Foundations of Molecular Biophysics (BIOC2001)

Course overview

Biophysics is an interdisciplinary science which uses methods and techniques that have their origins in physics and chemistry, and applies these to study the structure, functional properties and behaviour of molecules, cells and organisms in a quantitative manner. This course provides students with a strong, foundational understanding of the concepts that define biological processes at the molecular scale. Lectures and workshops also introduce core biophysical techniques; these ultimately open windows that allow biological processes to be visualised and better understood.

Understanding the molecular basis of life is like trying to solve a giant, ever-evolving puzzle. In studying BIOC2001, you will be provided with the instruction manual for solving this enigmatic riddle.

Biophysics is a subject that lies at the crossroads of biology, physics, and chemistry. It is not simply “hard biology”. Rather it is an interdisciplinary science that uses methods and techniques that have their origins in physics (and chemistry) to study the structure, functional properties, and behaviour of molecules, cells and organisms in a quantitative manner. In doing so, we learn progressively more about the way cells and biomolecules behave, thus inching every close to solving the mystery of life itself.

BIOC2001 arms students with the tools to develop their understanding of the life sciences at a fundamental level. It provides an introduction to concepts that include the interaction of radiation

with matter, thermodynamic principles that guide e.g. protein folding and stability, and quantitative modelling of biological systems. It also provides an introduction to techniques that are widely used throughout the biotech and life sciences research and industry sectors for characterisation of biological macromolecules (i.e. proteins, nucleic acids, lipids, and carbohydrates). Thus, the course provides a foundational learning experience for students who plan to pursue subsequent studies and/or career paths that require an understanding of biological molecules.

BIOC2001 is a compulsory course for students undertaking a BSc or other eligible program that wish to graduate with a minor in Biophysics. BIOC2001 is likely to be of interest to students from a range of BSc majors (e.g. Chemistry/Chemical Sciences, Biochemistry & Molecular Biology, Physics) as well as students from other majors or programs with an interest in molecular systems, including (but not limited to) Biotechnology, Biomedical Science, Nanotechnology, Computational Science, Molecular Microbiology and Engineering. For students who have taken BIOC2000 and who plan to take BIOC3000 in the future, BIOC2001 is an excellent bridging course which many past students have found to be highly beneficial to their understanding of advanced concepts in Biochemistry.

Note that prior to 2023, this course was coded as BIPH2000.

Course requirements

Assumed background

Biophysics is a discipline positioned at the nexus of chemistry, biology and physics. This course therefore welcomes students from either chemical/biochemical/biological sciences backgrounds, or from physical/engineering sciences backgrounds. As a discipline, Biophysics welcomes people from diverse backgrounds and in recognising that this leads to a diverse student cohort, we endeavour to bring everyone up to speed in the first few weeks of semester.ﾠﾠ

Notwithstanding the above,ﾠstudents will benefit most from having a background that satisfies one of the following requirements:

1) Have studied a combination of biology (e.g. BIOL1020) or chemistry (e.g. CHEM1100 or CHEM1200)ﾠand physics (e.g. PHYS1171 orﾠPHYS1002) at first level

OR

2) Have studied biochemistry (BIOC2000) at second level.

OR

3) Have an engineering or chemical sciences background and an interest in biophysics; students in this category may have acquired the necessary background knowledge from one of many courses and should discuss with the course coordinator prior to enrolling.

NOTE: Regardless of background, Yr 11/12 Physics and Maths (or equivalent) is assumed pre-knowledge. Students should be familiar with basic calculus and algebra.ﾠ
ﾠ

If you have any queries or concerns about whether your background is appropriate for the course, please contact the course coordinator before enrolling.

ﾠ

Prerequisites

You'll need to complete the following courses before enrolling in this one:

BIOC2000 or BIOC2900 or BIOE1001 or PHYS1171 or PHYS1002

Incompatible

You can't enrol in this course if you've already completed the following:

PHYS2170 and BIPH2000

Course contact

Course staff

Timetable

The timetable for this course is available on the UQ Public Timetable.

Additional timetable information

Check your online timetable regularly.

Aims and outcomes

This course focuses on how principles and techniques originally derived from physics, physical chemistry and maths can be applied to biological systems and used to obtain a quantitative understanding of biomolecular systems at a molecular and cellular level. For the chemistry, biochemistry or biomedical sciences student, the course provides an introduction to the biophysical principles at the heart of modern biochemistry, molecular medicine, and physiology. For the physics student the course offers an introduction to cellular and molecular biology with an emphasis on the quantitative analysis of the relevant physical properties. In particular, the course will focus on the fundamentals and applications of a range of biophysical techniques used to characterize biomolecular systems including mass spectrometry, sedimentation, thermodynamics, macromolecular x-ray crystallography, magnetic resonance, and cryo-electron microscopy. The course will provide all students with a detailed understanding of tools used in the quantitative analysis of biomolecular systems and cellular substructures.

Learning outcomes

After successfully completing this course you should be able to:

Assessment

Assessment summary

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

Workshop Exercises

• Hurdle

Mode

Written

Category

Tutorial/ Problem Set

Weight

25%

Due date

2pm 24/07/2024 - 23/10/2024

Each completed workshop assessment task will be due for submission one week after the workshop at 2pm.

Learning outcomes

L01, L02, L03, L04, L05, L06, L07, L09

Task description

Hurdle requirements

Submission guidelines

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.

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.

This assignment must be submitted via the appropriate Turnitin submission point found on the course Blackboard site. Late penalties will apply at 10% per day or part day if your submission is late. It is your responsibility to check that your submitted document is correct and that you have received a Turnitin receipt.

Experimental techniques

• Hurdle
• Identity Verified

Mode

Product/ Artefact/ Multimedia

Category

Presentation

Weight

15%

Due date

25/10/2024 2:00 pm

Other conditions

Student specific.

See the conditions definitions

Learning outcomes

L07, L08, L10

Task description

Hurdle requirements

Submission guidelines

Submit your recording through the course Turnitin submission point in Blackboard. Before submitting your assessment item to Turnitin please name your file in the following way. FAMILY NAME_GivenName_StudentID_CourseCode_AssignmentName For example: Bob Smith (ID: 54329876) would name his ABCD1234 essay 1 in the following way. SMITH_Bob_54329876_ABCD1234_Essay1

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.

Biophysics

• Hurdle
• Identity Verified
• In-person

Mode

Written

Category

Examination

Weight

60%

Due date

End of Semester Exam Period

2/11/2024 - 16/11/2024

Other conditions

Time limited.

See the conditions definitions

Learning outcomes

L01, L02, L03, L04, L05, L06, L07, L09

Task description

Hurdle requirements

Exam details

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.

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):

1. You must obtain an overall mark of 50% or more; and

2. You must obtain an overall mark of 40% or more in the end of semester exam; and

3. You must obtain a minimum weighted average mark of 40% across all other non-examination course assessment items and learning tasks; and

4. You mustﾠcomplete and submit ALL workshop-related assessment.

The maximum grade you will receive will be a 2 if you:

1. Obtain an overall mark of 30% or less on the end of semester exam; and/or

2. Obtain a weighted average mark of 30% or less on the non-examination course assessment items and learning tasks.

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.

Please ensure you receive and save the submission confirmation for all submitted items, you may be asked to produce this as evidence of your submission.

Turnitin

By submitting work through Turnitin you are deemed to have accepted the following declaration “I certify that this assignment is my own work and has not been submitted, either previously or concurrently, in whole or in part, to this University or any other educational institution, for marking or assessment”.

All students must ensure they receive their Turnitin receipt on submission of any assessments. A valid Turnitin receipt will be the only evidence accepted if one or more of your submissions are missing. Without evidence, the assessment will receive the standard late penalty, or after seven days, will receive zero. In the case of a Blackboard outage, please contact the Course Coordinator as soon as possible to confirm the outage with ITS.

Assessment/Attendance

Please 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 Electronic Course Profile (ECP) for your course also 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

Any student who enrols in a course must not be given exemption or partial credit from their previous attempt(s) for any individual piece of assessment. Instead, the student must successfully complete all of the learning activities and assessment items within the study period of enrolment (PPL Assessment - Procedures Section: Assessment integrity).

If the same assessment item is set from one year to the next, repeating students are allowed to submit the same work they submitted in previous attempts at the course. Where possible SCMB recommends that you use the feedback you received in your last attempt to improve parts of the item where you lost marks. Resubmission of an altered or unaltered assessment item by a repeating student (where the same assessment has been set) will not be considered as self-plagiarism.

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 are encouraged to read the UQ Academic Integrity and Plagiarism policy at: ppl.app.uq.edu.au/content/3.60.04-student-integrity-and-misconduct

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.

Additional learning resources information

Blackboard

Please check the Announcements section of the Blackboard site regularly for information updates.

Learning activities

The learning activities for this course are outlined below. Learn more about the learning outcomes that apply to this course.

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.