Chapter 12 amino acids and proteins

Chapter 12 : Amino Acids and Proteins
FCH 0226
CHEMISTRY II
SEM II SESSION 2014/2015

Outlines
12.1 : Introduction
12.2 : IUPAC Nomenclature
12.3 : Classification
12.4 : Physical Properties
12.5 : Optical Activity
12.6 : Zwittetions and Isoelectronic Point
12.7 : Reactions
12.8 : Peptides
12.9 : Applications

Amino acidAmino acid: a compound that contains
both an amino group, -NH2 and a
carboxyl group, -COOH
αα-amino acid:-amino acid: an amino acid in which
the amino group is on the carbon
adjacent to the carboxyl group
α
CH3CH2 C COOH
H
NH2
12.1 : Introduction
NH2 C COOH
H
CH2CH3

H C COOH
H
NH2
i)
ethanoic acid
2 1
2-amino
H C COOH
CH3
NH2
ii)
2 1
3
propanoic acid2-amino
H C COOH
CH2OH
NH2
iii)
2 1
3
propanoic acid
2-amino-3-hydroxy
IUPAC Name
12.2 : Naming

pentanoic acid2,5-diamino
hexanedioic acid2-amino
2 1
3 4 5
H C COOH
CH2CH2CH2COOH
NH2
v)
H C COOH
CH2CH2CH2NH2
NH2
iv)
2 1
3 4 5 6
IUPAC Name
12.2 : Naming

Exercise: Name the following structures.
CH2N COOH
H
CH2 CH2 COOH
CH3
CH2N
H
C
H
COOH CH3
CH2 OH

Acidic
12.3 : Classification – Neutral, Acidic and Basic
• Amino acid can be classified as;
• Neutral, Acidic or Basic
• Depends on the structure of RBasic
Neutral

Acidic
• R has carboxyl –COOH group
• Those whose side chains can carry a
negative charge at certain pH values
• Typically aspartic acid, glutamic acid.
Glutamic acid Aspartic acid

Basic
• If R contains an amine functional
group,
• the amino acid produces a basic solution
because the extra amine group is not
neutralized by the acid group
• Amino acids which have basic side
chains include: lysine and arginine
Lysine • Arginine

Neutral
• Since an amino acid has both an amine
and acid group which have been
neutralized in the zwitterion,
• If neither (Carbonyl group or Amine
group) are present on the R side the
whole amino acid is neutral.
Glycine Phenylalanine

Exercise: Classify the following structures as acid, basic or neutral..
H2N C C OH
CH3
OH
H2N C C OH
CH2
C
CH3
HCH3
O
H
H2N C C OH
CH2
OH
C O H
O H2N C C OH
CH2CH2CH2CH2
OH
NH2

Solid with high melting points at room
conditions due to formation of zwitterions
(dipolar ions) Strong ionic bond between
NH3
+
& COO-
ions
Solubility:
 Soluble in water (Polar solvent)
 Insoluble in non-polar solvent
Form hydrogen bonds with water & with its
own molecules.
12.4 : Physical Properties

All α - amino are optically active except Glycine
(no chiral centres)
Optically active molecules have an asymmetry
such that they are not superimposable on their
mirror image in the same way that a left hand is not
superimposable on its mirror image, a right hand.
Left and right hand corresponding molecules are
called enantiomers.
All amino acid found naturally have the
configuration as L-(-) glyceraldehyde which are L-
isomer
12.5 : Optical Activity

Molecule with positive charge on one
atom and negative charge on another
atom in the same molecule.
H C COOH
CH2CH2CH3
NH2
(neutral)
H C COO
CH2CH2CH3
NH3
-
+
(dipolar ion @
zwitterion)
Zwitterion
Isoelectric point
Structures in:
Acidic
Basic
pI
12.6 : Zwitterion & Isoelectronic Point
Zwitterion

In general, zwitterion is electrically
neutral and exists at specific pH
Isoelectric Point (pI)
This particular pH is called isoelectric
points
Each amino acid has it’s specific pI
Example:
Zwitterion
Isoelectric point
Structures in:
Acidic
Basic
pI

Zwitterion
Isoelectric point
Structures in:
Acidic
Basic
pI
H2N─(CH2)4─CH ─COOH
│
NH2
H CH
NH2
COOH
HOOC─CH2─CH─COOH
│
NH2
Amino Acid Structure pI
Glycine
(Gly)
6.1
Lysine
(Lys)
9.7
Aspartic
acid
(Asp)
2.9

Exercise:
The chemical structure of serine is shown below. Given isoelectric point (pI)
of serine is 5.7.
HO C C C OH
O
H
H
H
NH2
a. Give the IUPAC name for serine.
b.Draw the structure of serine at
i. pH = 2.1
ii. pH = 9.3
iii. pH = 5.7

a) Reaction with HCl
R C NH2
COOH
R'
+ HCl R C NH3Cl
COOH
R' _+
Example:
Reactions of
–NH2 group:
HCl
NaNO2
H C NH2
COOH
CH2CH3
+ HCl
12.7 : Reactions of Amino Acids
H C NH3Cl
COOH
CH2CH3 _+

b) With Nitrous Acid (HNO2)
Reactions of
–NH2 group:
HCl
NaNO2
elimination of N2(g)
R C
COOH
R'
+
carbocation
H2O
2-hydroxy
carboxylic acid
Cl
-+
halocarboxylic
acid
- H
+
Alkenoic
acid
Observation: Bubbling
of gas (N2)
R C NH2
COOH
R'
R C N N
COOH
R'
+
diazonium ion
NaNO2 / HCl
-5 to 0 o
C

Example:
H C NH2
COOH
CH3
H C N N
COOH
CH3
+
diazonium ion
NaNO2 / HCl
elimination of N2(g)
H C
COOH
CH3
+
carbocation
H2O
H C OH
COOH
CH3
Cl
-+
H C Cl
COOH
CH3
- H
+
H C
COOH
CH2

c) Reaction with NaOH
Example:
NaOH
ROH
Reactions of
-COOH group:
R C NH2
COOH
R'
+ NaOH R C NH2
COO Na
R'
_ +
H C NH2
COOH
CH2CH3
+ NaOH H C NH2
COO Na
CH2CH3
_
+

Exercise:
CH3 CH2 C COOH
H
OH
C COOH
H
Cl
CH3CH2
C COOH
H
NH2
CH3CH2
I II
A B C
a. Give IUPAC names for A,B and C.
b. Give the reagents and reactions conditions for reactions I and II.
c. Explain why C exists as solid at room temperature.
d. Name the mechanism for reaction II.

Peptides are amino acid polymers
in which the individual amino acid
units, are linked together by amide
bonds, or peptide bonds
Peptide Bond
2 amino acids react together, H2O
is eliminated.
This is condensation reaction.Peptide bond
•2 amino acids form dipeptide
•3 amino acids form tripeptide
•15 – 30 amino acids form oligopeptide
•> 30 amino acids form polypeptide
12.8 : Peptides

Formation of dipeptide bond:
+
+
H2O
H2N CH2 C OH H N C COOH
H CH3
H
H2N CH2 C N C COOH
H CH3
H
O
O
amide bond /
peptide bond
A dipeptide
Notes:
N-terminal (with free –NH2) is
always written on the left and
C-terminal (with free –COOH) at
the right side
12.8 : Peptides
Peptide bond

Formation of tripeptide bond:
Write the structural formula of tripeptide with the following
sequence Gly-Ala-Tyr :
H2N CH2 C OH H N C COOH
H CH3
HO
H N C COOH
H H
CH2 OH
Gly Ala Tyr
H2N CH2 C N C C
H CH3
HO
N C COOH
H
CH2 OHO
H
A tripeptide

Importance of amino acids :
 Human beings can synthesize about half
of the amino acids needed to make
proteins.
 Other amino acids, called the essentialessential
amino acidsamino acids, must be provided in the
diet.
 The ten essential amino acids are :
arginine (Arg) valine (val) methionine (Met)
threonine (Thr) leucine (Leu) phenylalanine (Phe)
histidine (His) isoleucine (Ile) lysine (Lys)
trypthophan (Trp)
Importance
12.9 : Applications

Importance of proteins :
 Proteins are the most abundant organic
molecules in animals, playing important
roles in all aspects of cell structure and
function.
 Examples of protein functions :
Class of protein Examples Functions
structural protein collagen, keratin tendons, skin
hair, nails
enzymes DNA polymerase repair DNA
transport protein hemoglobin transport O2
Importance
12.9 : Applications

Name Structure
Glycine
Gly
Alanine
Ala
Valine
Val
H CH
NH2
COOH
H3C CH
NH2
COOH
HC CH
NH2
COOH
CH3
CH3
Common
Names of
Amino Acids
12.9 : Applications

Name Structure
Leucine
Leu
Isoleucine
Ile
Phenylalanine
Phe
CHCH2
CH3
CH3
CH
NH2
COOH
CH
NH2
COOHCH3CH2CH
CH3
CH2 CH
NH2
COOH
12.9 : Applications

Name Structure
Threonine
Thr
Cysteine
Cys
Methionine
Met
CH2 CH2
CH2 NH
C
COOH
H
HO CH2 CH
NH2
COOH
CH3 C
H
OH
CH
NH2
COOH
12.9 : Applications

Name Structure
Tryptophan
Trp
Proline
Pro
Serine
Ser
CH2 CH2
CH2 NH
C
COOH
H
HO CH2 CH
NH2
COOH
O
NH2NH
OH
12.9 : Applications

Name Structure
Threonine
Thr
Cysteine
Cys
Methionine
Met
CH3 C
H
OH
CH
NH2
COOH
HS CH
NH2
COOHCH2
CH
NH2
COOHCH3 S CH2CH2
12.9 : Applications

Name Structure
Tyrosine
Tyr
Asparagine
Asn
Glutamine
Gln
NH2─C─CH2─CH ─COOH
║ │
O NH2
NH2─C─CH2CH2─CH─COOH
║ │
O NH2
CH
NH2
COOHCH2HO
12.9 : Applications

Name Structure
Aspartic
acid
Asp
Glutamic
acid
Glu
Lysine
Lys
HOOC─CH2CH2─CH─COOH
│
NH2
HOOC─CH2─CH─COOH
│
NH2
H2N─CH2CH2CH2CH2─CH ─COOH
│
NH2
12.9 : Applications

12.9 : Applications
Exercise:
Draw the structures of the following peptide.
Val-Lys

12.9 : Applications
Answer:
H2N C C N C COOH
H
CH(CH3)2
O H (CH2)4NH2
H
Val-Lys

Chapter 12 amino acids and proteins

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