1. Course Description and Learning Outcomes

COURSE DESCRIPTION

This is a three-unit lecture course that focuses on the structure and function of biomolecular compounds: proteins, nucleic acids, carbohydrates, and lipids and their roles in energy transduction and metabolism.

COURSE LEARNING OUTCOMES

After completing the course, you should be able to:

1. Demonstrate knowledge of the fundamental concepts in biochemistry.
2. Discuss the reaction pathways involving biomolecules such as proteins, nucleic acids, carbohydrates and lipids.
3. Apply biochemical reaction pathways in the analysis of problems and situations accompanied by erroneous metabolism.
4. Solve common qualitative and quantitative problems in biochemistry

OER TEXTBOOKS

You can download the following Open Education Resources as your reference for this course. 

• Biochemistry Free For All.pdf 
• BiochemistryFreeandEasy3.pdf 

MAIN TEXTBOOK REFERENCES

Ahern, K., Rajagopal, I. (2015). Biochemistry: Free and Easy. Available at:  https://biochem.oregonstate.edu/files/biochem/ahern/BiochemistryFreeandEasy3.pdf.

Ahern, K., Rajagopal, I., Tan, T. (2018). Biochemistry: Free For All. Available at: https://open.umn.edu/opentextbooks/textbooks/biochemistry-free-for-all-ahern.

Alberts, B., Johnson, A., Lewis, J., Morgan, D., Raff, M., Roberts, K., Walter, P., (2015). Molecular Biology of the Cell, 6^th Ed. New York: Garland Science.

Berg, J., Tymoczko, J., Stryer, L., Gatto, G. (2012). Biochemistry, 7^th Ed. New York: W.H. Freeman and Company.

Campbell, M., Farrell, S., & McDougal, O. (2017). Biochemistry. Pacific Grove, CA: Brooks Cole.

Nelson, D., Cox, M. (2008). Lehninger Principles of Biochemistry, 5^th Ed. New York: W.H. Freeman and Company.

Voet, D., Voet, J. (2011). Biochemistry, 4^th Ed. New Jersey: John Wiley & Sons, Inc.

Copyright Notice

In compliance with intellectual property and fair use policies, no part of the materials here can be sold, distributed, or reproduced. Please note that permissions from attributed sources only allow the use of the materials within this class. Hence, uploading of class materials on sites like CourseHero etc. or sharing copies outside this class count as violations against the intellectual property rights of the attributed authors.  

2. Course Outline

INTRODUCTION: The Sense of Biochemistry

BUFFERS AND LIVING SYSTEMS: pH, pKa, Ka, titration curves, Henderson-Hasselbach

STRUCTURE AND FUNCTION OF BIOMOLECULES

1. Proteins
   1. Function of proteins
   2. Structure: 1°, 2°, 3°, 4°, pI
   3. Isolation and characterization methods
      1. Electrophoresis
      2. Chromatography
      3. Sequencing
      4. Others
   4. Enzymes
      1. Classification
      2. Kinetics: Km, Vmax, Michaelis-Menten, Lineweaver-Burke
      3. Minerals and coenzymes

Departmental Exam 1

2. Nucleic Acids

1. 1. Function
   2. Structure: 1°, 2° (A, B, Z), 3° (supercoiling), histones, chromatin
   3. Central dogma of molecular biology (Prokaryotes and Eukaryotes)
      1. Replication
      2. Transcription
      3. Post-transcriptional modifications
      4. Translation
      5. Post-translational modifications
   4. Mutation
      1. Types of mutation
      2. Effects of physical, chemical and viral agents on the structure and function of nucleic acids
      3. Protective mechanism and repair systems
   5. Isolation and Characterization methods
      1. Electrophoresis
      2. Polymerase chain reaction
      3. Recombinant DNA technology
      4. cDNA libraries
      5. Sequencing
      6. Others

Departmental Exam 2

3. Carbohydrates

1. 1. Structure and properties of carbohydrates
      1. Classifications and examples
      2. Chemical properties
      3. Physical properties
      Functions of polysaccharides
      1. Storage
      2. Structural
      3. Glycoproteins and proteoglycans

4. Lipids

1. 1. Structure and properties of lipids
      1. Simple neutral lipids
      2. Phospholipids
      3. Compound lipids
      Biological membranes
      1. Components
      2. Organization
      3. Function and Transport Processes

 METABOLISM

1. Introduction: Design, Phases, Stages and Regulation

2. Bioenergetics

1. 1. Free energy, high energy compounds and coupled reactions
   2. Substrate level phosphorylation, electron transport chain, oxidative phosphorylation
   3. Inhibitors of ATP production

3. Catabolic Pathways and Metabolism

1. 1. Carbohydrate metabolism
      1. Glycolysis
      2. Kreb’s cycle
      3. Glycogenolysis
      Lipid metabolism
      1. Lipolysis
      2. B – oxidation of fatty acids
      Degradation of amino acids
      1. Transamination, oxidative deamination, direct deamination
      2. Metabolic fate of the carbon skeleton
      3. Metabolic fate of nitrogen

Departmental Exam 3

1. Anabolic Pathways and Regulation
   1. Carbohydrate metabolism
      1. Gluconeogenesis
      2. Pentose phosphate pathway
      3. Biosynthesis of polysaccharides
   2. Lipid metabolism
      1. Biosynthesis of fatty acids
      2. Lipogenesis
      3. Ketogenesis
      4. Biosynthesis of cholesterol
   3. Nitrogen metabolism
      1. Biosynthesis of non essential amino acids
      2. Utilization of amino acids as precursors of non-protein compounds
   4. Nitrogen balance
   5. Metabolic pathways of purine and pyrimidines
      1. De novo synthesis
      2. Salvage pathways

INTEGRATION OF METABOLISM

1. Digestion and Absorption
2. Transport Processes of Biomolecules in the Blood
3. Role of Hormones and other Mediators in Metabolism
4. Post Absorption and Starvation

Departmental Exam 4

3. Weekly Schedule

The table below shows in which weeks and sessions specific modules will be taken up. 

You can also download this table here.

4. Mode of Delivery

For this Second Semester, AY 2020-2021, the course is delivered using our university’s learning management system (LMS), the UP Manila Virtual Learning Environment (VLE). The course is designed to enable independent and self-paced study among the learners through the posting of all the topics and important references that will serve as guide.

Asynchronous Sessions (required): Content will largely be delivered asynchronously meaning they can be accessed outside of the indicated SAIS class hours. Recorded lecture videos or live sessions, readings, and tasks will be uploaded. Materials on LMS as well as specific rubrics in activities will also serve as guide in the completion of requirements.

Synchronous Sessions (not required): Synchronous sessions will happen during our class hours which will also serve as our scheduled online consultation if you have any questions about the coverage.  

5. Course Requirements

PRE-FINAL CLASS STANDING (2/3)

1. Four (4) Departmental Exams (60%)
2. Class activities (20%)
3. Class quizzes and probsets (20%)

FINAL EXAM (1/3)

Grading System

%                                 Grade Eq.

[90, 100]                     1.00

[85, 90)                       1.25

[80, 85)                       1.50

[75, 80)                       1.75

[70, 75)                       2.00

[65, 70)                       2.25

[60, 65)                       2.50

[55, 60)                       2.75

[50, 55)                       3.00

[40, 50)                       4.00

[0, 40)                         5.00

6. Course Policies

By proceeding with this online class, you agree to the Code of Honor below:

"I will work on the activities on my own without the help of another person, unless said so by the instructor. I will not share course materials made available in the LMS to those who are not enrolled in this subject. I will not make solutions to homework and exams available in any way to other learners. I will not engage in any other activities that will dishonestly improve my results or dishonestly improve or damage the work of others." 

(edited and adopted from https://mooc.house/)

7. Guide for the Synchronous Sessions

Pre-session:

1. Install an application for viewing PDF files
2. Check that your phone/desktop is fully charged.
3. Check that you have your charger, headsets, and other necessary equipment that you might use during our Synchronous sessions
4. Log-in a few minutes early so you can check your audio and/or video prior to the start of the online session

During:

1. Use your UP Mail in joining Zoom/Google (or other online platform) meetings
2. Mute your microphone when you enter the room.
3. Use icons to express yourself ("clap", "thumbs up" etc.). You may use the “Raise Hand” icon you want to speak (available in Zoom).
4. Contact (Email or SMS) the instructor/classmate when you are having connectivity issues.

 Post-session:

1. Use the designated VLE forum or messaging for questions and concerns, so that the entire class can participate in them as well.

You will be receiving meeting details through the Announcement or Calendar blocks. These should be seen either at your Course Page or the Dashboard. 

8. Policies for Group Work, Submissions, Questions

Please practice ACADEMIC INTEGRITY AT ALL TIMES. 

Group work

1. Groups are assigned at random. Please get to know your group mates, group messaging is allowed so you can contact them through the VLE messaging platform:  (found in the upper right corner of your page).
   
2. Please use the forums for discussions so that your interactions and contributions are documented. You are allowed to speak in whatever language that suits you, however, we would like to emphasize respect and disbar foul language.
3. For Group submission, a single submission from a group member will suffice. 
4. You will be asked to rate your team members and their contributions to a group work. Please rate them objectively. 
5. To all members, please actively participate and contribute to your group. They are your accountability and study team in this remote education.

Individual Work

1. All assignment submissions will be via the VLE platform unless otherwise indicated by the instructor.
2. Please read and follow instructions carefully especially when submission types are specified. 
3. If multiple submissions are done, only the most recent submission will be checked. 
4. Take note of deadlines and try to follow them as much as you can. We will try to post activities ahead of time so that you can make contingency plans in the submissions like internet/gadget access. 

Quizzes

1. Please assume that this is a normal classroom quiz with closed notes and no other tabs or googling available unless stated otherwise. 
2. Please be ready with your gadgets and internet accessibility when taking quizzes especially the timed ones. 
3. Please let your instructor know right away when you have trouble accessing quizzes.

Forums/Discussions

1. This is the main platform for class interactions and for posting of questions or clarifications. 
2. For class concerns, please put them here so that others who might have the same questions will be included and will also receive the answer. DO NOT INDIVIDUALLY MESSAGE the instructor for this. It will spam our emails/message boards and we might not be able to get to your question. 
3. Use this platform to simulate a normal class conversation. Again, no language specifics - formal or informal is fine - as long as we are respectful of each other. 

For Clarifications/Questions/Concerns

1. As stated, the main platform for posting these is through the forums. 
2. The main methods for contacting the instructors are through the forums and message boards.  
3. Email addresses or mobile numbers are secondary means of communication if the first two methods fail.
4. Please give us 24-72 hrs to respond to your queries. 
5. Live consultations (synchronous sessions) will also be platforms to address questions accumulated throughout the week or for other discussions.  

9. Meet your Instructor

The Chem 40 Course Team
	Dr. Ma. Constancia Carrillo Mark Jeremiah Cleofas Ciara Christianne Lim Dr. Marcelina Lirazan Dr. Marilou Nicolas

Happy Sem, kiddos!

10. Explore the VLE platform

Get to know your learning platform and its features. Look around and see what you can do with it. 

Here are some sites you can check out for this:

• https://docs.moodle.org/20/en/Student_tutorials
• http://45.55.1.62/images/currentStudents/eLearning/studentResources/studentQuickStartMoodleGuide.pdf 

You can also download the Moodle mobile app on your phone/tablet and configure the VLE website (vle.upm.edu.ph) into it. 

For your dashboard, here are some of the things you might want to look around on: