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CBMS337 – Biochemistry and Cell Biology

2017 – S2 Day

General Information

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Unit convenor and teaching staff Unit convenor and teaching staff Unit Convenor and Lecturer
Paul Jaschke
Contact via Email
E8A 357
Upon request
Lecturer
Robert Willows
Lecturer
Morten Andersen
Lecturer
Mark Molloy
Credit points Credit points
3
Prerequisites Prerequisites
CBMS223 and CBMS224
Corequisites Corequisites
Co-badged status Co-badged status
CBMS837
Unit description Unit description
Biochemistry and cell biology are central to our understanding of medicine and biotechnology. Advances in these fields are dependent on an advanced understanding of the molecular basis of diverse cellular processes. This unit links important biochemical processes to functions and properties of eukaryotic cells. We explore advanced concepts including: enzyme function, properties of membranes, signal transduction, protein trafficking and transport, and protein turnover. These are linked to whole cell behaviours such as cell division and differentiation, programmed cell death, and general responses to external stimuli. Practical work complements lecture material and provides experience with a broad range of current techniques used in research and industry. Laboratory techniques used include analysis of signalling cascades, enzyme kinetics, spectrophotometry, and fluorescence and light microscopy.

Important Academic Dates

Information about important academic dates including deadlines for withdrawing from units are available at http://students.mq.edu.au/student_admin/enrolmentguide/academicdates/

Learning Outcomes

  1. Demonstrate an understanding of how eukaryotic cells are studied and summarise current knowledge of internal cell organisation, membrane trafficking, intracellular compartments, biochemical pathways, and intra- and extra-cellular signalling.
  2. Summarise the major eukaryotic cell regulation control points and how disturbances in these processes are involved in human disease.
  3. Design and execute laboratory experiments to characterise, quantitate and measure a range of fundamental cell processes.
  4. Critically analyse and communicate advanced molecular, cellular, and biochemical concepts from the primary literature in both verbal and written form.

General Assessment Information

 

Please refer to the Macquarie University Assessment policy regarding submission of assignments, plagarism, extensions, late submissions, etc.

Individual assessment criteria/marking rubrics can be found on the CBMS337/837 iLearn site.

Late Submissions

Tasks 10% or less - No extensions will be granted. Students who have not submitted the task prior to the deadline will be awarded a mark of 0 for the task. This penalty does not apply for cases in which an application for disruption of studies is made and approved. No submission will be accepted after solutions have been posted.

Tasks above 10% - No extensions will be granted. There will be a deduction of 10% of the total available marks made from the total awarded mark for each 24 hour period or part thereof that the submission is late (for example, 25 hours late in submission – 20% penalty). This penalty does not apply for cases in which an application for disruption of studies is made and approved. No submission will be accepted after solutions have been posted. 

Assessment Tasks

Name Weighting Due
Quiz 7% Week 3
Enzyme Kinetics Prac Report #1 7% Week 6
Enzyme Kinetics Prac Report #2 3% Week 7
Mid-Semester Exam 23% Week 7
Protein Localisation LabReport 15% Week 10
Phosphorylation Lab Report 5% Weeks 11/12
Hot Topics Seminar 8% Weeks 11/12
Final Exam 32% University Examination Period

Quiz

Due: Week 3
Weighting: 7%

An early quiz on material covered in weeks 1-3. In-class hard-copy written assessment.


This Assessment Task relates to the following Learning Outcomes:
  • Demonstrate an understanding of how eukaryotic cells are studied and summarise current knowledge of internal cell organisation, membrane trafficking, intracellular compartments, biochemical pathways, and intra- and extra-cellular signalling.
  • Summarise the major eukaryotic cell regulation control points and how disturbances in these processes are involved in human disease.

Enzyme Kinetics Prac Report #1

Due: Week 6
Weighting: 7%

Students will graph and analyze enzyme kinetics data. They will need to identify enzymatic mechanism and determine the kinetic constants. 


This Assessment Task relates to the following Learning Outcomes:
  • Design and execute laboratory experiments to characterise, quantitate and measure a range of fundamental cell processes.

Enzyme Kinetics Prac Report #2

Due: Week 7
Weighting: 3%

Students will graph and analyze enzyme kinetics data. They will need to identify enzymatic mechanism and determine the kinetic constants. 


This Assessment Task relates to the following Learning Outcomes:
  • Design and execute laboratory experiments to characterise, quantitate and measure a range of fundamental cell processes.

Mid-Semester Exam

Due: Week 7
Weighting: 23%

A written exam covering all materials and textbook readings associated with lectures 1-13. This assessment will be designed to give you specific feedback on your understanding of the topics up to this stage in the unit. In-class hard-copy written assessment.


This Assessment Task relates to the following Learning Outcomes:
  • Demonstrate an understanding of how eukaryotic cells are studied and summarise current knowledge of internal cell organisation, membrane trafficking, intracellular compartments, biochemical pathways, and intra- and extra-cellular signalling.
  • Summarise the major eukaryotic cell regulation control points and how disturbances in these processes are involved in human disease.

Protein Localisation LabReport

Due: Week 10
Weighting: 15%

A scientific report of the results from practicals 2, 3, 7, 8. The report will be written in the form of a peer reviewed journal article. Handed in via Turnitin.


This Assessment Task relates to the following Learning Outcomes:
  • Demonstrate an understanding of how eukaryotic cells are studied and summarise current knowledge of internal cell organisation, membrane trafficking, intracellular compartments, biochemical pathways, and intra- and extra-cellular signalling.
  • Summarise the major eukaryotic cell regulation control points and how disturbances in these processes are involved in human disease.
  • Design and execute laboratory experiments to characterise, quantitate and measure a range of fundamental cell processes.
  • Critically analyse and communicate advanced molecular, cellular, and biochemical concepts from the primary literature in both verbal and written form.

Phosphorylation Lab Report

Due: Weeks 11/12
Weighting: 5%

A short report analysing the results from practicals 9 and 10 regarding changes to cellular protein phosphorylation patterns in response to a chemical. Handed in via iLearn.


This Assessment Task relates to the following Learning Outcomes:
  • Demonstrate an understanding of how eukaryotic cells are studied and summarise current knowledge of internal cell organisation, membrane trafficking, intracellular compartments, biochemical pathways, and intra- and extra-cellular signalling.
  • Summarise the major eukaryotic cell regulation control points and how disturbances in these processes are involved in human disease.
  • Design and execute laboratory experiments to characterise, quantitate and measure a range of fundamental cell processes.
  • Critically analyse and communicate advanced molecular, cellular, and biochemical concepts from the primary literature in both verbal and written form.

Hot Topics Seminar

Due: Weeks 11/12
Weighting: 8%

Prepare and present a short oral presentation (seminar) on a "hot topic" in cell biology and/or biochemistry. 


This Assessment Task relates to the following Learning Outcomes:
  • Demonstrate an understanding of how eukaryotic cells are studied and summarise current knowledge of internal cell organisation, membrane trafficking, intracellular compartments, biochemical pathways, and intra- and extra-cellular signalling.
  • Summarise the major eukaryotic cell regulation control points and how disturbances in these processes are involved in human disease.
  • Critically analyse and communicate advanced molecular, cellular, and biochemical concepts from the primary literature in both verbal and written form.

Final Exam

Due: University Examination Period
Weighting: 32%

This assessment is designed to test understanding of topics presented in all of the lectures and practicals, and to evaluate the student's ability to apply this knowledge to new problems. Hard-copy 3 hour written exam.


This Assessment Task relates to the following Learning Outcomes:
  • Demonstrate an understanding of how eukaryotic cells are studied and summarise current knowledge of internal cell organisation, membrane trafficking, intracellular compartments, biochemical pathways, and intra- and extra-cellular signalling.
  • Summarise the major eukaryotic cell regulation control points and how disturbances in these processes are involved in human disease.

Delivery and Resources

Required Text

B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, P. Walter (2015) "Molecular Biology of the Cell" (6th Edition), ISBN 978-0815344322. Available at the Co-op and a few copies for reference in the library.

Your lectures will cover parts of many chapters from this text and your success in the unit will be greatly enhanced by having this textbook.

Unit Web Page

The web page for this unit is at Macquarie University's iLearn site accessed here.

The iLearn site for CBMS337/837 will be used to deliver lecture and laboratory notes and will feature a discussion forum, digital lecture recordings and other learning resources. To view the lecture notes and other PDF files on the website, you will require a PDF viewer. Free PDF viewers can be found online (e.g. Adobe Reader).

Active Learning Platform

Some lectures will feature interactive lecture presentations using a technology called the Echo360 Active Learning Platform. This is a new system, different from Lecture Tools which you may be more familiar with. Additionally, this technology is different from the Echo360 Lecture Recordings you may be more familiar with.

To participate in the Active Learning Platform the student will need to bring their laptop, tablet, or smart phone to class, or participate while live-streaming the class (if this service is available).

Guides and videos on how to use the Active Learning Platform can be found here.

Active Learning Platform - Getting Started

http://help.echo360.org/#t=Student_Guide%2FGetting_Students_Started.htm%23bc-1&rhtocid=2.0_1

During Class

A video guide to using the Active Learning Platform during class 

https://vimeo.com/album/3456016/video/125803882

Viewing a presentation

http://help.echo360.org/#t=Student_Guide%2FViewing_Classes.htm

Responding to interactive slides

http://help.echo360.org/#t=Student_Guide%2FAnswering_Questions_Class.htm

Taking notes

http://help.echo360.org/#t=Student_Guide%2FTaking_Notes.htm

Posting a question

http://help.echo360.org/#t=Student_Guide%2FPosting_Questions_About_Class_Presentations.htm

Responding to a question

http://help.echo360.org/#t=Student_Guide%2FResponding_to_Questions_about_Class_Presentations.htm  

Flagging confusion slides and bookmarking

http://help.echo360.org/#t=Student_Guide%2FFlagging_Bookmarking_Content.htm 

After Class

After class video guide

https://vimeo.com/album/3456016/video/125735236

Review personal study guide (student notes and bookmarks)

http://help.echo360.org/#t=Student_Guide%2FReviewing_Study_Guide.htm

Questions and answers

http://help.echo360.org/#t=Student_Guide%2FParticipate_in_Class_Q_A.htm

Downloading notes

http://help.echo360.org/#t=Student_Guide%2FDownloading_Notes.htm

Echo360 Lecture Recordings

All lectures (but not pracs) will be recorded using the Echo360 Lecture Recording technology. A guide to this technology is available here. The Echo360 recordings can be accessed from the Echo360 Active Learning Platform block on the right side of the CBMS337/837 iLearn page.

 

Learning and Teaching Activities

Lectures

Lectures from staff in CBMS summarising a wide range of advanced topics in eukaryotic cell biology and biochemistry. You are highly encouraged to attend lectures in person. Past experience has shown that students who attend lectures tend to receive higher marks in the unit.

Practicals

Practicals give you an opportunity to put into practice your knowledge of biochemistry and cell biology and to develop real laboratory skills that are valued in academic and industry professions.

Self-Study

To succeed in this unit you are expected to spend time outside formal instruction reading assigned sections of the textbook, reviewing notes taken in class, and exploring other sources of information on advanced biochemistry and cell biology. To self-assess your degree of understanding and to practice problem solving skills you are expected to attempt problems from the text and other resources.

Policies and Procedures

Macquarie University policies and procedures are accessible from Policy Central. Students should be aware of the following policies in particular with regard to Learning and Teaching:

Academic Honesty Policy http://mq.edu.au/policy/docs/academic_honesty/policy.html

Assessment Policy http://mq.edu.au/policy/docs/assessment/policy_2016.html

Grade Appeal Policy http://mq.edu.au/policy/docs/gradeappeal/policy.html

Complaint Management Procedure for Students and Members of the Public http://www.mq.edu.au/policy/docs/complaint_management/procedure.html​

Disruption to Studies Policy http://www.mq.edu.au/policy/docs/disruption_studies/policy.html The Disruption to Studies Policy is effective from March 3 2014 and replaces the Special Consideration Policy.

In addition, a number of other policies can be found in the Learning and Teaching Category of 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/support/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 Enquiry Service

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

Equity 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.

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

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

  • Demonstrate an understanding of how eukaryotic cells are studied and summarise current knowledge of internal cell organisation, membrane trafficking, intracellular compartments, biochemical pathways, and intra- and extra-cellular signalling.
  • Summarise the major eukaryotic cell regulation control points and how disturbances in these processes are involved in human disease.
  • Design and execute laboratory experiments to characterise, quantitate and measure a range of fundamental cell processes.
  • Critically analyse and communicate advanced molecular, cellular, and biochemical concepts from the primary literature in both verbal and written form.

Assessment tasks

  • Quiz
  • Enzyme Kinetics Prac Report #1
  • Enzyme Kinetics Prac Report #2
  • Mid-Semester Exam
  • Protein Localisation LabReport
  • Phosphorylation Lab Report
  • Hot Topics Seminar
  • Final Exam

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

  • Demonstrate an understanding of how eukaryotic cells are studied and summarise current knowledge of internal cell organisation, membrane trafficking, intracellular compartments, biochemical pathways, and intra- and extra-cellular signalling.
  • Summarise the major eukaryotic cell regulation control points and how disturbances in these processes are involved in human disease.
  • Design and execute laboratory experiments to characterise, quantitate and measure a range of fundamental cell processes.
  • Critically analyse and communicate advanced molecular, cellular, and biochemical concepts from the primary literature in both verbal and written form.

Assessment tasks

  • Quiz
  • Enzyme Kinetics Prac Report #1
  • Enzyme Kinetics Prac Report #2
  • Mid-Semester Exam
  • Protein Localisation LabReport
  • Phosphorylation Lab Report
  • Hot Topics Seminar
  • Final Exam

Commitment to Continuous Learning

Our graduates will have enquiring minds and a literate curiosity which will lead them to pursue knowledge for its own sake. They will continue to pursue learning in their careers and as they participate in the world. They will be capable of reflecting on their experiences and relationships with others and the environment, learning from them, and growing - personally, professionally and socially.

This graduate capability is supported by:

Learning outcomes

  • Demonstrate an understanding of how eukaryotic cells are studied and summarise current knowledge of internal cell organisation, membrane trafficking, intracellular compartments, biochemical pathways, and intra- and extra-cellular signalling.
  • Summarise the major eukaryotic cell regulation control points and how disturbances in these processes are involved in human disease.
  • Design and execute laboratory experiments to characterise, quantitate and measure a range of fundamental cell processes.
  • Critically analyse and communicate advanced molecular, cellular, and biochemical concepts from the primary literature in both verbal and written form.

Assessment tasks

  • Quiz
  • Enzyme Kinetics Prac Report #1
  • Enzyme Kinetics Prac Report #2
  • Mid-Semester Exam
  • Protein Localisation LabReport
  • Phosphorylation Lab Report
  • Hot Topics Seminar
  • Final Exam

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

  • Demonstrate an understanding of how eukaryotic cells are studied and summarise current knowledge of internal cell organisation, membrane trafficking, intracellular compartments, biochemical pathways, and intra- and extra-cellular signalling.
  • Summarise the major eukaryotic cell regulation control points and how disturbances in these processes are involved in human disease.
  • Design and execute laboratory experiments to characterise, quantitate and measure a range of fundamental cell processes.
  • Critically analyse and communicate advanced molecular, cellular, and biochemical concepts from the primary literature in both verbal and written form.

Assessment tasks

  • Quiz
  • Enzyme Kinetics Prac Report #1
  • Enzyme Kinetics Prac Report #2
  • Mid-Semester Exam
  • Protein Localisation LabReport
  • Phosphorylation Lab Report
  • Hot Topics Seminar
  • Final Exam

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

  • Demonstrate an understanding of how eukaryotic cells are studied and summarise current knowledge of internal cell organisation, membrane trafficking, intracellular compartments, biochemical pathways, and intra- and extra-cellular signalling.
  • Summarise the major eukaryotic cell regulation control points and how disturbances in these processes are involved in human disease.
  • Design and execute laboratory experiments to characterise, quantitate and measure a range of fundamental cell processes.
  • Critically analyse and communicate advanced molecular, cellular, and biochemical concepts from the primary literature in both verbal and written form.

Assessment tasks

  • Quiz
  • Enzyme Kinetics Prac Report #1
  • Enzyme Kinetics Prac Report #2
  • Mid-Semester Exam
  • Protein Localisation LabReport
  • Phosphorylation Lab Report
  • Hot Topics Seminar
  • Final Exam

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

  • Demonstrate an understanding of how eukaryotic cells are studied and summarise current knowledge of internal cell organisation, membrane trafficking, intracellular compartments, biochemical pathways, and intra- and extra-cellular signalling.
  • Summarise the major eukaryotic cell regulation control points and how disturbances in these processes are involved in human disease.
  • Design and execute laboratory experiments to characterise, quantitate and measure a range of fundamental cell processes.
  • Critically analyse and communicate advanced molecular, cellular, and biochemical concepts from the primary literature in both verbal and written form.

Assessment tasks

  • Quiz
  • Enzyme Kinetics Prac Report #1
  • Enzyme Kinetics Prac Report #2
  • Mid-Semester Exam
  • Protein Localisation LabReport
  • Phosphorylation Lab Report
  • Hot Topics Seminar
  • Final Exam

Capable of Professional and Personal Judgement and Initiative

We want our graduates to have emotional intelligence and sound interpersonal skills and to demonstrate discernment and common sense in their professional and personal judgement. They will exercise initiative as needed. They will be capable of risk assessment, and be able to handle ambiguity and complexity, enabling them to be adaptable in diverse and changing environments.

This graduate capability is supported by:

Learning outcomes

  • Design and execute laboratory experiments to characterise, quantitate and measure a range of fundamental cell processes.
  • Critically analyse and communicate advanced molecular, cellular, and biochemical concepts from the primary literature in both verbal and written form.

Assessment tasks

  • Enzyme Kinetics Prac Report #1
  • Enzyme Kinetics Prac Report #2
  • Protein Localisation LabReport
  • Phosphorylation Lab Report
  • Hot Topics Seminar

Changes from Previous Offering

The 2017 offering of this unit will feature several changes from the 2016 offering. These changes include: two additional assessment tasks, changes to the content of several of the practical labs, change to lecturers.