1.

Structure and function

of proteins

Primary Structure

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An example of relevance of proteins’ structure:
Antibodies - immunology

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 Levels of organisation
in proteins:

Regions of sequence
with regular structure Polypeptide chains associated in
Packing of elements functional assemblies
AA sequence
of II-ary structure into
one or more compact units
called domains
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3D structure
of myoglobin

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Proteins are polymers of
-amino acids

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Cell  mitochondria 
proteins  atoms

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Stereochemistry
of -amino acids

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Some amino acids not found in proteins, not
coded by DNA, but biologically important

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 Properties of aa side-chains
 Aliphatic aa:

 Flexible and hydrophobic, the most Ile;

 Found in the hyodrophobic core of proteins
 Pro: exception, rigid ring as side chain, often a structure
breaker

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 Hydroxyl-, sulfur- side chains
 Weakly polar side chains

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Aromatic side-chains

Absorbance

Detection of proteins
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 Easy detection of proteins:
Absorbance
 Absorbance: spectrophotometer

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Basic side-chains

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Acidic side-chains
and amides

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 Proteins are polyampholites

 pI: isoelectric point

pI

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 
 
 

 

 

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Post-
translational
processing

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Peptide bond

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A tetrapeptide

Glu-Gly-Ala-Lys
EGAK

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Analysis of proteins’ primary
structure:

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 Chemical degradation

1. HCl: Complete
degradation, 6M HCl at
105ºC

2. Cyanogen bromide

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 5. Edman degradation

3. ß-mercaptoethanol

4. Performic acid

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 Peptide analysers

 The two major direct methods of protein

sequencing are the Edman degradation
reaction and mass spectrometry.
 Proteomics

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 N-terminal and C-terminal
blocking

N-terminal and
C-terminal
block groups

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Enzymatic degradation:
Proteases:

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Protease active sites

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Mechanism of protease
activity

Pg 210

Pg 208

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Mechanism of protease activity

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Outline of what
you must now know:
 Amino acids:
 Formulae
 Properties
 Stereochemistry
 Reactivity: properties of the side chains
 Peptide bond
 Proteins as polyampholites: pI
 Primary structure of proteins
 Example of how aa side chains give properties to
proteins: Mechanism of proteases activity
 Post-translational modifications
 Protein analysis:
 Chemical analysis
 Enzymatic analysis - proteases
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 Possibili domande
 Descrivi con l’uso di formule:
 le proprieta’ comuni degli aminoacidi
 le proprieta’ delle catene laterali
 le proprieta’ del legame peptidico
 Scrivi le formule degli amminoacidi divisi per
gruppo illustrando e discutendo le loro proprieta’
chimico-fisiche.
 Descrivi le proprieta’ di dissociazione degli
aminoacidi e delle loro catene laterali con i valori di
punto isoelettrico (pI)
 Analisi della struttura I aria delle proteine: descrivi i
metodi di degradazione chimica ed enzimatica
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