CLASS SYLLABUS. Prerequisite(s): CHEM 112; Biology 30. Note: Students with credit for BIOC 200 will not receive credit for BMSC 200.

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1 Please Note: This Class Syllabus is an important step in updating the format of our distance courses. If for any reason the Class Syllabus does not match the print Course Guide or online class information, the Class Syllabus shall be taken as correct. CLASS SYLLABUS COURSE TITLE: Biomolecules COURSE CODE: BMSC 200 TERM: Winter 2016 COURSE CREDITS: 3 DELIVERY: Online COURSE SECTION: W02-W99 START DATE: January 5, 2016 END DATE: April 7, 2016 Course Description An introduction to the structures, general properties, and functions of simple and complex biomolecules: amino acids, peptides, proteins, enzymes, carbohydrates, lipids and nucleic acids as well as membranes and solute transport. Prerequisite(s): CHEM 112; Biology 30. Note: Students with credit for BIOC 200 will not receive credit for BMSC 200. Course Objectives By the end of this course, students should be able to: 1. Identify and draw the molecules that represent the building blocks of the four classes of biomolecules to be studied in this course; proteins, nucleic acids, carbohydrates and lipids. This would include the amino acids, nucleotides, select monosaccharides and basic lipid structures. 2. Describe and draw the nature of the linkages between the various building blocks to the creation of higher order structures. This would include peptide bonds, glycosidic linkages and phosphodiester linkages. 3. Describe the various forces, covalent and non-covalent, contribute to the formation and stabilization of the various biomolecules. 4. Describe how the various structures of different biomolecules contributes to their biological functions. For example, oxygen storage/delivery by hemoglobin and myoglobin, reaction catalysis by enzymes, information storage/utilization by nucleic acids, energy storage by carbohydrates and lipids, membrane formation and transport by lipids and proteins. November 16, 2015 jt ck pk od

2 Course Overview This online course presents recorded video lectures over 10 learning modules and was created by Dr. Scott Napper. Each module covers new foundational concepts and theories that will guide you through the learning process to achieve the course objectives. Each module contains an overview of the content which includes the learning objectives for that module, some instructions as to how to proceed through the learning materials, a list of your required readings, a list of key terms and concepts that you should look for within the content, a list of frequently asked questions, review questions and answers, learning activities, and discussion questions. These sections, along with approximately three recorded video lectures per module and a PDF of the lecture slides should provide you with the learning materials you need to achieve the course objectives. Your Instructor Contact Information Dr. Oleg Dmitriev: , 3D30.7, Academic Health Sciences Bldg, Oleg.Dmitriev@usask.ca Students are encouraged to communicate with Dr. Dmitriev through . Inquiries can expect to receive a reply within 24 hours during the work-week and 48 hours on week-ends. Any changes to the course or anticipated delays in responses will be communicated to the class as a whole through notifications. Office Hours During the workday Dr. Dmitriev will be checking his s on an hourly basis. Profile Dr. Dmitriev is a Professor in the Department of Biochemistry at the University of Saskatchewan. His research interests focus on proteins that transport ions and small molecules across the cell membranes, and the role of these proteins in human disease. Dr. Dmitriev s lab uses Nuclear Magnetic Resonance spectroscopy and methods of protein biochemistry to study the function of three very different but equally exciting membrane transporters: ATP synthase, the power plant of most living cells, Wilson disease protein, which is responsible for handling copper in human cells, and multidrug transporter MdfA that protects bacterial cells against antibiotics and disinfectants. A list of recent publications from Dmitriev lab can be found here. Outside the lab, Dr. Dmitriev is interested in new models of disseminating scientific information and serves as Academic Editor of PLOS One on-line journal. Required Resources Readings/Textbooks/Online Resources Biochemistry: A Short Course with Launchpad 3rd Edition (2015), Tymoczko, John Textbooks are available from the University of Saskatchewan Bookstore: Page 2 of 8

3 Mobile Access Blackboard Mobile Learn TM is an app that is available on many devices including ios and Android for those occasional times when you may want mobile access. It is still recommended that you use a laptop or desktop computer for the majority of your online studies Class Schedule Week Module Readings 1 Module 1: Introduction to Biochemistry Stryer 3 rd Edition All of Chapter Module 2: Water Stryer 3 rd Edition All of Chapter Module 3: Amino Acids, Peptides and Proteins Module 4: Three Dimensional Structure of Proteins Stryer 3 rd Edition All of Chapter 3 Stryer 3 rd Edition All of Chapter 4 5 Module 5: Protein Function Stryer 3 rd Edition All of Chapter 9 MIDTERM EXAM Module 6: Enzymes 8 Module 7: Carbohydrates 9 Module 8: Lipids February 13, 2016 (9:00-10:30 a.m.) Stryer 3 rd Edition All of Chapters 6, 7 and 8 Stryer 3 rd Edition All of Chapter 10 Stryer 3 rd Edition All of Chapter Module 9: Biological Membranes and Transport Stryer 3 rd Edition All of Chapter Module 10: Nucleic Acids Stryer 3 rd Edition All of Chapter 33 TBA FINAL EXAM Note: If for any reason the Class Syllabus Reading List does not match the Module Reading List, the Class Syllabus shall be taken as correct. Page 3 of 8

4 Grading Scheme Midterm Exam 35% Final Exam 65% Total 100% Information on literal descriptors for grading at the University of Saskatchewan can be found at: Please note: There are different literal descriptors for undergraduate and graduate students. More information on the Academic Courses Policy on course delivery, examinations and assessment of student learning can be found at: The University of Saskatchewan Learning Charter is intended to define aspirations about the learning experience that the University aims to provide, and the roles to be played in realizing these aspirations by students, instructors and the institution. A copy of the Learning Charter can be found at: Evaluation Components There will be two comprehensive examinations on the content of the course, as outlined below. The format of the midterm and final examinations will consist of multiple-choice questions. However, the format of any deferred or special deferred final examinations may be a short answer or essay format. Midterm Exam Value: 35% of final grade Date: February 13, 2016 Length: 1.5 hours Purpose: The midterm exam will be a comprehensive exam covering materials of Modules 1 through 5. You will be notified through your PAWS and on the course site of the exact location. All students will write the midterm in Saskatoon UNLESS you reside more than 110 KM from Saskatoon. For those students that are more than 110 KM from Saskatoon you will need to complete the Special Centre Form for the Midterm Examination. This application form is available at Application must be submitted no later than January 20, 2016 Students writing in Saskatoon do not need to complete this form. Page 4 of 8

5 Final Exam Value: Date: Length: Purpose: 65% of final grade See Class Schedule 3 hours The final exam will be a comprehensive exam covering all the material of the course. Emphasis of the exam (75% of the questions) will be placed on post midterm material. Description: The final exam will consist of 100 multiple-choice questions. The exam will be a closed- book exam. Calculators are permitted. Term 2 examination period runs from April 9-30, Date and time of your final examination will be posted in the Final Examination schedule in your PAWS account in early February. More details will also be posted in your online class. All students will write the final exam in Saskatoon UNLESS you reside more than 110 KM from Saskatoon. For those students that are more than 110 KM from Saskatoon you will need to complete the Application for Final Examination Form. This application form is available at Application must be submitted no later than March 4, Students writing in Saskatoon do not need to complete this form. Additional Information Students who do not complete the midterm exam without seeking arrangement and approval from Dr. Dmitriev will be assigned a grade of 0% for the midterm. In exceptional circumstances (medical or compassionate) students will be allowed to write the midterm on an alternate date. Integrity Defined (from the Office of the University Secretary) Integrity is expected of all students in their academic work class participation, examinations, assignments, research, practica and in their non-academic interactions and activities as well. (Office of the University Secretary) It is your responsibility to be familiar with the University of Saskatchewan Guidelines for Academic Conduct. More information is available at Page 5 of 8

6 Module Objectives Module 1 Introduction to Biochemistry 1. To appreciate the differences and similarities of prokaryotes and eukaryotes. 2. Appreciate how chirality and stereochemistry relate to biochemistry. 3. To consider life from a thermodynamic perspective. 4. To appreciate the genetic basis of living organisms and how this relates to evolution. 5. Understand the basic chemical groups that are found in biomolecules. Module 2 Water 1. To be able to describe the physical characteristics of water and their importance to biological systems. 2. To be able to explain the chemical mechanisms of buffers and describe their importance to biological systems. 3. To be able to summarize the mechanisms and abilities of water to act as a solvent for biomolecules. 4. To be able to describe the four different types of non-covalent interactions that predominant within biological systems. Module 3 Amino Acids, Peptides and Proteins 1. To be able to identify or draw all of the amino acids and explain their structural characteristics. 2. To be able to assign the correct one & three letter codes to the amino acids. 3. Be able to construct and interpret titration curves for all of the amino acids, including being able to calculate isoelectric points. 4. To be able to draw the peptide bond and explain its structural characteristics. Module 4 Three Dimensional Structure of Proteins 1. To be able to describe the forces that drive protein folding and stabilization. 2. To be able to articulate the four levels of protein structure. 3. Understand the characteristics of different types of secondary structure. 4. To be able to express the structure/function relationship of select proteins. Module 5 Protein Function 1. To be able to articulate how the structures of hemoglobin and myoglobin contribute to their unique biological functions. 2. To be able to describe the various physiological signals which regulate hemoglobin s affinity for oxygen. 3. To be able to describe the molecular mechanisms of allosteric regulation of hemoglobin. 4. To be able to explain the molecular basis of sickle cell anemia and how it relates to malaria. Page 6 of 8

7 Module 6 Enzymes 1. To be able to describe the relationship between free energy and reaction properties, including how enzymes influence these parameters and the kinetic consequences. 2. To be able to describe specific mechanisms (binding effects and chemical effects) by which enzymes catalyze reactions. 3. To be able to describe the catalytic mechanism of a serine protease. 4. To be able to describe mechanisms, and kinetic consequences, of reversible and irreversible enzyme inhibition. 5. To be able to describe various physiological mechanisms for regulation of enzyme activity (allosteric and covalent modifications). Module 7 Carbohydrates 1. To be able to describe the different physiological roles of carbohydrates and interpret these functions with respect to their structures. 2. To be able to recognize and draw the common monosaccharides in linear and cyclic forms. 3. To be able to assign proper scientific names to disaccharides. Module 8 Lipids 1. To be able to describe the structure-function properties of lipids. 2. To be able to identify critical lipid structures and describe their biological functions. 3. To be able to articulate how the structures of lipid monomers contribute to higher order structures. 4. To be able to describe the diverse physiological roles of lipids. Module 9 Biological Membranes and Transport 1. To be able to describe the composition and complexity of biological membranes. 2. To be able to describe the degrees and mechanisms of specialization that exist within biological membranes. 3. To be able to compare and contrast the different categories of membrane proteins. 4. To be able to discuss the dynamic nature of membranes in terms of their composition and structure. 5. To be able to describe the events involved in membrane fusion. 6. To be able to compare and contrast the different categories of membrane transport systems. Module 10 Nucleic Acids 1. To be able to apply the system for nomenclature of nucleosides and nucleotides. 2. To be able to describe the physiological functions of nucleotides and nucleosides. 3. To be able to describe the structure and function of the various nucleic acids (DNA, mrna, trna, rrna). 4. To be able to describe the mechanisms and importance of DNA-protein interactions (histones and restriction enzymes). Page 7 of 8

8 Acknowledgements Course Author(s) Dr. Scott Napper, Ph.D., Professor, Department of Biochemistry, College of Medicine, University of Saskatchewan Instructional Design and Course Development Jordan Epp, BFA, M.Ed. (Instructional Designer, Distance, Off-campus, and Certificate Programs, Centre for Continuing & Distance Education, University of Saskatchewan) Jeanette McKee, M.Ed. (Instructional Designer, Distance, Off-campus, and Certificate Programs, Centre for Continuing & Distance Education, University of Saskatchewan) Page 8 of 8