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 tour of the University's structural biology facilities.

Contact hours:

	Autumn	Spring	Summer
Lectures		12
Practicals classes and workshops		24
Guided independent study:		64
Total hours by term		100
Total hours for module	100

Summative Assessment Methods:

Method	Percentage
Written exam	60
Written assignment including essay	20
Practical skills assessment	10
Class test administered by School	10

Summative assessment- Examinations:
A one-and-a-half hour examination

Summative assessment- Coursework and in-class tests:

Summative assessments will include interactive quiz questions and/or discussions to be held at regular intervals during the lectures/practicals, which will help to reinforce and recap on the key points raised. The quizzes and discussions will help to improve student attainment, as well as being used to monitor the group progress and understanding of the module material. 

Formative assessment methods:
Formative assessments will include interactive quiz questions and/or discussions to be held at regular intervals during the lectures, which will help to reinforce and recap on the key points raised. The quizzes and discussions will help to improve student attainment, as well as being used to monitor the group progress and understanding of the module material.

Penalties for late submission:

The Support Centres will apply the following penalties for work submitted late:

• where the piece of work is submitted after the original deadline (or any formally agreed extension to the deadline): 10% of the total marks available for that piece of work will be deducted from the mark for each working day (or part thereof) following the deadline up to a total of five working days;
• where the piece of work is submitted more than five working days after the original deadline (or any formally agreed extension to the deadline): a mark of zero will be recorded.

The University policy statement on penalties for late submission can be found at: https://www.reading.ac.uk/cqsd/-/media/project/functions/cqsd/documents/cqsd-old-site-documents/penaltiesforlatesubmission.pdf
You are strongly advised to ensure that coursework is submitted by the relevant deadline. You should note that it is advisable to submit work in an unfinished state rather than to fail to submit any work.

Assessment requirements for a pass:
A mark of 40% overall

Reassessment arrangements:
Re-examination in August/September

Additional Costs (specified where applicable):

1) Required text books:  None

2) Specialist equipment or materials:  None

3) Specialist clothing, footwear or headgear:  None

4) Printing and binding:  None

5) Computers and devices with a particular specification:  None

6) Travel, accommodation and subsistence:  None

Last updated: 30 March 2023