Students

CBMS332 – Protein Discovery and Analysis

2018 – S1 Day

General Information

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Unit convenor and teaching staff Unit convenor and teaching staff Coordinator
Bridget Mabbutt
bridget.mabbutt@mq.edu.au
Unit Convenor
Phani Rekha Potluri
phani-rekha.potluri@mq.edu.au
Contact via By email
E8A 306
Tuesday 11am-12pm
Credit points Credit points
3
Prerequisites Prerequisites
6cp from CBMS200-CBMS233
Corequisites Corequisites
Co-badged status Co-badged status
Unit description Unit description
This unit outlines molecular principles underlying today's developments in protein science and biomedical research. As well as detailing modern separation technologies, the course addresses structural biology, protein analysis and bioinformatics. Practices common in the biotechnology and pharmaceutical industries to isolate recombinant proteins are emphasized. Analysis methods are introduced in relation to proteomics, genomics and biochemical research. Molecular properties leading to the 3D shape of proteins are detailed and contemporary structure methods outlined.

Important Academic Dates

Information about important academic dates including deadlines for withdrawing from units are available at https://www.mq.edu.au/study/calendar-of-dates

Learning Outcomes

On successful completion of this unit, you will be able to:

  • Assimilate and interpret methods used today to isolate and handle proteins
  • Comprehend the molecular behaviour of proteins (gene products), both in vivo and in vitro
  • Develop a sound knowledge of protein structure and how it is encoded in a protein (or gene) sequence
  • Gain hands-on practical experience in protein characterisation, and competency with contemporary web tools
  • Be able to analyze and describe biomolecular forms and architectures
  • Extract and interpret information from a variety of scientific sources concerning proteins
  • Develop presentation skills (written, oral) relevant in biomolecular science

General Assessment Information

  • Four modes of assessment are used to determine your progress in CBMS332.

Assessment Tasks

Name Weighting Hurdle Due
Take-home mid-year exam 15% No April 10
Protein workshop report 15% No April 30
Molecular graphics report 10% No May 18
“Pet Protein” Structure 20% No June 1
Final examination 40% No University Examination period

Take-home mid-year exam

Due: April 10
Weighting: 15%

  • A protein purification scenario and questions will be uploaded for a three-day period (April 7-9).  This task will test material covered within lectures 1-11. 
  • Hand-written responses will be required from each student and must be submitted via the assignment box located in the FSE student centre (Level 2, MUSE building C7A). Submissions must include a completed and signed cover sheet stapled to the front cover. 
  • Turnitin submission is not required for this task.
  • Marks will be deducted for reports handed in after the due date (10% of the total mark/ day).
On successful completion you will be able to:
  • Assimilate and interpret methods used today to isolate and handle proteins
  • Comprehend the molecular behaviour of proteins (gene products), both in vivo and in vitro
  • Gain hands-on practical experience in protein characterisation, and competency with contemporary web tools

Protein workshop report

Due: April 30
Weighting: 15%

  • A full report must be made of experimental data and discussion and analysis of your findings. Separate sections for Aims; Methods; Results & Discussion; References must all be included. 
  • Submit the report via the assignment box located in the FSE student centre (Level 2, MUSE building C7A) including a completed and signed cover sheet stapled to the front cover. 
  • Electronic submission to the Turnitin program (see iLearn site) is also required for this task by the due date. 
  • Bibliography listings must conform to an acceptable style (for guidance, see http://libguides.mq.edu.au/Referencing Mq library link), or the reports will be returned unmarked for correction and re-submission. 
  • Marks will be deducted for reports handed in after the due date (10% of the total mark/ day).
On successful completion you will be able to:
  • Assimilate and interpret methods used today to isolate and handle proteins
  • Gain hands-on practical experience in protein characterisation, and competency with contemporary web tools
  • Extract and interpret information from a variety of scientific sources concerning proteins
  • Develop presentation skills (written, oral) relevant in biomolecular science

Molecular graphics report

Due: May 18
Weighting: 10%

  • Submit the work-sheets filled on the day of practical to FSE Student Centre (Level 2, MUSE building C7A). 
  • Marks will be deducted for reports handed in after the due date (10% of the total mark/ day).
  • All marked work will be returned via FSE student centre, generally within 3 weeks.
On successful completion you will be able to:
  • Assimilate and interpret methods used today to isolate and handle proteins
  • Gain hands-on practical experience in protein characterisation, and competency with contemporary web tools
  • Extract and interpret information from a variety of scientific sources concerning proteins
  • Develop presentation skills (written, oral) relevant in biomolecular science

“Pet Protein” Structure

Due: June 1
Weighting: 20%

  • This is assessment of research and analytical skills, and continues throughout the semester to enhance each topic area.
  • Students will be assigned an individual “Pet Protein” as a basis for structural analysis during Week 6. 
  • You are required to transmit your understanding of the individual protein to your fellow students via seminars and presentation of your own constructed three-dimensional protein model:
  • Overall, project work will be assessed according to:
    • the quality and extent of your research
    • the depth and molecular detail of your analysis
    • appropriate use of internet tools
    • the clarity of your communication (verbal and written) and molecular analysis
    • the extent to which your model successfully shows the shape and form of your protein in three-dimensions

On successful completion you will be able to:
  • Develop a sound knowledge of protein structure and how it is encoded in a protein (or gene) sequence
  • Be able to analyze and describe biomolecular forms and architectures
  • Extract and interpret information from a variety of scientific sources concerning proteins
  • Develop presentation skills (written, oral) relevant in biomolecular science

Final examination

Due: University Examination period
Weighting: 40%

  • This written exam will incorporate problem-solving exercises.
  • The paper will be scheduled within the University Examination period for First Half Year 2018. All students must ensure that they are available until the final day of this official examination period.
On successful completion you will be able to:
  • Assimilate and interpret methods used today to isolate and handle proteins
  • Comprehend the molecular behaviour of proteins (gene products), both in vivo and in vitro
  • Develop a sound knowledge of protein structure and how it is encoded in a protein (or gene) sequence
  • Gain hands-on practical experience in protein characterisation, and competency with contemporary web tools
  • Be able to analyze and describe biomolecular forms and architectures

Delivery and Resources

Classes:

  • Lectures will be twice weekly: Thursday 12-1pm in E7BT2 and Friday 9-10am in E7BT5. 
  • The course syllabus is defined by the subject material presented in all  lectures (including guest lectures) and practicals, much of which is beyond standard textbooks.
  • From week 1, tutorials run for all students. You are required to attend for either of the three sessions: Wednesday 12-1pm (E7B 200), Thursday 11-12pm (C5A 229), Thursday 1-2pm (E3B 217). These are structured as problem-solving workshops and will help you at exam time.

 

Laboratory Sessions:

A block chromatography workshop (workshop_1 to workshop_5) is scheduled in the first week of mid-semester break, i.e. from April 16-20, 9am-5pm.

CBMS 332 students are required to attend ONLY Workshop 1 on Apr 16 (Mon) from 9am-11am and WORKSHOP 2 and 3 scheduled for Apr 17-18 (Tues-Wed) from 9am-5pm.

  • During session, practicals (named Practical_1 in the University timetable) are scheduled on four allocated Fridays from Week 10 (10am-2pm) in E5A270.  You will attend for 4 occasions, according to your allocated laboratory group.
  • You will be allocated a lab group (Group 1 or Group 2) by the Unit convenor and communicated via the iLearn interface.
  • Participation is compulsory on the allocated days of class. If you are sick, please consult with the Unit Convenor to ensure all laboratory and project work is completed. 
  • Please carefully check the location of each laboratory activity, as classes start promptly.  Latecomers may be excluded from class.
  • You are not permitted to change groups during semester.

Required and Recommended texts

  • The textbook of which you are expected to purchase a personal copy is: “Physical Biochemistry: Principles and Applications”, David Sheehan, John Wiley (2nd ed, 2002). Online access of the text is available on the MQ Library website.
  • Because of the multidisciplinary nature of this course, you will be expected to read more widely than this, however.  The library has an excellent collection of up-to-date reference material to cover the course and laboratory subjects - explore it!!
  • Strongly recommended reference texts available in the library (short-term loan only):
    • “Proteins: Structure and Function”, D. Whitford, John Wiley, 2005
    • “Protein Structure and Function”, Petsko & Ringe, New Science Press, 2009
    • “Introduction to Protein Structure”, Branden & Tooze, Garland, 1999
    • “Purifying proteins for proteomics : a laboratory manual” ed. R.J. Simpson. Cold Spring Harbor Laboratory Press, 2004
  • Other general references that you may find useful are:
    • R. Scopes, "Protein purification: principles and practice", New York, Springer-Verlag, 1994
    • Garrett & Grisham, “Biochemistry” (esp. Chs 4 – 6), Harcourt Brace, 2013
    • T. Creighton, “Proteins: Structures and Molecular Properties”, Freeman, 1993

 

Web resources

The Unit will run as an online unit within iLearn (http://learn.mq.edu.au).  Within this Unit, you will be introduced to Web-based tools, search engines and graphics software that are commonly used today in protein science. There are many excellent websites, apps and YouTube presentations to show how protein are made and constantly move around. 

It is an expectation that you will become familiar with the following sites during the course:

 

Technology Requirements

  • You will require access to the internet and have a computer available for accessing the iLearn site, web browsing, preparation of your reports and presentations (Word and PowerPoint software), molecular viewing and case study analysis.  Printer access is required to generate hard copy of reports.
  • Your project and laboratory reports will be electronically submitted via the online Turnitin program within the CBMS332/732/832 iLearn portal.
  • Your practical reports will require you to carry out minor computational tasks, for which a calculator and access to basic statistical software will be required.
  • We place a strong emphasis on correct referencing style in all your reports. Use of the program EndNote (http://libguides.mq.edu.au/EndNoteMac, http://libguides.mq.edu.au/EndNotePC ) is encouraged, but not essential.
  • The capacity to download and install a simple molecular graphics program will assist you greatly in the Unit. Your model-building assessment task can be carried out with very simple materials; it is not an expectation that expensive art supplies need be purchased.

Unit Schedule

Lectures

 

1 - 3  

 

FUNCTIONAL GROUPS IN PROTEINS
4 

 ISOLATING BIOMOLECULES

recombinant sources; quantitation & detection
5 & 6  

SEPARATION OF PROTEIN MIXTURES

separation  by precipitation; gel filtration for separation 
7 - 10   

CHROMATOGRAPHY FOR PURIFICATION

ion exchange; hydrophobic/reversed-phase; affinity chromatography
11 -13  

 PROTEIN ANALYSIS METHODS

 2D gel electrophoresis;  mass spectrometry; sugar/glycoprotein analysis

14 - 16

PROTEIN  FOLDS AND DOMAINS

all alpha-structures (globin fold, helix bundles); all beta structures (antiparallel barrels, the beta helix); mixed  alpha/beta folds
17- 19             

TERTIARY STRUCTURE DETERMINATION

 x-ray crystallography;  NMR spectroscopy
20-22

HOW PROTEINS FOLD IN SOLUTION

circular dichroism;thermodynamics of protein folds; invivo folding
23 & 24

BIOINFORMATICS

structure prediction methods;  the CASP project
25

 MEMBRANE PROTEINS

Policies and Procedures

Macquarie University policies and procedures are accessible from Policy Central (https://staff.mq.edu.au/work/strategy-planning-and-governance/university-policies-and-procedures/policy-central). Students should be aware of the following policies in particular with regard to Learning and Teaching:

Undergraduate students seeking more policy resources can visit the Student Policy Gateway (https://students.mq.edu.au/support/study/student-policy-gateway). It is your one-stop-shop for the key policies you need to know about throughout your undergraduate student journey.

If you would like to see all the policies relevant to Learning and Teaching visit Policy Central (https://staff.mq.edu.au/work/strategy-planning-and-governance/university-policies-and-procedures/policy-central).

Student Code of Conduct

Macquarie University students have a responsibility to be familiar with the Student Code of Conduct: https://students.mq.edu.au/study/getting-started/student-conduct​

Results

Results shown in iLearn, or released directly by your Unit Convenor, are not confirmed as they are subject to final approval by the University. Once approved, final results will be sent to your student email address and will be made available in eStudent. For more information visit ask.mq.edu.au.

Student Support

Macquarie University provides a range of support services for students. For details, visit http://students.mq.edu.au/support/

Learning Skills

Learning Skills (mq.edu.au/learningskills) provides academic writing resources and study strategies to improve your marks and take control of your study.

Student Services and Support

Students with a disability are encouraged to contact the Disability Service who can provide appropriate help with any issues that arise during their studies.

Student Enquiries

For all student enquiries, visit Student Connect at ask.mq.edu.au

IT Help

For help with University computer systems and technology, visit http://www.mq.edu.au/about_us/offices_and_units/information_technology/help/. 

When using the University's IT, you must adhere to the Acceptable Use of IT Resources Policy. The policy applies to all who connect to the MQ network including students.

Graduate Capabilities

Creative and Innovative

Our graduates will also be capable of creative thinking and of creating knowledge. They will be imaginative and open to experience and capable of innovation at work and in the community. We want them to be engaged in applying their critical, creative thinking.

This graduate capability is supported by:

Learning outcomes

  • Be able to analyze and describe biomolecular forms and architectures
  • Develop presentation skills (written, oral) relevant in biomolecular science

Assessment tasks

  • Protein workshop report
  • Molecular graphics report
  • “Pet Protein” Structure

Discipline Specific Knowledge and Skills

Our graduates will take with them the intellectual development, depth and breadth of knowledge, scholarly understanding, and specific subject content in their chosen fields to make them competent and confident in their subject or profession. They will be able to demonstrate, where relevant, professional technical competence and meet professional standards. They will be able to articulate the structure of knowledge of their discipline, be able to adapt discipline-specific knowledge to novel situations, and be able to contribute from their discipline to inter-disciplinary solutions to problems.

This graduate capability is supported by:

Learning outcomes

  • Assimilate and interpret methods used today to isolate and handle proteins
  • Comprehend the molecular behaviour of proteins (gene products), both in vivo and in vitro
  • Develop a sound knowledge of protein structure and how it is encoded in a protein (or gene) sequence
  • Gain hands-on practical experience in protein characterisation, and competency with contemporary web tools

Assessment tasks

  • Take-home mid-year exam
  • Protein workshop report
  • Molecular graphics report
  • Final examination

Critical, Analytical and Integrative Thinking

We want our graduates to be capable of reasoning, questioning and analysing, and to integrate and synthesise learning and knowledge from a range of sources and environments; to be able to critique constraints, assumptions and limitations; to be able to think independently and systemically in relation to scholarly activity, in the workplace, and in the world. We want them to have a level of scientific and information technology literacy.

This graduate capability is supported by:

Learning outcomes

  • Comprehend the molecular behaviour of proteins (gene products), both in vivo and in vitro
  • Develop a sound knowledge of protein structure and how it is encoded in a protein (or gene) sequence
  • Extract and interpret information from a variety of scientific sources concerning proteins

Assessment tasks

  • Take-home mid-year exam
  • Protein workshop report
  • Molecular graphics report
  • Final examination

Problem Solving and Research Capability

Our graduates should be capable of researching; of analysing, and interpreting and assessing data and information in various forms; of drawing connections across fields of knowledge; and they should be able to relate their knowledge to complex situations at work or in the world, in order to diagnose and solve problems. We want them to have the confidence to take the initiative in doing so, within an awareness of their own limitations.

This graduate capability is supported by:

Learning outcomes

  • Assimilate and interpret methods used today to isolate and handle proteins
  • Gain hands-on practical experience in protein characterisation, and competency with contemporary web tools
  • Extract and interpret information from a variety of scientific sources concerning proteins

Assessment tasks

  • Protein workshop report
  • “Pet Protein” Structure
  • Final examination

Effective Communication

We want to develop in our students the ability to communicate and convey their views in forms effective with different audiences. We want our graduates to take with them the capability to read, listen, question, gather and evaluate information resources in a variety of formats, assess, write clearly, speak effectively, and to use visual communication and communication technologies as appropriate.

This graduate capability is supported by:

Learning outcomes

  • Be able to analyze and describe biomolecular forms and architectures
  • Develop presentation skills (written, oral) relevant in biomolecular science

Assessment tasks

  • Take-home mid-year exam
  • Protein workshop report
  • Molecular graphics report
  • “Pet Protein” Structure
  • Final examination