This module provides an extensive description of the structures of biological macromolecules and their interactions. It aims to show how the basis of their reactivity can be understood in terms of chemical laws and concepts.

a) mechanistically depict the typical reactivity of amino acids, nucleotides and simple carbohydrates;

b) depict the primary, secondary, tertiary and quaternary structures of proteins, polysaccharides, nucleic acids and phospholipid bilayers, discuss their size and describe how their biological functions relate to their chemical structure and reactivity;

c) explain the different types of non-covalent interactions at the molecular level and be able to translate the concepts of hydrogen-bonding, van der Waals interactions, hydrophobic interactions, hydrophilic interactions and salt bridges into a description of macromolecular structure and how small ligands interact with enzymes;

d) give an overview of how enzymes function within biological systems, and write mechanisms for specific examples of hydrolytic and redox enzymes;

e) explain the Michaelis-Menten model of enzyme kinetics and be able to quantitatively describe enzyme catalysed reactions using the Michaelis-Menten equation;

f)  explain the chemistry of DNA replication, mutagenesis and repair processes;

g) depict the chemistry underlying transcription and translation, and explain how this can be used to manufacture a protein with a given amino acid sequence;

h) draw mechanisms for Edman degradation of proteins and the reaction with cyanogen bromide.

17 x 1 h lectures, 3 x 1h workshops, 7 h practical

Intellectual Skills:

On completion of the module the student will be able to:

a) rationalise biological reaction mechanisms using the curly arrow formalism of organic chemistry;

b) suggest biological functions and biologically relevant reactivity of previously unseen molecules.

Discipline Specific (including practical) Skills:

On completion of the module the student will have a greater awareness of how to apply the principles of chemical reactivity to more complex biological systems. The student will be able to use on-line databases to search for function and structure of biological macromolecules.

A written exam (2 h) will test the student’s knowledge and understanding as elaborated under the learning outcomes. The coursework (workshops and tutorials) will allow the student to demonstrate his/her ability to judge and critically review relevant information.  Practical skills will be assessed via a laboratory-based exercise.

Biomacromolecules and their building blocks – amino acids, carbohydrates and nucleotides.

Amino acid side chain functional groups - classification into hydrophobic, hydrophilic, charged, aromatic.

pK_a and ionization states of amino acids under physiological conditions.

Cysteine - ability to oxidize.

Polypeptides/proteins - amide bonds - electronic structure and geometry.

Primary structure - the 3 letter / 1 letter codes for amino acids and the convention for writing peptide sequences.

Importance of non-covalent interactions in biological systems.

Torsion angles. Hydrogen bonding in alpha helix and beta sheet, Ramachandran plots.

Tertiary structure - hydrophobic interactions, salt bridges, cystine, H bonds - combinations of helices and sheets.

Quaternary structure - protein-protein interactions.

Introduction to databases of protein sequences and structures.

Biological catalysis.

Reaction free energy profiles, types of catalysis - general acid/base, nucleophilic catalysis.

Examples – esterases, serine and cysteine proteases.

Michaelis-Menten kinetics.

Introduction to cofactors/coenzymes/prosthetic groups.

Sugars - monosaccharides - structure and Fischer/Haworth projections.

Chemistry of hemiacetals, ring/chain equilibria. Pyranose and furanose forms. Anomers.

Glycosides, disaccharides - maltose, cellobiose.

Polysaccharides - linear and branching, cellulose, starch and glycogen.

Complex carbohydrates – aminosugars, proteoglycans, glycosaminoglycans and peptidoglycans.

Nucleic acids - heterocyclic bases, H-bonding, base pairing (classical and non-classical).

Sugars - ribose, deoxyribose, in a biological context.

Phosphate esters – reactions, kinetics and thermodynamics.

Nucleosides, nucleotides and the double helix (DNA vs. RNA conformation).

Polymerases - DNA replication, transcription and reverse transcription.

Chemical reactions of mutation and DNA repair processes.

Transcription and translation.

Introduction to recombinant DNA technology and molecular biology.

Foundations of Molecular Biology, C. M. Dobson, J. A. Garrard, A. J. Pratt, Oxford Chemistry Primers.

Lehninger Principles of Biochemistry, 4^th edition or later, David L. Nelson and Michael M. Cox, W. H. Freeman.

Fundamentals of General, Organic and Biological Chemistry, 5^th edition, John McMurry, Mary E. Castellion, David S. Ballantine, Pearson Prentice Hall 2007.

Please see Essential Reading List.