PEPTIDES NOTES
The Basics
The Proteinogenic α-amino acids
Amino Acid Abbreviation Side Chain (R)
Glycine Gly H
Alanine Ala Me
Valine Val CHMe2
Leucine Leu CH2CHMe2
Isoleucine Ile CH(Me)CH2Me
Phenylalanine Phe CH2Ph
Tyrosine Tyr CH2(4-hydroxyphenyl)
Tryptophan Trp CH2(3-indolyl)
Methionine Met CH2CH2SMe
Cysteine Cys CH2SH
Serine Ser CH2OH
Threonine Thr CH(Me)OH
Arginine Arg CH2CH2CH2NHC(=NH)NH2
Lysine Lys (CH2)4NH2
Histidine His CH2(4-imidazolyl)
Glutamic Acid Glu CH2CH2CO2H
Aspartic Acid Asp CH2CO2H
Glutamine Gln CH2CH2CONH2
Asparagine Asn CH2CONH2
Peptides
What they do:
Hormones – insulin and oxytocin.
Antibiotics – penicillin.
Drugs – zoladex (prostate cancer), crixivan (AIDS).
Structure Determination
Usually by chemical degradation, although Physical Methods can also be used.
1) Oxidise S-S bridges with peracid.
2) C-terminal: hydrazinolysis
These Notes are copyright Alex Moss 2003. They may be reproduced without need for permission.
www.alchemyst.f2o.org
, 3) N-terminal:
Sanger Method –
Edman Method –
4) Selective Fragmentation – add BrCN at Met residues.
5) Protease Enzymes, e.g. trypsin (cleaves basic side chains – Lys, Arg).
4 & 5 are often combined – overlap sequences and thus helps structure assignment.
Synthesis Overview
Unsymmetrical dipeptides:
Need to protect them selectively –
Depicted as:
These Notes are copyright Alex Moss 2003. They may be reproduced without need for permission.
www.alchemyst.f2o.org
, Protecting Groups
1. Easy to introduce.
2. Protect Functional Group during amide formation.
3. Removable without harming rest of the molecule.
4. No loss of stereochemistry in 1-3.
α-amino Protection
Alkoxycarbonyl Protection
Also known as urethanes or carbamates. They are both amides and esters. As amides, they have
low nucleophilic reactivity at nitrogen. As esters, they have relatively low reactivity wrt acyl-
oxygen fission, but they can be degraded alkyl-oxygen fission to carbamic acids, which
decarboxylate spontaneously under practically all conditions, regenerating the parent amine.
They are also good because they are nearly immune to racemisation.
Benzyloxycarbonyl (Z)
Less reactive acylating agents (i.e. not the chloroformate) are sometimes preferred to prevent
dipeptide formation:
Hence use reagents such as:
Mildly basic or nucleophilic reagents do not generally affect the Z group at ambient temperature.
The main exception to this is hydantoin formation:
However, this is only really significant with ZXaaGly-peptides.
Mildly acidic conditions (e.g. half an hour with neat TFA in an ice-bath) are also without effect.
This allows it to be carried through synthesis with more acid-labile protecting groups
(orthogonality).
Cleavage conditions are HBr/AcOH or catalytic hydrogenolysis. HBr/AcOH proceeds by an SN2-
like mechanism:
The conditions are quite severe though, but most peptides survive it undamaged, unless
susceptible side-chains are present. This is usually due to the generation of electrophilic species
such as benzyl cations which attack electron-rich side chains (e.g. Trp, Tyr, Met). Additives like
These Notes are copyright Alex Moss 2003. They may be reproduced without need for permission.
www.alchemyst.f2o.org
The Basics
The Proteinogenic α-amino acids
Amino Acid Abbreviation Side Chain (R)
Glycine Gly H
Alanine Ala Me
Valine Val CHMe2
Leucine Leu CH2CHMe2
Isoleucine Ile CH(Me)CH2Me
Phenylalanine Phe CH2Ph
Tyrosine Tyr CH2(4-hydroxyphenyl)
Tryptophan Trp CH2(3-indolyl)
Methionine Met CH2CH2SMe
Cysteine Cys CH2SH
Serine Ser CH2OH
Threonine Thr CH(Me)OH
Arginine Arg CH2CH2CH2NHC(=NH)NH2
Lysine Lys (CH2)4NH2
Histidine His CH2(4-imidazolyl)
Glutamic Acid Glu CH2CH2CO2H
Aspartic Acid Asp CH2CO2H
Glutamine Gln CH2CH2CONH2
Asparagine Asn CH2CONH2
Peptides
What they do:
Hormones – insulin and oxytocin.
Antibiotics – penicillin.
Drugs – zoladex (prostate cancer), crixivan (AIDS).
Structure Determination
Usually by chemical degradation, although Physical Methods can also be used.
1) Oxidise S-S bridges with peracid.
2) C-terminal: hydrazinolysis
These Notes are copyright Alex Moss 2003. They may be reproduced without need for permission.
www.alchemyst.f2o.org
, 3) N-terminal:
Sanger Method –
Edman Method –
4) Selective Fragmentation – add BrCN at Met residues.
5) Protease Enzymes, e.g. trypsin (cleaves basic side chains – Lys, Arg).
4 & 5 are often combined – overlap sequences and thus helps structure assignment.
Synthesis Overview
Unsymmetrical dipeptides:
Need to protect them selectively –
Depicted as:
These Notes are copyright Alex Moss 2003. They may be reproduced without need for permission.
www.alchemyst.f2o.org
, Protecting Groups
1. Easy to introduce.
2. Protect Functional Group during amide formation.
3. Removable without harming rest of the molecule.
4. No loss of stereochemistry in 1-3.
α-amino Protection
Alkoxycarbonyl Protection
Also known as urethanes or carbamates. They are both amides and esters. As amides, they have
low nucleophilic reactivity at nitrogen. As esters, they have relatively low reactivity wrt acyl-
oxygen fission, but they can be degraded alkyl-oxygen fission to carbamic acids, which
decarboxylate spontaneously under practically all conditions, regenerating the parent amine.
They are also good because they are nearly immune to racemisation.
Benzyloxycarbonyl (Z)
Less reactive acylating agents (i.e. not the chloroformate) are sometimes preferred to prevent
dipeptide formation:
Hence use reagents such as:
Mildly basic or nucleophilic reagents do not generally affect the Z group at ambient temperature.
The main exception to this is hydantoin formation:
However, this is only really significant with ZXaaGly-peptides.
Mildly acidic conditions (e.g. half an hour with neat TFA in an ice-bath) are also without effect.
This allows it to be carried through synthesis with more acid-labile protecting groups
(orthogonality).
Cleavage conditions are HBr/AcOH or catalytic hydrogenolysis. HBr/AcOH proceeds by an SN2-
like mechanism:
The conditions are quite severe though, but most peptides survive it undamaged, unless
susceptible side-chains are present. This is usually due to the generation of electrophilic species
such as benzyl cations which attack electron-rich side chains (e.g. Trp, Tyr, Met). Additives like
These Notes are copyright Alex Moss 2003. They may be reproduced without need for permission.
www.alchemyst.f2o.org
