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BIOT9002 - Structural Biology

Title:Structural Biology
Long Title:Structural Biology
Module Code:BIOT9002
Credits: 10
NFQ Level:Expert
Field of Study: Biotechnology
Valid From: Semester 1 - 2011/12 ( September 2011 )
Module Delivered in 1 programme(s)
Module Coordinator: BRENDAN O CONNELL
Module Author: HUGH MC GLYNN
Module Description: The aim of this module is to acquire a knowledge of the advanced mechanisms of protein evolution and to use this to inform and guide the process of relating protein structure, function and primary sequence data.
Learning Outcomes
On successful completion of this module the learner will be able to:
LO1 Appraise the classification systems underlying the main protein structural databases (CATH, SCOP, FSSP/DALI).
LO2 Critically evaluate the use of Rasmol and Jmol for displaying three-dimensional images of proteins in a range of different display types and colour schemes.
LO3 Interpret the main experimental sources of data in the Protein Data Bank (PDB) and compare their precision.
LO4 Demonstrate an understanding of the mechanisms underlying protein structure and function.
LO5 Demonstrate an understanding of the forces shaping protein structure and function.
LO6 Critically appraise pattern and profile methods to identify homologues of low sequence identity (PROSITE, PRINTS, PFAM).
LO7 Apply comparative modelling and the fundamental steps in the modelling process.
LO8 Demonstrate the ability to carry out comparative modelling on a target protein.
Pre-requisite learning
Module Recommendations
This is prior learning (or a practical skill) that is strongly recommended before enrolment in this module. You may enrol in this module if you have not acquired the recommended learning but you will have considerable difficulty in passing (i.e. achieving the learning outcomes of) the module. While the prior learning is expressed as named CIT module(s) it also allows for learning (in another module or modules) which is equivalent to the learning specified in the named module(s).
No recommendations listed
Incompatible Modules
These are modules which have learning outcomes that are too similar to the learning outcomes of this module. You may not earn additional credit for the same learning and therefore you may not enrol in this module if you have successfully completed any modules in the incompatible list.
No incompatible modules listed
Co-requisite Modules
No Co-requisite modules listed

This is prior learning (or a practical skill) that is mandatory before enrolment in this module is allowed. You may not enrol on this module if you have not acquired the learning specified in this section.

No requirements listed
No Co Requisites listed

Module Content & Assessment

Indicative Content
Ramachandran maps
The use of Ramachandran maps to obtain and convey information about favourable energy geometries in protein models.
Protein Domains, Folds and Motifs
A detialed overview of condserved prtein domains and their role in protein identification and classification.
Classifications of Protein Structure
An insight into the classification systems underlying the main structural databases (CATH, SCOP, FSSP/DALI).
Prediction of Protein Secondary Structure
An overview of the principal methods for prediction of secondary structure and interpretation the results in terms of protein function.
Protein Evolution
An introduction to evolutionary relationships which exist between given proteins, taking into account comparisons in sequence, structure and function.
Comparative Modelling
Three dimensional protein structure prediction. Specifically, the use of fold recognition (threading) methods to detect distant structural and evolutionary relationships.
Assessment Breakdown%
Course Work100.00%
Course Work
Assessment Type Assessment Description Outcome addressed % of total Assessment Date
Multiple Choice Questions 50 MCQ questions with negative marking 1,2,3,4,5,6,7,8 70.0 Sem End
Practical/Skills Evaluation in silico problem based assessment with detailed write-ups to be submitted online. 1,2,3,4,5,6,7,8 30.0 Every Week
No End of Module Formal Examination
Reassessment Requirement
Repeat examination
Reassessment of this module will consist of a repeat examination. It is possible that there will also be a requirement to be reassessed in a coursework element.

The institute reserves the right to alter the nature and timings of assessment


Module Workload

Workload: Full Time
Workload Type Workload Description Hours Frequency Average Weekly Learner Workload
Lecture face to face and blended learning 3.0 Every Week 3.00
Lab in silico problem based learning 3.0 Every Week 3.00
Independent & Directed Learning (Non-contact) eportfolio 8.0 Every Week 8.00
Total Hours 14.00
Total Weekly Learner Workload 14.00
Total Weekly Contact Hours 6.00
This module has no Part Time workload.

Module Resources

Recommended Book Resources
  • Gary Walsh, Proteins [ISBN: 0-471-899070]
This module does not have any article/paper resources
This module does not have any other resources

Module Delivered in

Programme Code Programme Semester Delivery
CR_SCMPB_9 Master of Science in Computational Biology 1 Mandatory

Cork Institute of Technology
Rossa Avenue, Bishopstown, Cork

Tel: 021-4326100     Fax: 021-4545343
Email: help@cit.edu.ie