Students

CBMS736 – Molecular Biology and Genomics

2016 – S1 Day

General Information

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Unit convenor and teaching staff Unit convenor and teaching staff Convenor
Ian Paulsen
ian.paulsen@mq.edu.au
Contact via x8152
E8A 202
Lecturer
Paul Haynes
paul.haynes@mq.edu.au
Lab Technician
Ray Duell
Credit points Credit points
4
Prerequisites Prerequisites
Admission to MRes
Corequisites Corequisites
Co-badged status Co-badged status
Unit description Unit description
Molecular biology is a central science in twenty-first century biology and biotechnology. Understanding the fundamentals of molecular biology is essential for many other fields in the life sciences, including microbiology, cell biology, immunology and development. Molecular biology makes a significant and increasing contribution to major sectors of our society including agriculture and medicine, and is also important in environmental science and forensics. In this unit we explore topics that allow students to obtain an advanced understanding of the mechanisms of molecular biology, including those of DNA replication and recombination, prokaryotic gene expression, eukaryotic gene expression, mobile elements, the functions of the nucleus, and epigenetics. We also address topics on the rapidly changing technologies in molecular biology, including those used in genome sequencing, metagenomics and microarray analysis. Practical sessions complement the lectures and provide students with hands-on experience with a range of critical laboratory skills including those required for DNA and RNA isolation, PCR and RT-PCR, cloning and bioinformatics. Students gain experience in working with both bacterial and eukaryotic systems in the laboratory classes so that their skills and experience are valuable for a variety of positions in both industry and research.

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:

  • Students will be proficient in the theory and practice of a range of molecular biology experimental techniques, including PCR, restriction enzyme digestion, gel electrophoresis, cloning, site-directed mutagenesis, DNA sequencing and DNA hybridization.
  • Students will have a thorough understanding of essential molecular processes in the cell, especially as related to DNA and RNA. These molecular processes include transcription, translation, DNA replication, recombination, DNA repair, and transposition.
  • Students will have an understanding of the revolutionary impact of genomics across all biological sciences.
  • Students will also display evidence of good report-writing skills including appropriate scientific referencing.
  • Students will develop hands-on expertise at conducting bioinformatic analyses of genomic data
  • Students will develop skills in critical thinking and analysis, and written and oral presentation of scientific information

General Assessment Information

Assignments

  • All assignments must be submitted to the FSE Student Centre

 

  • All assignments are to be submitted by midday on the date specified and must include a completed and signed coversheet stapled to the front cover.

 

Problem Set

Problems 1 - 12 should be done in time for marking and discussion during the practical session of the Week 12.

 

Requirements

  • Students are required to satisfactorily complete all components of the unit to pass.

Satisfactory completion of all components includes the practical assignments and the problem sets which are both integral components of the unit.  Apart from the marks formally allocated to these components, a comprehensive understanding of them will greatly assist you in the final exam.  You should remember that the final exam covers ALL components of the unit. 

  • Attendance at the practical sessions is compulsory.

Assessment Tasks

Name Weighting Due
Laboratory Reports 15% Apr 13, Apr 27, Jun 1
Bioinformatic Report 10% June 8
Mid-Semester Test 10% Week 7
Problem Set 5% Week 12
Final Examination 50% University Examination Period
Essay 10% May 11

Laboratory Reports

Due: Apr 13, Apr 27, Jun 1
Weighting: 15%

3 lab reports, 1500 words each
On successful completion you will be able to:
  • Students will be proficient in the theory and practice of a range of molecular biology experimental techniques, including PCR, restriction enzyme digestion, gel electrophoresis, cloning, site-directed mutagenesis, DNA sequencing and DNA hybridization.
  • Students will have a thorough understanding of essential molecular processes in the cell, especially as related to DNA and RNA. These molecular processes include transcription, translation, DNA replication, recombination, DNA repair, and transposition.
  • Students will also display evidence of good report-writing skills including appropriate scientific referencing.
  • Students will develop skills in critical thinking and analysis, and written and oral presentation of scientific information

Bioinformatic Report

Due: June 8
Weighting: 10%

Report on Bioinformatic Analysis
On successful completion you will be able to:
  • Students will have an understanding of the revolutionary impact of genomics across all biological sciences.
  • Students will also display evidence of good report-writing skills including appropriate scientific referencing.
  • Students will develop hands-on expertise at conducting bioinformatic analyses of genomic data
  • Students will develop skills in critical thinking and analysis, and written and oral presentation of scientific information

Mid-Semester Test

Due: Week 7
Weighting: 10%

Multiple Choice Test carried out during regularly scheduled laboratory time.
On successful completion you will be able to:
  • Students will be proficient in the theory and practice of a range of molecular biology experimental techniques, including PCR, restriction enzyme digestion, gel electrophoresis, cloning, site-directed mutagenesis, DNA sequencing and DNA hybridization.
  • Students will have a thorough understanding of essential molecular processes in the cell, especially as related to DNA and RNA. These molecular processes include transcription, translation, DNA replication, recombination, DNA repair, and transposition.
  • Students will develop skills in critical thinking and analysis, and written and oral presentation of scientific information

Problem Set

Due: Week 12
Weighting: 5%

12 Question Problem Set in Prac Manual.
On successful completion you will be able to:
  • Students will be proficient in the theory and practice of a range of molecular biology experimental techniques, including PCR, restriction enzyme digestion, gel electrophoresis, cloning, site-directed mutagenesis, DNA sequencing and DNA hybridization.
  • Students will develop skills in critical thinking and analysis, and written and oral presentation of scientific information

Final Examination

Due: University Examination Period
Weighting: 50%

2 essays, 20 short answer questions
On successful completion you will be able to:
  • Students will be proficient in the theory and practice of a range of molecular biology experimental techniques, including PCR, restriction enzyme digestion, gel electrophoresis, cloning, site-directed mutagenesis, DNA sequencing and DNA hybridization.
  • Students will have a thorough understanding of essential molecular processes in the cell, especially as related to DNA and RNA. These molecular processes include transcription, translation, DNA replication, recombination, DNA repair, and transposition.
  • Students will have an understanding of the revolutionary impact of genomics across all biological sciences.
  • Students will also display evidence of good report-writing skills including appropriate scientific referencing.
  • Students will develop skills in critical thinking and analysis, and written and oral presentation of scientific information

Essay

Due: May 11
Weighting: 10%

1000 word research essay
On successful completion you will be able to:
  • Students will have a thorough understanding of essential molecular processes in the cell, especially as related to DNA and RNA. These molecular processes include transcription, translation, DNA replication, recombination, DNA repair, and transposition.
  • Students will have an understanding of the revolutionary impact of genomics across all biological sciences.
  • Students will also display evidence of good report-writing skills including appropriate scientific referencing.
  • Students will develop skills in critical thinking and analysis, and written and oral presentation of scientific information

Delivery and Resources

Classes There are two weekly lectures of 1 hour (C5C Collaborative Forum, 12pm Tuesday, 11am Thursday) and a weekly practical session of 3 hours (F7B102-105, 2 – 5pm Tuesday or 9am-12pm Wednesday). In weeks 10 and 11, the practical class is replaced with a bioinformatic workshop in the same location. Attendance at practical sessions (and bioinformatic workshop) is a compulsory component of this unit. Lecture recordings and graphics slides are available online through iLearn (https://ilearn.mq.edu.au/login/MQ/), although lecture attendance in person is highly recommended. The practical manual is also available online through iLearn.  

Required and Recommended Texts The course syllabus is defined by all of the subject material presented in lectures and practicals, much of which is beyond standard textbooks. The prescribed text for this unit is Molecular Biology Fifth edition by Robert F Weaver. Available from the Co-op bookshop. The following texts may also be useful and are available in the library:

GenesIX by Benjamin Lewin

Mobile Genetic Elements by Sherratt

Molecular Cloning: A Laboratory Manual by Maniatis, Fritsch and Sambrook

An Introduction to Genetic Engineering by Des Nicholl.

Technology Requirements Within this Unit, you will be introduced to Web-based search engines that are commonly used in molecular biology. Our expectation is that you will be able to readily access the internet and have a computer available to you for web browsing and preparation of your laboratory reports. Handwritten reports will not be accepted. Your laboratory reports will be submitted and circulated via the online Turnitin program, for which access instructions will be given at submission time. Your practical reports will require you to carry out minor computational tasks, for which a calculator and access to basic statistical tools will be required. We place a large emphasis on correct referencing style in all your reports, and use of the program EndNote is encouraged, but not essential.

Unit Schedule

Week

Date

Lecture

Title

Lecturer

1

Mar 1

1

Introduction/What is Molecular Biology/Genome Structure

Haynes

Mar 3

2

Gene Organization/function

Haynes

2

Mar 8

3

Molecular Biology Techniques

Haynes

Mar 10

4

Molecular Biology Techniques

Haynes

3

Mar 15

5

Molecular Cloning

Paulsen

Mar 17

6

Tools for studying Gene Activity

Paulsen

4

Mar 22

7

Transcription in Prokaryotes

Paulsen

Mar 24

8

Structure of Prokaryotic Operons

Paulsen

5

Mar 29

9

Bacterial Gene Regulation

Paulsen

Mar 31

10

Transcription in Eukaryotes

Paulsen

6

Apr 5

11

Eukaryotic Gene Regulation

Paulsen

Apr 7

12

Nucleosomes/Histones/Chromatin

Paulsen

 

 

 

Semester break

 

 

7

Apr 26

13

Messenger RNA splicing

Paulsen

Apr 28

14

Mechanism of Translation

Paulsen

8

May 3

15

Ribosomes and transfer RNA

Paulsen

May 5

16

DNA replication

Paulsen

9

May 10

17

DNA recombination

Paulsen

May 12

18

DNA repair

Paulsen

10

May 17

19

Mobile DNA elements

Paulsen

May 19

20

Mobile DNA elements

Paulsen

11

May 24

21

Genome Sequencing

Paulsen

May 26

22

Genomes, Pan-Genomes and Metagenomics

Paulsen

12

May 31

23

Bioinformatics and Genome Annotation

Paulsen

Jun 2

24

Functional Genomics and Systems Biology

Paulsen

13

Jun 7

25

Synthetic Biology

Paulsen

Jun 9

26

Revision

Paulsen

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

New Assessment Policy in effect from Session 2 2016 http://mq.edu.au/policy/docs/assessment/policy_2016.html. For more information visit http://students.mq.edu.au/events/2016/07/19/new_assessment_policy_in_place_from_session_2/

Assessment Policy prior to Session 2 2016 http://mq.edu.au/policy/docs/assessment/policy.html

Grading Policy prior to Session 2 2016 http://mq.edu.au/policy/docs/grading/policy.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 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

PG - Capable of Professional and Personal Judgment and Initiative

Our postgraduates will demonstrate a high standard of discernment and common sense in their professional and personal judgment. They will have the ability to make informed choices and decisions that reflect both the nature of their professional work and their personal perspectives.

This graduate capability is supported by:

Learning outcomes

  • Students will be proficient in the theory and practice of a range of molecular biology experimental techniques, including PCR, restriction enzyme digestion, gel electrophoresis, cloning, site-directed mutagenesis, DNA sequencing and DNA hybridization.
  • Students will develop hands-on expertise at conducting bioinformatic analyses of genomic data
  • Students will develop skills in critical thinking and analysis, and written and oral presentation of scientific information

Assessment tasks

  • Laboratory Reports
  • Bioinformatic Report
  • Mid-Semester Test
  • Problem Set
  • Final Examination
  • Essay

PG - Discipline Knowledge and Skills

Our postgraduates will be able to demonstrate a significantly enhanced depth and breadth of knowledge, scholarly understanding, and specific subject content knowledge in their chosen fields.

This graduate capability is supported by:

Learning outcomes

  • Students will be proficient in the theory and practice of a range of molecular biology experimental techniques, including PCR, restriction enzyme digestion, gel electrophoresis, cloning, site-directed mutagenesis, DNA sequencing and DNA hybridization.
  • Students will have a thorough understanding of essential molecular processes in the cell, especially as related to DNA and RNA. These molecular processes include transcription, translation, DNA replication, recombination, DNA repair, and transposition.
  • Students will have an understanding of the revolutionary impact of genomics across all biological sciences.
  • Students will develop hands-on expertise at conducting bioinformatic analyses of genomic data

Assessment tasks

  • Laboratory Reports
  • Bioinformatic Report
  • Mid-Semester Test
  • Problem Set
  • Final Examination
  • Essay

PG - Critical, Analytical and Integrative Thinking

Our postgraduates will be capable of utilising and reflecting on prior knowledge and experience, of applying higher level critical thinking skills, and of integrating and synthesising learning and knowledge from a range of sources and environments. A characteristic of this form of thinking is the generation of new, professionally oriented knowledge through personal or group-based critique of practice and theory.

This graduate capability is supported by:

Learning outcomes

  • Students will be proficient in the theory and practice of a range of molecular biology experimental techniques, including PCR, restriction enzyme digestion, gel electrophoresis, cloning, site-directed mutagenesis, DNA sequencing and DNA hybridization.
  • Students will have a thorough understanding of essential molecular processes in the cell, especially as related to DNA and RNA. These molecular processes include transcription, translation, DNA replication, recombination, DNA repair, and transposition.
  • Students will have an understanding of the revolutionary impact of genomics across all biological sciences.
  • Students will also display evidence of good report-writing skills including appropriate scientific referencing.
  • Students will develop hands-on expertise at conducting bioinformatic analyses of genomic data
  • Students will develop skills in critical thinking and analysis, and written and oral presentation of scientific information

Assessment tasks

  • Laboratory Reports
  • Bioinformatic Report
  • Mid-Semester Test
  • Problem Set
  • Final Examination
  • Essay

PG - Research and Problem Solving Capability

Our postgraduates will be capable of systematic enquiry; able to use research skills to create new knowledge that can be applied to real world issues, or contribute to a field of study or practice to enhance society. They will be capable of creative questioning, problem finding and problem solving.

This graduate capability is supported by:

Learning outcomes

  • Students will be proficient in the theory and practice of a range of molecular biology experimental techniques, including PCR, restriction enzyme digestion, gel electrophoresis, cloning, site-directed mutagenesis, DNA sequencing and DNA hybridization.
  • Students will develop hands-on expertise at conducting bioinformatic analyses of genomic data
  • Students will develop skills in critical thinking and analysis, and written and oral presentation of scientific information

Assessment tasks

  • Laboratory Reports
  • Bioinformatic Report
  • Mid-Semester Test
  • Problem Set
  • Final Examination
  • Essay

PG - Effective Communication

Our postgraduates will be able to communicate effectively and convey their views to different social, cultural, and professional audiences. They will be able to use a variety of technologically supported media to communicate with empathy using a range of written, spoken or visual formats.

This graduate capability is supported by:

Learning outcomes

  • Students will also display evidence of good report-writing skills including appropriate scientific referencing.
  • Students will develop hands-on expertise at conducting bioinformatic analyses of genomic data
  • Students will develop skills in critical thinking and analysis, and written and oral presentation of scientific information

Assessment tasks

  • Laboratory Reports
  • Bioinformatic Report
  • Mid-Semester Test
  • Problem Set
  • Final Examination
  • Essay

PG - Engaged and Responsible, Active and Ethical Citizens

Our postgraduates will be ethically aware and capable of confident transformative action in relation to their professional responsibilities and the wider community. They will have a sense of connectedness with others and country and have a sense of mutual obligation. They will be able to appreciate the impact of their professional roles for social justice and inclusion related to national and global issues

This graduate capability is supported by:

Learning outcome

  • Students will develop skills in critical thinking and analysis, and written and oral presentation of scientific information

Assessment tasks

  • Laboratory Reports
  • Bioinformatic Report
  • Mid-Semester Test
  • Problem Set
  • Final Examination
  • Essay