Third year organic chemistry

Amino Acids, Peptides and Proteins Convener : Dr.. Fawaz Aldabbagh Third Year Organic Chemistry CO-303 Natural Product Chemistry Primary, Secondary, Tertiary and Quaternary structures of

Amino Acids, Peptides and Proteins

Convener : Dr Fawaz Aldabbagh

Third Year Organic Chemistry

CO-303 Natural Product Chemistry

Primary, Secondary, Tertiary and Quaternary structures of Proteins.

Isoelectric Point Prosthetic Group Investigation of amino acid structure of a protein Peptide Synthesis

H 2 N

(L) - Amino Acids (-) -

=

CHO

CH 2 OH H

HO

(S) - Glyceraldehyde (-) -

R

CH

H2N CO2H

All DNA encoded aa are α

All are chiral,

L-Of the 20 aa, only proline is not a primary aa

NH2C (H3C)2HC

R

NH 2

O

OH N

H

Proline (Secondary aa)

aa are high melting point solids! Why?

Answer = aa are ionic compounds under normal conditions

C

OOHR

NH3

C

OOR

NH3

C

OOR

For aa with basic R-groups, we require higher pHs, and

for aa with acidic R-groups, we require lower pHs

to reach the Isoelectric Point

(CH 2 ) 2 CH

Preparation of Amino Acids

Preparation of Optically active Amino Acids

- (Asymmetric Synthesis)

Prepare the target aa in racemic form, and separate the enantiomers afterwards

Resolution

One salt preferentially crystallizes out

Chiral ion

1 Crystallisation with a chiral Counter-ion

N O

O

N

H H

H H

H

Strechnine

COOH

H NHAc R

R NH * 2

COO AcHN H

R

R NH * 2

H NHAc R

R*-NH 3

Diastereomeric ammonium salts Enantiomers

NaOH, H 2 O

(S)-2 Form Diastereotopic Peptides

R

+

COO

H NHAc R

Hog-kidney acylase

easily separated

Test for Amino Acids - Ninhydrin

O

O

O O

H H

aa are covalently linked by amide bonds

(Peptide Bonds) The resulting molecules are called

Peptides & Proteins

2 Planar to allow delocalisation

3 Restricted Rotation about the amide bond

4 Rotation of Groups (R and R’) attached to the amide

bond is relatively free

aa that are part of a peptide or protein are referred

to as residues

Peptides are made up of about 50 residues, and do not

possess a well-defined 3D-structure

Proteins are larger molecules that usually contain at least 50

residues, and sometimes 1000 The most important feature of

proteins is that they possess well-defined 3D-structure.

Primary Structure is the order (or sequence) of amino acid residues

Peptides are always written and named

with the amino terminus on the left and

the carboxy terminus on the right

Strong Acid Required to hydrolyse peptide bonds

O CH 2 OH

C

N H

(CH 2 ) 4 NH 2

H 2 N C

H N

O

S

C

N H

O

OH

C

O H

N

O

H 2 N Ph

Lys Cys PhePhe Ser Cys

1 RSH

2 6 M HCl hydrolysis

Lys + 2 Cys + 2 Phe + Ser

Cysteine residues create

Disulfide Bridges

between chains

This does not reveal

Primary Structure

Prof Linus Pauling

Tertiary Structure

This is the 3D structure resulting from further regular

folding of the polypeptide chains using H-bonding, Van der Waals, disulfide bonds and electrostatic forces –

Often detected by X-ray crystallographic methods

Globular Proteins – “Spherical Shape” , include Insulin, Hemoglobin, Enzymes, Antibodies

-polar hydrophilic groups are aimed outwards towards water,

whereas non-polar “greasy” hydrophobic hydrocarbon portions cluster inside the molecule, so protecting them from the hostile

aqueous environment - Soluble Proteins

Fibrous Proteins – “Long thin fibres” , include Hair,

wool, skin, nails – less folded - e.g keratin - the α-helix

strands are wound into a “superhelix” The superhelix makes one complete turn for each 35 turns of the α-helix

In globular proteins this tertiary structure or

macromolecular shape determines biological properties

Bays or pockets in proteins are called Active Sites

Enzymes are Stereospecific and possess Geometric Specificity

Emil Fischer formulated the lock-and-key mechanism for enzymes

The range of compounds that an enzyme excepts varies

from a particular functional group to a specific compound

All reactions which occur in living cells are mediated by enzymes and

are catalysed by 10 6 -10 8

Some enzymes may require the presence of a Cofactor

This may be a metal atom, which is essential for its redox activity.

Others may require the presence of an organic molecule, such as

NAD + , called a Coenzyme

If the Cofactor is permanently bound to the enzyme, it is called a

Prosthetic Group

For a protein composed of a single polypeptide molecule, tertiary

structure is the highest level of structure that is attained

Myoglobin and hemoglobin were the first proteins to be

successfully subjected to completely successful X-rays

analysis by J C Kendrew and Max Perutz (Nobel Prize for

Chemistry 1962)

Quaternary

Structure

When multiple sub-units are held together in

aggregates by Van der Waals and electrostatic

forces (not covalent bonds)

Hemoglobin is tetrameric myglobin

For example, Hemoglobin has four heme units, the protein

globin surrounds the heme – Takes the shape of a giant

tetrahedron – Two identical α and β globins.

The α and β chains are very similar but distinguishable in both

primary structure and folding

C

R OH

N H H

H +

O C

N H

O OH

X R

H 2 N

HN

NH O

Unprotected Coupling Three Competing Nucleophiles

Three Criteria for a Good Protecting Group?

What is the best way to activate the Carboxyl group?

CH 3 N

H

Boc t

H 2 N

O

OR +

Dicyclohexylcarbodiimide (DCC)

CH 3 N

OH

Protecting Groups

CH 3 N H

C

O OH

O O C

CH 3

H 3 N

O O

PEPTIDE SYNTHESIS PROTECT

De-PROTECT mild acid and neutralize

CH 3

H 3 N

O N

H

COO Leu

CH 3

H 3 N

O O

Protecting NH 2

O

O Cl Ph

O

O

O O

O O

Cl = Fmoc-Cl

Much Milder Conditions are required

to Break an ester as compared to an amide bond.

H+, H2O HEAT

SN1 mechanism