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Unit of study_

BCMB2901: Biochemistry and Molecular Biology (Advanced)

Semester 1, 2022 [Normal day] - Remote

Without cells, life as we know it would not exist. These dynamic assemblies, packed with biological molecules are constantly in action. But how do cells work? Why is the food that you eat so important for cellular function? How is information transmitted from generation to generation? And, what happens as a result of disease or genetic mutation? In this unit of study, you will learn how cells work at the molecular level, with an emphasis on human biochemistry and molecular biology. We will focus initially on how genetic information is regulated in eukaryotes, including replication, transcription and translation, and molecular aspects of the cell cycle, mitosis and meiosis. Then we will explore cellular metabolism and how cells extract and store energy from fuels like fats and carbohydrates, how the use of fuels is modulated in response to exercise, starvation and disease, and how other key metabolites are processed. The advanced laboratory component will provide students with an authentic research laboratory experience while in the theory component, current research topics will be presented in a problem-based format through tutorial sessions. This material will be assessed by creative student-centered activities supported by eLearning platforms.

Unit details and rules

Unit code BCMB2901
Academic unit Life and Environmental Sciences Academic Operations
Credit points 6
Prohibitions
? 
BCHM2072 or BCHM2972 or MBLG2071 or MBLG2971 or BMED2405 or BCMB2001 or MEDS2003
Prerequisites
? 
A mark of at least 70 from (BIOL1XX7 or MBLG1XX1) and (CHEM1XX1 or CHEM1903)
Corequisites
? 
None
Assumed knowledge
? 

None

Available to study abroad and exchange students

Yes

Teaching staff

Coordinator Giselle Yeo, giselle.yeo@sydney.edu.au
Lecturer(s) Keng Kwang Jason Low, jason.low@sydney.edu.au
Matthew Clemson, matthew.clemson@sydney.edu.au
Giselle Yeo, giselle.yeo@sydney.edu.au
Alice Huang, alice.huang@sydney.edu.au
Type Description Weight Due Length
Final exam (Record+) Type B final exam Final exam
Final exam for metabolism lectures and theory of practical
25% Formal exam period 1.5 hours
Outcomes assessed: LO1 LO2 LO3 LO8 LO9 LO10 LO11
Skills-based evaluation Electronic laboratory notebook (LabArchives)
Data analysis and interpretation, laboratory calculations, assay design.
30% Multiple weeks Notebooks completed after each practical
Outcomes assessed: LO7 LO11 LO10 LO9 LO8
Tutorial quiz Lecture revision quiz
Short multiple-choice quiz related to lecture concepts
5% Week 03
Due date: 11 Mar 2022 at 23:59

Closing date: 11 Mar 2022
30 minute quiz
Outcomes assessed: LO4 LO6 LO5
In-semester test (Record+) Type B in-semester exam In-semester test
In-semester test for molecular biology lectures and theory of prac
25% Week 07
Due date: 08 Apr 2022 at 10:00
1.5 hours
Outcomes assessed: LO8 LO9 LO10 LO11 LO4 LO5 LO6 LO7
Assignment Cloning presentation
Recorded presentation about new cloning techniques
10% Week 09
Due date: 01 May 2022 at 23:59

Closing date: 01 May 2022
Five-minute video
Outcomes assessed: LO7 LO11
Tutorial quiz Lecture revision quiz
Short multiple-choice quiz related to lecture concepts
5% Week 10
Due date: 06 May 2022 at 23:59

Closing date: 06 May 2022
30 minute quiz
Outcomes assessed: LO1 LO3 LO2
Type B final exam = Type B final exam ?
Type B in-semester exam = Type B in-semester exam ?

Assessment summary

Detailed information of the contribution of each assessment task to the final mark can be found on Canvas. 

It should be appreciated that a pass mark in both the theory and the practical components of the course are required to achieve a passing grade overall.

Electronic Laboratory Notebook (ELN): One write-up for each of the four practical classes, and a final assessment in assay design in week 12. The write-ups need to be completed 7 days after the practical session.

Revision Quizzes: Multiple choice questions based on the lecture material. The first quiz will be for molecular biology lectures and the second quiz will be for metabolism lectures.

In-semester test: This will cover all molecular biology material from lectures and theory of practical from the first two practical classes. There multiple choice and short answer questions.

Cloning Presentation (BCMB2901): This will involve presenting a 5-minute video about a cloning technique.

Final Exam: This will cover all metabolism material from lectures and theory of practical from the last two practical classes. There multiple choice and short answer questions.

Final exam: This assessment is compulsory and failure to attend, attempt, or submit will result in the award of an AF grade.

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.

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

Mastery of topics showing extensive integration and ability to transfer knowledge to novel contexts; treatment of tasks shows an advanced synthesis of ideas; demonstration of initiative, complex understanding and analysis; work is very well presented; all criteria addressed and learning outcomes achieved to an outstanding level

Distinction

75 - 84

Excellent achievement, consistent evidence of deep understanding and application of knowledge in biochemistry; treatment of tasks shows advanced understanding of topics; demonstration of initiative, complex understanding and analysis; work is well-presented; all criteria addressed and learning outcomes achieved to a superior level

Credit

65 - 74

Confident in explaining biochemistry processes, with evidence of solid understanding and achievement; occasional lapses indicative of unresolved issues; treatment of tasks show a good understanding of topic; work is well-presented with a minimum of errors; all criteria addressed and learning outcomes achieved to a high level

Pass

50 - 64

Satisfactory level of engagement with and understanding of topic; some inconsistencies in understanding and knowledge of biochemistry; work is adequately presented, with some errors or omissions, most criteria addressed and learning outcomes achieved to an adequate level

Fail

0 - 49

Unsatisfactory achievement and engagement with the biochemistry discipline; inadequate understanding or fundamental misunderstanding of topics; most criteria and learning outcomes not clearly or adequately addressed or achieved; lack of effort/involvement in the unit

For more information see sydney.edu.au/students/guide-to-grades.

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.

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.

You may only use artificial intelligence and writing assistance tools in assessment tasks if you are permitted to by your unit coordinator, and if you do use them, you must also acknowledge this in your work, either in a footnote or an acknowledgement section.

Studiosity is permitted for postgraduate units unless otherwise indicated by the unit coordinator. The use of this service must be acknowledged in your submission.

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.

WK Topic Learning activity Learning outcomes
Week 01 1. Introduction; 2. Nucleic acid structure; 3. Prokaryotic replication Lecture (3 hr) LO4 LO5
Introduction to labs Tutorial (1 hr) LO7 LO10
Week 02 1. Eukaryotic replication; 2. DNA synthesis in lab; 3. Eukaryotic genome Lecture (3 hr) LO4 LO5 LO7
1. Genotyping PCR; 2. Cloning ligation Practical (4 hr) LO7 LO8 LO9 LO10
Week 03 1. Prokaryotic transcription; 2. Eukaryotic transcription; 3. Post-transcriptional processing Lecture (3 hr) LO4 LO5 LO6
1. Genotyping PCR; 2. Cloning Ligation Tutorial (1 hr) LO7 LO8 LO9 LO10
Week 04 1. Translation in prokaryotes; 2. Translation in eukaryotes; 3. Translational regulation Lecture (3 hr) LO6
1. Electrophoresis of amplicons; 2. Cloning transformation Practical (4 hr) LO7 LO8 LO9 LO10
Week 05 1. Molecular biology techniques part 1; 2. Molecular biology techniques part 2 Lecture (3 hr) LO6 LO7
1. Electrophoresis of amplicons; 2. Cloning transformation Tutorial (1 hr) LO7 LO8 LO9 LO10
Week 08 1. Introduction to Metabolism 2. Carbohydrate Catabolism and Storage Lecture (2 hr) LO1 LO2
1. Spectrophotometry; 2. Cloning - plasmid isolation and digest Practical (4 hr) LO7 LO8 LO9 LO10
Week 09 1. Carbohydrate Catabolism and Storage II 2. Gluconeogenesis Lecture (2 hr) LO1 LO2
1. Spectrophotometry; 2. Cloning - plasmid isolation and digest Tutorial (1 hr) LO7 LO8 LO9 LO10
Week 10 1. Krebs Cycle 2. Respiratory Chain 3. Oxidative Phosphorylation Lecture (3 hr) LO1 LO2
1. Enzyme-linked Metabolite Assay (ELMA); 2. Cloning - plasmid digest gel Practical (4 hr) LO7 LO8 LO9 LO10
Week 11 1. Fat Catabolism and Storage 2. Fat Catabolism and Storage II 3. Central Control of Metabolism Lecture (3 hr) LO1 LO2
1. Enzyme-linked Metabolite Assay (ELMA); 2. Cloning - plasmid digest gel Tutorial (1 hr) LO7 LO8 LO9 LO10
Week 12 1. Tissue Specific Metabolism 2. Fuel Supply During Exercise 3. Fuel Supply During Fasting Lecture (3 hr) LO1 LO2 LO3
Design assay Practical (4 hr) LO8 LO9 LO10
Week 13 1. Protein and Nucleotide Metabolism 2. Integration of Metabolism 3. Revision Lecture (3 hr) LO1 LO2 LO3

Attendance and class requirements

All lectures, practicals and tutorials are delivered live. Attendance for all practicals and tutorials is compulsory. Lecture attendance is optional. All lectures will be recorded and made available.

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 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.

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

  • LO1. describe in detail the main anabolic and catabolic processes in the cell and discuss how variations in energy demand and supply affect these processes
  • LO2. compare and contrast the integration of anabolic and catabolic processes in the cells and predict how perturbations to these processes, including fuel selection and genetic mutation, affect the cell and whole organism
  • LO3. summarise the catabolic and anabolic fates of dietary nitrogen and predict how the synthesis and degradation of nitrogenous biopolymers are affected in contexts such as starvation, diabetes and cancer
  • LO4. describe the complexity of the eukaryotic genome and its structure in detail and identify the key constituent elements
  • LO5. outline the specific processes by which genetic information is transmitted from one generation to the next and analyse the flow of this information within the cell
  • LO6. describe and evaluate the steps involved in gene transcription and translation and evaluate the different ways by which gene expression can be regulated
  • LO7. evaluate the main concepts and power of modern molecular biology techniques and select the appropriate technique for specific applications in life science and medical research
  • LO8. explain, with examples, the difference between qualitative and quantitative measurements; obtain quantitative measurements of metabolite concentrations and enzyme activities, in an accurate and reproducible manner
  • LO9. adapt, develop and trouble-shoot recognised procedures for novel contexts and requirements
  • LO10. assess the quality of, interpret and draw conclusions from data obtained in the laboratory
  • LO11. summarise and identify the key points from topical biochemical data from a number of published sources; synthesise and communicate the findings.

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
GQ1 GQ2 GQ3 GQ4 GQ5 GQ6 GQ7 GQ8 GQ9

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

In response to student feedback: 1. the number of assessments has been reduced; 2. the tutorials support the practical assessments; 3. the molecular biology and metabolism components of the unit will be assessed separately.

To achieve an overall pass mark, students are expected to pass both the theory and practical components of the course.

Work, health and safety

We are governed by the Work Health and Safety Act 2011, Work Health and Safety Regulation 2011 and Codes of Practice. Penalties for non-compliance have increased. Everyone has a responsibility for health and safety at work. The University’s Work Health and Safety policy explains the responsibilities and expectations of workers and others, and the procedures for managing WHS risks associated with University activities.

General Laboratory Safety Rules

  • No eating or drinking is allowed in any laboratory under any circumstances
  • A laboratory coat and closed-toe shoes are mandatory
  • Follow safety instructions in your manual and posted in laboratories
  • In case of fire, follow instructions posted outside the laboratory door
  • First aid kits, eye wash and fire extinguishers are located in or immediately outside each laboratory
  • As a precautionary measure, it is recommended that you have a current tetanus immunisation. This can be obtained from University Health Service: unihealth.usyd.edu.au

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.