Outline

Overview

Diseases are ultimately the result of an imbalance of cellular function. Causes for such dysfunction are diverse and include mutations of our DNA, altered gene expression and external stimuli such as infection. This unit will investigate how defects in key cell functions including gene expression, signalling, biomolecular interactions and metabolic processes lead to diseases. The molecular causes and biochemical processes that underlie cancer, aging and neurodegeneration will be used to illustrate the relationships between these processes and how our understanding of these commonalities is allowing us to solve complex health problems. Associations to other diseases will be integrated into the course to give a broader understanding of how key biochemical processes are linked to a wide range of disorders. In the practicals you will use experimental approaches to study cell proliferation and death, protein misfolding, the hallmarks of cancer and some neurodegenerative diseases. By the end of this unit you will have gained foundational skills and knowledge that will support further studies and careers in the life and medical sciences. The lecture component of this advanced unit will be the same as for the mainstream unit BCMB3003. In the practicals you will investigate similar concepts, however, the experiments are designed to cover a wider range of techniques, and you will analyse the results in more depth. You will present scientific findings in a poster session to academics from the School of Life and Environmental Sciences (SOLES). In addition, to relate the course content to current research and application, you will attend a series of four research seminars relating to the lecture content that will be given by experts in their field.

Unit details and rules

Academic unit	Life and Environmental Sciences Academic Operations
Credit points	6
Prerequisites ?	An average mark of 75 or above in [12 credit points from (BCHM2X71 or BCHM2X72 or BCMB2X01 or BCMB2X02 or MEDS2003 or MBLG2X01) or [6 credit points from (BCHM2X71 or BCHM2X72 or BCMB2X01 or BCMB2X02 or MEDS2003 or MBLG2X01) and 6 credit points from (AMED3001 or BCHM3XXX or BCMB3XXX or BIOL2X29 or BMED2401 and BMED2405 or GEGE2X01 or MEDS2002 or PCOL2X21 or QBIO2001)] or 12 credit points from (BMED2401 and BMED2405)]
Corequisites ?	None
Prohibitions ?	BCMB3003 or (BCHM3X72 and BCHM3X82)
Assumed knowledge ?	Protein chemistry and biochemistry concepts at 2000-level units
Available to study abroad and exchange students	Yes

Teaching staff

Coordinator	Markus Hofer, markus.hofer@sydney.edu.au
Lecturer(s)	Ann Kwan, ann.kwan@sydney.edu.au
Lecturer(s)	Markus Hofer, markus.hofer@sydney.edu.au
Tutor(s)	Giselle Yeo, giselle.yeo@sydney.edu.au

Assessment

The census date for this unit availability is 2 September 2024

Details
Criteria

Type	Description	Weight	Due	Length
Supervised exam ?	Final exam Final exam incl. theory of prac & theory of lecture components & seminars	55%	Formal exam period	2 hours
Outcomes assessed:
Skills-based evaluation	Additional task experiment 1 Additional task experiment 1. See Canvas for details	5%	Week 04	online questions and/or file upload.
Outcomes assessed:
Tutorial quiz	In semester theory of prac quiz In class online quiz with MCQs and SAQs held during week 9. COMPULSORY	25%	Week 09	30 minutes online incl. file upload.
Outcomes assessed:
Skills-based evaluation	Additional task experiment 2 Additional task experiment 2. See Canvas for details	5%	Week 12	file upload
Outcomes assessed:
Presentation	Presentation for Lay audience Presentation on scientific data aimed at a lay audience	5%	Week 13	5-10 min
Outcomes assessed:
Skills-based evaluation	Lab report of experiment 2 lab report for experiment 2. See Canvas for details	5%	Week 13	200 words plus figures/legends
Outcomes assessed:
= hurdle task ?

Assessment summary

The in semester theory of practical quiz is compulsory. Collectively, all in semester assessments must be passed, that is 22.5 out of 45 possible marks or more must be obtained.

Short scientific paper: Students will evaluate, and discuss their own results in the context of the class results and published literature in the form of a short scientific paper. The paper forms part of the in semester quiz and will be uploaded as a pre-written file. For details see Canvas.
Oral presentation: Students will give a brief oral presentation; details ind instructions will be provided during the course.
Lab reports of experiment 2: The aim of the lab report is to supply a written record or your results including figures and data interpretation. Different aspects of the lab reports may have different deadlines with the full lab report due before the last session of each experiment. For due dates, details and breakdown of partial marks see Canvas. The lab reports are written in Labarchives and contain experimental aim, plan, raw and processed data, figures and legends, sumary of results and discussion points, as well as a brief methods section.
Additional tasks for experiment 1 and 2: The additional tasks cover assumed knowledge and aspects of theory of prac. In addition, experimental design and planning are included. For due dates and details see Canvas.
In semester theory of prac quiz: The quiz will be held in week 9 and attendance is compulsory. It is an online quiz consisting of short answer and multiple choice questions. The quiz will cover the theory of prac for experiment 1 as well as important concepts in experimental molecular biology and biochemistry. In addition, upload of a pre-written short scientific paper will be required (see above). Note if the in-semester quiz is missed, an alternative, written or oral assignment will be given. The alternative assessment will meet the same learning outcomes as the original in-semester quiz. The decision as to the format and details of the replacement will be made by the Unit of Study coordinator.
End of semester exam: The end of semester exam consists of two parts, which will cover the theory of prac and theory of lectures, respectively. If a second replacement exam is required, this exam may be delivered via an alternative assessment method, such as a viva voce (oral exam). The alternative assessment will meet the same learning outcomes as the original exam. The format of the alternative assessment will be determined by the unit coordinator.

Detailed information for each assessment can be found on Canvas

Assessment criteria

The University awards common result grades, set out in the Coursework Policy 2014 (Schedule 1).

As a general guide, a high distinction indicates work of an exceptional standard, a distinction a very high standard, a credit a good standard, and a pass an acceptable standard.

Result name	Mark range	Description
High distinction	85 - 100	Able to write a coherent and flowing report in good English. Using a variety of viewpoints to argue the process for identifying the problem. Excellent discussion of management strategies to manage this problem. References are used wisely and the student shows an ability to critique the literature. Sources included at least three refereed journal articles and these were presented in the correct format in the reference list and using the correct in text citation.
Distinction	75 - 84	Able to write a coherent report in good English. Presented at least two points of view to argue the process for identifying the problem. Good discussion of management strategies to manage this problem. Sources included at least three refereed journal articles and these were presented in the correct format in the reference list and using the correct in text citation.
Credit	65 - 74	Presented a report in good English. Presented at least two points of view to argue the process for identifying the problem. Reasonable discussion of management strategies to manage this problem. Sources included at least two refereed journal articles and these were presented in the correct format in the reference list and using the correct in text citation.
Pass	50 - 64	Presented and report in good English that defined the problem and came to a recommendation. Sources included two refereed journal articles, in a reference list.
Fail	0 - 49	When you don’t meet the learning outcomes of the unit to a satisfactory standard. Presented a report that did not address the problem or was poorly constructed and grammatically incorrect. Did not provide any recommendations. Did not use any refereed journal papers.

For more information see guide to grades.

Late submission

In accordance with University policy, these penalties apply when written work is submitted after 11:59pm on the due date:

Deduction of 5% of the maximum mark for each calendar day after the due date.
After ten calendar days late, a mark of zero will be awarded.

This unit has an exception to the standard University policy or supplementary information has been provided by the unit coordinator. This information is displayed below:

Written assignments submitted late without permission (see Special Considerations: http://sydney.edu.au/students/special-consideration-and-arrangements.html) will incur a late penalty equal to 5% of the maximum awardable mark per day. These deductions will continue for 10 calendar days or until a solution for the assignment is released or marked assignments are returned to other students. At that point the mark awarded will be zero.

Academic integrity

The Current Student website provides information on academic integrity and the resources available to all students. The University expects students and staff to act ethically and honestly and will treat all allegations of academic integrity breaches seriously.

We use similarity detection software to detect potential instances of plagiarism or other forms of academic integrity breach. If such matches indicate evidence of plagiarism or other forms of academic integrity breaches, your teacher is required to report your work for further investigation.

Use of generative artificial intelligence (AI) and automated writing tools

You may only use generative AI and automated writing tools in assessment tasks if you are permitted to by your unit coordinator. If you do use these tools, you must acknowledge this in your work, either in a footnote or an acknowledgement section. The assessment instructions or unit outline will give guidance of the types of tools that are permitted and how the tools should be used.

Your final submitted work must be your own, original work. You must acknowledge any use of generative AI tools that have been used in the assessment, and any material that forms part of your submission must be appropriately referenced. For guidance on how to acknowledge the use of AI, please refer to the AI in Education Canvas site.

The unapproved use of these tools or unacknowledged use will be considered a breach of the Academic Integrity Policy and penalties may apply.

Studiosity is permitted unless otherwise indicated by the unit coordinator. The use of this service must be acknowledged in your submission as detailed on the Learning Hub’s Canvas page.

Outside assessment tasks, generative AI tools may be used to support your learning. The AI in Education Canvas site contains a number of productive ways that students are using AI to improve their learning.

Learning support

Simple extensions

If you encounter a problem submitting your work on time, you may be able to apply for an extension of five calendar days through a simple extension.  The application process will be different depending on the type of assessment and extensions cannot be granted for some assessment types like exams.

Special consideration

If exceptional circumstances mean you can’t complete an assessment, you need consideration for a longer period of time, or if you have essential commitments which impact your performance in an assessment, you may be eligible for special consideration or special arrangements.

Special consideration applications will not be affected by a simple extension application.

Using AI responsibly

Co-created with students, AI in Education includes lots of helpful examples of how students use generative AI tools to support their learning. It explains how generative AI works, the different tools available and how to use them responsibly and productively.

Support for students

The Support for Students Policy 2023 reflects the University’s commitment to supporting students in their academic journey and making the University safe for students. It is important that you read and understand this policy so that you are familiar with the range of support services available to you and understand how to engage with them.

The University uses email as its primary source of communication with students who need support under the Support for Students Policy 2023. Make sure you check your University email regularly and respond to any communications received from the University.

Learning resources and detailed information about weekly assessment and learning activities can be accessed via Canvas. It is essential that you visit your unit of study Canvas site to ensure you are up to date with all of your tasks.

If you are having difficulties completing your studies, or are feeling unsure about your progress, we are here to help. You can access the support services offered by the University at any time:

Support and Services (including health and wellbeing services, financial support and learning support)
Course planning and administration
Meet with an Academic Adviser

Weekly schedule

WK	Topic	Learning activity
Multiple weeks	Lecture Block 1: Stem cells: Brief history of stem cell research; definition of embryonic vs. adult stem cells; potency, plasticity, trans-differentiation; stem cell niche, stem cells and aging, stem cells and cancer; mechanism of pluripotency & self-renewal, reprogramming of somatic cells into pluripotent stem cells, stem cell differentiation, 3D organoids; Practical and therapeutic potentials, embryonic development, disease modelling, drug screening and toxicity	Lecture (4 hr)
	Lecture Block 2A: Cell cycle: Outline and description of the phases of the cell cycle, DNA duplication, telomere biology, ageing; introduction of the molecular components of the cell cycle and their regulators; how to measure cell cycle experimentally (flow cytometry, microscopy, centrifugal elutriation); analysis of the cell cycle using Omics approaches (Proteomics, RNA-Seq); regulation of cell cycle by external factors (mitogens) and DNA mutations. Chromosomal damage affecting cell cycle.	Lecture (4 hr)
	Lecture Block 2B: Mitosis, meiosis and molecular motors: Comparison of mitosis and meiosis; purpose of meiosis, differences in male vs. female organisms; microtubules, kinesin, microtubule based molecular motors; molecular motors in mitosis and meiosis.	Lecture (2 hr)
	Lecture Block 3: Cellular stress and cell death: Forms of cellular stress (oxidative stress, hypoxia, toxins, infection, replication, cell death) and adaptation of metabolism (Warburg effect); cell death to control cell number and fate; extrinsic versus intrinsic pathways of apoptosis; methods for detecting apoptotic cells; the DNA damage response and cell cycle regulation; mechanisms of avoiding apoptosis; Necrosis, necroptosis, pyroptosis and other forms of cell death.	Lecture (4 hr)
	Lecture Block 4A: Protein misfolding diseases of the brain: components of the brain, cells and their function in the CNS, definition of the term “neurodegeneration”; brief revision of protein folding and misfolding. Overview of protein misfolding as a feature in diseases and potential causes; how protein misfolding and/or problem with protein degradation pathways lead to protein aggregation - overview of the history, biological mechanisms and experimental evidence.	Lecture (3 hr)
	Lecture Block 4B: Protein misfolding diseases: Parkinson’s and Huntington’s disease: possibly pathogenic mechanism, experimental evidence (including animal models); Alzheimer’s disease: causes and consequences of protein misfolding, counter mutations, amyloid vaccine, immunotherapy and treatment development; prion diseases: How can a protein can be infectious? Protein aggregation and systemic amyloidosis (e.g. light chain /AL amyloidosis).	Lecture (5 hr)
	Experiment 1: Investigating the effects of drugs on cell proliferation, cell number and cell death. Learning the use of common cell and molecular techniques including cell culture, antibody-based techniques and flow cytometry; data analysis and interpretation with a focus on quantitative and qualitative measurements; write a scientific paper to communicate experimental results effectively.	Practical (12 hr)
	Experiment 2: Design and perform an experiment to measure protein aggregation and critically evaluate results.	Practical (12 hr)
	Research presentations by internal and external invited speakers that extend on lecture content and present new aspects or research related to human diseases.	Seminar (4 hr)
	Presentation of published experimental results with a focus to communicate complex scientific information to a lay audience.	Presentation (2 hr)

Attendance and class requirements

Students must attend a minimum of 10 out of 12 practical sessions, all 4 advanced seminars, the lay talks, the in-semester quiz and the final exam.

To obtain a pass degree you must satisfy the requirements in BOTH the theory and practical components of the course, AND collectively all in semester assignments must be passed, that is 22.5 out of 45 possible marks or more must be obtained.

Study commitment

Typically, there is a minimum expectation of 1.5-2 hours of student effort per week per credit point for units of study offered over a full semester. For a 6 credit point unit, this equates to roughly 120-150 hours of student effort in total.

Learning outcomes

Learning outcomes are what students know, understand and are able to do on completion of a unit of study. They are aligned with the University's graduate qualities and are assessed as part of the curriculum.

Outcomes
Graduate qualities

At the completion of this unit, you should be able to:

LO1. Describe the components involved in the cell cycle and predict how specific gene mutations will affect the cell cycle and cell proliferation.
LO2. Adapt experimental techniques to address a specific question and analyse aspects of the cell cycle and cell proliferation using biochemical assays.
LO3. Design an experimental plan to study aspects of cell proliferation and cell death, and conduct the experiment.
LO4. Explain the processes involved in protein folding and misfolding and evaluate experimental studies in that area.
LO5. Perform and evaluate a biochemical assays to determine protein concentrations in solutions using different approaches.
LO6. Evaluate and communicate experimental data by composing a scientific presentation based on your own experimental results.
LO7. Critically evaluate experimental data.
LO8. Collaborate by working in a small team to solve a scientific problem.
LO9. Obtain and explain the difference between qualitative and quantitative measurements and data.
LO10. Judge validity of data and solve scientific calculations.

Graduate qualities

The graduate qualities are the qualities and skills that all University of Sydney graduates must demonstrate on successful completion of an award course. As a future Sydney graduate, the set of qualities have been designed to equip you for the contemporary world.

GQ1	Depth of disciplinary expertise Deep disciplinary expertise is the ability to integrate and rigorously apply knowledge, understanding and skills of a recognised discipline defined by scholarly activity, as well as familiarity with evolving practice of the discipline.
GQ2	Critical thinking and problem solving Critical thinking and problem solving are the questioning of ideas, evidence and assumptions in order to propose and evaluate hypotheses or alternative arguments before formulating a conclusion or a solution to an identified problem.
GQ3	Oral and written communication Effective communication, in both oral and written form, is the clear exchange of meaning in a manner that is appropriate to audience and context.
GQ4	Information and digital literacy Information and digital literacy is the ability to locate, interpret, evaluate, manage, adapt, integrate, create and convey information using appropriate resources, tools and strategies.
GQ5	Inventiveness Generating novel ideas and solutions.
GQ6	Cultural competence Cultural Competence is the ability to actively, ethically, respectfully, and successfully engage across and between cultures. In the Australian context, this includes and celebrates Aboriginal and Torres Strait Islander cultures, knowledge systems, and a mature understanding of contemporary issues.
GQ7	Interdisciplinary effectiveness Interdisciplinary effectiveness is the integration and synthesis of multiple viewpoints and practices, working effectively across disciplinary boundaries.
GQ8	Integrated professional, ethical, and personal identity An integrated professional, ethical and personal identity is understanding the interaction between one’s personal and professional selves in an ethical context.
GQ9	Influence Engaging others in a process, idea or vision.

Outcome map

Learning outcomes	Graduate qualities
Learning outcomes

Responding to student feedback

This section outlines changes made to this unit following staff and student reviews.

This course will be offered as a face-to-face unit only. Based on student feedback, some adjustments on the format and due dates/times for assignments have been made. These have been approved by the relevant School and Faculty committees.

Additional information

More information can be found on Canvas and/or will be provided in class.

Additional costs

There are no additional costs for this unit.

Site visit guidelines

There are no site visit guidelines for this unit.

Work, health and safety

Personal and communal safety is of the highest importance. Students must familiarise themselves with and observe the safety procedures outlined in the Introduction section of the Lab Manual and the WHS Guidelines for Undergraduate Teaching of the School of Life and Environmental Sciences, which can be found on the Canvas site. Additional WHS documents including Risk Assessments, Safe Work Procedures and Safety Data Sheets are deposited on LabArchives.

Students with health concerns and/or relevant health conditions should discuss these with the Unit of Study Coordinator.

All students are required to bring a suitable lab coat and safety glasses or goggles to all practical classes. Appropriate footwear (enclosed and made of non-adsorbent material) must be worn during practical classes.

Disclaimer

The University reserves the right to amend units of study or no longer offer certain units, including where there are low enrolment numbers.

To help you understand common terms that we use at the University, we offer an online glossary.

Current students

Overview

Overview

Unit details and rules

Teaching staff

Assessment

Assessment

Assessment summary

Assessment criteria

Late submission

Academic integrity

Learning support

Learning support

Simple extensions

Special consideration

Using AI responsibly

Support for students

Weekly schedule

Weekly schedule

Attendance and class requirements

Study commitment

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Additional costs

Site visit guidelines

Work, health and safety

Disclaimer

On this page

Useful links

Media

Student links

About us

Connect

Current students

BCMB3903: Biochemistry of Human Disease (Advanced)

Semester 2, 2024 [Normal day] - Camperdown/Darlington, Sydney

Overview

Overview

Unit details and rules

Teaching staff

Assessment

Assessment

Assessment summary

Assessment criteria

Late submission

Academic integrity

Learning support

Learning support

Simple extensions

Special consideration

Using AI responsibly

Support for students

Weekly schedule

Weekly schedule

Attendance and class requirements

Study commitment

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Additional costs

Site visit guidelines

Work, health and safety

Disclaimer

On this page

Useful links

Media

Student links

About us

Connect