Course coordinator
Dr Justin Ridge
Course overview
- Study period
- Semester 1, 2025 (24/02/2025 - 21/06/2025)
- Study level
- Postgraduate Coursework
- Location
- St Lucia
- Attendance mode
- In Person
- Units
- 2
- Administrative campus
- St Lucia
- Coordinating unit
- Chemistry & Molec Biosciences
This course allows students to gain core molecular biological laboratory skills. This course focuses on techniques and protocols used in molecular biology providing an in-depth understanding of the principles behind them. Students will also gain experience in the interpretation of protocols, dealing with and interconverting units, and communicating results in a number of commonly used means. This course is designed for students who will soon be, or are currently, undertaking a lab-based research project and is one of the core courses of the Master of Molecular Biology programme.
This course builds on the concepts and experience gained in BIOC6001. The course will cover advanced aspects of working with both nucleic acids and proteins in the laboratory.
This course will provide the opportunity to apply your understanding of common molecular biology protocols in completing a project across the course of the semester. You will look to achieve a common goal of many laboratories that use molecular biology: the amplification and cloning of a protein coding region and then going on to express, purify, and characterise the expressed protein.
The learning activities and assessment will provide you with the skills to develop your own experimental plans to successfully clone, express, and purify almost any protein.
Course requirements
Assumed background
Knowledge of the mechanisms of theﾠflow of biological information from DNA to RNA to protein (central dogma of molecularﾠbiology). An understanding of the theory and practice of common molecular biology laboratory protocols (BIOC6001 and BIOC6040 or equivalent)
Prerequisites
You'll need to complete the following courses before enrolling in this one:
BIOC6001
Course contact
Course staff
Lecturer
Dr Justin Ridge
Professor Gary Schenk
Dr Nichaela Harbison-Price
Timetable
The timetable for this course is available on the UQ Public Timetable.
Aims and outcomes
The aim of this course is to provide you with experience of a range of laboratory techniques used in modern molecular genetics, and the theory and principles that underlie them, so that you can gain these important skills. Completion of this course will enhance your skill set and your research capabilities.
Learning outcomes
After successfully completing this course you should be able to:
LO1.
Competently carry out laboratory protocols.
LO2.
Maintain accurate and legible records of experimental procedures.
LO3.
Interpret and critically appraise experimental results.
LO4.
Successfully communicate the experimental findings.
LO5.
Develop workable plans to achieve experimental goals utilising molecular biology.
Assessment
Assessment summary
| Category | Assessment task | Weight | Due date |
|---|---|---|---|
| Practical/ Demonstration |
Laboratory Participation and Experimental Plans
|
20% Pass/Fail |
Experimental Plan 1 26/03/2025 2:00 pm Experimental Plan 2 2/04/2025 2:00 pm Experimental Plan 3 9/04/2025 2:00 pm Experimental Plan 4 30/04/2025 2:00 pm |
| Paper/ Report/ Annotation, Product/ Design |
In Silico Cloning & Cloning Strategy
|
20% |
16/04/2025 2:00 pm |
| Paper/ Report/ Annotation |
Feasibility Report
|
20% |
28/05/2025 2:00 pm |
| Examination |
End-of-semester written exam
|
40% |
End of Semester Exam Period 7/06/2025 - 21/06/2025 |
A hurdle is an assessment requirement that must be satisfied in order to receive a specific grade for the course. Check the assessment details for more information about hurdle requirements.
Assessment details
Laboratory Participation and Experimental Plans
- Hurdle
- In-person
- Mode
- Activity/ Performance, Written
- Category
- Practical/ Demonstration
- Weight
- 20% Pass/Fail
- Due date
Experimental Plan 1 26/03/2025 2:00 pm
Experimental Plan 2 2/04/2025 2:00 pm
Experimental Plan 3 9/04/2025 2:00 pm
Experimental Plan 4 30/04/2025 2:00 pm
- Learning outcomes
- L01, L02, L05
Task description
This assessment item has two components:
- An assessment of participation and good lab citizenship in each lab session (Pass/Fail).
- Written Experimental Plans 1-4 submitted every second week. (20%; 5% per plan)
Participation and good lab citizenship
In each laboratory session your participation and behaviour will be assessed by your tutor against written criteria. A passing grade for the session will be granted if your average competency is rated at "Competent with supervision" or better. A passing grade for the course will be awarded if you achieve a pass in ≥75% of the lab sessions. For details on the criteria and the marking see the BIOC7001 Protocol Booklet.
Experimental Plans
You will be expected to draft a short (1 A4 page) Experimental Plan that outlines how you intend to complete a specific experimental task. Each plan will be submitted approximately 1 week before the activities it describes will be attempted in the lab.
- Experimental Plan 1: Colony PCR
- Experimental Plan 2: DNA sequencing
- Experimental Plan 3: Protein expression
- Experimental Plan 4: Enzyme assays
Use of Artificial Intelligence (AI) and Machine Translation (MT)
Artificial Intelligence (AI) and Machine Translation (MT) are emerging tools that may support students in completing this assessment task. Students may appropriately use AI and/or MT in completing this assessment task. Students must clearly reference any use of AI or MT in each instance.
A failure to reference generative AI or MT use may constitute student misconduct under the Student Code of Conduct.
Hurdle requirements
See ADDITIONAL COURSE GRADING INFORMATION for the hurdle/s relating to this assessment item.Submission guidelines
Each Experimental Plan must be submitted via the appropriate Turnitin submission point found on the course Blackboard site. Late penalties will apply if your submission is late. It is your responsibility to check that each document is correctly submitted.
Deferral or extension
You may be able to apply for an extension.
Applications for Extensions
Information on applying for an extension can be found here: my.UQ Applying for an extension.
Extension applications must be received by the assessment due date and time.
If you are unable to provide approved documentation to support your application by the due date and time, you must still submit your application by the deadline but with an attached Word document that outlines why you cannot provide the approved documentation by the deadline. You will then need to acquire and upload the approved documentation to your request within 24 hours. Please note: When an extension request has been submitted and is pending, students are expected to continue to work on the assessment item, with the aim of submitting by the requested due date and time.
Prolonged Absence
If you have been ill or unable to attend class for more than 14 days, we advise you to carefully consider whether you are capable of successfully completing your courses this semester.
Extensions with Student Access Plans (SAP)
For extensions up to 7 days, your SAP is all that is required as documentation to support your application. However, extension requests longer than 7 days (for any one assessment item) will require the submission of additional supporting documentation e.g. a medical certificate.
Late submission
A penalty of 10% of the maximum possible mark will be deducted per 24 hours from time submission is due for up to 7 days. After 7 days, you will receive a mark of 0.
You are required to submit assessable items on time. If you fail to meet the submission deadline for any assessment item, then 10% of the maximum possible mark for the assessment item (assessment ‘marked from’ value) will be deducted as a late penalty for every day (or part day) late after the due date. For example, if you submit your assignment 1 hour late, you will be penalised 10%; if your assignment is 24.5 hours late, you will be penalised 20% (because it is late by one 24-hour period plus part of another 24-hour period). 10% will be deducted per day for up to 7 calendar days, at which point your submission will receive a mark of zero (0) unless an extension has been approved.
In most instances one or more hurdles will apply to your assessment item so you will need to submit it to fulfil the requirements of the course regardless of how late it is and the mark you are likely to be awarded.
In Silico Cloning & Cloning Strategy
- Hurdle
- Mode
- Product/ Artefact/ Multimedia, Written
- Category
- Paper/ Report/ Annotation, Product/ Design
- Weight
- 20%
- Due date
16/04/2025 2:00 pm
- Learning outcomes
- L05
Task description
For this assessment you will:
- Design appropriate PCR primers to enable amplification and cloning of the target coding region.
- Create a plasmid map of the construct that you will make.
- Create an annotated flow chart of protocols that will successfully achieve the amplification and cloning of your target protein coding region, plus validate the resultant plasmids.
For the flow chart, each step will be annotated with a description that includes:
- What the step achieves.
- An indication if samples should be taken and what these samples should be.
- An estimation of the time required.
You will be assigned a target coding sequence to work with and have a limited range of plasmid vectors to choose from. You will be able to use the SnapGene software to design PCR primers and create a plasmid map.
Use of Artificial Intelligence (AI) and Machine Translation (MT)
Artificial Intelligence (AI) and Machine Translation (MT) are emerging tools that may support students in completing this assessment task. Students may appropriately use AI and/or MT in completing this assessment task. Students must clearly reference any use of AI or MT in each instance.
A failure to reference generative AI or MT use may constitute student misconduct under the Student Code of Conduct.
Hurdle requirements
See ADDITIONAL COURSE GRADING INFORMATION for the hurdle/s relating to this assessment item.Submission guidelines
The annotated flow chart must be submitted via the appropriate Turnitin submission point found on the course Blackboard site. It is your responsibility to check that your submitted document is correct. The plasmid construct data file you create must also be submitted by the due date as a SnapGene file (.dna) file to the appropriate Blackboard assessment portal. Late penalties may apply if your submission is late. For the determination of on-time submission, the written submission and the plasmid data file will be treated as a single item (i.e., if one item is late and penalties are applied, they will be applied to both items).
Deferral or extension
You may be able to apply for an extension.
Applications for Extensions
Information on applying for an extension can be found here: my.UQ Applying for an extension.
Extension applications must be received by the assessment due date and time.
If you are unable to provide approved documentation to support your application by the due date and time, you must still submit your application by the deadline but with an attached Word document that outlines why you cannot provide the approved documentation by the deadline. You will then need to acquire and upload the approved documentation to your request within 24 hours. Please note: When an extension request has been submitted and is pending, students are expected to continue to work on the assessment item, with the aim of submitting by the requested due date and time.
Prolonged Absence
If you have been ill or unable to attend class for more than 14 days, we advise you to carefully consider whether you are capable of successfully completing your courses this semester.
Extensions with Student Access Plans (SAP)
For extensions up to 7 days, your SAP is all that is required as documentation to support your application. However, extension requests longer than 7 days (for any one assessment item) will require the submission of additional supporting documentation e.g. a medical certificate.
Late submission
A penalty of 10% of the maximum possible mark will be deducted per 24 hours from time submission is due for up to 7 days. After 7 days, you will receive a mark of 0.
You are required to submit assessable items on time. If you fail to meet the submission deadline for any assessment item, then 10% of the maximum possible mark for the assessment item (assessment ‘marked from’ value) will be deducted as a late penalty for every day (or part day) late after the due date. For example, if you submit your assignment 1 hour late, you will be penalised 10%; if your assignment is 24.5 hours late, you will be penalised 20% (because it is late by one 24-hour period plus part of another 24-hour period). 10% will be deducted per day for up to 7 calendar days, at which point your submission will receive a mark of zero (0) unless an extension has been approved.
In most instances one or more hurdles will apply to your assessment item so you will need to submit it to fulfil the requirements of the course regardless of how late it is and the mark you are likely to be awarded.
Feasibility Report
- Hurdle
- Mode
- Written
- Category
- Paper/ Report/ Annotation
- Weight
- 20%
- Due date
28/05/2025 2:00 pm
- Learning outcomes
- L03, L04
Task description
The enzyme isoforms the class will express and characterise in the lab all have the potential to be used in the production of biofuels. However, differences in enzymatic properties and tolerance of high temperatures may make one variant a better choice.
You will write a Feasibility Report describing how each of the isoforms may (or may not) be suitable for use in an industrial setting. A detailed description of what should be included in the report will be available on the course Blackboard site.
Use of Artificial Intelligence (AI) and Machine Translation (MT)
Artificial Intelligence (AI) and Machine Translation (MT) are emerging tools that may support students in completing this assessment task. Students may appropriately use AI and/or MT in completing this assessment task. Students must clearly reference any use of AI or MT in each instance.
A failure to reference generative AI or MT use may constitute student misconduct under the Student Code of Conduct.
Hurdle requirements
See ADDITIONAL COURSE GRADING INFORMATION for the hurdle/s relating to this assessment item.Submission guidelines
This assignment must be submitted via the appropriate Turnitin submission point found on the course Blackboard site. Late penalties will apply if your submission is late. It is your responsibility to check that your submitted document is correct.
Deferral or extension
You may be able to apply for an extension.
Applications for Extensions
Information on applying for an extension can be found here: my.UQ Applying for an extension.
Extension applications must be received by the assessment due date and time.
If you are unable to provide approved documentation to support your application by the due date and time, you must still submit your application by the deadline but with an attached Word document that outlines why you cannot provide the approved documentation by the deadline. You will then need to acquire and upload the approved documentation to your request within 24 hours. Please note: When an extension request has been submitted and is pending, students are expected to continue to work on the assessment item, with the aim of submitting by the requested due date and time.
Prolonged Absence
If you have been ill or unable to attend class for more than 14 days, we advise you to carefully consider whether you are capable of successfully completing your courses this semester.
Extensions with Student Access Plans (SAP)
For extensions up to 7 days, your SAP is all that is required as documentation to support your application. However, extension requests longer than 7 days (for any one assessment item) will require the submission of additional supporting documentation e.g. a medical certificate.
Late submission
A penalty of 10% of the maximum possible mark will be deducted per 24 hours from time submission is due for up to 7 days. After 7 days, you will receive a mark of 0.
You are required to submit assessable items on time. If you fail to meet the submission deadline for any assessment item, then 10% of the maximum possible mark for the assessment item (assessment ‘marked from’ value) will be deducted as a late penalty for every day (or part day) late after the due date. For example, if you submit your assignment 1 hour late, you will be penalised 10%; if your assignment is 24.5 hours late, you will be penalised 20% (because it is late by one 24-hour period plus part of another 24-hour period). 10% will be deducted per day for up to 7 calendar days, at which point your submission will receive a mark of zero (0) unless an extension has been approved.
In most instances one or more hurdles will apply to your assessment item so you will need to submit it to fulfil the requirements of the course regardless of how late it is and the mark you are likely to be awarded.
End-of-semester written exam
- Hurdle
- Identity Verified
- In-person
- Mode
- Written
- Category
- Examination
- Weight
- 40%
- Due date
End of Semester Exam Period
7/06/2025 - 21/06/2025
- Learning outcomes
- L03, L05
Task description
This will be an on-campus, in-person exam.
This exam will test your ability to apply the knowledge you have gained throughout the semester.
N.B. Calculators or a similar device will be required for this exam. These should be of the approved type see: https://my.uq.edu.au/services/manage-my-program/exams-and-assessment/sitting-exam/approved-calculators
Use of Artificial Intelligence (AI) and Machine Translation (MT)
This assessment task is to be completed in-person. The use of generative Artificial Intelligence (AI) or Machine Translation (MT) tools will not be permitted. Any attempted use of AI or MT may constitute student misconduct under the Student Code of Conduct.
Hurdle requirements
See ADDITIONAL COURSE GRADING INFORMATION for the hurdle/s relating to this assessment item.Exam details
| Planning time | 10 minutes |
|---|---|
| Duration | 120 minutes |
| Calculator options | (In person) Casio FX82 series only or UQ approved and labelled calculator |
| Open/closed book | Closed Book examination - no written materials permitted |
| Exam platform | Paper based |
| Invigilation | Invigilated in person |
Submission guidelines
Deferral or extension
You may be able to defer this exam.
Course grading
Full criteria for each grade is available in the Assessment Procedure.
| Grade | Description |
|---|---|
| 1 (Low Fail) |
Absence of evidence of achievement of course learning outcomes. Course grade description: The student does not demonstrate knowledge of the basic factual information presented in the course. The student shows no ability to integrate and process information. The student showsﾠno ability to maintain a laboratory note book, carry out laboratory procedures or present information in a professional manner. The minimum percentage required for this grade is: 0% |
| 2 (Fail) |
Minimal evidence of achievement of course learning outcomes. Course grade description: The student demonstrates a rudimentary knowledge of the basic factual information presented in the course. The student shows little ability to integrate and process information. The student shows little ability to maintain a laboratory note book, carry out laboratory procedures or present information in a professional manner, and at a level well below that considered necessary as a basis for professional practice. The minimum percentage required for this grade is: 30% |
| 3 (Marginal Fail) |
Demonstrated evidence of developing achievement of course learning outcomes Course grade description: The student demonstrates a rudimentary understanding of the material presented in the course. The student shows limited ability to integrate and process information. The student shows limited ability to maintain a laboratory note book, carry out laboratory procedures or present information in a professional manner, but at a level below that considered necessary as a basis for professional practice. The minimum percentage required for this grade is: 45% |
| 4 (Pass) |
Demonstrated evidence of functional achievement of course learning outcomes. Course grade description: The student demonstrates a level of understanding of the factual information and general concepts presented in the course. The student shows some ability to integrate and process the information. The student is able to present material in at least one professional mode. The student shows some ability to maintain a laboratory note book and carry out laboratory procedures at a level that provides a minimal basis for professional practice. The minimum percentage required for this grade is: 50% |
| 5 (Credit) |
Demonstrated evidence of proficient achievement of course learning outcomes. Course grade description: The student demonstrates a good level of understanding of the factual information and general concepts presented in the course. The student shows good ability to integrate and process the information. The student is able to present material in more than one professional mode. The student shows good ability to maintain a laboratory note book and carry out laboratory procedures at a level that provides a sound basis for professional practice. The minimum percentage required for this grade is: 65% |
| 6 (Distinction) |
Demonstrated evidence of advanced achievement of course learning outcomes. Course grade description: The student demonstrates a high level of understanding of the factual and conceptual information presented in the course together with goodﾠ ability to integrate different aspects of that knowledge and evaluate problems. The student displays good grasp of relevant ethical issues and the ability to reflect and evaluate these issues. The student is accomplished in the presentation of scientific material in more than one professional mode. The student shows high ability to maintain a laboratory note book and carry out laboratory procedures at a level that provides a good basis for professional practice. The minimum percentage required for this grade is: 75% |
| 7 (High Distinction) |
Demonstrated evidence of exceptional achievement of course learning outcomes. Course grade description: The student demonstrates a very high level of understanding of the factual and conceptual information presented in the course together with excellent ability to integrate different aspects of that knowledge and evaluate problems. The student displays wide understanding of ethical issues and insight into factors which influence these issues. The student is accomplished in the presentation of scientific material in all professional mode. The student shows very high proficiency in maintaining a laboratory note book and carrying out laboratory procedures at a level that provides an excellent basis for professional practice. The minimum percentage required for this grade is: 85% |
Additional course grading information
Assessment Hurdles
In order to pass this course, you must meet ALL of the following requirements (if you do not meet these requirements, the maximum grade you will receive will be a 3):
- You must obtain an overall course mark of 50% or more; and
- You must obtain an overall mark of 40% or more on the end of semester exam; and
- You must obtain a minimum weighted average mark of 40% across all other non-examination course assessment items; and
- You must complete 100% of the laboratory component of the course.
Practical Sessions
Students are expected to complete all practical sessions. Where practical sessions clash with timetabled activities in other courses the student should contact the course coordinator as soon as possible. Students who are unable to be present on any day or part day of laboratory work for reasons other than timetable clashes must submit an explanation in writing to the course coordinator.
Supplementary assessment
Supplementary assessment is available for this course.
Should you fail a course with a grade of 3, you may be eligible for supplementary assessment. Refer to my.UQ for information on supplementary assessment and how to apply.
Supplementary assessment provides an additional opportunity to demonstrate you have achieved all the required learning outcomes for a course.
If you apply and are granted supplementary assessment, the type of supplementary assessment set will consider which learning outcome(s) have not been met.
Supplementary assessment can take any form (such as a written report, oral presentation, examination or other appropriate assessment) and may test specific learning outcomes tailored to the individual student, or all learning outcomes.
To receive a passing grade of 3S4, you must obtain a mark of 50% or more on the supplementary assessment.
Additional assessment information
Assessment Submission
It is the responsibility of the student to ensure the on time, correct and complete submission of all assessment items.
Students are responsible for retaining evidence of submission by the due date for all assessment items, in the required form (for example, screenshot, email, photo, and an unaltered copy of submitted work).
In the case of a Blackboard outage, contact the Course Coordinator as soon as possible to confirm the outage with ITS.
Assessment/Attendance
Notify your Course Coordinator as soon as you become aware of any issue that may affect your ability to meet the assessment/attendance requirements of the course. The my.UQ website and the Course Profile (CP) for your course provide information about your course requirements, the rules associated with your courses and services offered by the University.
A note for repeating students in this course
Only learning activities and/or assessment items completed during the study period of enrolment, including any approved extensions, may contribute to your grade in this course. The whole or partial use of assessment items previously submitted for the same course, for a course at any institution, or for published material, is not permitted without written permission of the Course Coordinator.
Important Note
Turnitin is to be used for assignments/laboratory reports to check for plagiarism. Penalties can be severe for plagiarism.
The University has adopted the following definition of plagiarism: Plagiarism is the act of misrepresenting as one's own original work the ideas, interpretations, words or creative works of another either intentionally or unintentionally. These include published and unpublished documents, designs, music, sounds, images, photographs, computer codes and ideas gained through working in a group. These ideas, interpretations, words or works may be found in print and/or electronic media.
Students should read the UQ Student Integrity and Misconduct Policy.
Learning resources
You'll need the following resources to successfully complete the course. We've indicated below if you need a personal copy of the reading materials or your own item.
Library resources
Find the required and recommended resources for this course on the UQ Library website.
Other course materials
If we've listed something under further requirement, you'll need to provide your own.
Required
| Item | Description | Further Requirement |
|---|---|---|
| Lab coat | A lab coat is part of the essential personal protective equipment (PPE) required for working in the teaching lab. | own item needed |
| Safety glasses/goggles | Lab safety glasses/goggles are part of the essential personal protective equipment (PPE) required for working in the teaching lab. | own item needed |
| Lab notebook | A suitable notebook is needed to record your activities in the lab. A recommendation of which notebook is suitable will be provided on Blackboard. | own item needed |
| SnapGene software package | This software will be used to complete some of the assessment items. You will be provided with a time-limited licence for this software for no charge. | |
| GraphPad Prism | This software will be used in one of the workshops and can be used to complete the Feasibility Report. This software can be obtained from UQ. |
Additional learning resources information
Blackboard
Any information required to complete this course will be posted to the BIOC7001 Blackboardﾠsite learn.uq.edu.au
Please check the Announcements section of the Blackboard site regularly for information updates.
Digital Essentials and CLIPS
These are two collections of resources you may find useful in your studies.
- The Digital Essentials site is hosted by UQ Library and contains self-directed learning modules about a range of things including: navigating UQ online systems; finding and using media; and working with data.
- The CLIPS website has been developed by academics within the Faculty of Science and provides resources and information about communicating as a scientist. It includes guides on presentations, posters, and presenting data.
Software
As a student in BIOC7001 it is essential that you source the following software packages and install them on your laptop:
- Graphpad Prism – this is a specialist graphing software that is very useful to plot and fit data. You can obtain a copy of this as a UQ student via the "Free student software for personal use" webpage on the UQ website.
- SnapGene – this is a software package that allows you to visualise, interrogate, and manipulate nucleic acid sequence data. You will be provided with details on how to install a fully licenced version of this for free. You will need this software to complete the "In Silico Cloning & Cloning Strategy" assessment item.
Learning activities
The learning activities for this course are outlined below. Learn more about the learning outcomes that apply to this course.
Filter activity type by
Please select
| Learning period | Activity type | Topic |
|---|---|---|
Multiple weeks From Week 1 To Week 13 |
Lecture |
Weekly Lectures These lectures will introduce advanced concepts in molecular biology. You will learn how to specifically apply key molecular biological protocols. A more detailed timetable will be posted to Blackboard. Learning outcomes: L03, L05 |
Multiple weeks From Week 2 To Week 13 |
Tutorial |
Weekly Tutorials These tutorials will be used as a forum to apply knowledge gained in the lectures, provide guidance in using software tools, and review assessment items. When appropriate we will use these session to review and analyse outcomes from the laboratory sessions. Learning outcomes: L03, L05 |
Multiple weeks From Week 2 To Week 11 |
Practical |
Heterologous Expression Lab Project Weekly laboratory practical sessions in which students will clone a target gene and validate the resultant plasmid constructs and then use these to express a heterologous protein. The expressed protein will then be purified and characterised. Learning outcomes: L01, L02, L03, L04, L05 |
Policies and procedures
University policies and procedures apply to all aspects of student life. As a UQ student, you must comply with University-wide and program-specific requirements, including the:
- Student Code of Conduct Policy
- Student Integrity and Misconduct Policy and Procedure
- Assessment Procedure
- Examinations Procedure
- Reasonable Adjustments - Students Policy and Procedure
Learn more about UQ policies on my.UQ and the Policy and Procedure Library.