topic 2 amino acid and peptide abbrev

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 Amino Acid and Peptide:

Lecture OutlineThe amino acids of protein

• General properties• Peptide bonds• Classifications

• Acid-base properties

Optical Activity• Chirality

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Amino Acids

Amino acids are carboxylic acids whichalso contain an amino (- NH2) group.

Those occuring in proteins are almost

exclusively -amino acids ie the carboxyland amino groups are attached to thesame carbon atom (the -carbon)

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General structural formula for -

amino acids.

   P  a  g

  e

   6   5

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Zwitterionic form of the

-amino acids thatoccur at physiological

pH values.

   P  a  g  e

   6   5

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Classification AA are classified according to the side chain, R:

the most useful way to do this according to their

hydrophobicity, which determines their functionin proteins.

The most hydrophobic are those with large apolarside chains, the most hydrophilic those with

charged side chains.

The structures of the 20 aas commonly occurringin proteins are given.

AA are often denoted by abbreviations of threeletters (in most cases the first 3 letters of thename)

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Condensation of two -amino acids to form a dipeptide.

   P  a  g  e

   6   8

The peptide bond is shown in red

The aa polymerize through theelimination of a water molecule

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Linear polymers of aa have one -NH2 and one -COOH which are not involved in the peptide bondformation

The aa bearing these are known as the N-terminusand C-terminus respectively

AA sequences are conventionally written from N-

terminus to C-terminus

Asp-Arg-Val-Tyr-Ile-His-Pro-Leu-Phe

N-terminus C-terminus

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What is CHIRALITY ?

A chiral object is notsuperimposible on its

mirror image.Examplesinclude hands, socks andkeys…..

The two forms of a chiralobject are known asEnantiomers, namely (R)-and (S)-enantiomers.Enantiomers are mirrorimages of each other.

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• AA are all optically active.

• Optically active molecules are chiralcompounds.

• This situation is characteristics ofsubstances that contain tetrahedral Catoms that have four different

substituents.

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Nonstandard AA

• The 20 common aa are not the only aathat occur in the biological systems.

• Nonstandard aa residues are often imp.Constituents of proteins.

• These residues result from the specific

chemical modifications of aa residues inpreexisting proteins.

• Roles of these aa includes as

neurotransmitters, metabolicintermediates and poisons.

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Some uncommon amino acid residues

that are components of certainproteins.