Learning Guide - Summary Metabolism PDF

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School of Science and Health

300848 Metabolism Spring 2019

Unit Details Unit Code:

300848

Unit Name:

Metabolism

Credit Points:

10

Unit Level:

2

Assumed Knowledge:

Not Applicable

Note: Students with any problems, concerns or doubts should discuss those with the Unit Coordinator as early as they can.

Unit Coordinator Name: Dr Mark R. Jones Phone: 4570 1444 Location: Building K12, room G.53, HWK campus Email: [email protected] Consultation Arrangement: Immediately prior to/following lectures on each campus, or by appointment. Note: Student emails routinely receive responses between 8am & 10am Weekdays.

Edition: Spring 2019 Copyright 2019 c University Western Sydney trading as Western Sydney University ABN 53 014 069 881 CRICOS Provider No: 00917K No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or by any information storage and retrieval system, without the prior written permission from the Dean of the School. Copyright for acknowledged materials reproduced herein is retained by the copyright holder. All readings in this publication are copied under licence in accordance with Part VB of the Copyright Act 1968.

Contents 1 About Metabolism 1.1 An Introduction to this Unit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.2 What is Expected of You . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.3 Changes to Unit as a Result of Past Student Feedback . . . . . . . . . . . . . . . . . . . . . . . . .

2 2 2 2

2 Assessment Information 2.1 Unit Learning Outcomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.2 Approach to Learning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.3 Assessment Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.4 Assessment Details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.4.1 Laboratory Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.4.2 Quiz . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.4.3 Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.4.4 Intra-session Exam (On-line, Take-home) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.4.5 Final Exam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.5 General Submission Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

3 3 3 5 6 6 9 10 13 14 15

3 Teaching and Learning Activities

17

4 Learning Resources 19 4.1 Recommended Readings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Note: The relevant Learning Guide Companion supplements this document 1

1

About Metabolism

1.1

An Introduction to this Unit

Organisms degrade food molecules to generate energy and converts excess food molecules into internal fuel stores. This unit will cover topics including: bioenergetics; the structures of key molecules; glycolysis, gluconeogenesis, glycogen synthesis and breakdown; fatty acid oxidation and synthesis; amino acid catabolism; urea synthesis; citric acid cycle; electron transport and oxidative phosphorylation. Emphasis will be on the regulation and integration of these pathways, including their responses to hormonal regulation. The effects of altered dietary and hormonal status on metabolic pathways and their consequences for the organism will be discussed.

1.2

What is Expected of You

Study Load A student is expected to study an hour per credit point a week. For example a 10 credit point unit would require 10 hours of study per week. This time includes the time spent within classes during lectures, tutorials or practicals. Attendance Attendance at practical and workshop activity is mandatory. Students must attend a minimum 5 of the 6 practicals/workshop sessions. Online Learning Requirements Unit materials will be made available on the unit’s vUWS (E-Learning) site (https://vuws.westernsydney.edu.au/). You are expected to consult vUWS at least twice a week, as all unit announcements will be made via vUWS. Teaching and learning materials will be regularly updated and posted online by the teaching team. Special Requirements Essential Equipment: Safety glasses, Lab coat, enclosed footwear and Laboratory Notebook Legislative Pre-Requisites: Not Applicable

1.3

Changes to Unit as a Result of Past Student Feedback

The University values student feedback in order to improve the quality of its educational programs. The feedback provided helps us improve teaching methods and units of study. The survey results inform unit content and design, learning guides, teaching methods, assessment processes and teaching materials. You are welcome to provide feedback that is related to the teaching of this unit. At the end of the semester you will be given the opportunity to complete a Student Feedback on Unit (SFU) questionnaire to assess the unit. You may also have the opportunity to complete a Student Feedback on Teaching (SFT) questionnaire to provide feedback for individual teaching staff. As a result of student feedback, the following changes and improvements to this unit have recently been made: – Enhance linkage between lecture topics and Work Integrated Learning (WIL) practical activity via a 10min online Quiz during lectures. – Further emphasis crystalising core concepts and WIL key information in the Report (Part A & B) by reducing the word count and assessment weighting. – Establish problem solving and analytical skills through development of a biochemical procedure (laborartory manual) from first principles, using industry standard models. – Develop competency in time management through addressing practical acivity milestones and reporting progress against industry expectations (WIL).

2

2 2.1

Assessment Information Unit Learning Outcomes

Much of modern medicine and biotechnology depends on the understanding and exploitation of various metabolic pathways in micro-organisms, plants and animals, either to obtain large quantities of specific metabolites (e.g. amino acids, vitamins), to provide organisms with new metabolic capabilities, or to develop new drugs and strategies for controlling disease. Metabolism is concerned with the nature and regulation of the chemical processes by which cells obtain energy from complex organic fuel molecules and use this energy to synthesise their own organic molecules from simple precursors. This unit aims to develop a basic understanding of the biochemical pathways central to degradation and synthesis of carbohydrates, fats, and proteins and develop concepts of metabolic regulation, with reference to altered hormonal, dietary and disease states particularly in humans. Upon successfully completing this unit, you should be able to:

Outcome 1

Describe the molecular mechanisms by which dietary macromolecules (carbohydrates, lipids, proteins) are metabolised to generate energy or, alternatively, to store energy

2

Demonstrate an understanding of the mitochondrial electron transport system and the mechanism by which this system is coupled to ATP synthesis in oxidative phosphorylation

3

Describe the different roles of the major tissues in energy metabolism. Know the general structural types and functional classifications of regulatory molecules such as hormones, growth factors, cytokines, neurotransmitters

4

Explain how disruption of a metabolic pathway affects changes in other metabolic pathways in order to maintain homeostasis

5

Demonstrate competency in; biochemical techniques, use of standard biochemical equipment, graphical skills, biochemical calculations and utilization of professional databases in the research, diagnostic, treatment and policy sectors

6

Organise, present and interpret experimental observations in clear, concise written and spoken English. Identify, retrieve, read and analyse scientific literature relevant to the study of metabolism

7

Demonstrate competency of time management through identifying milestones and reporting progress against milestones in accordance with human resource management and industry expectations

2.2

Approach to Learning

The Metabolism Lecture, Practical and Assessment strategy is designed to: 1. Supplement and reinforce the lecture course in Metabolism. 2. Illustrate key elements of metabolic regulation, at the cellular and whole organism level. 3. Broaden the student’s range of biochemical skills in terms of: - Work Integrated Learning (WIL) - including Work Health & Safety (WHS) issues. - using laboratory equipment. - critical analysis and calculations. 4. Enable student to maintain a laboratory notebook, use industry standard biochemical procedures to establish a biochemical assay protocol/manual and present outcomes at a professional standard (WIL). 5. Expand the student’s ability to acquire data and analyse experimental results (WIL). 6. Develop the student’s ability to write and present clear, concise interpretations and discussions of experimental work (WIL) sector/industry imperatives.

3

7. Enhance critical thinking and time/resource management skills through Inquiry/Problem Based Learning (PBL).

The Report (Part A & B) integrates regulatory aspects of metabolism, enhancing lecture and laboratory activity to enable students to understand the role Research, Diagnostic, Treatment and Policy sectors rely on biochemistry (WIL). With an emphasis on developing scientific arguments across sectors that use data to direct research and development as well as policy. Please Note: Scheduled activity may alter as a consequence of changing circumstance.

4

2.3

Assessment Summary

The assessment items in this unit are designed to enable you to demonstrate that you have achieved the unit learning outcomes. Completion and submission of all assessment items which have been designated as mandatory or compulsory is essential to receive a passing grade. To pass this unit you must: Complete and submit all compulsory assessment items listed below. Attendance at practical and workshop activity is mandatory. Students must attend a minimum 5 of the 6 practical sessions (Workshops and related Modules), as well as achieve at least 50% overall to be eligible to pass this unit. Item

Weight

Due Date

ULOs Assessed

Threshold

Laboratory Report

20%

Weeks 1-14

1, 2, 5, 6, 7

No

Quiz

10%

Weeks 1-7 and 10-14, during lectures.

1-4

No

Report

10%

Report Part A due 9am 13 September and Report Part B due 9am 25 October.

4-7

No

Intra-session Exam (On-line, Take-home)

10%

Week 8 (9am Tuesday 10 Sept - 5pm Friday 13 Sept), inclusive.

1-4

No

Final Exam

50%

University Exam period

1-4

No

Feedback on Assessment Feedback is an important part of the learning process that can improve your progress towards achieving the learning outcomes. Feedback is any written or spoken response made in relation to academic work such as an assessment task, a performance or product. It can be given to you by a teacher, an external assessor or student peer, and may be given individually or to a group of students. As a Western Sydney University student, it is your responsibility to seek out and act on feedback that is provided to you as a resource to further your learning. Assessment item feedback will be given as General Feedback in class (Lectures and Practicals), and personal (in Practicals) on-line (via Metabolism (300848) vUWS) and by appointment.

5

2.4

Assessment Details

2.4.1

Laboratory Report

Weight:

20%

Type of Collaboration:

Individual

Due:

Weeks 1-14

Submission:

Hardcopy Laboratory Notebook (Industry Standard) submitted to Supervisor or Demonstrator, prior to completion of each scheduled practical Workshop (Weeks 4, 6, 8,12 & 14).

Format:

Includes: - Signed Risk Assessment/Safety Data Sheet (of hazardous reagents) required to enter laboratory and undertake Laboratory Module 1 - 5 activity, and be eligible for Module 1 - 5 assessment outcomes. - Laboratory Report - Laboratory Notebook (12%) maintenance for Module 1-4 (3% each) addressing Module 1-5: Biochemical Assay Development Milestones & Objectives (available on vUWS), including determination of WIL assay analysis, assessed by the Supervisor/Demonstrator during the accompanying Workshop. - Laboratory Report - Team Leader (5%) - Student Team Leaders coordinate achievement of Module Milestones and Objectives (including: experiment design, apportioning resources, responsibilities, data acquisition, analysis and interpretation), give an oral presentation (3-5min) using one (1) PowerPoint slide during the accompanying Workshop, addressing the experiment outcomes and analysis achieved by the team for Module 1-4 activity. Further, Team leaders are responsible for the WIL assay standard curve calculations and sample determination for the team. - Laboratory Report - Assay Analysis (3%) - individual student determination of Module 5 Quality Control sample values and questions pertaining to biochemical assays, accessed and submitted to vUWS Assessment folder within 24 hours following completion of the Module 5 practical session. Note: Incomplete or inappropriate maintenance of Laboratory Notebooks, late arrival (>10min past scheduled laboratory start time), late departure (>10min past laboratory activity end time), unauthorised use of electronic devices in the laboratory, will result in automatic forfeit of part or all of module assessment outcomes.

Length:

1,500 words maximum

Curriculum Mode:

Log/Workbook

Students will be expected to develop a basic understanding of the following biochemical procedures and their use through Work Integrated Learning (WIL) to: 1. 2. 3. 4. 5. 6.

Assay biochemical pathways in cell free extracts. Determine analyte concentration in tissue and cell fractionation. Use of enzymes as analytical tools. Accurately measure various metabolites and end-products. Perform biochemical calculations. Establish a laboratory protocol to detect and measure a biochemical analyte (using industry protocols as examplars)

All students are required to work in teams of no more than 3. Each Team will have a nominated Team Leader, required to coordinate and present Team experiment data and outcomes in the Laboratory Workshop (week following experimentation) and present one (1) PowerPoint slide within 3-5min/student. Note: All students will be required to be a Team Leader and investigators will be rotated into new teams for each of Module 1-4.

6

GENERAL COMMENTS Reading/reviewing of any suggested background material is essential. For each Experiment Module 1 - 5, it is expected that students will complete most, if not all of the ’wet work’ in the first week of the experiment. The time following the wet work of each Module will be devoted mostly to data analysis, calculations, interpretation of results and Team Leader presentation and class discussion. Maintenance of the Laboratory Notebook is essential throughout the lab classes. Note: Pre-work must be completed before attending class and both Pre- and Post-work will be monitored in the Laboratory and assessed via the Laboratory Notebook, Lab Analysis (on-line) and in the Final Exam. Students are obliged to attend ALL practical sessions to fulfil the requirements of this unit. Students who miss a session MUST contact the Unit Coordinator or Laboratory Supervisor at the earliest possible opportunity and provide a medical certificate or other relevant documentation. Failure to attend laboratory classes may be grounds for failing the unit. Students who miss more than one practical session, even with a medical certificate, may find they are required to complete their practical work the next time the unit is offered (i.e. Spring 2020). Students may not be permitted to enter the laboratory if they arrive after briefing notices advising WH&S or other experiment specific issues: This will be at the discretion of laboratory staff.

REQUIRED EQUIPMENT Each student must bring the following items to every practical session: – – – – – –

a laboratory notebook (Industry Standard) a laboratory coat a felt-tip pen for marking glass (water insoluble ink) a pad of linear metric graph paper (1mm graph paper is preferred) a calculator safety glasses

Workshops: The workshops will cover laboratory issues and data analysis (Module 1-4) or preparation for preceding Module 2 including: Background information, Experiment design, Protocols and procedures and analysis/calculations. Signed Risk Assessment/Safety Data Sheet (of hazardous reagents) required to enter laboratory and undertake Experiment Module 1-5 activity, and be eligible for Module assessment outcomes. The Laboratory Notebook is an integral part of every scientific laboratory in both the public and the private sectors. It documents the day-to-day accomplishments (experimental purpose, methods used, observations, results and conclusions). It has two main purposes. First, it is a valuable resource of methods and results. Second, it is a legal document that can be used to establish whether proper procedures were followed or which researcher was the first to make a ground-breaking discovery. Refer to the Metabolism vUWS site for additional information (incl: Module 1-5: Biochemical Assay Development Milestones & Objectives).

Exemplar: Refer to the Metabolism (300848) vUWS site Laboratory Program Folder. Resources: Each student must ensure they have an electronic device to access vUWS during Module 1-5 and Workshop activity. Workshops: The workshops will be used cover Instructional videos/calculations, laboratory issues and data analysis or preparation for preceding Experiments including: Background information, Experiment design, Protocols and procedures and analysis/calculations. Module 1-5: Biochemical Assay Development Milestones & Objectives available on vUWS.

7

Signed Risk Assessment/Safety Data Sheet (of hazardous reagents) required to enter laboratory and undertake Module 1 - 5 activity, and be eligible for Module assessment outcomes. Marking Criteria: Laboratory Report - Notebook

Value 0 or 1

Title & Aim: Accurate Materials: Complete (including pre-work/calculations) Methods: Reproducible Data/Results: Replicates for each dilution/time point All calculation steps with logical/orderly layout Appropriate decimal, significant figure, unit(s) of measure Tables/graphs formatted incl: title, legend, scale & labelled axes Outcomes: Appropriate analysis & interpretation of data/results Explains the importance of assay parameter Organization: Legible, logical/orderly layout, correct spelling & grammar Total

/10 marks (= 3%)

Laboratory Report - Team Leader

Format:

Va...