Proteins (Oxford AQA International A Level Chemistry)

Revision Note

Philippa Platt

Written by: Philippa Platt

Reviewed by: Stewart Hird

Proteins

  • 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

  • This is a condensation reaction so a small molecule is eliminated (H2O)

  • 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

Formation of a dipeptide and tripeptide

Nitrogen Compounds - Formation of Peptide Bonds, downloadable AS & A Level Chemistry revision notes
A peptide bond is an amide bond between two amino acids

Polypeptides

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

 The structure of a polypeptide

Nitrogen Compounds - Polypeptides, downloadable AS & A Level Chemistry revision notes
A polypeptide is a long chain of amino acid molecules joined together

The structure of proteins

  • There are three main structures of proteins:

    • Primary

    • Secondary

    • Tertiary

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 structure is held together by covalent bonding

Diagram to show the structure of a primary 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)

Secondary

  • The secondary structure of a protein occurs when the weak negatively charged nitrogen and oxygen atoms interact with the weak positively charged hydrogen atoms to form hydrogen bonds

  • There are two shapes that can form within proteins due to the hydrogen bonds:

    • α-helix

    • β-pleated sheet

  • The α-helix shape occurs when the hydrogen bonds form between every fourth peptide bond (between the oxygen of the carboxyl group and the hydrogen of the amine group)

  • The β-pleated sheet shape forms when the protein folds so that two parts of the polypeptide chain are parallel to each other enabling hydrogen bonds to form between parallel peptide bonds

  • Most fibrous proteins have secondary structures (e.g. collagen and keratin)

  • The secondary structure only relates to hydrogen bonds forming between the amino group and the carboxyl group (the ‘protein backbone’)

The structures of secondary proteins

Diagram to show the structure of secondary protiens
The secondary structure of a protein with the α-helix and β-pleated sheet shapes highlighted. The magnified regions illustrate how the hydrogen bonds form between the peptide bonds

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 structure of tertiary proteins

Structure of tertiary 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

Type of Bond

Protein Structure

Primary

Secondary

Tertiary

Peptide

Hydrogen

x

between NH2 and COOH groups

between NH2, COOH and R groups

Disulfide

x

x

Ionic

x

x

Hydrophobic interactions

x

x

Examiner Tips and Tricks

You should be able to draw the peptide formed by the joining of up to three amino acids.

Protein Hydrolysis

  • 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 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 enzymes, the reaction occurs at room temperature

Hydrolysis of proteins

Diagram to show hydrolysis of proteins
Amino acids are bonded together by covalent peptide bonds to form a dipeptide in a condensation reaction

Identification of Amino Acids

  • After hydrolysis, the amino acid components from polypeptides can be identified by using the technique of thin layer chromatography (TLC)

  • 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 Rf values for compounds

  • These values can be used alongside other analytical data to deduce composition of mixtures

  • The Rf value (retention factor) can be determined and use to identify a specific amino acid

A diagram to show how to calculate Rf value
Rf values can be calculated by taking two measurements from the TLC plate

Two dimensional TLC

  • 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 90o and run through the second solvent

  • Two Rvalues are determined allowing greater confidence in identifying the amino acids

2D TLC for amino acids, downloadable AS & A Level Chemistry revision notes
Two dimensional TLC allows greater confidence in identifying amino acids

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Philippa Platt

Author: Philippa Platt

Expertise: Chemistry

Philippa has worked as a GCSE and A level chemistry teacher and tutor for over thirteen years. She studied chemistry and sport science at Loughborough University graduating in 2007 having also completed her PGCE in science. Throughout her time as a teacher she was incharge of a boarding house for five years and coached many teams in a variety of sports. When not producing resources with the chemistry team, Philippa enjoys being active outside with her young family and is a very keen gardener

Stewart Hird

Author: Stewart Hird

Expertise: Chemistry Lead

Stewart has been an enthusiastic GCSE, IGCSE, A Level and IB teacher for more than 30 years in the UK as well as overseas, and has also been an examiner for IB and A Level. As a long-standing Head of Science, Stewart brings a wealth of experience to creating Topic Questions and revision materials for Save My Exams. Stewart specialises in Chemistry, but has also taught Physics and Environmental Systems and Societies.