Biology Online Module Handbook

BL3301 Protein Structure and Function

(BL3301 online module handbook version 13)

cover image

image: Image from: Govaerts et al. PNAS 101, 8342 (2004)

This module builds an understanding of more advanced aspects of protein structure and enzymology. The module begins by considering the protein-folding problem. The energetics of protein folding and the dependence of structure on sequence are examined. Protein folding diseases like spongiform encephalopathies are used as examples to highlight the significance of protein folding. The molecular basis of prion diseases is discussed in detail. The second part of the module focuses on the mechanisms of enzymes. This in turn leads into the phenomena of allosteric regulation, signalling cascades and transporter systems and is followed by a consideration of enzymes as pharmacological targets. The third part of the module introduces the major techniques for protein structure determination that are at the heart of modern biochemistry, molecular biology and drug discovery. Strategies for obtaining three-dimensional images of macromolecules by electron microscopy, X-ray crystallography and nuclear magnetic resonance are discussed. The laboratory course associated with this module introduces the fundamentals of safe laboratory practice. It provides grounding in the basic laboratory techniques, including associated calculations, as well as those associated with the study of proteins and enzymes.*

Credits: 20*

Semester: 1

Module Organiser
Dr Uli Schwarz-Linek
us6@st-andrews.ac.uk
01334 467188
Pre-requisite Modules:
BEFORE TAKING THIS MODULE YOU SHOULD PASS BL2306 AND ( PASS BL2302 OR PASS BL2309 ). BEFORE TAKING THIS MODULE YOU MUST PASS BL2306 AND ( PASS BL2302 OR PASS BL2309 )*
Anti-requisite Modules:
None*
Post-requisite Modules:
BL4212, BL4215, BL4223*
Additional Module Information:
Please check MMS regularly for additional module information


Biology Teaching Office:
Room 1.17, Biomolecular Sciences Building, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST

Email: bioteach@st-andrews.ac.uk      Tel: 01334  463602

BL3301: Timetable

The regular hours for lectures and tutorials are 9-10am on Mondays, Tuesdays and Wednesdays.

Legend (not all modules have every event type):
lecture
tutorial
workshop
practical
other

Semester 1: Week 1

DATE & TIMEVENUESTAFFEVENT
Monday
18-09-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Uli Schwarz-Linek

Lecture L1: Module Introduction
2017-8_BL3301_L1
Tuesday
19-09-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Uli Schwarz-Linek

Lecture L2: Reminder: The basics of protein structure
2017-8_BL3301_L2
Wednesday
20-09-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Uli Schwarz-Linek

Lecture L3: The protein folding problem
2017-8_BL3301_L3

Semester 1: Week 2

DATE & TIMEVENUESTAFFEVENT
Monday
25-09-2017
09:00 to 10:00
Purdie Building
Lecture Theatre D
Dr Uli Schwarz-Linek

Lecture L4: Assisted protein folding I
2017-8_BL3301_L4
Tuesday
26-09-2017
09:00 to 10:00
Purdie Building
Lecture Theatre D
Dr Uli Schwarz-Linek

Lecture L5: Assisted protein folding II
2017-8_BL3301_L5
Wednesday
27-09-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Uli Schwarz-Linek

Lecture L6: Protein misfolding and disease I
2017-8_BL3301_L6
Thursday
28-09-2017
10:00 to 17:00
Purdie Building
Teaching Lab
Dr Uli Schwarz-Linek

Practical P1: Introductory Techniques and SDS PAGE
2017-8_BL3301_P1
Class section A
Friday
29-09-2017
10:00 to 17:00
Purdie Building
Teaching Lab
Dr Uli Schwarz-Linek

Practical P2: Introductory Techniques and SDS PAGE
2017-8_BL3301_P2
Class section B

Semester 1: Week 3

DATE & TIMEVENUESTAFFEVENT
Monday
02-10-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Uli Schwarz-Linek

Lecture L7: Protein misfolding and disease II
2017-8_BL3301_L7
Tuesday
03-10-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Uli Schwarz-Linek

Lecture L8: Protein misfolding and disease III
2017-8_BL3301_L8
Wednesday
04-10-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Uli Schwarz-Linek

Lecture L9: Protein misfolding and disease IV
2017-8_BL3301_L9

Semester 1: Week 4

DATE & TIMEVENUESTAFFEVENT
Monday
09-10-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Prof Terry Smith

Lecture L10: Michaelis-Menten and beyond
2017-8_BL3301_L10
Tuesday
10-10-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Prof Terry Smith

Lecture L11: The kinetics of inhibition I
2017-8_BL3301_L11
Wednesday
11-10-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Prof Terry Smith

Lecture L12: The kinetics of inhibition II
2017-8_BL3301_L12

Semester 1: Week 5

DATE & TIMEVENUESTAFFEVENT
Monday
16-10-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Prof Terry Smith

Lecture L13: Two-substrate reactions
2017-8_BL3301_L13
Tuesday
17-10-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Rafael Guimaraes da Silva

Lecture L14: Chemistry basics for enzymology
2017-8_BL3301_L14
Wednesday
18-10-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Jacqueline Nairn

Lecture L15: Biophysical techniques
2017-8_BL3301_L15

Semester 1: Week 7

DATE & TIMEVENUESTAFFEVENT
Monday
30-10-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Rafael Guimaraes da Silva

Lecture L16: Rate enhancement and enzyme catalysis
2017-8_BL3301_L16
Tuesday
31-10-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Rafael Guimaraes da Silva

Lecture L17: The chemistry of cofactors
2017-8_BL3301_L17
Wednesday
01-11-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Rafael Guimaraes da Silva

Lecture L18: Allostery and cooperativity
2017-8_BL3301_L18
Friday
03-11-2017
09:00 to 13:00
Irvine Building
PC lab
Dr Jacqueline Nairn

Practical P3: Plotting kinetic data
2017-8_BL3301_P3

Semester 1: Week 8

DATE & TIMEVENUESTAFFEVENT
Monday
06-11-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Jacqueline Nairn

Lecture L19: How to explore an enzyme mechanism
2017-8_BL3301_L19
Tuesday
07-11-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Jacqueline Nairn

Lecture L20: Proteases
2017-8_BL3301_L20
Wednesday
08-11-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Jacqueline Nairn

Lecture L21: Two-substrate reactions - LDH and ADH
2017-8_BL3301_L21
Thursday
09-11-2017
09:00 to 17:00
Purdie Building
Teaching Lab
Dr Jacqueline Nairn

Practical P4: Gathering, plotting and analysing kinetic data
2017-8_BL3301_P4
Class section Y
Friday
10-11-2017
09:00 to 17:00
Purdie Building
Teaching Lab
Dr Jacqueline Nairn

Practical P5: Gathering, plotting and analysing kinetic data
2017-8_BL3301_P5
Class section Z

Semester 1: Week 9

DATE & TIMEVENUESTAFFEVENT
Monday
13-11-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Jacqueline Nairn

Lecture L22: Enzyme substitution mechanism
2017-8_BL3301_L22
Tuesday
14-11-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Rafael Guimaraes da Silva

Lecture L23: Kinetic isotope effects and transition-state geometry
2017-8_BL3301_L23
Tuesday
14-11-2017
11:00 to 12:00
Biomolecular Sciences Building
Lecture Theatre
Dr Rafael Guimaraes da Silva

Tutorial T1: Enzyme mechanisms
2017-8_BL3301_T1
Wednesday
15-11-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Tracey Gloster

Lecture L24: Introduction to Protein Structure Determination
2017-8_BL3301_L24

Semester 1: Week 10

DATE & TIMEVENUESTAFFEVENT
Monday
20-11-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Tracey Gloster

Lecture L25: X-Ray Crystallography I
2017-8_BL3301_L25
Tuesday
21-11-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Tracey Gloster

Lecture L26: X-Ray Crystallography II
2017-8_BL3301_L26
Wednesday
22-11-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Tracey Gloster

Lecture L27: X-Ray Crystallography III
2017-8_BL3301_L27

Semester 1: Week 11

DATE & TIMEVENUESTAFFEVENT
Monday
27-11-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Uli Schwarz-Linek

Lecture L28: Nuclear Magnetic Resonance I
2017-8_BL3301_L28
Tuesday
28-11-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Uli Schwarz-Linek

Lecture L29: Nuclear Magnetic Resonance II
2017-8_BL3301_L29
Wednesday
29-11-2017
09:00 to 10:00
Biomolecular Sciences Building
Lecture Theatre
Dr Uli Schwarz-Linek

Lecture L30: Nuclear Magnetic Resonance III
2017-8_BL3301_L30
Thursday
30-11-2017
09:00 to 17:00
Purdie Building
Teaching Lab
Dr Jacqueline Nairn

Practical P6: Protein ligand interactions
2017-8_BL3301_P6
Friday
01-12-2017
09:00 to 17:00
Purdie Building
Teaching Lab
Dr Jacqueline Nairn

Practical P7: Protein ligand interactions
2017-8_BL3301_P7

Semester 1: Week 12

DATE & TIMEVENUESTAFFEVENT
Tuesday
05-12-2017
11:00 to 12:00
Purdie Building
Lecture Theatre D
Dr Jacqueline Nairn

Workshop W1: Exam prep workshop
2017-8_BL3301_W1
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
School of Biology Symbiosis Database (module organisers only)
University of St Andrews MMS (St Andrews users only)

BL3301: Reading List

Click for BL3301 reading list

BL3301: Assessment

3-hour Written Examination = 66%, Coursework = 34%*

Assessment:
Module essay
Due by:
30/10/2017 12:00
Feedback due by:
20/11/2017 12:00
Type:
Single Upload
Weight:
50%
Assessment:
Week 7 practical report
Due by:
08/11/2017 12:00
Feedback due by:
29/11/2017 12:00
Type:
Single Upload
Weight:
0%
Assessment:
Week 8 practical report
Due by:
20/11/2017 12:00
Feedback due by:
11/12/2017 12:00
Type:
Single Upload
Weight:
50%
Assessment:
Week 11 practical report
Due by:
01/12/2017 17:00
Feedback due by:
22/12/2017 17:00
Type:
Single Upload
Weight:
0%

(MMS assessment data cached: 17 November 2017 23:20:14.)


The following related information applies to all Biology modules:

School of Biology Marking Criteria: See School of Biology Undergraduate Handbook
Late submission of continuous assessment work:

All late submissions of coursework that do not require electronic submission should be made via the late submissions box in the Biomolecular Science Building (beside the Teaching Office)
Exam details: See School of Biology Undergraduate Handbook
Exam timetable: see http://www.st-andrews.ac.uk/students/academic/examinations/examtimetablescurrent/
Expected attendance: See School of Biology Undergraduate Handbook for detailed attendance requirements.
Good Academic Practice & Avoiding Academic Misconduct: See School of Biology Undergraduate Handbook
University Student Handbook: University Student Handbook
School and University regulations in the School and University Undergraduate Handbook relating to absence reporting, penalties and rules for late submission of work, extensions for coursework, return of coursework, S-coding, good academic practice and Academic Alerts.: School of Biology Undergraduate Handbook University Student Handbook
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
School of Biology Symbiosis Database (module organisers only)
University of St Andrews MMS (St Andrews users only)

Who to ask

(Information in this section applies to all Biology Modules)

Questions about different aspects of the module should be directed to different people:

Questions about Contact
General teaching matters Biology Teaching Office ( bioteach@st-andrews.ac.uk )
Rescheduled or cancelled events Check your University email
Lecture or practical content The lecturer who presented the material
Completing assessed practical assignments The lecturer who set the assignment
Completing assessments Module Organiser (Dr Uli Schwarz-Linek us6@st-andrews.ac.uk)
Marking on continuous assessment The Demonstrator or Module Organiser (Dr Uli Schwarz-Linek us6@st-andrews.ac.uk)
Marking on exams Module Organiser (Dr Uli Schwarz-Linek us6@st-andrews.ac.uk)
Rearranging practical days Grant Brown
Absence and/or extensions Module Organiser (Dr Uli Schwarz-Linek us6@st-andrews.ac.uk) and the Biology Teaching Office ( bioteach@st-andrews.ac.uk )

Difficulties with academic progress which impact more than one module:

Year Coordinator

See School of Biology Undergraduate student handbook for list: http://biology.st-andrews.ac.uk/documents/UndergraduateHandbook.pdf

Overall performance, progress or future directions:

Advisor of Studies

Disability:

Disability Coordinator (Dr Jacqueline Nairn jn37@st-andrews.ac.uk)

Biology Teaching Office:

Room 1.17, Biomolecular Sciences Building, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST

Email: bioteach@st-andrews.ac.uk

Tel: 01334 463602

BL3301: Contributing Staff

Dr Uli Schwarz-Linek

Dr Uli Schwarz-Linek
(Module Organiser)

Lecturer in Biomolecular Sciencesus6@st-andrews.ac.uk
Dr Tracey GlosterDr Tracey GlosterWellcome Trust Research Fellowtmg@st-andrews.ac.uk
Dr Rafael Guimaraes da SilvaDr Rafael Guimaraes da SilvaResearch Fellowrgds@st-andrews.ac.uk
Dr Jacqueline NairnSenior Lecturer (Education Focused)jn37@st-andrews.ac.uk
Dr Uli Schwarz-LinekDr Uli Schwarz-Linek
(Module Organiser)
Lecturer in Biomolecular Sciencesus6@st-andrews.ac.uk
Prof Terry SmithProf Terry SmithProfessortks1@st-andrews.ac.uk
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
School of Biology Symbiosis Database (module organisers only)
University of St Andrews MMS (St Andrews users only)

BL3301: Learning Outcomes

Students completing module BL3301 successfully should be able to:

  • Describe protein structure & folding using a range of examples
  • Relate protein structure to protein function
  • Outline the methods used to characterise protein-ligand interactions
  • Demonstrate the use of enzyme kinetics to characterise an enzyme
  • Design experiments to explore enzyme activity
  • Describe the methods used to explore protein structure
  • Use in silico tools to characterise proteins, including biomolecular databases and molecular viewers
  • Outline the methods used to characterise protein-ligand interactions
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
School of Biology Symbiosis Database (module organisers only)
University of St Andrews MMS (St Andrews users only)

BL3301: Acquired Skills

Practical Skills

  • Buffers
  • Enzyme assay
  • Kinetic data analysis
  • Molecular viewer software
  • Pipetting
  • Protein quantitation
  • SDS PAGE

Transferable Skills

  • "Short" practical write-up (e.g. completed worksheet)
  • Short essay (1000-2000 words)
  • Finding literature
  • Referencing
  • Searching databases
  • Lab safety awareness
  • Calculations/equations
  • Concentrations
  • Dilutions
  • Volumes
  • Working in pairs/small groups
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
School of Biology Symbiosis Database (module organisers only)
University of St Andrews MMS (St Andrews users only)

Policies

(Information in this section applies to all Biology Modules)