BI2BL5-Protein Structure and Function

Module Provider: School of Biological Sciences
Number of credits: 10 [5 ECTS credits]
Level:5
Terms in which taught: Spring term module
Pre-requisites:
Non-modular pre-requisites:
Co-requisites:
Modules excluded:
Current from: 2023/4

Module Convenor: Prof Kimberly Watson
Email: k.a.watson@reading.ac.uk

Type of module:

Summary module description:

To understand protein structure at the primary, secondary, tertiary and quaternary levels, the properties of amino acids and chemistry of polypeptides. To know the principles of methods for determining protein three-dimensional structure To be able to relate protein structure to function for important types of proteins. To gain experience of using molecular graphics tools and the Web to investigate the structure of a protein and its relation to function To understand the principles of enzyme catalysis (kinetics, thermodynamics and allostery).

Aims:
To understand protein structure at the primary, secondary, tertiary and quaternary levels, the properties of amino acids and chemistry of polypeptides.
To know the principles of methods for determining protein three-dimensional structure
To be able to relate protein structure to function for important types of proteins.
To gain experience of using molecular graphics tools and the Web to investigate the structure of a protein and its relation to function
To understand the principles of enzyme catalysis (kinetics, thermodynamics and allostery).

Assessable learning outcomes:

By the end of the module students should be able to:

• Describe a range of functions undertaken by proteins


• Categorise amino acids on the basis of different chemical and structural properties


• Draw the basic mechanism of peptide bond formation and label the associated torsion angles


• Describe the 4 levels of protein structure and the principles behind structure classification


• Demonstrate the relationship between secondary structure and the Ramachandran plot


• Describe the major types of molecular forces and their implication in protein structure and interactions


• Discuss the principles of catalysis in structural terms


• Give examples of structural and non-structural co-factors showing how they interact with proteins and describing their importance


• Demonstrate a knowledge of basic thermodynamics and chemical and enzyme kinetics


• Discuss the effects of allostery and its biological advantages


• Describe the use of X-ray crystallography for determining protein structure

Discuss the structure and function of the following:

• DNA binding proteins, serine proteases, membrane proteins, molecules of the immune system, kinases and viruses


• Extract information about the protein structure and function from on-line resources (Protein Data Bank)


• Use molecular graphics tools to display and create images of protein structures.

Additional outcomes:

Outline content:
Lectures will cover:
Examples of protein function. Types of proteins. Amino acids and their properties. Chemistry and geometry of the peptide bond. The Ramachandran Plot. Primary, secondary, super-secondary, tertiary and quaternary structure. Motifs, domains, folds, classes and classification. Molecular Forces (covalent, non-covalent, hydrophobic).X-ray crystallography for determining protein structure. DNA and DNA-binding proteins. Enzymes and allostery. Structure and function of serine proteases; membrane proteins; viruses; molecules of the immune system and kinases.

Practicals will cover:
Visualization of protein structures using PyMol. Web practicals on amino acids, peptide bonds, protein folds and molecular forces. Building peptide structures. Viewing examples of protein interactions. Accessing web-based databases of protein structure. Visit to structural biology facilities on the University campus.

Brief description of teaching and learning methods:
Teaching will be through a series of 12 lectures with supporting practicals. Practicals will mostly be computer-based. Independent study based around web-based material will be expected. One practical will involve a