BTEC8007
Protein Biotechnology
TOPIC INFORMATION 2018
CONTENTS
Syllabus…………………………………………………………………………………………………………… 1
Educational Aims of the Topic …………………………………………………………………………… 1
Expected Learning Outcomes of the Topic ………………………………………………………….. 2
Topic Content…………………………………………………………………………………………………… 2
Teaching Team…………………………………………………………………………………………………. 3
Topic Schedule…………………………………………………………………………………………………. 3
Textbooks & Resources …………………………………………………………………………………….. 4
Assessment………………………………………………………………………………………………………. 6
Assignment 1: Answer to 16 Questions and Class Instruction…………………………….. 7
Assignment 2: Group Report/Oral Presentation ………………………………………………… 8
Assignment 3: Literature Review ………………………………………………………………….. 10
Academic Integrity………………………………………………………………………………………….. 11
Referencing……………………………………………………………………………………………………. 11
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Syllabus
In this topic students will learn about the functions of cellular proteins and contemporary approaches that are used for the study and characterisation of proteins. Students will review the process of protein translation, and then examine the post-translational events that affect the structure, function and cellular location of proteins. Traditional techniques for the study of proteins such as protein purification, electrophoresis, Western-blotting and enzyme kinetics will be contrasted with more contemporary techniques such as mass spectrometry techniques for identification of entire proteomes and computer based approaches for evaluating protein structure and function.
Protein Biotechnology is a selective topic supporting the Master students who do not have sufficient knowledge prerequisite for them to do the Topic BIOL9005 Protein to Proteome GE. Therefore this Topic will teach the students the foundational knowledge and techniques in contemporary protein biochemistry and biotechnology to bridge the gaps for them to successfully study BIOL9005 GE. In this Topic, the students will learn about protein structures, protein folding, electrophoresis, western-blotting, molecular cloning and manipulation of recombinant DNA, protein expression in E. coli, protein purification, enzymes and enzymatic catalysis, protein-protein interactions, DNA binding, and basic biophysical characterization of protein structures. This Topic will focus on building the knowledge bases of students to further learn the functions of cellular proteins and contemporary approaches of protein characterization. A range of teaching strategies will be employed, including lectures, tutorials, workshops, self-directed learning and computer simulation, to best address the students learning outcomes.
Educational Aims of the Topic
The aims of this topic are to:
1. Prepare the students with foundational knowledge and techniques on protein biochemistry and biotechnology required for the Topic BIOL9005 GE
2. Develop students’ understanding of basic protein biochemistry including protein structure, protein folding, protein-protein interactions and DNA binding
3. Familiarize the students with basic protein characterization techniques, including electrophoresis, western-blotting, enzymes and enzymatic catalysis
4. Develop students’ basic knowledge of protein molecular biology including molecular cloning and manipulation of recombinant DNA, protein expression in E. coli, and protein purification
5. Develop students’ generic skills in problem-solving, self-directed learning, independence and teamwork, good written and oral communication, and critical thinking
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Expected Learning Outcomes of the Topic
At the completion of the topic, students are expected to be able to:
1. Demonstrate understanding of the foundational knowledge and techniques on protein biochemistry and biotechnology required for the Topic BIOL9005 GE
2. Demonstrate understanding of basic protein biochemistry including protein structure, protein folding, protein-protein interactions and DNA binding
3. Demonstrate understanding of basic protein characterization techniques, including electrophoresis, western-blotting, enzymes and enzymatic catalysis
4. Gain basic knowledge of protein molecular biology including molecular cloning and manipulation of recombinant DNA, protein expression in E. coli, and protein purification
5. Display effective skills in self-directed learning, peer-learning, critical literature analysis, communication, independence and team work skills, and problem-solving
Topic Content
This topic consists of:
o Lectures
o Tutorials
o PASS sessions
o 3 Modules / assignments
o Workshops
Peer Assisted Study Sessions (PASS)
It is anticipated that the students may need additional assistance with course instruction to what is provided in lectures and tutorials. In addition, students may encounter challenges and obstacles with the independent learning exercises that are part of the three modules. Thus, some of the timeslots designated in the course timetable as tutorial sessions will be utilized as PASS sessions, which are designed so that students learn from one another in an informal setting. A major part of these PASS sessions will involve students working in small groups on pre-designed activities with the help of ‘facilitators’, students with previous knowledge and experience in biochemistry. The role of the facilitators will be to guide learning and discussion by the groups. All students need to attend and participate in these PASS sessions.
The benefits of the PASS program are mentioned below and can be found at the following link: http://www.flinders.edu.au/staff/pass/how-students-benefit-from-pass.cfm
Benefits of PASS:
A Flinders University PASS session will typically have between 15-28 students, and 2 PASS Facilitators. Sessions are informal; however they may contain structured activities for the class to work through in small groups.
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The relaxed environment enables students to seek help from their facilitators without the anxiety associated with approaching academics.
Most importantly PASS Facilitators are not teachers so they do not provide students with the answers to problems. Facilitators guide students towards discovering the answer themselves, which, from an educational perspective is much more rewarding.
Peer learning programs like PASS have been around for approximately 35 years resulting in a vast amount of literature documenting the benefits. These benefits include:
• Improved academic performance (increased mean exam & final grade, see fig. 1).
• Increased retention into higher year topics.
• Increased persistence towards and timely graduation.
• Enables transition of first year students to university, both academically and socially.
• Development of efficient study skills.
• Increased efficiency of study during PASS as compared to individual study.
• Enhanced learning via provision of immediate feedback and discussion of difficult problems.
• Students are motivated to keep up with weekly topic content.
• Greater student satisfaction in topics.
• And importantly, students make friends!
Teaching Team
Topic coordinator: Professor Wei Zhang
Telephone: 08 7221 8557
Email: Wei.Zhang@flinders.edu.au
Office location: Health Sciences Building Room #4.21
Other teaching team members:
Name
Role
Phone #
Email address
A/Prof Kathleen Soole
Lecturer
8201 2032
Kathleen.Soole@flinders.edu.au
A/Prof Munish Puri
Lecturer
7221 8573
Munish Puri@flinders.edu.au
A/Prof Cathy Abbott
Lecturer
8201 2078
8201 3836
Cathy.Abbott@flinders.edu.au
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PROTEIN BIOTECHNOLOGY
BTEC 8007 LECTURES, WORKSHOPS AND SEMINARS TIMETABLE – SEM 2 2018
Lectures: Health Sciences Lecture Theatre Complex (HSLTC) – Room 3.06/3.07
Tutorials: Physics Sciences Building (PHYS) – Room 0007
Workshops: Physics Sciences Building (PHYS) – Room 0006
Week
Date
Time
Event
Venue
Lecturer
Wk 1
Wed
25 Jul
1.00pm-2.00pm
Aptitude test
HSLTC 3.06/3.07
Wei Zhang/
Kathleen Soole
Wed
25 Jul
4.00pm-5.00pm
1h Lecture – Course Introduction
HSLTC 3.06/3.07
Wei Zhang
Wk 2
Wed
1 Aug
1.00pm-3.00pm
2h Lecture (introductory lecture for BIOL9005 GE)
HSLTC 3.06/3.07
Kathleen Soole
Wk 3
Wed
8 Aug
1.00pm-3.00pm
2h Lecture (introductory lecture for BIOL9005 GE)
HSLTC 3.06/3.07
Kathleen Soole
Wk 4
Wed
15 Aug
Written assignment due for Module 1
(provide answers to 16 Q’s)
Students
Wed
15 Aug
9.00am-10.00am
1h Tutorial (for Module 1)
PHYS 0007
M Puri
Wed
15 Aug
1.00pm-3.00pm
2h Lecture (introductory lecture for BIOL9005 GE)
HSLTC 3.06/3.07
Cathy Abbott
Wk 5
Wed
22 Aug
9.00am-10.00am
1h Tutorial
PHYS 0007
PASS Facilitator
Wk 6
Wed
29 Aug
9.00am-10.00am
1h Tutorial (for Module 2)
PHYS 0007
M Puri
Wed
29 Aug
1.00pm-5.00pm
3h Workshop
(for module 1; students individually to present to class on given topics)
Written assignment due for
module 1
PHYS 0006
M Puri
Students
Wk 7
Wed
5 Sep
9.00am-10.00am
1h Tutorial
Written assignment due for
Module 2
PHYS 0007
PASS Facilitator
Students
Wed
5 Sep
1.00pm-2.00pm
1h Tutorial
HSLTC 3.06/3.07
Wei Zhang
5
Wk 8
Wed
12 Sep
1.00pm-5.00pm
3h Workshop
(for module 2; group oral presentations)
PHYS 0006
Wei Zhang
Break
Mon
17 Sep – Sun
30 Sep
Semester 2 Break
Wk 9
Mon
1 Oct
Labour Day Public Holiday
NO LECTURES
Wk 10
Wed
10 Oct
9.00am-10.00am
1h Tutorial (for module 3)
PHYS 0007
Wei Zhang
Wed
10 Oct
1.00pm-2.00pm
1h Tutorial (PASS)
HSLTC 3.06/3.07
PASS Facilitator
Wk 11
Wed
17 Oct
9.00am-10.00am
1h Tutorial
PHYS 0007
Wei Zhang
Wk 12
Wed
24 Oct
9.00am-10.00am
1h Tutorial
PHYS 0007
PASS Facilitator
Wed
24 Oct
4.00pm-5.00pm
1h Lecture
Final Exam
HSLTC 3.06/3.07
Wei Zhang
Wk 13
Wed
31 Oct
Written assignment due for Module 3 (literature review)
Students
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Textbooks & Resources
Hardcopy:
Textbooks should help provide you some basic concepts and secure the foundations of your understanding in protein biochemistry. Two recommended textbooks available in the Flinders library that you may refer to are:
Nelson, D.L. and Cox, M.M. (2008) Lehninger Principles of Biochemistry. 5th edn.
Brandon, C. and Tooze, J. (1991) Introduction to Protein Structure. 1st edn. This is a protein biochemistry textbook; a newer 1999 edition can be purchased from bookstores or online websites, but is ~$90 – 100.
Free online resources:
Biochemistry – Second Edition (Garret & Grishan) http://biosource.blogspot.com/2007/09/free-biochemistry-book-online.html
Biochemistry Online: An Approach Based on Chemical Logic
http://employees.csbsju.edu/hjakubowski/classes/ch331/bcintro/default.html
Wikipedia: Biochemistry/Proteins/Introduction online e-book
http://en.wikibooks.org/wiki/Biochemistry
‘Foundations of Biochemistry’ online activities textbook; it has a variety of questions and activities for biochemistry students
http://www.pcrest2.com/biochemistry/flip/index.html
Assessment
The assessment strategy tests a range of skills and knowledge. In particular, it focuses on assessment of individual understanding of the topics as well as their ability to present what they have learned in both written form and orally, which will allow an opportunity for the students to teach one another. Students will also be assessed on their ability to work well in a group, since team work is an important aspect of working and developing a career in the biotechnology industry.
Where each assignment should be submitted is detailed in the Statement of Assessment Methods. Most of the assignments are to be handed in electronically using the Assignment Dropbox on FLO. You must ensure that you know how to use this tool before the due date. The university provides computers on campus and there is a FLO Helpdesk in the Central Library. Therefore, computer problems are not an excuse for late submission.
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The assessment consists of the following exercises:
o Workshop (Module 1: Protein Biochemistry) – answer 16 Q’s and present to/teach class
o Team Project (Module 2: Protein Characterisation) – group written report/oral presentation
o Written Assignment (Module 3: Protein Molecular Biology) – individual literature review
o Exam: To test the students’ overall understanding of basic concepts and applications in protein biotechnology
Nature of component
Number of assessment pieces
Relative weighting(%)
Learning outcomes assessed
Workshop
1
20
1-5
Team Project
1
20
1,3,5
Written Assignments
1
20
1-5
Examination
1
40
1-5
Assignment 1: Answer to 16 Questions and Class Instruction
Module 1: Protein biochemistry
For Module 1, you will learn basic protein biochemistry using a self-directed, peer-assisted and problem-based learning approach. You will be provided with a list of 16 questions, which you will need to provide answers along with a brief explanation as necessary. These answers must be submitted as a written assignment due at the beginning of the workshop in week 35 (Wednesday 30 August). If the assignment is not completed, then you cannot attend the workshop. For the workshop, answers to the 16 questions will be presented individually orally to the entire class. For these oral presentations, students will be asked randomly to come up to the front of the lecture room to present to the class on one or two of the topics (using the whiteboard and marker, if desired). You will be assessed and graded in the workshop based on your presentation (eg how well you cover the topic(s)) as well as your participation in asking questions and discussing the topics presented by the other students
Refer to the ‘Textbooks & Resources’ section above for resources to help answer these questions.
Questions:
1) What are proteins composed of (ie basic building blocks)?
2) List the amino acids and diagram their organic structure (C-N bonds).
3) What gives proteins a charge or neutrality?
4) What are the basic secondary structures of proteins and how do they form?
5) What are some common protein motifs or domains? Describe three of them.
6) How are proteins generated within a cell?
7) What are the different types of protein-protein interactions? Describe each, including the different kinds of domains that are used.
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8) What are the different types of proteins within a cell (eg membrane proteins, signal transducers, etc)? Name at least 4 and describe the role of each.
9) How is protein structure determined/analysed (provide at least 2 different methodologies)?
10)How and when does protein unfolding occur?
11)What are chaperones and how do they do their job?
12)What is an enzyme and how is it a specialised protein?
13)Describe what Km and Vmax are for an enzyme.
14)What equation links these parameters (Km and Vmax)? How are they calculated?
15)What is an allosteric effector and how does it affect Km and Vmax?
16)Describe the different types of inhibition you can get for enzyme reactions.
How assignment 1 will be assessed
This assignment will be assessed based on three main components:
1) written answers to questions (40%)
– Students must hand in answers at beginning of workshop; responses will be graded on how thoroughly, yet concisely they answer the questions. The amount of information to cover will depend on the question, but a paragraph to ½ page should be sufficient in most cases.
2) presentations (30%)
– Students will be assessed on their ability to present the material clearly and concisely within a 5 minute time-frame.
3) answers to questions by lecturer/students and participation (30%)
– Questions will be posed to each presenter at the completion of their ‘instruction’. For this component, all students will be assessed for their participation in asking and answering questions; all students need to ask at least 1 question during the course of the workshop to receive full credit for this component. The presenter will be marked on their ability to answer the question(s) thoroughly and clearly appropriate for the audience (ie students in a basic protein biochemistry course).
Assignment 2: Group Report/Oral Presentation
Module 2: Protein characterisation
For module 2, you will work as a group of 4 students (3 at least). Each group will be required to research the following 4 areas relating to protein characterisation techniques:
1) electrophoresis (eg 1D/2D gels, native gels, SDS-PAGE, capillary electrophoresis)
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2) Western blotting (eg how it is done – membranes, antibodies, etc, what information you obtain from it, limitations to this technique, associated methods: eg immunoprecipitation, pull-down assays, etc)
3) enzymes (eg what are enzymes, how do they function, what are common features of active sites, what are the different kinds of enzymes in cells)
4) enzyme catalysis (eg substrate docking – induced fit vs transition state stabilisation, enzyme inhibition, enzyme kinetics, measuring enzyme activity).
You will need to meet as a group to decide on which area of protein characterisation each of you will research. You will be required to write an overview of the chosen topic using a maximum of 500 words per section plus short introduction and summary sections (2500 total for the group). References and diagrams should be provided (these will not be included in the total word count). This written assignment is due on Friday 8 September. You will also need to meet as a group to teach each other the different topic areas and prepare an oral presentation (eg using PowerPoint). On Wednesday 13 September you will present the information as a group, but each person will present on a different area than they researched, which will be selected randomly by the lecturer. In addition, the presentation should begin with 1-2 introduction slides and end with 1-2 summary slides; the students in the group can decide how to divide this part up. The presentation has a 20 minute time limit with a 5 minute limit for each topic area (each individual presentation).
References need to be provided using the Harvard referencing system as mentioned later in this handbook. It is recommended to use a citation manager program such as Endnote or Reference Manager, which makes creating bibliographies much easier.
How assignment 2 will be assessed
This assignment will be assessed based on three main components:
1) written component (40%)
– individual mark (50% of written component) – based on each individual’s selected section of the report (eg thoroughness in covering topic area, clarity, keeping to word limit, proper referencing, etc).
– group mark (50% of written component) – based on flow and quality of the entire report (eg whether all sections are present, appropriate use of diagrams, quality of transitions between sections, sufficient background information and citations for the introduction section, overall summary of protein characterisation with reference to current research use and future applications, and proper referencing style usage).
2) oral component (40%)
– individual mark (75% of oral component) – based on each individual’s presentation as part of the group (clear, concise, enough details to explain topic, engagement of the audience, within time limit).
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– group mark (25% of oral component) – based on overall group presentation (ie flow of the presentation, transitions, adherence to time limit, ability to answer questions).
3) peer assessment (20%)
– students will be given an opportunity to anonymously assess the effort and performance of each of the other students in their group on both the written and oral components; specific assessment criteria will be provided later. Examples of assessment criteria include: level of contribution to report and oral presentation (including the introduction, summary and referencing sections), ability to work well as a team member, availability for meetings, etc.
Assignment 3: Literature Review
Module 3: Protein molecular biology
For module 3, you will each do an individual literature review on protein molecular biology, covering the following topics:
1) molecular cloning (eg methods commonly used, cDNA libraries, genome sequencing, peptide sequencing, chromosome walking, etc.)
2) manipulation of recombinant DNA (eg restriction enzymes, PCR, plasmid vectors, viral vectors)
3) protein expression in E. coli (eg plasmid vectors, fusion proteins, use of fluorescent markers, antibiotic resistance, plasmid purification for cell transfections)
4) protein purification [eg chromatography (silica gel, liquid, gas), gel electrophoresis, HPLC, column purification, dialysis], including importance of purity for crystallography, NMR and mass spectometry
For this assignment you will need to submit a written document in the form of a review consisting of up to 2000 words (not including references). Besides the topic areas, you should include ‘Introduction’ and ‘Summary’ sections to provide some background on protein molecular biology as well as a summary of the current methodologies employed in research.
How assignment 3 will be assessed
This assignment will be marked individually based on the following criteria:
1) Introduction: provide sufficient background information to introduce the topic
2) Main body: provide sufficient detail describing the 4 main areas (subsections) stated above with appropriate citations (ideally peer-reviewed journal articles)
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3) Summary: give an overall summary of protein molecular biology and its use in current research as well as future applications in industry and medicine
4) Quality of references and correct use of Harvard referencing system
NOTE: Going over word limit will reduce your overall mark
Academic Integrity
In an academic context we show respect for other people’s work and demonstrate our professionalism by being honest and trustworthy, and acting with fairness, respect and responsibility.
(The Center for Academic Integrity (1999), The Fundamental Values of Academic Integrity, Duke University, North Carolina)
All students are expected to be familiar with Statute 5.4 of the Student Policy & Procedures at http://www.flinders.edu.au/ppmanual/student/assessment1.html .
The University recognises that some acts of academic dishonesty, particularly plagiarism, may arise from genuine ignorance of the use of academic conventions but will not accept ignorance as an excuse. It is therefore the obligation of all students to understand and respect the rules concerning academic integrity.
To find out more about maintaining your academic integrity use the “ACINT001_o Academic Integrity Flinders” site in FLO.
Referencing
There are many variations of the Harvard referencing style. This handout has been modified to match the current requirements for Biotechnology written work at Flinders University as on 28 May 2008. The following is a summary of the referencing format required – see FLO or the Student learning Centre for further detail.
There are 2 parts to the Harvard referencing system:
1. The in-text reference
2. The reference list
1. The In-text Referencing – as requested for Biotechnology theses
Please note that the comma before the year in in-text referencing is optional. In-text referencing is based on the authors’ surnames, the year of publication of the discussion or idea you are referring to.
Smith (2005) argues that ‘the relative seriousness of the two kinds of errors differs from situation to situation’.
It has been argued that ‘the relative seriousness of the two kinds of errors differs from situation to situation’ (Smith, 2005).
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If you paraphrase material (express someone else’s ideas in your own words) you must make it clear that you are referring to someone else’s work:
A recent study (Jones & Chan, 2002) has shown…
When the authors’ names are incorporated within the text, you must write the word ‘and’ instead of the symbol &:
Jones and Chan (2002) have shown that…
For Works with three or more authors, include only the surname of the first author and the abbreviation et al. (meaning ‘and the others’). In the following example, the citation refers to work done by Lim, Smith, Brown and Nguyen:
A recent study (Lim et al., 2006) has shown…
For two or more authors with the same surname, distinguish between them by using the authors’ initials or full names:
A recent study by CL Jones (2005) has shown … but A Jones (2006) has suggested…
For secondary references (when one author discusses another author’s work), both sources must be acknowledged in your in-text reference. However, only the book or article you actually used (the secondary reference) should appear in your reference list. In the example below, Marini is the primary reference and Jones is the secondary reference:
Marini (Jones, 2005) states…
Marini’s study in 2003 (cited in Jones, 2005) states…
Jones (2005), in reporting Marini’s study of 2003, states…
The process was shown to be more complex than at first thought (Marini, 2003 cited in Jones, 2005).
2. The Reference List
The reference list is placed at the end of the assignment. It is arranged in alphabetical order of authors’ surnames and chronologically for each author, with the items marked below with an asterisk (*) being essential.
When using the Harvard system for books, the following information is required in this order:
author’s surname & initials *
year of publication *
title of publication (in italics) *
title of series (if applicable)
volume number or number of volumes (if applicable)
edition (if applicable)
editor, reviser, compiler or translator (if other than the author) *
publisher *
place of publication *
page numbers (when applicable, e.g. for a chapter in a book)
Book
Angelil-Carter, S 2000, Stolen language? Plagiarism in writing, Longman, London.
Chapter in an edited book
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Fox R 2000, ‘Online technologies changing university practices’, in A Herrmann & M Kulski (eds), Futures in university teaching, Centre for Educational Advancement, Curtin University of Technology, Perth, pp. 235-243.
When referencing material from journals (periodicals) the following order is required:
author’s surname & initials *
year of publication *
title of article (in inverted commas) *
title of journal or periodical (in italics)*
title of series (if applicable)
place of publication (if needed to distinguish between different periodicals with the same title
volume number *
issue number (if applicable)
month (if applicable) – not required for Biotechnology Theses
page number or numbers *
Example as requested for Biotechnology written work:
Campbell, M 2003, ‘Dorothy Smith and knowing the world we live in’, Journal of Sociology and Social Welfare, 30: 3-22.
When referencing World Wide Web pages, the following order is required:
author – the person or organisation responsible for the page
site date (either the date it was last updated, a copyright date or n.d. (no date), if date not available)
name and place of sponsor of website
the date you viewed the site
the web address
Flinders University n.d., Flinders University homepage, viewed 14 December 2006, <http://www.flinders.edu.au>.
For further examples, see FLO or the Student Learning Centre.