BIOL2771 Topic Manual 2022 PDF

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Topic Manual for BIO2271 2022...

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COLLEGE OF SCIENCE AND ENGINEERING

BIOL 2771 BIOCHEMISTRY TOPIC GUIDE

Structural hierarchy in the molecular organization of cells (Lehninger)

BIOL2771 BIOCHEMISTRY

ACADEMIC TIMETABLE First Semester classes start

28 February

Mid Semester Break

11 April – 24 April

Classes end

10 June

Exams

20 June – 1 July You are advised to refer to the Semester 1 Critical Dates for Enrolment 2022 at http://www.flinders.edu.au/current-students/dates/critical-enrolment-dates.cfm TEACHING STAFF INVOLVED IN BIOCHEMISTRY

Topic coordinator

Dr Sunita Ramesh [email protected]

Room #

Building

321

Biol. Sc.

314

Biol. Sc.

Lecturer

Dr Crystal Sweetman

Recommended Textbook: Nelson, D.L. and Cox, M.M. (2017) Lehninger, Principles of Biochemistry. 8th edn.

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TABLE OF CONTENTS GENERAL INFORMATION ........................................................................................ 4 EDUCATIONAL AIMS OF THE TOPIC ........................................................ 4 EXPECTED LEARNING OUTCOMES OF THE TOPIC ............................... 4 SYLLABUS OF THE TOPIC ........................................................................... 5 STRUCTURE OF THE TOPIC ......................................................................... 5 ATTENDANCE................................................................................................. 5 GETTING STARTED ....................................................................................... 5 LECTURE TIMETABLE .................................................................................. 7 TUTORIAL TIMETABLE ................................................................................ 8 PRACTICAL TIMETABLE.............................................................................. 9 LABORATORY EXERCISES .................................................................................... 10 GENERAL INFORMATION & SAFETY GUIDELINES ............................. 10 PREPARATION FOR PRACTICAL SESSIONS .......................................... 11 PRACTICAL 1: SKILL DEVELOPMENT (WEEK 2) .................................. 13 PILOT STUDY 1: PROTEIN STANDARD CURVE AND ASSAY OF UNKNOWN PROTEIN SAMPLES (WEEK 2) ................................. 19 PRACTICAL 2_1: QUANTITATING PROTEIN CONTENT AND INVESTIGATING THE EFFECT OF TREATMENTS ON PROTEIN FUNCTION (WEEKS 4 AND 6) ........................................................ 25 PRACTICAL 2_2: DETECTION OF SUGARS (GLUCOSE AND FRUCTOSE) IN FOOD SAMPLES (WEEKS 4 AND 6)................... 32 PRACTICAL 2_3: QUANTITAING TOTAL STARCH CONTENT OF SAMPLES CONTAINING RESISTANT STARCH .......................... 41 PRACTICAL 3_1: INVESTIGATION OF HEXOKINASE ENZYME ACTIVITY (WEEK 8)……………………………………………………… 46 PRACTICAL 3_2: INVESTIGATION OF HEXOKINASE ENZYME ACTIVITY _ MICHAELIS MENTEN KINETICS (WEEK 10) ........ 51 CALCULATIONS ....................................................................................................... 55 UNDERGRADUATE LABORATORY SAFETY PROCEDURES .......................... 57

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BIOL2771 BIOCHEMISTRY

GENERAL INFORMATION EDUCATIONAL AIMS OF THE TOPIC The overall aim of this topic is to develop students’ knowledge and understanding of food and energy metabolism and to provide opportunities to apply this knowledge and understanding to the solution of ‘real-world’ problems related to enzyme function, nutritional deficiencies, and metabolic disorders. EXPECTED LEARNING OUTCOMES OF THE TOPIC On completion of this topic, students will be expected to be able to: 

Explain clearly in both oral and written form the processes and regulation of food and energy metabolism covered in this topic.  Apply their knowledge to the diagnosis and treatment of nutritional deficiencies and metabolic disorders.  Collaborate effectively with colleagues to solve problems.  Interpret experimental data in the context of current knowledge in the field of biochemistry.  Understand the likely artefacts inherent in working with biological materials and be cognisant of the use of controls to identify artefacts. Practical specific  Maintain a laboratory notebook such that others can reproduce their work.  Perform routine calculations required for the preparation of laboratory reagents.  Present experimental results in tables and graphs in a format suitable for publication in a scientific journal.  Be familiar with the basic properties of carbohydrates, proteins, and enzymes.  Understand that protein structure affects protein function.  Understand the meaning of the terms native and denatured when applied to proteins.  Understand how protein (enzyme) structure and function is affected by heat, acid, and nondenaturing precipitants (e.g., ammonium sulphate, polyethylene glycol).  Know how to test the validity of an enzyme assay.  Understand the concepts underlying the Beer-Lambert law, max and the molar extinction coefficient (ε).  Understand the relationship between substrate concentration and reaction rate for an enzyme catalyzed reaction; basic Michaelis-Menten enzyme kinetics; Km, Vmax.  Be able to generate a protein standard curve and understand the use of standard curves.  Work competently in a molecular biology laboratory and produce reliable and reproducible data.

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BIOL2771 BIOCHEMISTRY

SYLLABUS OF THE TOPIC In this topic, students will learn the underlying biochemistry of food and energy metabolism with a focus on carbohydrates, proteins, fats, vitamins and minerals and the regulation of metabolism by hormones such as glucagon, adrenaline, and insulin. The topic includes lectures, problem-based learning (PBL) tutorials and laboratory-based practicals. In the lectures, students will gain an overview of the most important enzymes, metabolic pathways, and regulatory mechanisms. In the PBL tutorials, students will apply their knowledge by working in teams to solve cases and suggest remedies for ‘patients’ suffering from nutritional deficiencies or metabolic disorders. In the practicals, students will quantitate sugars, starch and protein from different sources and investigate enzyme activity and learn scientific report writing. STRUCTURE OF THE TOPIC  Pre-recorded lecture videos (Tuesday)  Wednesday workshop related to lecture content ‘live’ via collaborate (recorded)  One 1-hour tutorial session per week (starting week 3)  One 3-hour practical session per fortnight (starting week 2)  Two 1 h workshops in alternate weeks to the practical for help with calculations and design of experiments (starting week 3)  One workshop face to face (not recorded)  One workshop “live’ via collaborate (not recorded) ATTENDANCE Attendance at tutorials and practicals is compulsory (Please refer to SAM on FLO). Attendance at workshops is strongly recommended. GETTING STARTED Teaching philosophy  Our teaching philosophy is student-centred, and student driven. We have designed our faceto-face teaching activities to be interactive. In these activities we provide an opportunity to apply knowledge gained through the online resources and extend understanding of the content. How do I find information about topic assessment?  Please refer to FLO for the Statement of Assessment Methods (SAM).  Assignment instructions and feedback rubrics can also be found on FLO. Lecture Notes  Lecture notes can be downloaded from Flinders Learning Online (FLO)  It is strongly recommended that you view the pre-recorded lecture videos and download the lecture notes before attending the workshop so that you can participate in problem solving in class. Attending workshops  Attendance at workshops is not compulsory but it is strongly recommended. What if I miss workshop 1?  Workshop 1 (Wednesdays) will be recorded. The recordings can be accessed through FLO. Attending tutorials  Attendance at tutorials is compulsory.  Students should register themselves in a tutorial class by going to the Flinders University

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BIOL2771 BIOCHEMISTRY

homepage.  Students should attend the same tutorial class for the whole semester. What do I need to bring to tutorials?  Information for the tutorials will be available on the topic FLO site or it will be handed out in the tutorial. Students should check the topic FLO site regularly. What if I miss a tutorial?  If you cannot attend your usual tutorial class, you should attempt to catch up by attending another tutorial class in the same week by rescheduling via the FLO page. If you need to change your tutorial class, you must e-mail [email protected] with a valid reason. Attending practicals  Attendance at practicals is compulsory.  Students should register themselves in a practical class by going to the “Student System (student login)” link on the Flinders University homepage.  Students should attend the same practical class for the whole semester. What do I need to bring to practicals?  Topic manual and a bound A4 sized laboratory notebook dedicated to this topic this semester.  Blue or black ink pen, a fine water-resistant marker pen, a ruler, and a calculator.  Laboratory coat, safety glasses, closed-in shoes, not sandals and certainly not thongs. *All students should supply their own safety glasses and lab coats.  You must wear a “mask” at all times in the laboratory.  USB drive.  Lap top computer (if you have one). What if I miss a practical?  If you cannot attend your usual practical class, you should attempt to catch up by attending another practical class in the same week by rescheduling via the FLO page. If you need to change your practical class, you must e-mail [email protected] with a valid reason.

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BIOL2771 BIOCHEMISTRY

LECTURE TIMETABLE Lectures: Tuesday: Pre-recorded and available via FLO. Workshop 1: Wednesday: 9:00 – 9:50am ‘live’ via collaborate. o o WEEK

1

This session is interactive, and preparation is required. Recording will be made available via FLO following the live class.

DAY

LECTURE TITLE

STAFF

Tues

Fundamentals of Biochemistry/Overview of transport across cell membranes/ion channels and regulation

Wed

Pre-recorded SR Collaborate

Workshop 1 Tues

VENUE

Carbohydrates and proteins

Pre-recorded

2

SR Wed

Workshop 1

Tues

Glycolysis and Gluconeogenesis

Collaborate Pre-recorded

3

SR Wed

Workshop 1

Tues

Glycogen / Coordinated regulation of Glycolysis and Gluconeogenesis

Collaborate

4

Pre-recorded SR

Wed

Workshop 1

Tues

Pyruvate Dehydrogenase Complex (PDHC)/ Vitamins in metabolism

Collaborate

5

Pre-recorded CS

Wed Tues 6 Wed

Workshop 1

Collaborate Pre-recorded

Tricarboxylic Acid Cycle

CS Collaborate

Workshop 1 MID-SEMESTER BREAK

Tues

Oxidative Phosphorylation

Pre-recorded

7

CS Wed

Workshop 1

Tues

Protein Digestion and Amino Acid Catabolism

Collaborate Pre-recorded

8

CS Wed

Workshop 1

Tues

Fats as Fuels / Fatty acid synthesis

Collaborate Pre-recorded

9

CS Wed

Workshop 1

Collaborate

Tues

Hormonal regulation / Metabolic perturbations and disease

10

Pre-recorded CS

Wed

Workshop 1

Tues

Water and ion movement across membranes

Collaborate Pre-recorded

11

SR Wed

Workshop 1

Tues

Ion movement, neurotransmission, and disease

Collaborate Pre-recorded

12

SR Wed

Workshop 1

Collaborate

Tues 13

Pre-recorded Integrating metabolism as revision

SR

Wed

Collaborate

Tues 14

SR/CS

Exam revision lecture Wed

Abbreviations used: SR, Dr Sunita Ramesh; CS, Dr Crystal Sweetman

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BIOL2771 BIOCHEMISTRY

TUTORIAL TIMETABLE  Tutorials commence in week 3.  Please register for a class via student systems.  Attendance is compulsory. WEEK

TUTORIAL TITLE

ASSESSMENT

1

No tutorials

2

No tutorials

3

Introductory PBL tutorial

4

Case 1 – Introduction of case (group work)

5

Case 1 – Resolution of case (group work)

6

No tutorials

Tutorial Formative Quiz 1 on FLO due week 6

MID-SEMESTER BREAK 7

Case 2 – Introduction of case (group work)

8

Case 2 – Resolution of case (group work)

9

No tutorials

10

Case 3 – Introduction of case (group work)

11

Case 3 – Resolution of case (group work)

12

No tutorials

13

No tutorials

Tutorial Formative Quiz 2 on FLO due week 9

Tutorial Formative Quiz on FLO due week 12 Video presentation of case (group) uploaded to dropbox on FLO

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BIOL2771 BIOCHEMISTRY

PRACTICAL TIMETABLE  Practicals commence in week 2 and are held in laboratory 5 in the Biology Discovery Centre (level 1).  Register for a class via student systems.  Attendance is compulsory.

WEEK

PRACTICAL TITLE

ASSESSMENT

1

No practicals

2

Skill development and Pilot study (Protein standard curve and assaying for unknown proteins)

3

Workshop 2: Calculations and experimental design

4

Detection of Starch and Sugars in samples (Part 1)

5

Workshop 2: Calculations and experimental design

6

Detection of Starch and Sugars in samples (Part 2)

Pre-lab quiz 1

Pre-lab quiz 2

Pre-lab quiz 3

Formative assessment of lab notebook 7

Workshop 2: Calculations and experimental design

8

Investigation of Hexokinase enzyme activity (Part 1)

9

Workshop 2: Calculations and experimental design

10

Investigation of Hexokinase enzyme activity (Part 2) and Laboratory notebook assessment

11

Workshop 2: Calculations

12

Laboratory notebook assessment (summative) and assignment feedback

Laboratory notebook (based on week’s 2-10)

13

No practicals

Practical report

9

Pre-lab quiz 4

Pre-lab quiz 5 and laboratory notebook (based on week’s 2-10)

BIOL2771 BIOCHEMISTRY

LABORATORY EXERCISES GENERAL INFORMATION & SAFETY GUIDELINES Laboratory classes are designed to give you technical skills, which support the theoretical information you learn in lectures. They form an essential and assessable component of this topic. You will enrol in a particular practical session that is compatible with your timetable. The role of laboratory demonstrators Each laboratory will be assigned teaching staff (demonstrators), whose task it is to oversee the successful running of the practical, and to assist you. The demonstrators assigned to your practical session will also assess your practical work. Demonstrators are usually doctoral students from the many research laboratories in the College, and most have completed their undergraduate degrees at Flinders as well, so they are also familiar with the topic from a student perspective. You should feel free to approach them for help with any questions you may have during the practical sessions. Practical assessment All demonstrators within this topic are provided with supporting information about the exercises they supervise, so that they are sufficiently familiar with the background to be able to help you. They are provided with marking criteria and weightings for assessment purposes to minimise any differences between demonstrators. Be assured that we are constantly monitoring this process. Safety guidelines Safety is of primary concern in any laboratory, and we ask you treat this issue seriously. The following guidelines should be adhered to at all times in the laboratory. 

Wash your hands when entering or exiting the laboratory.



Wear a buttoned laboratory coat to prevent contamination of your clothing.



Wear closed shoes.



Always wear a mask.



Wear safety glasses always.



Keep your workbench free of articles not currently in use.



No food or drink is to be brought into the laboratory and avoid placing objects on the bench that may be consciously or unconsciously transferred to the mouth (e.g., stationery).



If in doubt as to how to conduct a laboratory procedure, seek advice from the demonstrator.



Report any accidents to your demonstrator immediately.



Please refer to the safety instructions at end of manual for further information.

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PREPARATION FOR PRACTICAL SESSIONS Your laboratory notebook should be treated as a formal exercise. It is routine practice in research and industrial laboratories for employees to keep a detailed daily record of their activities. Knowing the experimental aims is an essential part of practical session preparation, as you will need to know them to properly understand the practical experiments. To assist you with this, and understanding the concepts relevant to each practical session, ensure you complete the pre-laboratory quiz on FLO relevant to each practical session. Laboratory notebook Most laboratory notebooks follow a similar format. The aim of the notebook is to present an accurate and complete record of your activities, in a way that demonstrates your understanding of the exercises completed. Your laboratory notebook is a record of your aims, experimental procedures, observations, data, and interpretations from a given laboratory session. Thus, the laboratory notebook should be used during the laboratory session to record your experiments. We expect that all relevant information is recorded in the laboratory notebook by the end of the laboratory session. Although you are working in pairs during the laboratory session, everyone must keep their own laboratory notebook. The information recorded in the laboratory notebook will be assessed through the laboratory notebook assessment and used to write the laboratory report. Where to buy the laboratory notebook? 

An A4 bound, lined notebook can be purchased from any newsagency. Alternatively, a Flinders University laboratory notebook can be purchased on campus from the Post Office. The benefit of this laboratory notebook is that it includes a table of contents, numbered and ruled pages.

How to fill in the laboratory notebook? 

The laboratory notebook must be filled in with permanent black or blue ink. No white out is to be used. If a mistake is made...