Chemistry 301 Introduction to Biochemistry

Course Orientation

Introduction

Welcome to Chemistry 301: Biochemistry, a three‑credit, intermediate‑level course. This course has a strong chemical emphasis, and stresses these two principles: biological processes obey accepted “chemical” laws; and successful chemical designs are used over and over in biological processes.

The Course Orientation document, which you are now reading, contains information you will need to successfully complete the course. Please read it through carefully and return to it often.

Course Materials

All of the course materials for this, including the textbook, are available online, on the course home page.

Textbook

https://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy

Using the Textbook

The course textbook is available online, through the link provided on the course home page. For easy access, we also link to a PDF of each unit’s textbook readings from within the Study Guide. Please note that these PDFs are not interactive; however, the Study Guide contains links to recommended online videos associated with the textbook.

Athabasca University Materials

Chemistry 301: Introduction to Biochemistry: Course Orientation. Athabasca, AB: Athabasca University, 2016.

Chemistry 301: Introduction to Biochemistry: Study Guide. Athabasca, AB: Athabasca University, 2016.M.

Student Manual. Athabasca, AB: Athabasca University.

Forms

The forms you will need to request an examination, apply for an extension, or inform Athabasca University of a change in your status are available through your myAU portal.

Course Design and Outcomes

The course materials have been prepared for self instruction and individualized study. What you should learn and how you should learn it are described in the Study Guide, which you will use in conjunction with the textbook. The Study Guide is designed to direct you through the course. Each unit in the Study Guide contains introductory remarks, learning objectives, required readings, a glossary of biochemical terms used in the unit, commentary on the textbook readings, and study questions with answers. The textbook is the main source of information, and has been chosen principally for its excellent figures and diagrams. Additional resources are also available through links in the Study Guide and the digital textbook.

Read the introduction to each unit in the Study Guide to determine the overall theme of the unit. Pay particular attention to the objectives—they describe what you will need to know to complete the course successfully. Then do the required readings, and use the study questions to test your understanding of the material. If your answers to the study questions do not agree with the answers provided, review the appropriate sections of the required reading. Your Academic Expert (AE) can also assist you if you are having difficulty. The two assignments ask you to apply the principles in the units to demonstrate that you have understood and can meet the objectives.

Upon successful completion of this course, you will be able to

• describe the organization of a eukaryotic and prokaryotic cell.
• explain the synthesis of proteins, lipids, nucleic acids, and carbohydrates and their role in metabolic pathways.
• describe the function of vitamins and cofactors, and provide examples of each group.
• use graphical techniques to analyze and describe simple, unimolecular enzyme activities.
• explain the chemical differences between DNA and RNA.
• describe nucleic acid structures, replication, transcription and translation.
• explain the major differences and similarities between the synthesis of DNA and that of RNA.
• describe how eukaryotic protein synthesis is controlled.
• apply the genetic code to translate mRNA sequences into (protein) amino acid sequences.

Using the Textbook

Ahern, Kevin, and Rajagopal, Indira. (2012/2013). Biochemistry Free and Easy. Version 2.0. All rights reserved.

This is a digital textbook in an interactive PDF format. You can access the textbook by clicking on the link provided on the course website.

The textbook provides a strong fundamental overview of the many important concepts in biochemistry and is well illustrated. It also contains lectures that you can click on to access if you choose to supplement your learning from the textbook and Study Guide. The Study Guide, written by the Course Professor and provided by AU, contains additional commentary and links, adding valuable information and detail.

AU Landing

The Athabasca Landing is social networking site hosted at Athabasca University. It provides a host of communications, networking, and information management tools including blogs, photos, wikis, groups, social bookmarks, profiles, and more. It is similar to Facebook but with two important differences: a) Permissions allow each individual to control who sees each item they share on the landing – the user can set whether each item can be seen only by a few colleagues, or whether it can be seen only by certain groups, and so on up to everyone online; b) it is a “boutique network” offering a special place, accessible only to Athabasca University students, staff, faculty, and alumni. If you are a member of any of these groups, sign in at https://landing.athabascau.ca using your normal student or staff ID and password.

The Landing group for this course is named Chemistry 301: Introduction to Biochemistry. The site offers a few activities that allow you to interact with other students as well as academic experts, and to further your learning of topics covered in the course. A discussion board enables you to ask questions. This is mediated by the academic experts and the course professor, who may answer some of the questions, but many of the questions are answered by students, so the students are helping each other learn.

The other two Landing activities are the study buddy exercise and online bookmarking. Students receive 1 overall bonus mark for the course if they participate in each activity. The bookmarking activity involves students posting online resources in biochemistry. Other students in the Landing may then access these, so this activity enriches the course content and the larger Landing group site. The study buddy activity allows students to connect and work with other students on a similar schedule, and helps them stay on track. Students must write a report at the end of the course describing how they worked with another student and how the activity affected their experience in the course. Please contact the course professor, Dr. Zenteno (shaunaz@athabascau.ca), regarding bonus marks for activities in the Landing.

Course Outline

Chemistry 301 consists of ten units.

Unit 1: Cells, Water, and Buffers

Lesson 1: Introduction to Biochemistry and Biochemical Research Literature
Lesson 2: Cells: The Bio of Biochemistry
Lesson 3: Water
Lesson 4: pH and Buffers

Unit 2: Energy

Lesson 1: Energy Reactions
Lesson 2: Thermodynamics
Lesson 3: Cellular Phosphorylations and Electron Transport
Lesson 4: Energy Efficiency
Lesson 5: Metabolic Controls

Unit 3: Structure and Function

Lesson 1: Proteins
Lesson 2: Nucleic Acids
Lesson 3: Carbohydrates
Lesson 4: Lipids
Lesson 5: Membranes and Transport
Lesson 6: Vitamins and Cofactors

Unit 4: Catalysis

Lesson 1: Activation Energy
Lesson 2: Enzyme Catalysis
Lesson 3: Enzyme Kinetics
Lesson 4: Enzyme Inhibition
Lesson 5: Control of Enzymes

Unit 5: Flow of Genetic Information

Lesson 1: DNA Replication
Lesson 2: DNA Repair
Lesson 3: Transcription
Lesson 4: Regulation of Transcription
Lesson 5: RNA Processing
Lesson 6: Translation

Unit 6: Metabolism I

Lesson 1: Overview of Metabolic Concepts
Lesson 2: Glycolysis, Fermentation, and Gluconeogenesis
Lesson 3: Citric Acid and Glyoxylate Cycles
Lesson 4: Acetyl-CoA and Cholesterol Metabolism
Lesson 5: Ketone Bodies
Lesson 6: Fatty Acid Oxidation and Synthesis

Unit 7: Metabolism II

Lesson 1: Carbohydrate Storage and Breakdown
Lesson 2: Pentose Phosphate Pathway
Lesson 3: Calvin Cycle
Lesson 4: Urea Cycle
Lesson 5: Nitrogen Fixation
Lesson 6: Amino Acid Metabolism and Catabolism
Lesson 7: Nucleotide Metabolism and de novo Biosynthesis

Unit 8: Signaling

Lesson 1: Cell Signaling
Lesson 2: Ligand‑gated Ion Channel Receptors
Lesson 3: Nuclear Hormone Receptors
Lesson 4: G‑protein Coupled Receptors (GPCRs)
Lesson 5: Receptor Tyrosine Kinases (RTKs)

Unit 9: Biochemical Techniques

Lesson 1: Cell Disruption and Fractionation
Lesson 2: Chromatography
Lesson 3: Electrophoresis
Lesson 4: Blotting
Lesson 5: DNA Techniques

Unit 10: Synthesis of Concepts in Biochemistry

Overview

Study Schedule

The following study schedule details the lessons and assignments for which you will be responsible in this course. We have indicated the approximate amount of time that you should spend on each lesson or assignment. You have a maximum of six months from your start date to complete the course, but please note that the schedule is based on a twenty‑week period. This time frame is more closely in line with the schedules of similar courses in traditional institutions, and allows you some leeway in case an unforeseen circumstance interrupts your studies.

If you find yourself falling behind, contact your AE to discuss the situation.

This course is challenging, but you should have no difficulty meeting these guidelines, if you set aside a study period every week, and do not procrastinate. You may read more about your course contract, and applying for extensions if required, in the Student Manual.

Note: Students who are receiving financial assistance or those in a grouped-study version of this course should check their course registration for special restrictions on the length of registration, and should be prepared to adjust their schedules.

Click here for a pdf version of the Study Schedule.

Student Evaluation

Your final grade in this course is based on the grades you achieve in two assignments and two examinations (a mid-term and a final). The table below summarizes these evaluation mechanisms and their weight. You may wish to use it to track the grades you achieve.

To pass the course, you must achieve 50% on each assignment and examination.

Each assignment consists partly of problems and partly of an analysis of one or more biochemical research papers.

Examinations

Each examination consists of multiple‑choice (20 marks) and short-answer (80 marks) questions. The mid-term examination will cover Units 1‑5, and the final examination will cover Units 6‑10. The final examination is not cumulative.

When you feel you are ready to take the mid‑term or final examination, you may request it by using the online examination request system. Please consult “Procedures for Applying for and Writing Examinations” in the Student Manual. Remember to arrange your exam well in advance of your course contract expiry date.

If you are not satisfied with your grade on the final exam, or you receive a grade below 50%, you are urged to re‑study the material and write a supplemental examination. Please refer to the Student Manual.

Appeals

Appeals to examination or assignment grades should be discussed first with your AE. For the correct procedure, see “Student Code of Conduct and Right to Appeal Regulations” in the current Athabasca University Calendar.

Your Academic Expert (AE)

Your AE has excellent academic qualifications, and is committed to helping you learn at a distance. He or she is available to answer your questions about course content or how to approach a problem or an assignment, and can direct you to the right person or department to help you with other problems that may be hindering your progress in your course or program. In addition, your AE will be responsible for marking your assignments.

We suggest that you call your AE as soon as you begin the course, and then get into the habit of contacting them regularly, when you complete a unit or when you run into any special problem. We have found that students who maintain regular contact with their AEs are most likely to be successful in completing their courses, so do keep in touch. You may read more about Athabasca University academic experts in the Student Manual.

In general, you should contact your AE first, through the Student Success Centre, with any queries about Athabasca University. You should have received an email from the Faculty of Science and Technology with information about the FST Student Success Centre and how to obtain information on AU procedures or have your academic questions answered by your AE or Course Professor.

For administrative inquiries or assistance from the course professor, please contact the Student Success Centre and indicate the type of assistance you require. The course professor is able to answer many of your questions that for some reason cannot be answered by your AE. The FST administrative staff is exceptional at providing quick and accurate answers to administrative procedures and deadlines.

Faculty of Science and Technology Student Success Centre:

Monday to Friday, 8:30 a.m. to 4:30 p.m. MT
Phone: 1-855-362-2870 (Toll free Canada and US)
E-mail: fst_success@athabascau.ca

You can also contact the Student Success Centre by clicking on the “Make a Request” button on the top right hand corner of your CHEM 301 course website.

Athabasca University Calendar

You are encouraged to refer to the current Athabasca University Calendar for important information concerning the University’s policies, practices, and procedures.