Module Specification
The information contained in this module specification was correct at the time of publication but may be subject to change, either during the session because of unforeseen circumstances, or following review of the module at the end of the session. Queries about the module should be directed to the member of staff with responsibility for the module.
Title Structure and Dynamics of Macromolecules
Code LIFE203
Coordinator Dr I Barsukov
Biochemistry
I.Barsukov@liverpool.ac.uk
Year CATS Level Semester CATS Value
Session 2016-17 Level 5 FHEQ First Semester 15

Pre-requisites before taking this module (other modules and/or general educational/academic requirements):
LIFE104 None 

Modules for which this module is a pre-requisite:
LIFE303 

Co-requisite modules:
 

Linked Modules:
 

Teaching Schedule
  Lectures Seminars Tutorials Lab Practicals Fieldwork Placement Other TOTAL
Study Hours 24
Lectures to introduce key concepts
        6
Problem solving and data handling sessions
30
Timetable (if known) Timetabled lectures will develop knowledge and understanding
  		           
Private Study 120
TOTAL HOURS 150

Assessment
EXAM Duration Timing
(Semester)		 % of
final
mark		 Resit/resubmission
opportunity		 Penalty for late
submission		 Notes
Unseen Written Exam  2h  Semester 1  70  Yes    Exam 
CONTINUOUS Duration Timing
(Semester)		 % of
final
mark		 Resit/resubmission
opportunity		 Penalty for late
submission		 Notes
Coursework  2h  Semester 1  10  Yes  Standard UoL penalty applies  In-class assignment 
Coursework  1000 words  Semester 1  20  Yes  Standard UoL penalty applies  Essay Notes (applying to all assessments) Assessment 1 (203) will be short answer questions. Assessment 2 (203.1) will be short answer questions. Assessment 3 (203.2) will be an extended written assignment (essay). Full compensation operates between all assessment elements  

Aims

  • This module aims to:

     
    Provide students with knowledge and understanding of the latest methodologies and techniques that are used to study the fine detail of macromolecules;

  • Expla in how the structure of macromolecules determines their function

  • Describe how altered protein function can result in disease;

  • Outline the importance of applying the techniques used to solve macromolecular structure and function can be applied to drug discovery programmes

  • Develop knowledge and understanding in structural biology, and ability to apply, evaluate and interpret this knowledge to solve problems

    		•

    Learning Outcomes

    Explain the key chemical and structural features of proteins and describe how these features relate to biological function

    Discuss how knowledge of biomolecular structure relates to applications in medicine, the pharmaceutical industry and bio- and nano-technology

    Describe techniques used to determine protein structure and dynamics and discuss the advantages and limitations of each technique

    Discuss the chemical and structural basis of some central biological processes by describing the structure and function of enzymes, membrane proteins and macromolecular complexes of biomolecules

    Discuss the latest ideas on the evolution of protein function

    Describe the principles of structural biology, and how this knowledge has been applied to solve fundumental biological questions

    Conduct basic analysis of optical and NMR spectra of proteins


    Teaching and Learning Strategies

    Lecture - Lectures to introduce key concepts

    Timetabled lectures will develop knowledge and understanding

    Workshop - Problem solving and data handling sessions

    Syllabus
    1 

    Block 1. The experimental tools of protein biochemists and structural biologists.
     
    The forces that hold molecules together: The hydrogen bond, hydrophobic interactions, Van der Waals forces, electrostatic interactions. Amino acid chemistry.
     
    Architectural principles of protein structure: Secondary structure. Folds, domains, motifs. Visualising protein structure.
     
    Purification and analysis of proteins: Sources of proteins; natural versus recombinant. Protein chromatography and electrophoresis.
     
    Mass spectrometry of proteins. Fu ndamentals. Peptide mass, MS-MS sequencing. Proteomics; Identification of proteins in complex mixtures.
     
    X-ray crystallography fundamentals: X-ray crystallography 1: Introduction to crystallisation and X-ray diffraction
     
    X-ray crystallography practice: Introduction to phasing and model bu ilding
     
    NMR fundamentals: Structural information from NMR spectra
     
    Additional methods of structural analysis : Electron microscopy, atomic force microscopy, circular dichroism, fluorescence and small angle X-ray scattering.
     
    Block 2. Understanding the structural basis of central biochemical processes.
     
    Thermodynamics in protein function and interactions:   Thermodynamic parameters and reaction rates.
     
    Main protein domains, their folds and functions: Examples of protein domains, multi-domain proteins

    Membrane proteins: Protein architecture of membrane proteins and protein-lipid interactions.
     

    Nucleic Acid structure: Chemical composition and structural principles of DNA and RNA
     
    Protein-nucleic acid complexes: Principles of the interaction of proteins and DNA
     
    Structural basis of receptor signalling: G-protein coupled receptors. Structural and functional classes.
     
    Structural basis of disease: How structural techniques have given us insights into the causes and treatments of devastating human diseases.
     
    Regulation of protein function 1: Why regulate protein function? Regulation by covalent modification, regulation without covalent modification: Alloster ic control by effectors.
     
    Regulation of protein function 2: Regulation by change in quaternary structure. Binding of inhibitors to catalytic site. Regulation by environment e.g. pH.
     
    Evolution of protein function 1: New function: mutation, domain duplication. Homology, orthology, paralogy. Conservation of structure while sequence changes.
     
    Evolution of protein function 2: Conservation of function with respect to sequence identity. Detection of sequence similarity and significance for genome annotation. Moonlighting proteins. Convergent evolution. Molecular mimicry.

    Recommended Texts
    Reading lists are managed at readinglists.liverpool.ac.uk. Click here to access the reading lists for this module.
    Explanation of Reading List: