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*Revision Materials and Past Papers* 1 Atomic Structure 2 Amounts of Substance 3 Bonding 4 Energetics 5 Kinetics 6 Chemical Equilibria & Kc 7 Redox Equations 8 Thermodynamics 9 Rate Equations 10 Kp (Equilibrium Constant) 11 Electrode Potentials & Cells 12 Acids and Bases 13 Periodicity 14 Group 2: Alkaline Earth Metals 15 Group 7: The Halogens 16 Period 3 Elements & Oxides 17 Transition Metals 18 Reactions of Ions in Aqueous Solution 19 Intro to Organic Chemistry 20 Alkanes 21 Halogenoalkanes 22 Alkenes 23 Alcohols 24 Organic Analysis 25 Optical Isomerism 26 Aldehydes & Ketones 27 Carboxylic Acids & Derivatives 28 Aromatic Chemistry 29 Amines 30 Polymers 31 Amino Acids, Proteins & DNA 32 Organic Synthesis 33 NMR Spectroscopy 34 Chromatography RP1–RP12 Required Practicals

3.13 Amino Acids, Proteins and DNA (A-level only)

3.13.1 Amino Acids 3.13.2 Proteins 3.13.3 Enzymes 3.13.4 DNA 3.13.5 Action of Anti-Cancer Drugs

Proteins

Specification Reference Organic chemistry, Amino acids, proteins and DNA 3.3.13.2

Quick Notes

  • Proteins are polymers made up of amino acid monomers joined by peptide bonds (−CONH−).
  • Proteins have complex shapes that are described in terms of a Primary, Secondary and Tertiary structure.
    • Primary structure refers to the sequence of amino acids bonded together.
    • Secondary structure includes α-helices and β-pleated sheets, stabilised by hydrogen bonding between C=O and N−H groups from different amino acids.
    • Tertiary structure is the 3D folding of proteins, stabilised by hydrogen bonds, disulfide bonds (S−S), ionic bonds, and hydrophobic interactions between R groups on different amino acids.
  • Hydrolysis of proteins breaks peptide bonds, forming the constituent amino acids.
  • Amino acids can be separated and identified by thin-layer chromatography (TLC).
    • As amino acids are colourless, ninhydrin or UV light is used with a chromatogram, and amino acids are identified by Rf values.

Full Notes

Structure of Proteins

Proteins are naturally occurring polymers of amino acids linked by peptide bonds (−CONH−).

AQA A-Level Chemistry diagram showing a protein as a polymer chain made from amino acids linked by peptide bonds

Peptide bonds form by condensation reactions between amino acids, releasing water:

AQA A-Level Chemistry diagram showing two amino acids forming a dipeptide linked by a peptide bond

The process can keep happening between more amino acids, forming a polypeptide chain (polymer).

AQA A-Level Chemistry condensation reaction forming a peptide bond with water as a by-product

Peptide bonds can be broken apart in hydrolysis reactions. The hydrolysis of proteins (with acid or alkali) releases the amino acids that made up the protein .

AQA A-Level Chemistry hydrolysis of a peptide bond giving two amino acids
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The conditions used for hydrolysis determine the form of the amino acids released.

  • If acidic conditions are used, then the amino acids may exist as positively charged ions with the NH2 group accepting a H+ ion to form NH3+
  • If alkaline conditions are used, then the carboxylic acid groups may be forced to lose H+ ions and exist as carboxylate ions (COO−)

Levels of Protein Structure

Proteins can have very complicated shapes that are difficult to analyse. We describe the structure of proteins in terms of a Primary, Secondary and Tertiary structure. (Proteins made up of more than one polymer chain also have a quaternary structure, however you don’t need to learn that for AQA A-Level Chemistry!).

Primary Structure

The primary structure is the sequence of amino acids in a polypeptide chain.

AQA A-Level Chemistry overview of protein structure levels including primary sequence, secondary shapes and tertiary folding

Determines the overall structure and function of the protein.

Secondary Structure

The secondary structure describes two types of shape (α-helix and β-pleated sheet) that arise from hydrogen bonding between C=O and N−H bonds from different amino acids in the polymer chain

AQA A-Level Chemistry α-helix and β-pleated sheet depictions as common secondary structures

α-helix – a spiral structure stabilised by hydrogen bonds

β-pleated sheet – strands linked side by side with hydrogen bonds

AQA A-Level Chemistry hydrogen bonding between C=O and N−H groups forming secondary structure

Tertiary Structure

The tertiary structure describes the 3D folding of the protein due to interactions between R groups.

AQA A-Level Chemistry tertiary protein structure formed by interactions between R groups

The interactions between different R groups causes the protein to ‘fold’ into complicated shapes, with the final shape between determined by the locations (and type) of amino acids in the chain.

AQA A-Level Chemistry diagram showing hydrogen bonds, disulfide bonds, ionic bonds and hydrophobic interactions that stabilise tertiary structure

The type of interaction depends on the R groups interacting - only certain R groups can interact with each other.

Hydrolysis of Proteins

Proteins are examples of condensation polymers and can be broken apart into amino acids by hydrolysis. See Condensation Polymers for more detail.

AQA A-Level Chemistry diagram showing protein hydrolysis to give amino acids using acid or alkali

Peptide bonds (−CONH−) are hydrolysed by acid, alkali, or enzymes to release amino acids. The form of amino acid(s) produced is based on the conditions used (see Amino Acids for more detail).

Reagents:

Separation and Identification of Amino Acids by Thin-Layer Chromatography (TLC)

After a protein is hydrolysed and broken apart into its amino acids, the amino acids can be separated and identified using Thin-Layer Chromatography (TLC) – see Required Practical 12.

AQA A-Level Chemistry TLC of amino acids with solvent front and spots for Rf calculation

Summary