Chapter 12 amino acids and proteins

Chapter 12 : Amino Acids and Proteins

FCH 0226CHEMISTRY 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 acid2 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 acid2-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

CH2NHC

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

OHH2N C C OH

CH2

C

CH3

HCH3

OH

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

smb://upload.wikimedia.org/wikipedia/commons/e/e8/Chirality_with_hands.svg


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

OH

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'

+

carbocationH2O

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 oC



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

CH3Cl

-+

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

CH3CH2C 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 essential essential 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

GlycineGly

AlanineAla

ValineVal

H CH

NH2

COOH

H3C CH

NH2

COOH

HC CH

NH2

COOH

CH3

CH3

Common Names of

Amino Acids

12.9 : Applications


Name Structure

LeucineLeu

IsoleucineIle

PhenylalaninePhe

CHCH2

CH3

CH3

CH

NH2

COOH

CH

NH2

COOHCH3CH2CH

CH3

CH2 CH

NH2

COOH

12.9 : Applications


Name Structure

ThreonineThr

CysteineCys

MethionineMet

CH2 CH2

CH2 NHC

COOH

H

HO CH2 CH

NH2

COOH

CH3 C

H

OH

CH

NH2

COOH

12.9 : Applications


Name Structure

TryptophanTrp

ProlinePro

SerineSer

CH2 CH2

CH2 NHC

COOH

H

HO CH2 CH

NH2

COOH

O

NH2NH

OH

12.9 : Applications


Name Structure

ThreonineThr

CysteineCys

Methionine

Met

CH3 C

H

OH

CH

NH2

COOH

HS CH

NH2

COOHCH2

CH

NH2

COOHCH3 S CH2CH2

12.9 : Applications


Name Structure

TyrosineTyr

AsparagineAsn

GlutamineGln

NH2─C─CH2─CH ─COOH ║ │ O NH2

NH2─C─CH2CH2─CH─COOH ║ │ O NH2

CH

NH2

COOHCH2HO

12.9 : Applications


Name Structure

Aspartic acidAsp

Glutamic acidGlu

LysineLys

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

The End

Chapter 12 amino acids and proteins

Education

amino group

coohamino acid

proteinsall amino

methylpentanedioic acid2amino

acid groupamino acids

classification neutral

proteinsamino acid

basicamino acid