Outline

Overview

A single human cell contains billions of protein molecules that are constantly in motion. Why so many? What are they doing? And, how are they doing it? In simple terms, proteins define the function of and drive almost every process within cells. In this unit of study you will learn about the biochemistry of proteins in their natural environment - within cells - with a focus on eukaryotes including plant and other cell types. You will discover the dynamic interplay within and between proteins and other cellular components and how the physical properties of proteins dictate function. You will discover how proteins are compartmentalized, modified, folded, transported in and between cells, the mechanisms by which proteins regulate biological activities, interact and transport molecules across membranes, and how mutations in proteins can lead to pathological consequences. Our practicals, other guided and online learning sessions will introduce you to a wide range of currently utilised techniques for protein biochemistry ranging from protein visualization, quantification, purification and enzymatic activity, to in silico studies and cellular targeting experiments. By the end of this unit you will be equipped with foundational skills and knowledge to support your studies in the cellular and molecular biosciences.

Unit details and rules

Academic unit	Life and Environmental Sciences Academic Operations
Credit points	6
Prerequisites ?	6cp of (BIOL1XX7 or MBLG1XXX) and 6cp of (CHEM1XX1 or CHEM1903)
Corequisites ?	None
Prohibitions ?	BCHM2071 or BCHM2971 or BCMB2902
Assumed knowledge ?	None
Available to study abroad and exchange students	Yes

Teaching staff

Coordinator	Sandro Fernandes Ataide, sandro.ataide@sydney.edu.au

Type	Description	Weight	Due	Length
Final exam (Record+)	Final exam Invigilated - 48 MCQ and 6 SAQ	50%	Formal exam period	2 hours
Outcomes assessed:
Assignment	Project Report their online experiments	5%	Week 06 Due date: 11 Sep 2022 at 23:59	2 weeks
Outcomes assessed:
Small test	Quiz 1 Quiz	5%	Week 07 Due date: 18 Sep 2022 at 23:59	20MCQ - 90 min
Outcomes assessed:
Assignment	Project/presentation perform an online VR experiment	5%	Week 11 Due date: 23 Oct 2022 at 23:59	4 weeks
Outcomes assessed:
Small test	Quiz 2 Quiz	5%	Week 12 Due date: 30 Oct 2022 at 23:59	20MCQ - 90 min
Outcomes assessed:
Small continuous assessment	Post-lab work report ( x7) Experiment report	30%	Weekly	during prac or 1 week after prac
Outcomes assessed:
= hurdle task ? = Type B final exam ?

Assessment summary

-Post-Lab work: This assignment requires you to write a prac report with the data that you have obtained. It will include the data analysis, calculation and interpretations of the data. Some will be short reports and some longer reports depending on the prac. All the pracs have a pre-prac quiz consisting of 3 MCQ questions to be completed before the pracs.

-Quizzes: The quizzes consists of 20 MCQs covering the material from lectures and practical classes.

-Project 1: This assignemt requries you to perfomr some bioninformatic analysis online and write a report with your findings integrating information form Lectures and Practical classes.

-Project/presentation: This assignment requires you to perfomern a VR prac online and undertake their quiz. There will be a discussion of your VR experiment during a tutorial.

Final exam: The exam will cover all material in the unit from both lectures and practical classes. The exam will have a mixture of multiple choice questions ( 24MCQ from lectures and 24 MCQs from practical classes) and 6 short answer questions from Lectures.

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.

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

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.

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:

deduction of 5% per day for late submission

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
Week 01	1. Introduction lecture; 2. The sugar story; 3. Proteins: introduction to structure and function	Lecture (1 hr)
Week 01	1. Structure of proteins in detail; 2. Protein folding: primary, secondary, tertiary and quaternary structures, forces involved in the folding; 3. Ramachandran plot; diseases relating to misfolding of proteins	Lecture (1 hr)
Week 02	1. Introduction to globular and fibrous proteins; 2. Determining the sequence of a peptide; 3. Evolutionary relationships from protein sequences	Lecture (1 hr)
	1. Protein synthesis of housekeeping genes and protein sorting; 2. Protein sorting pathways; 3. Soluble protein stays in cytosol or gets transported to other cellular compartments	Lecture (1 hr)
	Dry lab 1 protein visualization and modeling - ONLINE	Practical (3 hr)
Week 03	1. Cell membranes; 2. Properties & functions of membranes; component parts, curvature, cholesterol, lipid rafts, diffusion through versus flipping across	Lecture (1 hr)
	1. Integral membrane proteins, peripheral, amphitropic; 2. TM helical and B- proteins; 3. Directionality; hydrophobicity & charge distribution; 4. Lipid anchors and glycosylation; interaction with lipids; 5. Working with membrane proteins	Lecture (1 hr)
	Dry lab - pigments extractions and identification - Calculations - ONLINE	Practical (3 hr)
Week 04	Membrane permeability, membrane potential, membrane transport, permeases, carriers – passive, primary active and secondary active	Lecture (1 hr)
	1. Channels; 2. Ion channels size/charge selectivity; 3. Gating: ligand, voltage, mechanosensitive, light sensitive; 4. Action potentials – ligand and voltage gates channel working in series	Lecture (1 hr)
	Dry lab 2 principles of protein purification - protein alignment/ secondary structure prediction (project)/ ONLINE	Practical (3 hr)
Week 05	1. Protein modulation of membranes; 2. Transport vesicles and SNARE system, Clathrin and vesicle formation; 3. Dynamin and kinesin intermediate filaments	Lecture (1 hr)
	1. Stages of secretory pathways – ER and GOLGI; 2. Targeting to organelles – mitochondria and chloroplasts; 3. Lysosomes and peroxisomes – functions, storage and trafficking	Lecture (1 hr)
	Wet lab - protein purification and SDS-PAGE (Part 1) - Face-to-Face/ ONLINE	Practical (3 hr)
Week 06	1. Nuclear transport – nuclear import and export, nuclear pore complex; 2. Nuclear localisation sequences; 3. Importins, the RAN cycle	Lecture (1 hr)
	1. Nuclear hormone receptors (STATS) in to trigger transcription; 2. Export of RNA; 3. Nuclear bodies	Lecture (1 hr)
	Wet lab - protein purification and native gel (Part 2) - Face-to-Face/ ONLINE	Practical (3 hr)
Week 07	1. Enzymes are catalysts; the transition state; 2. Enzyme classification; 3. Cofactors; 4. Rate constants, free energy changes, activation energy, binding energy; 5. Rate-limiting steps in catalysis; 6. Reaction coordinate diagrams; 7. Rate enhancements; 8. Weak interactions between enzyme and substrate	Lecture (1 hr)
	1. The enzyme-substrate (ES) complex; 2. Enzyme specificity and catalysis; 3. Physical and thermodynamic factors affecting activation energy; 4. Induced fit; 5. General enzyme mechanisms; mechanisms of hexokinase, enolase, lysozyme; 6. Enzyme mutants	Lecture (1 hr)
	Dry lab 3 VR project (Kinetics) / Quiz 1 - ONLINE	Practical (3 hr)
Week 08	1. Michaelis Menten kinetics and the MM equation; 2. Substrate-to-enzyme ratio; 3. Initial velocity in enzyme kinetics; 4. Enzyme saturation; 5. Pre-steady state and steady state; 6. The Lineweaver-Burk plot; 7. Limitations of Michaelis-Menten kinetics; 8. Turnover number	Lecture (1 hr)
	1. Reversible/ irreversible inhibitors and kinetics; 2. Competitive; 3. Non-competitive and mixed inhibition; 4. Enzyme inhibitors in identifying reaction mechanisms; 5. Effects of inhibition on the Michaelis-Menten constant and maximum velocity	Lecture (1 hr)
	Wet lab - methods of protein determination and quantification - Face-to-Face/ ONLINE	Practical (3 hr)
Week 09	1. Plant Biochemistry -differences in cell structure; 2. Chloroplasts; 3. Photosynthesis - the light reactions/Calvin cycle	Lecture (1 hr)
	Photosynthesis – the dark cycle	Lecture (1 hr)
	Wet lab - enzyme kinetics and analysis - Face-to-Face / ONLINE	Practical (3 hr)
Week 10	Nutrient assimilation – nitrogen sulfur	Lecture (1 hr)
	1. Secondary metabolites; 2. Plant hormones	Lecture (1 hr)
	Wet lab - mechanism of enzymes - chymotrypsin - Face-to-Face / ONLINE	Practical (3 hr)
Week 11	1. Introduction to post-translational modifications; 2. How many gene-products / proteins does the genome make? 3. Diversity in protein structure / function; 4. Major classes of PTM, including phosphorylation, glycosylation, acetylation, redox modifications and disulfide bonds, deamidation	Lecture (1 hr)
	1. Cell signaling by phosphorylation; 2. Concentrating on the insulin signaling pathway to demonstrate how a stimulus (signal) is transmitted by kinase-mediated phosphorylation and phosphatase mediated de-phosphorylation to result in changes to gene expression and response to the stimulus	Lecture (1 hr)
	Dry lab 4 tutorial / Review - ONLINE	Independent study (3 hr)
Week 12	1. Protein glycosylation I; 2. Why are glycans important? Classes of glycan? Glycan biosynthesis and structure of N-linked glycans; 3. Functions of glycosylation in health and disease	Lecture (1 hr)
	1. Disulfide bonds and redox modifications of proteins; 2. Formation of disulfide bonds and their role in protein structure; 3. Oxidative stress and oxidative modifications of proteins; 4. Diversity of redox modifications; 5. Function of redox modifications; 6. Redox signaling	Lecture (1 hr)
	1. Dry lab 5- Quiz 2 - ONLINE	Practical (3 hr)
Week 13	Review	Lecture (1 hr)

Attendance and class requirements

You must pass the theory and practical components of the course to pass the unit of study. To pass the practical component, you must complete 6 out of the 7 Labs and their corresponding Lab reports (part of the reports are due during the Labs). Make-up sessions will be available for students with special consideration or misadventure.

Referencing guide: if you use someone’s actual words you must use quotation marks as well as an appropriate reference. If you use someone’s ideas, formulas, methods, evidence, tables or images you must use a reference. You must not present someone’s artistic work, musical creation, programming code or any other form of intellectual property as your own. If referring to any of these, you must always present them as the work of their creator and reference in an appropriate way.

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

Lehninger Principles of Biochemistry 7th edition, by Nelson & Cox
Molecular Cell Biology 8th edition, by Lodish
Any other Biochemistry and Molecular Biology textbook can be referred to in the course.

Any one of these reference textbooks would be useful to those wishing to continue with Biochemistry and Molecular Biology in second semester and beyond.

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. Outline the basic principles and describe in detail the constituent elements of protein structure; attribute these properties to protein and cellular function.
LO2. Identify the different types of compartments and other types of organisation within cells and describe the intrinsic properties and specific functions of these organelles and other compartments.
LO3. Discuss the movement of proteins inside the cell. Evaluate how these dynamics are achieved and why they are important for cellular function.
LO4. Identify the various ways in which proteins can be modified after translation, describe how these modifications are achieved and evaluate how they affect the physical properties of proteins.
LO5. Classify the types of communication necessary for cells; differentiate the different ways by which molecules are transported within and between cells.
LO6. Compare and evaluate the similarities and differences in biochemical processes between plants and other eukaryotes.
LO7. Explain, with examples, the difference between a qualitative and a quantitative measurement; determine which of the different technique should be used, and implement methods to visualize and analyse the structure and function of proteins, in an accurate and reproducible manner.
LO8. Adapt, develop and trouble-shoot experimental procedures for novel contexts and requirements.
LO9. Assess the quality of data, interpret and draw conclusions from data obtained in the laboratory.
LO10. 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
Learning outcomes

Responding to student feedback

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

Pracs and tutorials have been rearranged and due dates for lab reports changed accordingly

Additional information

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.

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

Required readings

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Work, health and safety

Disclaimer

On this page

Useful links

Media

Student links

About us

Connect

Current students

BCMB2002: Proteins in Cells

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

Required readings

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Work, health and safety

Disclaimer

On this page

Useful links

Media

Student links

About us

Connect