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.

Unit details and rules

Academic unit	Life and Environmental Sciences Academic Operations
Credit points	6
Prerequisites ?	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 ?	BCMB3903 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)	Markus Hofer, markus.hofer@sydney.edu.au
	Giselle Yeo, giselle.yeo@sydney.edu.au
	Ann Kwan, ann.kwan@sydney.edu.au

Type	Description	Weight	Due	Length
Final exam (Record+)	Final exam Final exam includes theory of prac and theory of lecture components	55%	Formal exam period	2 hours
Outcomes assessed:
Skills-based evaluation	Summary of experiment 1 Online task + descr. of results from exp1. Due at start/end of session 4.	7%	Week 05	200 w plus figures/legends + online;
Outcomes assessed:
Skills-based evaluation	Summary of experiment 2 Online task + Descr. of results from exp2. Due at start/end of session 6.	7%	Week 07	200 words plus figures/legends + online
Outcomes assessed:
Tutorial quiz	In semester theory of prac quiz In class online quiz with MCQs and SAQs held during week 9.	10%	Week 09	30 minutes
Outcomes assessed:
Assignment	Short scientific paper - discussion Online questions with ability to pre-write answers	14%	Week 10 Due date: 10 Oct 2022 at 09:00	500 Words
Outcomes assessed:
Skills-based evaluation	Summary of experiment 3 Online task + Descr. of results from exp.3. Due w12 / end of last session.	7%	Week 13	200 words plus figures/legends + online
Outcomes assessed:
= hurdle task ? = Type B final exam ?

Assessment summary

All assessments are compulsory and failure to attend, attempt, or submit and pass them, will result in the award of an AF grade.

Discussion for experiment 1: Students will evaluate and discuss their own results in the context of the class results and published literature. The discussion consists of multiple parts and will be ~ 500 words in length.
Summaries of experiments 1, 2 and 3: these are due at the end of the last laboratory session for the particular experiment. The summaries are written in Labarchives and contain experimental aim, plan, raw and processed data, figures and legends as well as a brief methods section. Additional assignments that cover the theory and content of the respective experiments are included.
In semester theory of prac quiz: The quiz will be held during the normal practical classes either in week 7 or 9. It is an online quiz consisting of short answer and multiple choice questions. The quiz will cover the theory of prac as well as important concepts in experimental molecular biology and biochemistry. 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

Result name	Mark range	Description
High distinction	85 - 100	Awarded when you demonstrate the learning outcomes for the unit at an exceptional standard, as defined by grade descriptors or exemplars outlined by your faculty or school.
Distinction	75 - 84	Awarded when you demonstrate the learning outcomes for the unit at a very high standard, as defined by grade descriptors or exemplars outlined by your faculty or school.
Credit	65 - 74	Awarded when you demonstrate the learning outcomes for the unit at a good standard, as defined by grade descriptors or exemplars outlined by your faculty or school.
Pass	50 - 64	Awarded when you demonstrate the learning outcomes for the unit at an acceptable standard, as defined by grade descriptors or exemplars outlined by your faculty or school.
Fail	0 - 49	When you don’t meet the learning outcomes of the unit to a satisfactory standard.

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. The summaries for experiments 1, 2 and 3 must be submitted at the end of the last laboratory session for the particular experiment and the associated assignments by the due date.

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.

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 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: Use of ELISAs to quantify soluble molecules in complex solutions. Design and perform experiments to measure the amount of specific molecules in biological solutions; analysis of the data and critical evaluation of the results; comparison of different approaches and their validity.	Practical (6 hr)
	Experiment 3: Measure protein aggregation using different photometrical techniques; determine protective and enhancing mechanisms on protein aggregation; design and perform an experiment to measure protein aggregation and critically evaluate results.	Practical (12 hr)

Attendance and class requirements

Students are required to attend all practical classes. Any absences must be documented through the University’s Student Administration Services (SAS). Students must complete a minimum of 80 % of the practical sessions in order to fulfil the attendance requirements independent of Special Consideration.

To obtain a pass degree you must sastisfy the requirments in BOTH the theory and practical components of the course, AND submit all assignments at a pass level.

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 paper 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.

Based on student feedback and due to the easing pandemic, this course will be primarily offered as a face-to-face unit. Where remote learning is/will be required, we will attempt to provide online tools and interactive sessions as done in previous years.

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.

For this Unit of Study, you are required to read a Safety Awareness Statement. This will be available from Canvas and must be completed before you can access the full Canvas site.

All students are required to bring a suitable lab coat and safety glasses or goggles to all 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

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

BCMB3003: Biochemistry of Human Disease

Semester 2, 2022 [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

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