Protein structure and Properties

Basic Definitions:
 

  • Polypeptide: linear heteropolymer (more than one type of monomer) composed of amino acids linked by peptide bonds

  • Protein: one or more polypeptides linked either covalently (disulphide) or non-covalently (e.g ionic)

  • Protein subunit: individual polypeptide

  • Prosthetic group: non-amino acid component

 

  • Functions are diverse and depends on: chemical structure and molecular conformation

  • Often involved in molecular recognition

 

Amino Acids:

  • Proteins have the same standard set of 20 AA

  • A-amino acids

  • Primary amino groups

  • Carboxylic group (carboxyl-COOH) group which is attached to central carbon atom adjacent to carboxyl group

 

  • Contain at least; one amine group and carboxyl group

  • Amine group attached to A-carbon = A-amino acid

  • B-carbon = B-amino acid

  • A-carbon = C adjacent to carboxyl

 

 

  • Attached to Ca Atom = hydrogen atom and 'R' group

  • Secondary amino group

  • Three letters or single letter

 

 

 

 

Stereochemistry (3D chem):

  • All amino acids = four differently arranged tetrahedrally around central Ca atom

  • Has a chiral centre, meaning its not superimposable except glycine

 

 

 

 

Enantiomers:

  • Physically and chemically indistinguishable

  • Distinguished by different optical rotation and plane-polarised light

  • Dextrorotatory (D: greek 'dextro' = right)

  • Levorotatory (L; Greek 'levo' = left)

  • Rotate plane of plane-polarised light clockwise or anticlockwise

  • D and L so enzymes can distinguish

  • L-amino acids in proteins, D-amino acids are rare and found in nature

 

SIde chains:

  • Standard 20 AA = 'R' groups differ

  • Subdivided = properties of their side chain

  • Different properties depending on side chains:

    - Acidic; basic

    - small-large; bulky

    - aromatic; aliphatic

    - polar; non-polar

    - hydrogen bonding

  •  

 

 

Amino Acids with Ionisable Side Chains:

 

  • Acidic and Basic

 

Acids and bases;

  • Bases accept hydrogen ions (decrease [H+] leads to increase pH)

  • Acids donate H+ (increase [H+] leads to decrease pH)

  • Every acid has a (conjugate) base and every base has a (conjugate) acid

 

Amino acids with acidic side chains;

  • Ionised at typical cellular pH values

  • Negatively charged; unionised forms

  •  

 

 

 

Amino acids with basic side chains;

  • Ionised at typical cellular pH values

  • Positively charged

 

Amino Acids with Polar, Non-Ionisable Side Chains:
 

  • Polar (from previous image)

 

Amino acids with alcoholic side chains;

  • Good at hydrogen bonding

  • Modifiable – phosphorylation – glcosylation

 

 

Amino acids with amide side chains;

  • Amide can form two hydrogen bonds

 

Cysteine;

  • Good at hydrogen bonding

  • Forms disulphide bridges

 

Amino acids with non-polar side chains:

  • Non-polar from previous image

 

AAs with aliphatic side chains;

  • Side cahins contain only carbon and hydrogen

  • Hydrophobic

Glycine; simplest amino acid, no stereoisomers