Unit convenor and teaching staff |
Unit convenor and teaching staff
Lecturer
Hasinika Gamage
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Credit points |
Credit points
3
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Prerequisites |
Prerequisites
CBMS103 or CBMS107) and BIOL115
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Corequisites |
Corequisites
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Co-badged status |
Co-badged status
CBMS624
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Unit description |
Unit description
The combination of CBMS223 with this unit provides an essential core of biochemistry and molecular biology. This unit aims to provide students with further insights into the molecular processes of the living cell, and at the same time help students to understand the complex language of molecular biology. Topics covered include: molecular biological techniques, prokaryotic and eukaryotic gene regulation and genome organisation, transcription of RNA, translation of RNA to proteins, replication of DNA, bacterial and animal viruses, photosynthesis, and proteomics. The practical program is designed to give students a broad introduction to modern molecular biology techniques including extraction of DNA and RNA from cells, reverse transcriptase PCR, agarose- and SDS-polyacrylamide-gel electrophoresis, cloning of cDNA, DNA sequencing, and heterologous protein expression in E. coli and analysis of the expressed protein products. As such it is highly recommended for all biomolecular sciences students.
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Information about important academic dates including deadlines for withdrawing from units are available at https://www.mq.edu.au/study/calendar-of-dates
On successful completion of this unit, you will be able to:
All practical assessment items must be submitted BOTH as a hard copy and online via turnitin.
Assessments conform to the current assessment policy: http://www.mq.edu.au/policy/docs/assessment/policy_2016.html
10% penalty per day for late assessments. Assessment items submitted more than 1 week late will not be marked, except for serious and unavoidable disruptions (See http://mq.edu.au/policy/docs/disruption_studies/policy.html )
Name | Weighting | Hurdle | Due |
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Practical report outline | 5% | No | 24th August |
Mid-semester test | 10% | No | Week 6 |
Student seminar | 10% | No | Week 11 |
Practical examination | 10% | No | Week 12 |
Practical Report | 10% | No | Week 12 |
Final Exam | 55% | No | TBA |
Due: 24th August
Weighting: 5%
The title, abstract and introduction will need to be submitted on Thursday of week 4 together with a flow diagram of the practical. It is expected that you will know the name of your Chlamydomonas gene and have done some literature searching together with searching http://www.ncbi.nlm.nih.gov/ pub med and protein databanks to work out what is known about your gene and gene product from Chlamydomonas. You will also have read ALL of the practical notes and worked out a flow diagram of the practical components placed in a logical order for cloning, expressing and analysing your gene and gene product.
This is worth 5%. It is expected that you will revise and update the abstract and introduction to include in the final report.
Due: Week 6
Weighting: 10%
The Mid-semester Test will cover lecture material and give you an idea of the types of questions that will be asked in the final examination. Held during lecture time.
Due: Week 11
Weighting: 10%
The seminar will provide you with the opportunity to research the current literature and to begin to understand the formal writing style of scientific papers. You will present the overview of a specific topic in the biomolecular science area to the class, thus gaining experience in presentation techniques and public speaking.
The review topic will be assigned to you through iLearn during the mid semester break. To help you start a review article on that topic will be supplied but you may use additional published reviews. Note that the topics are broad and you should check the detailed information on the iLearn web site as to what is expected for this seminar.
You must also submit a single sheet of 5 key points on your topic area.
Due: Week 12
Weighting: 10%
The practical exam is designed to test your practical skills. It will consist of two parts.
A practical theory component where you will be given data to analyze and interpret. This data is of a similar type that you have generated in the laboratory sessions during semester.
A hands on practical component. This is designed to test you laboratory skills such as pippeting acuracy and ability to interpret and follow a written method. The test is open book and you WILL require your laboratory manual to find and use the appropriate method.
Due: Week 12
Weighting: 10%
The Practical Report will provide you with the opportunity write a scientific paper using ALL of the experimental results obtained over the course of the semester. You will be primarily assessed on your data analysis and interpretation. Detailed marking criteria and an example report are available on the iLearn web site. This is to be handed in at the completion of the practical exam and can be used during the exam.
Due: TBA
Weighting: 55%
The final exam has three sections:
Multiple choice section (50 questions), 50% of the exam.
A short answer section similar to the midsemester exam, 30 % of exam.
One essay/long or extended answer question, 20% of exam. You will get a choice of three or four question for this section and are expected to write 1-3 pages.
It is important that you have a scientific calculator as hand-held calculators will be used in tutorials, practicals, for assignments, tests and in the final examination. Note that text retrieval calculators are not allowed in the in-semester tests or final examination.
Use will be made of Excel and other data processing and display software. Computers carrying this software are available in the teaching laboratories. Items of interest, links to other on-line material and iLectures will be placed on the unit iLearn website.
General use computers are provided by the University, but it would be advantageous to have your own computer and internet access.
The timetable for classes can be found on the University web site at: http://www.timetables.mq.edu.au/
• 2 x 1 hr lectures per week
• 3 hr Practical classes are interspersed with 2 hr tutorials/discussions of the practicals.
• CBMS224 will comprise 2 lectures (or equivalent) per week, with practical (usually 3 hours) sessions interspersed with tutorials (1 to 2 hours). Live lecture recordings, ECHO will be available through a link to iLectures.
• Students are expected to attend all practical and tutorial classes. You will be required to submit a formal lab report and keep an up to date laboratory book. In addition you will be required to give a seminar on a seminar topic related to the lecture topics.
• Satisfactory performance in BOTH the final exam and in the practical component is required to pass.
The assessment tasks are designed to give you feedback as well as to assess your progress within the unit. More specifically:
o The Mid-semester Test will cover lecture material and give you an idea of the types of questions that will be asked in the final examination.
o The seminar will provide you with the opportunity to research the current literature and to begin to understand the formal writing style of scientific manuscripts. You will present the results of a published paper to the class, thus gaining experience in presentation techniques and public speaking.
o The Practical Test is designed to test your practical skills.
o The Practical Report will provide you with the opportunity write a scientific paper using all of the experimental results obtained over the course of the semester
· Marked work and midsemester and practical exam results should be returned within 2 weeks of being submitted.
· Students are to hand in their assignments after the practical test in week 12. The practical test is open book and students may need their practical report results to complete the practical exam.
· The seminar presentation will be discussed with students during semester.
Late assignments will receive a 10% per day penalty. Assignments handed in more than 1 week late will not be marked. Extensions will only be given in extenuating circumstances and must be discussed with the unit convenor BEFORE the due date.
• There is no web page for this unit.
• The unit will utilise iLearn (https://ilearn.mq.edu.au). Select the CBMS224 link and log on with your student id and password.
None
• Prescribed or recommended text(s):
Garrett and Grisham BIOCHEMISTRY (Third edition, Saunders). Another suitable contemporary biochemistry text is BIOCHEMISTRY (Berg, Tymoczko, Stryer, 5th edition, 2002, Freeman Press).
Genuine molecular biology texts are a bit harder to find, but there is a new edition of the MOLECULAR BIOLOGY OF THE GENE (5th edition) by Watson and others (Benjamin-Cummings Publishers). Useful molecular biology can be found also in Lewin GENES VIII (Pearson Education) 2003) and in MOLECULAR BIOLOGY OF THE CELL (Alberts et al., Garland Science, 2002). Other information may be obtained from Prescott, Harley, Klein: MICROBIOLOGY (McGraw-Hill 1999) or other microbiology texts. Several of these books are also recommended for other Units so this will influence decisions as to whether to invest in them.
• Prescribed unit materials:
Practical notes are available from the bookshop
Tutorial (T) /Practical (P) |
Wed or Thurs
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Experiment no. and topic |
P1/T1 |
Week 1
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P1- Lab induction. Compulsory. T1 Introductory Tutorial/Workshop on: Gene control, lac operon, transcription, DNA replication |
P1 |
Week 2
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A1 Preparation of E. coli competent cells A2 ‘Miniprep’ extraction of plasmid DNA from E. coli A3 Transformation of E. coli competent cells with plasmid DNA |
P2/T2 |
Week 3
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B1 Growth of transformant E. coli cells and inducible expression of proteins T2 Recombinant DNA, Introduction to physical mapping |
P3 |
Week 4
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C1 Extraction of RNA from Chlamydomonas C2 RT-PCR of RNA with a primer set to amplify a Chlamydomonas cDNA Practical Outline: Due Thursday at science centre. Turnitin submission required. |
P4 (2hr) T3 (1hr) |
Week 5
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D1 Analysis of RNA, plasmid and PCR product by agarose gel electrophoresis D2 Set up of DNA sequencing reaction T3: Translation and protein synthesis |
No lab or tut |
Week 6
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Midsemester test |
P5(2hr) T4(1hr) |
Week 7
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E1 SDS-PAGE of total protein from induced and uninduced transformant cells E2 Bioinformatics: Analysis of sequencing results Tutorial:More genetic engineering, cloning strategies |
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Mid-semester break |
P6(2hr) T5(1hr) |
Week 8
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F1 Preparation of induced SDS-PAGE gel band for MS analysis Tutorial: Review mid-semester test; Eukaryotic genomes |
P7(3hr) |
Week 9
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G1 Extraction and MS analysis of induced protein from gel plug |
P8(2hr) |
Week 10
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H1 Bioinformatics: Analysis of MS results |
T6 |
Week 11
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Student seminars: Wonders of the biomolecular world |
Prac Test |
Week 12
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· Practical Test · Hand in hard copy of Practical Report: Turnitin submission also required. |
T7 |
Week 13
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Revision tutorial; trial exam questions |
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 (in effect until Dec 4th, 2017): http://www.mq.edu.au/policy/docs/disruption_studies/policy.html
Special Consideration Policy (in effect from Dec 4th, 2017): https://staff.mq.edu.au/work/strategy-planning-and-governance/university-policies-and-procedures/policies/special-consideration
In addition, a number of other policies can be found in the Learning and Teaching Category of Policy Central.
Macquarie University students have a responsibility to be familiar with the Student Code of Conduct: https://students.mq.edu.au/support/student_conduct/
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.
Macquarie University provides a range of support services for students. For details, visit http://students.mq.edu.au/support/
Learning Skills (mq.edu.au/learningskills) provides academic writing resources and study strategies to improve your marks and take control of your study.
Students with a disability are encouraged to contact the Disability Service who can provide appropriate help with any issues that arise during their studies.
For all student enquiries, visit Student Connect at ask.mq.edu.au
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.
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Rephrasing and clarification of the learning outcomes