Biology Online Module Handbook

BL2306 Biochemistry

(BL2306 online module handbook version 31)

cover image
Due to recent technological developments, metabolism and its regulation has re-emerged as an important area of Biology. This module will examine major biological macromolecules, the common motifs which occur in metabolic reactions, explore the properties of enzymes catalysing these reactions and consider the approaches to characterise the small molecule complement (metabolites) of biological systems. A number of central metabolic pathways and their control will be studied in detail, alongside examples of their importance in disease and recent metabolomic studies. *

Credits: 15*

Semester: 2

Module Organiser
Dr Jacqueline Nairn
jn37@st-andrews.ac.uk
01334 463604
Pre-requisite Modules:
BEFORE TAKING THIS MODULE YOU MUST PASS BL1101 AND PASS BL1102*
Anti-requisite Modules:
YOU CANNOT TAKE THIS MODULE IF YOU TAKE BL2104*
Post-requisite Modules:
BL3301, BL3302, BL3303, BL3310, BL3322*
Additional Module Information:
Please check MMS regularly for additional module information


Biology Teaching Office:
The Biology Hive, New Technology Centre, University of St Andrews, North Haugh, St Andrews, Fife KY16 9SR

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

BL2306: Timetable

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

Semester 2: Week -1

DATE & TIMEVENUESTAFFEVENT
Friday
26-01-2018
09:00 to 10:00
Physics Building
Lecture Theatre B
Dr Jacqueline Nairn

Lecture L1: Module Introduction & Introduction to Practical 1 Lab Skills
2017-8_BL2306_L1

Semester 2: Week 1

DATE & TIMEVENUESTAFFEVENT
Monday
29-01-2018
14:00 to 17:00
Chemistry
Purdie Lab
Dr Jacqueline Nairn

Practical P1: Practical 1 - Lab Skills
2017-8_BL2306_P1
Tuesday
30-01-2018
14:00 to 17:00
Chemistry
Purdie Lab
Dr Jacqueline Nairn

Practical P2: Practical 1 - Lab Skills
2017-8_BL2306_P2
Thursday
01-02-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Tracey Gloster

Lecture L2: The building blocks of life I
2017-8_BL2306_L2
Friday
02-02-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Tracey Gloster

Lecture L3: The building blocks of life II
2017-8_BL2306_L3

Semester 2: Week 2

DATE & TIMEVENUESTAFFEVENT
Wednesday
07-02-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Tracey Gloster

Lecture L4: The building blocks of life III
2017-8_BL2306_L4
Thursday
08-02-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Tracey Gloster

Lecture L5: The building blocks of life IV
2017-8_BL2306_L5
Friday
09-02-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Tracey Gloster

Lecture L6: Introduction to Practical 2 Visualising Molecules
2017-8_BL2306_L6

Semester 2: Week 3

DATE & TIMEVENUESTAFFEVENT
Monday
12-02-2018
14:00 to 17:00
Irvine Building
PC lab
Dr Tracey Gloster

Practical P3: Practical 2 - Visualising Molecules
2017-8_BL2306_P3
Tuesday
13-02-2018
14:00 to 17:00
Irvine Building
PC lab
Dr Tracey Gloster

Practical P4: Practical 2 - Visualising Molecules
2017-8_BL2306_P4
Thursday
15-02-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Tracey Gloster

Lecture L7: The building blocks of life V
2017-8_BL2306_L7
Friday
16-02-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Tracey Gloster

Lecture L8: Revision - the building blocks of life
2017-8_BL2306_L8

Semester 2: Week 4

DATE & TIMEVENUESTAFFEVENT
Wednesday
21-02-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Carlos Penedo-Esteiro

Lecture L9: Enzyme kinetics I
2017-8_BL2306_L9
Thursday
22-02-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Carlos Penedo-Esteiro

Lecture L10: Enzyme kinetics II
2017-8_BL2306_L10
Friday
23-02-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Tracey Gloster
Dr Carolin Kosiol
Lecture L11: Introduction to Practical 3 Lysozyme Study
2017-8_BL2306_L11

Semester 2: Week 5

DATE & TIMEVENUESTAFFEVENT
Monday
26-02-2018
14:00 to 17:00
Bute Building
PC lab
Dr Tracey Gloster
Dr Carolin Kosiol
Practical P5: Practical 3 - Lysozyme Study
2017-8_BL2306_P5
Tuesday
27-02-2018
14:00 to 17:00
Irvine Building
PC lab
Dr Tracey Gloster
Dr Carolin Kosiol
Practical P6: Practical 3 - Lysozyme Study
2017-8_BL2306_P6
Thursday
01-03-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Carlos Penedo-Esteiro

Lecture L12: Enzyme kinetics III
2017-8_BL2306_L12
Friday
02-03-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Carlos Penedo-Esteiro

Lecture L13: Enzymes: Mechanism of Action
2017-8_BL2306_L13

Semester 2: Week 6

DATE & TIMEVENUESTAFFEVENT
Wednesday
07-03-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Carlos Penedo-Esteiro

Lecture L14: Revision - Enzyme Kinetics
2017-8_BL2306_L14
Thursday
08-03-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Jacqueline Nairn

Lecture L15: Metabolic Control Strategies I
2017-8_BL2306_L15
Friday
09-03-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Carlos Penedo-Esteiro

Lecture L16: Introduction to Practical 4 - Enzyme kinetics
2017-8_BL2306_L16

Semester 2: Week 7

DATE & TIMEVENUESTAFFEVENT
Monday
12-03-2018
14:00 to 17:00
Chemistry
Purdie Lab
Dr Carlos Penedo-Esteiro

Practical P7: Practical 4 -Enzyme kinetics
2017-8_BL2306_P7
Tuesday
13-03-2018
14:00 to 17:00
Chemistry
Purdie Lab
Dr Carlos Penedo-Esteiro

Practical P8: Practical 4 -Enzyme kinetics
2017-8_BL2306_P8
Thursday
15-03-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Jacqueline Nairn

Lecture L17: Metabolic Control Strategies II
2017-8_BL2306_L17
Friday
16-03-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Jacqueline Nairn

Lecture L18: How to Study Metabolism & Metabolomics
2017-8_BL2306_L18

Reading Week: 17-Mar-2018 to 01-Apr-2018

Semester 2: Week 8

DATE & TIMEVENUESTAFFEVENT
Wednesday
04-04-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Jacqueline Nairn

Lecture L19: Metabolic Control
2017-8_BL2306_L19
Bring your laptop
Thursday
05-04-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Jacqueline Nairn

Lecture L20: Glycolysis and Gluconeogenesis
2017-8_BL2306_L20
Friday
06-04-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Jacqueline Nairn

Lecture L21: Introduction to Practical 5 - Protein purification
2017-8_BL2306_L21

Semester 2: Week 9

DATE & TIMEVENUESTAFFEVENT
Monday
09-04-2018
14:00 to 17:00
Chemistry
Purdie Lab
Dr Jacqueline Nairn

Practical P9: Practical 5 - Protein purification
2017-8_BL2306_P9
Tuesday
10-04-2018
14:00 to 17:00
Chemistry
Purdie Lab
Dr Jacqueline Nairn

Practical P10: Practical 5 - Protein purification
2017-8_BL2306_P10
Thursday
12-04-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Jacqueline Nairn

Lecture L22: Link between Glycolysis and TCA
2017-8_BL2306_L22
Friday
13-04-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Jacqueline Nairn

Lecture L23: TCA and ETC
2017-8_BL2306_L23

Semester 2: Week 10

DATE & TIMEVENUESTAFFEVENT
Wednesday
18-04-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Jacqueline Nairn

Lecture L24: Fatty Acid Metabolism and Metabolism Revision
2017-8_BL2306_L24
Thursday
19-04-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Rafael Guimaraes da Silva

Lecture L25: Purine/Pyrimidine Metabolism I
2017-8_BL2306_L25
Friday
20-04-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Rafael Guimaraes da Silva

Lecture L26: Purine/Pyrimidine Metabolism II
2017-8_BL2306_L26

Semester 2: Week 11

DATE & TIMEVENUESTAFFEVENT
Monday
23-04-2018
14:00 to 17:00
Chemistry
Purdie Lab
Dr Jacqueline Nairn

Practical P11: Workshop 6 - Metabolomic poster session
2017-8_BL2306_P11
Bring your laptop
Tuesday
24-04-2018
14:00 to 17:00
Chemistry
Purdie Lab
Dr Jacqueline Nairn

Practical P12: Workshop 6 - Metabolomic poster session
2017-8_BL2306_P12
Bring your laptop
Thursday
26-04-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Rafael Guimaraes da Silva

Lecture L27: Amino acid metabolism
2017-8_BL2306_L27
Friday
27-04-2018
09:00 to 10:00
Mathematical Institute
Lecture Theatre C
Dr Rafael Guimaraes da Silva
Dr Jacqueline Nairn
Lecture L28: Revision of RGdS material & BL2306 exam preparation
2017-8_BL2306_L28
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)

BL2306: Reading List

Click for BL2306 reading list

BL2306: Assessment

2-hour Written Examination = 50%, Coursework = 50%*

Assessment:
Practical 2 Visualising Molecules
Due by:
14/02/2018 12:00
Feedback due by:
07/03/2018 12:00
Type:
Single Upload
Weight:
0%
Assessment:
Practical 3 Lysozyme Study
Due by:
28/02/2018 12:00
Feedback due by:
21/03/2018 12:00
Type:
Single Upload
Weight:
0%
Assessment:
Practical 4 Enzyme Kinetics
Due by:
20/03/2018 12:00
Feedback due by:
10/04/2018 12:00
Type:
Turnitin
Weight:
50%
Assessment:
Practical 5 Protein Purification
Due by:
17/04/2018 12:00
Feedback due by:
08/05/2018 12:00
Type:
Turnitin
Weight:
50%
Assessment:
Practical 6 Metabolomic Poster
Due by:
25/04/2018 12:00
Feedback due by:
16/05/2018 12:00
Type:
Single Upload
Weight:
0%

(MMS assessment data cached: 28 March 2018 22:20:20.)


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 Jacqueline Nairn jn37@st-andrews.ac.uk)
Marking on continuous assessment The Demonstrator or Module Organiser (Dr Jacqueline Nairn jn37@st-andrews.ac.uk)
Marking on exams Module Organiser (Dr Jacqueline Nairn jn37@st-andrews.ac.uk)
Rearranging practical days Grant Brown
Absence and/or extensions Module Organiser (Dr Jacqueline Nairn jn37@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:

The Biology Hive, New Technology Centre, University of St Andrews, North Haugh, St Andrews, Fife KY16 9SR

Email: bioteach@st-andrews.ac.uk

Tel: 01334 463602

BL2306: Contributing Staff

Dr Jacqueline Nairn
(Module Organiser)

Senior Lecturer (Education Focused)jn37@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 Carolin KosiolDr Carolin KosiolLecturerck202@st-andrews.ac.uk
Dr Jacqueline Nairn
(Module Organiser)
Senior Lecturer (Education Focused)jn37@st-andrews.ac.uk
Dr Carlos Penedo-EsteiroLecturerjcp10@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)

BL2306: Learning Outcomes

Students completing module BL2306 successfully should be able to:

  • Explain the chemistry and structure of the major biological macromolecules and how that determines their biological properties
  • Mine, manipulate and interpret data from small molecule and macromolecular databases
  • Use molecular viewers
  • Explain the chemical and thermodynamic principles underlying biological catalysis and the role of enzymes and other proteins in determining the function and fate of cells and organisms
  • Conduct experiments to explore enzyme activity
  • Demonstrate a critical understanding of essential features of cell metabolism and its control, including topics such as energy and signal transduction, respiration and photosynthesis
  • Appreciate the diversity of small molecules within cells, their dynamic concentration range and how to study these, both individually and as part of a metabolome
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)

BL2306: Acquired Skills

Practical Skills

  • Biomolecule isolation/characterisation
  • Buffers
  • Chromatography
  • Database interogation
  • Enzyme assay
  • Kinetic data analysis
  • Molecular viewer software
  • Pipetting
  • Protein characterisation
  • Protein purification
  • Protein quantitation

Transferable Skills

  • Preparing group poster on given topic
  • Q+A poster session
  • "Full" practical write-up (Intro, Methods, Results, Discussion)
  • "Short" practical write-up (e.g. completed worksheet)
  • Handout (for presentation or poster)
  • Critically evaluating sources/information
  • Finding information on the web
  • Finding literature
  • Referencing
  • Searching databases
  • Sourcing figures/tables
  • Lab safety awareness
  • Problem-solving questions
  • Calculations/equations
  • Concentrations
  • Data analysis
  • Data presentation
  • Dilutions
  • Draw a line of best fit
  • Produce graphs/figures
  • Produce tables
  • SI units
  • Use Excel
  • Use R or R Studio
  • 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)