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Unit outline_

BCMB2901: Biochemistry and Molecular Biology (Advanced)

Semester 1, 2020 [Normal day] - Camperdown/Darlington, Sydney

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 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. Then we will explore how genetic information is regulated in eukaryotes, including replication, transcription and translation, and molecular aspects of the cell cycle, mitosis and meiosis. 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 dedicated advanced tutorial sessions. This material will be assessed by creative student-centered activities supported by eLearning platforms.

Unit details and rules

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

None

Available to study abroad and exchange students

Yes

Teaching staff

Coordinator Giselle Yeo, giselle.yeo@sydney.edu.au
Laboratory supervisor(s) Alice Huang, alice.huang@sydney.edu.au
Lecturer(s) Gareth Denyer, gareth.denyer@sydney.edu.au
Giselle Yeo, giselle.yeo@sydney.edu.au
Type Description Weight Due Length
Final exam Take home exam for Theory Lecture 8-28
Canvas timed exam
30% Formal exam period 2 hours
Outcomes assessed: LO1 LO2 LO3 LO4 LO5 LO6 LO7
Skills-based evaluation Electronic laboratory notebook (LabArchives)
Data management, contextual narrative, data analysis and interpretation.
23% Multiple weeks As required
Outcomes assessed: LO8 LO11 LO10 LO9
Assignment PeerWise tutorial assessment
Exploration of theory concepts through question authoring
10% Multiple weeks As required
Outcomes assessed: LO1 LO2 LO3 LO4 LO5 LO6 LO7
Assignment Calculations assignment
Basic lab calculations
12% Week 09 As required
Outcomes assessed: LO8 LO10
Assignment Cloning Assignment
Presentation of practical results and literature research
5% Week 10 As required
Outcomes assessed: LO8 LO11 LO10 LO9
Skills-based evaluation ELMA design assay
Writing plans, analysing results
10% Week 13 As required
Outcomes assessed: LO8 LO11 LO10 LO9
Final exam Take home exam for Theory Lecture 1-7
Take home test/CANVAS timed open book
10% Week 13 1 hour
Outcomes assessed: LO4 LO7 LO6 LO5

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.

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 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
Laboratory Skills: Data management and calculations Tutorial (1 hr) LO9 LO10 LO11
Week 02 1. Applications to molecular biology; 2. The Eukaryotic genome; 3. Prokaryotic replication Lecture (3 hr) LO4 LO5 LO7
Introductory techniques and cloning ligation Practical (4 hr) LO8 LO10
Week 03 1. Eukaryotic replication; 2. Prokaryotic transcription; 3. Eukaryotic transcription Lecture (3 hr) LO4 LO5 LO6
Genome organisation and synthesis Tutorial (1 hr) LO4 LO5
Week 04 1. Post-transcriptional processing; 2. Translation in prokaryotes; 3. Traslation in eukaryotes Lecture (3 hr) LO6
DNA Fingerprinting 1 and cloning transformation Practical (4 hr) LO7 LO8 LO10
Week 05 1. Translational regulation; 2. Molecular biology techniques Lecture (3 hr) LO6 LO7
Flow of information inside cells from DNA to action molecules Tutorial (1 hr) LO5 LO6 LO7
Week 06 1. Training for data analysis assessment; 2. Principles of energy balance and fuel oxidation; 3. Oxidative phosphorylation Lecture (3 hr) LO1 LO2 LO10
DNA fingerprinting 2 and plasmid isolation Practical (4 hr) LO7 LO8 LO10
Week 07 1. Oxidative phosphorylation; 2. Central catabolic pathways Lecture (3 hr) LO1 LO2
Cloning techniques and overview of molecular biology Tutorial (1 hr) LO4 LO5 LO6 LO7
Week 08 1. Central catabolic pathways; 2. Integration of catabolism Lecture (3 hr) LO1 LO2
Plasmid identification Practical (4 hr) LO7 LO8 LO10
Week 09 Integration of catabolism Lecture (3 hr) LO1 LO2
Aspects of catabolism Tutorial (1 hr) LO1 LO2
Week 10 Anabolic strategies Lecture (3 hr) LO1 LO2
Enzyme-linked Metabolite Assay (ELMA) Practical (4 hr) LO8 LO9 LO10
Week 11 Anabolic strategies Lecture (3 hr) LO1 LO2
Aspects of anabolism Tutorial (1 hr) LO1 LO2 LO11
Week 12 1. Protein and nucleotide metabolism; 2. Extrapolations: Type 1 diabetes Lecture (3 hr) LO1 LO2 LO3 LO11
Design assay Practical (4 hr) LO8 LO9 LO10

Attendance and class requirements

Due to the exceptional circumstances caused by the COVID-19 pandemic, attendance requirements for this unit of study have been amended. Where online tutorials/workshops/virtual laboratories have been scheduled, students should make every effort to attend and participate at the scheduled time. Penalties will not be applied if technical issues, etc. prevent attendance at a specific online class. In that case, students should discuss the problem with the coordinator, and attend another session, if 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.

Required readings

All readings for this unit can be accessed through the Library eReserve, available on Canvas.

  • Biochemistry by Berg, Tymoczko, Gatto and Stryer, 8th Edition. Typically known as “Stryer”.

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.

No changes have been made since this unit was last offered

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.