Students

BMOL3402 – Molecular Biology and Genomics

2024 – Session 1, In person-scheduled-weekday, North Ryde

General Information

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Unit convenor and teaching staff Unit convenor and teaching staff Unit Convenor
Ian Paulsen
Contact via Email
By appointment
Lecturer
Paul Haynes
Contact via Email
By Appointment
Scientific Officer
Ashwini Nagaraja
Scientific Officer
Ammara Sajjad
Credit points Credit points
10
Prerequisites Prerequisites
130cp at 1000 level or above including BMOL2201 or CBMS201 or CBMS223
Corequisites Corequisites
Co-badged status Co-badged status
BMOL6432
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, systems and synthetic biology. 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:

  • ULO1: Describe the theory behind and demonstrate competency in the use of a range of molecular biology experimental techniques, including PCR, restriction enzyme digestion, gel electrophoresis, cloning, gene editing, DNA sequencing and DNA hybridization.
  • ULO2: Describe and discuss 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.
  • ULO3: Relate the revolutionary impact of genomics across all biological sciences.
  • ULO4: Analyse and interpret experimental data and present this in a structured report utilising appropriate scientific referencing.

General Assessment Information

Requirements to Pass this Unit

To pass this unit you must:

Attempt all assessments, and

Achieve at least 40% in the final examination

Note: There are no hurdle assessments 

 

Assignments

All assignments must be submitted as soft copy on the date specified.

All written work must be submitted to Turnitin for plagiarism checking. Instructions will be provided on iLearn.

Criteria and standards required for the assessment tasks will be available on iLearn.

 

Note the standardised 11:55pm submission time for assessments

Extensions will only be granted under exceptional circumstances.

Late Assessment Submission Penalty 

Unless a Special Consideration request has been submitted and approved, a 5% penalty (of the total possible mark of the task) will be applied for each day a written report or presentation assessment is not submitted, up until the 7th day (including weekends). After the 7th day, a grade of ‘0’ will be awarded even if the assessment is submitted. The submission time for all uploaded assessments is 11:55 pm. A 1-hour grace period will be provided to students who experience a technical concern.

For any late submission of time-sensitive tasks, such as scheduled tests/exams, performance assessments/presentations, and/or scheduled practical assessments/labs, please apply for Special Consideration

Late submissions will be accepted for all assessments in this unit with penalties. 

General Faculty Policy on assessment submission deadlines and late submissions: Online quizzes, in-class activities, or scheduled tests and exam must be undertaken at the time indicated in the unit guide. Should these activities be missed due to illness or misadventure, students may apply for Special Consideration.

Special Consideration

The Special Consideration Policy aims to support students who have been impacted by short-term circumstances or events that are serious, unavoidable and significantly disruptive, and which may affect their performance in assessment. If you experience circumstances or events that affect your ability to complete the assessments in this unit on time, please inform the convenor and submit a Special Consideration request through ask.mq.edu.au.

Off-shore students Off-shore students must email the convenor as soon as possible to discuss study options as this course has in person practical classes and attendance is mandatory. So this course cannot be completed off-shore.

Weekly practice-based tasks: To pass the unit you need to demonstrate ongoing development of skills and application of knowledge in all of the weekly practical classes. If you miss a weekly practical class due to a serious, unavoidable and significant disruption, contact your convenor ASAP as you may be able to attend another class that week. If it is not possible to attend another class, you should still contact your convenor for access to class material to review in your own time.

We will communicate with you via your university email or through announcements on iLearn. Queries to convenors can either be placed on the iLearn discussion board or sent to ian.paulsen@mq.edu.au from your university email address.

COVID Information and on-campus classes

For the latest information on the University’s response to COVID-19, please refer to the Coronavirus infection page on the Macquarie website: https://www.mq.edu.au/about/coronavirus-faqs. Remember to check this page regularly in case the information and requirements change during semester. If there are any changes to this unit in relation to COVID, these will be communicated via iLearn.

Assessment Tasks

Name Weighting Hurdle Due
Midsemester Test 10% No Week 8, Apr 8
Lab reports 35% No Week 6, Mar 26; Week 9, Apr 30; Week 13, May 28
Synthetic Biology Challenge 15% No Week 12, May 21
Final Examination 40% No Unversity Examination Period, June 2024

Midsemester Test

Assessment Type 1: Quiz/Test
Indicative Time on Task 2: 10 hours
Due: Week 8, Apr 8
Weighting: 10%

 

Test carried out during regularly scheduled laboratory time.

 


On successful completion you will be able to:
  • Describe the theory behind and demonstrate competency in the use of a range of molecular biology experimental techniques, including PCR, restriction enzyme digestion, gel electrophoresis, cloning, gene editing, DNA sequencing and DNA hybridization.

Lab reports

Assessment Type 1: Lab report
Indicative Time on Task 2: 30 hours
Due: Week 6, Mar 26; Week 9, Apr 30; Week 13, May 28
Weighting: 35%

 

Three lab reports 1500 words each

 


On successful completion you will be able to:
  • Describe the theory behind and demonstrate competency in the use of a range of molecular biology experimental techniques, including PCR, restriction enzyme digestion, gel electrophoresis, cloning, gene editing, DNA sequencing and DNA hybridization.
  • Analyse and interpret experimental data and present this in a structured report utilising appropriate scientific referencing.

Synthetic Biology Challenge

Assessment Type 1: Qualitative analysis task
Indicative Time on Task 2: 10 hours
Due: Week 12, May 21
Weighting: 15%

 

This is a written group-based report on the design phase of synthetic biology

 


On successful completion you will be able to:
  • Relate the revolutionary impact of genomics across all biological sciences.
  • Analyse and interpret experimental data and present this in a structured report utilising appropriate scientific referencing.

Final Examination

Assessment Type 1: Examination
Indicative Time on Task 2: 18 hours
Due: Unversity Examination Period, June 2024
Weighting: 40%

 

Final Examination held in university examination period

 


On successful completion you will be able to:
  • Describe the theory behind and demonstrate competency in the use of a range of molecular biology experimental techniques, including PCR, restriction enzyme digestion, gel electrophoresis, cloning, gene editing, DNA sequencing and DNA hybridization.
  • Describe and discuss 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.
  • Relate the revolutionary impact of genomics across all biological sciences.

1 If you need help with your assignment, please contact:

  • the academic teaching staff in your unit for guidance in understanding or completing this type of assessment
  • the Writing Centre for academic skills support.

2 Indicative time-on-task is an estimate of the time required for completion of the assessment task and is subject to individual variation

Delivery and Resources

Classes

There are two weekly lectures of 1 hour each on Tuesday 3-4pm and Wednesday 12-1pm which will be held at 23 Wally's Walk T1 and 23 Wally's Walk, T2. There is one weekly practical session of 3 hours on Monday 10-1pm (practical groups 1 and 2) and Monday 2-5pm (practical groups 3 and 4) at 14 Eastern Road Science Labs 130 and 150. Attendance at practical sessions 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 on iLearn, 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

Unit Schedule

Week

Date

Lecture

Title

Lecturer

1

Feb 20

1

Introduction/What is Molecular Biology/Genome Structure

Haynes

Feb 21

2

Gene Organization/function

Haynes

2

Feb 27

3

Molecular Biology Techniques

Haynes

Feb 28

4

Molecular Biology Techniques

Haynes

3

Mar 5

5

Molecular Cloning

Haynes

Mar 6

6

Tools for studying Gene Activity

Haynes

4

Mar 12

7

Transcription in Prokaryotes

Paulsen

Mar 13

8

Structure of Prokaryotic Operons

Paulsen

5

Mar 19

9

Bacterial Gene Regulation

Paulsen

Mar 20

10

Transcription in Eukaryotes and Eukaryotic Gene Regulation

Paulsen

6

Mar 26

11

Nucleosomes/Histones/Chromatin

Paulsen

Mar 27

12

Messenger RNA splicing

Paulsen

7

Apr 2

13

Mechanism of Translation

Paulsen

Apr 3

14

Ribosomes and transfer RNA

Cain

8

Apr 9

15

DNA replication

Cain

Apr 10

16

DNA recombination

Paulsen

                                                                                       SEMESTER BREAK :  Apr 13 - Apr 28

9

Apr 30

17

DNA Repair

Paulsen

May 1

18

Mobile DNA elements #1

Paulsen

10

May 7

19

Mobile DNA elements #2

Paulsen

May 8

20

Genome Sequencing

Paulsen

11

May 14

21

Genomes, Pan-Genomes and Metagenomics

Paulsen

May 15

22

Bioinformatics and Genome Annotation

Paulsen

12

May 21

23

Functional Genomics and Systems Biology

Paulsen

May 22

24

Synthetic Biology I

Paulsen

13 May 28 25 Synthetic Biology II

Paulsen

May 29 26 Revision

Paulsen

Policies and Procedures

Macquarie University policies and procedures are accessible from Policy Central (https://policies.mq.edu.au). Students should be aware of the following policies in particular with regard to Learning and Teaching:

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

To find other policies relating to Teaching and Learning, visit Policy Central (https://policies.mq.edu.au) and use the search tool.

Student Code of Conduct

Macquarie University students have a responsibility to be familiar with the Student Code of Conduct: https://students.mq.edu.au/admin/other-resources/student-conduct

Results

Results published on platform other than eStudent, (eg. iLearn, Coursera etc.) 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 connect.mq.edu.au or if you are a Global MBA student contact globalmba.support@mq.edu.au

Academic Integrity

At Macquarie, we believe academic integrity – honesty, respect, trust, responsibility, fairness and courage – is at the core of learning, teaching and research. We recognise that meeting the expectations required to complete your assessments can be challenging. So, we offer you a range of resources and services to help you reach your potential, including free online writing and maths support, academic skills development and wellbeing consultations.

Student Support

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

The Writing Centre

The Writing Centre provides resources to develop your English language proficiency, academic writing, and communication skills.

The Library provides online and face to face support to help you find and use relevant information resources. 

Student Services and Support

Macquarie University offers a range of Student Support Services including:

Student Enquiries

Got a question? Ask us via the Service Connect Portal, or contact Service Connect.

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.


Unit information based on version 2024.01R of the Handbook