Proteins (AQA A Level Chemistry)

• Each amino acid contains an amine (-NH₂) and carboxylic acid (-COOH) group
• The -NH₂ group of one amino acid can react with the -COOH group of another amino acid in a condensation reaction to form a dipeptide
  • The new amide bond between two amino acids is also called a peptide link or peptide bond

• Since this is a condensation reaction, a small molecule (in this case H₂O) is eliminated
• The dipeptide still contains an -NH₂ and -COOH group at each end of the molecule which can again participate in a condensation reaction to form a tripeptide

A peptide bond is an amide bond between two amino acids

• A polypeptide is formed when many amino acids join together to form a long chain of molecules

A polypeptide is a long chain of amino acid molecules joined together

The structure of proteins

• There are four levels of structure in proteins, three are related to a single polypeptide chain and the fourth level relates to a protein that has two or more polypeptide chains
• Polypeptide or protein molecules can have anywhere from 3 amino acids (Glutathione) to more than 34,000 amino acids (Titan) bonded together in chains

Primary

• The sequence of amino acids bonded by covalent peptide bonds is the primary structure of a protein
• The primary structure is specific for each protein (one alteration in the sequence of amino acids can affect the function of the protein)

The primary structure of a protein. The three-letter abbreviations indicate the specific amino acid (there are 20 commonly found in cells of living organisms)

Tertiary

• Further conformational change of the secondary structure leads to additional bonds forming between the R groups (side chains)
• The additional bonds are:
  • Hydrogen (these are between R groups)
  • Disulphide (only occurs between cysteine amino acids)
  • Ionic (occurs between charged R groups)
  • Weak hydrophobic interactions (between non-polar R groups)

• This structure is common in globular proteins

The tertiary structure of a protein with hydrogen bonds, ionic bonds, disulphide bonds and hydrophobic interactions formed between the R groups of the amino acids

Summary of the types of bonding in peptides Table

• Hydrolysis of proteins is the reverse reaction of condensation in which the peptide link is broken and water added, hence the term hydrolysis
• During hydrolysis reactions polypeptides are broken down to amino acids when the addition of water breaks the peptide bonds
• The condensation and hydrolysis of a dipeptide is shown here for reference, but the reaction is identical with a protein chain

Amino acids are bonded together by covalent peptide bonds to form a dipeptide in a condensation reaction

• The hydrolysis reaction can be carried out by chemical means or using enzymes
• Concentrated hydrochloric acid is the reagent used and the mixture is boiled for many hours as the reaction is slow
• With enzyme the reaction occurs at room temperature

• After hydrolysis, the amino acid components from polypeptides can be identified by using the technique of thin layer chromatography (TLC)
• This technique is described in more detail in a later section
• Although the amino acids have the same basic structure the R group changes the overall polarity of the molecule so the amino acids will rise up the TLC at different rates
• Since amino acids are colourless the TLC plate has to either be sprayed with a locating agent such as ninhydrin which stains the amino acids, or the plate must be illuminated under a UV light
• A TLC plate can be used to calculate R_f values for compounds
• These values can be used alongside other analytical data to deduce composition of mixtures
• The R_f value (retention factor) can be determined and use to identify a specific amino acid

R_f values can be calculated by taking 2 measurements from the TLC plate

• Sometimes amino acids have very similar values in the same solvent, so a further technique of two dimensional TLC can be used
• In this technique the same plate is run through two different solvents
• A square TLC plate is used and run through the first solvent, then the plate is turned through 90^o and run through the second solvent
• Two R_f  values are determined allowing greater confidence in identifying the amino acids

Two dimensional TLC allows greater confidence in identifying amino acids