide bonds (inter- and intra
chain)
• Determine the amino acid composition of each polypeptide
chain
• If subunits are too large, fragment them into shorter
polypeptide chains
• Determine the amino acid sequence of each fragment using
the Edman degradation method
24. End-group Analysis
• Number of chains can be determine by
identifying the number of N- and C-terminal.
• N-terminal analysis
– Dansyl chloride
– Phenylisothiocynate (PITC)/ Edman reagent
– Aminopeptidase
• C-terminal analysis
– carboxypeptidase
