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The University of Southampton

BIOL3013 Molecular Recognition

Module Overview

Most biological processes involve interactions between macromolecules. The module discusses selected examples and explains techniques used to study molecular interactions.

Aims and Objectives

Learning Outcomes

Learning Outcomes

Having successfully completed this module you will be able to:

  • describe the structure of DNA and the nature of interactions with proteins;
  • describe the structure of RNA and the nature of riboswitches;
  • describe GTPases as molecular protein switches;
  • describe how peptide motifs are recognised by interacting proteins;
  • multi-domain proteins, their structure and function;
  • describe protein ligand interactions;
  • regulation of kinase activity;
  • describe hydrogen–deuterium exchange in mass spectrometry to study molecular interaction.


The module discusses ways in which signal transduction events lead to altered gene expression. Cytokines and growth hormones and their receptors are discussed, affecting cell cycle regulation. Protein-peptide recognition will be introduced, and will see how viruses upset cell regulation through interfering peptides. The receptors themselves are often multi-domain proteins. Assembly of multiple domains is a requirement for regulation and efficient binding site presentation. The structure of DNA and the recognition of nucleic acids by interacting proteins such as histones, nucleases, and transcription factors is introduced. Also discussed are the structures of RNA and riboswitches. Methods to study macromolecular interactions are introduced in all sections. The seminal technique of mass spectrometry is covered in detail to explain protein-ligand interactions. Hydrogen–deuterium exchange (HDX) mass spectrometry allows to studying protein-protein interactions.

Learning and Teaching

Teaching and learning methods

Lectures and independent study.

Independent Study126
Total study time150



MethodPercentage contribution
Written assessment 100%


MethodPercentage contribution
Written assessment 100%

Linked modules

PRE-REQUISITES BIOL2010 and either of (BIOL2011 or BIOL2012)

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