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CHEMISTRY 151 : Biochemistry (Lecture) Department of Chemistry School of Science and Engineering Ateneo de Manila University

Nina Rosario L. Rojas, Ph.D. Schmitt Hall Room Ch-115

1st Semester, SY 2014-2015 Section A, 6:00-7:30 p.m., M & W

426-6001 local 5632 or leave message at local 5620

http://ch151admu.wordpress.com nrojas at ateneo dot edu

“As one scientist put it, carbon supplies life’s quantity… while much scarcer nitrogen supplies its quality…”

Michael Pollan (2006) The Omnivore’s Dilemma: A Natural History of Four Meals

COURSE DESCIPTION This is an introductory course in Biochemistry which covers structure-function relationships of the four major classes of biomolecules: carbohydrates, lipids, proteins and nucleic acids. The general scope of the course is as follows:

1. The Cell: its major chemical constituents; the role of water and its properties 2. Nucleic acids: structure-function relationships of DNA and RNA, replication, protein synthesis

(transcription and translation), gene expression and regulation 3. Proteins: amino acids, biosynthesis of amino acids, classification, structure, properties, structure-

function relationships, analysis of protein structure 4. Enzymes: classification, mechanism of action, regulation, and kinetics 5. Carbohydrates: nomenclature, classification and structure, properties and reactions, structure-

function relationships 6. Lipids: classification and structure, properties, structure-function relationships 7. Biological membranes and signaling systems 8. Overview of the cell's information processes 9. Techniques in genetic engineering

PREREQUISITE COURSES Prerequisite course: Organic Chemistry (CH 25 & 27, 25.5 & 27.5, or CH 21) or their equivalents. Note that these courses have their own prerequisites. COURSE OBJECTIVES At the end of the course, students should be able to

1. Recognize and write formulas and structures representative of the four classes of biomolecules. 2. Describe how relation between structure and properties of the biomolecules. 3. Relate the higher order structure and dynamics of the biomolecules to their functional groups and

physico-chemical properties. 4. Explain the biomolecules' functions in terms of their physico-chemical structure and properties 5. Explain the mechanism of enzyme action and its regulation. 6. Demonstrate a basic knowledge of gene expression and its control. 7. Discuss membrane structure and function, especially transport across biological membranes. 8. Discuss the basics of cell signaling. 9. Describe how key bioanalytical techniques work. 10. Explain through problems, cases, and the literature how bioanalytical techniques and approaches

are used to understand biochemical systems and to develop applications. 11. Explore current discoveries/trends in biochemical techniques/applications, especially those being

used in the Philippines and those which may have a significant impact in the local scene. 12. Discuss basic ethical concerns, if any, raised by these biochemical techniques and applications. 13. Read scientific literature in the field, identify key points in a journal research article, and present

them concisely and clearly in written and oral formats.

Note: Dr. Rojas will be away until June 25. In her absence Ms. Eunice Biteng will be the class instructor.

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HOMEWORK 1: Student Profile Sheet and ID picture are due June 23, 2014, Monday, via TurnItIn. Class ID = 8117102. Student Profile Sheet template is downloadable from the Downloads and Links page of the class website. (5 points for profile sheet, 5 points for ID photo, both via TurnItIn) COURSE OUTLINE AND PROPOSED SCHEDULE (subject to change due to weather, etc.)

Topic Dates Pratt & Cornely 2/E

I. Introduction and the chemical basis of life A. Self-review B. Quiz on June 18

Weeks 1-2

Ch 1

II. Review of aqueous chemistry Week 2 Ch 2

III. From genes to proteins Week 2-3 Ch 3

IV. Protein structure and function A. Protein structure B. Protein function

Weeks 4-6

Ch 4 Ch 5

First long quiz and feedback (around July 21) Week 6

V. Enzymes A. How enzymes work B. Enzyme kinetics and inhibition

Weeks 7-9 Ch 6 Ch 7

VI. Lipids and membranes A. Structure of lipids and membranes B. Membrane transport

Weeks 10-12 Ch 8 Ch 9

Second long quiz and feedback (around September 1) Week 12

VII. Signaling pathways Week 13 Ch 10

VIII. Carbohydrate structure and function Week 14 Ch 11

IX. A brief look at metabolism A. Overview of metabolism and free energy B. Glucose metabolism

Week 15 Ch 12 Ch 13

Third long quiz and feedback (around September 29) Week 16

Summary and review Week 17

Final Examination Week of Oct. 13-18

IMPORTANT NOTES:

Students are expected to read the material prior to the class session. Classroom sessions will be primarily devoted to class discussion, problem solving, and special topics.

Please solve the problems in the book! REQUIRED TEXT

Pratt CW & Cornely K (2011) Essential Biochemistry 2/E. Hoboken, NJ: John Wiley & Sons.

SUGGESTED READINGS Berg, J.M., Tymosczko, J.L., and Stryer, L. Biochemistry. New York: W.H. Freeman & Co., 5th or later

edition (2002 onwards). Boyer, Rodney. Concepts in Biochemistry 3rd Edition. New York: John Wiley and Sons, 2006. Campbell, M.K. and Farrell, S.O. Biochemistry 4th Ed. California: Thomson Brooks/Cole, 2005. Garrett, R.H. and Grisham, C.M. Biochemistry 3rd Ed. California: Thomson Brooks/Cole, 2005. Matthews, C.K., van Holde K.E., and Ahern K.G. Biochemistry 3rd Ed. San Francisco: Addison-Wesley,

2000. McKee, T. and McKee, J.R. Biochemistry. Boston: WCB/McGraw-Hill, latest edition. Nelson, D.L. and Cox, M.M. Lehninger Principles of Biochemistry 4th Ed. New York: W.H. Freeman and Co.,

2005 or later edition. ONLINE SOURCES Many sources and sites are on the downloads and links page of http://ch151admu.wordpress.com. Stryer 5th Edition Free Online Version (type in exact topics / section titles to access wanted info.):

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=stryer.TOC&depth=2 Garret and Grisham- 2nd Edition Free Online Version: http://web.virginia.edu/Heidi/home.htm

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National Center for Biotechnology Information Database (Check for free papers, books, and just about any biochem/molbio info you may need): http://www.ncbi.nlm.nih.gov

COURSE REQUIREMENTS AND GRADING

REQUIREMENT WEIGHT Letter Grade Range

Three long quizzes 60% A 92 and up

Quizzes, exercises, homework, problems, class participation, short class reports

5% B+ 87-91.99

Group project/presentation 15% B 80-86.99

Final examination (comprehensive) 20% C+ 75-79.99

TOTAL 100% C 68-74.99

Note: Finals have exemptions D 60-67.99

F Below 60

Students with a class standing of B+ or A are exempted from the final exam. Those with a B+ standing who wish to try to raise their grade to an A may take the final exam at no risk to their B+ grade. CLASS POLICIES Please see your student handbook for general class policies. The following are highlights and additions that apply to this class. ATTENDANCE

CUTS. There is no distinction between excused and unexcused cuts for attendance. Attendance is checked at the start of the class. If you are not present when your name is called, the seat plan is checked, or when the attendance sheet is passed, you are considered absent.

Excused absences are still considered cuts, but any activity missed (quizzes, etc.) will not be counted against the student’s grades. Students are excused for only the following reasons: (1) Students who will represent the school in an official activity and present a letter endorsed by the Associate Dean for Academic Affairs; (2) Students who are ill and present a medical certificate attesting to the illness endorsed by the Associate Dean for Academic Affairs.

HOMEWORK AND OTHER ASSIGNMENTS

For major requirements, such as take-home examinations: Submissions after the deadline will be given a 20% deduction per hour after the deadline.

For minor requirements, such as homework and exercises done outside the classroom: Submissions after the deadline will be given a 20% deduction per 24-hours after the deadline (electronic submissions) or for every day that the department office is open (physical submissions). Note: Minor requirements that are time-sensitive (e.g., material needed for class time) may have other penalties for late submission.

TESTS / QUIZZES/ OTHER INDIVIDUAL IN-CLASS REQUIREMENTS

Please use BLUE or BLACK ballpens only. Pencils can be used only when specified

Bring a scientific calculator to class when needed. Borrowing of calculators during tests is not allowed. Cellular phones and other electronic communication tools may not be used as calculators during tests.

Absence during exams merits a grade of zero. If you have an ADAA-endorsed excused absence coming up, please arrange AHEAD OF TIME with the instructor for a special exam.

In case of serious illness on your part, or death or serious illness in the immediate family that will require your absence during an exam, please call or email the instructor or department before the exam starts so we can consider arrangements for a special exam. Otherwise, you forfeit the exam.

ACADEMIC INTEGRITY

Keep in mind that by writing your name on a school requirement, you are claiming responsibility for its authorship.

Make sure that all your sources are properly acknowledged.

The minimum penalty for dishonesty (e.g. cheating, generating false data, plagiarism, etc.) is a grade of zero for the particular examination / report. University policies and procedures also apply.

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ELECTRONIC DEVICES

Cellular phones, music players, gaming or entertainment devices should not be used in class. Phones have to be turned off or on silent mode.

Cameras and recording equipment should not be used without permission of the instructor.

Computers may be used for class activities as noted by the instructor. ELECTRONIC REQUIREMENTS

Electronic requirements are also subject to the same rules and regulations as regular paper and inside-the-classroom requirements. Academic integrity should be maintained, regardless of communication medium used.

Some tips for electronic submissions for school work: (also at http://nrojas.wordpress.com/2011/09/08/some-tips-for-electronic-submissions/)

Always cc yourself and your groupmates when sending files to your profs, clients, etc. so you can test if the email service is working properly, the attachments are attached properly, etc.

Use a proper subject line to avoid getting your mail classified as spam.

In the body of your message, say something about what you are sending, and who are sending it (e.g., attached are files ____ from Group No. N, with members blah…, of course number XX section YY).

Rename the file you are sending in a way that makes sense to your recipient, so that it would be easy to track. Your papers are more likely to get lost of they say homework.doc vs. Ch151_HW2_Ch2problems.doc, or your cv for internship if it says cv.doc rather than DeLaCruz_Juan_cv2011.doc.

Do get a formal looking email account name for your professional life. Keep your sweetiepie@yahoo.com account for personal matters.

CONSULTATION HOURS Consultation hours are generally by appointment, because my schedule is somewhat irregular (I also teach at the Ateneo School of Medicine and Public Health, which runs by module). But please feel free to drop by my office, in case I am around. Please proceed to Ch-115, the end of the 1st Floor Hallway. My cubicle is 2nd from the right. You can also email me. In general, MWF are good. CLASS WEBSITE The general course site is: http://ch151admu.wordpress.com Make it a habit to check the site, especially for reminders and schedule concerns (e.g., what happens when classes are suspended). This can also be a venue for your comments and suggestions regarding our class. My main website is at http://nrojas.wordpress.com. You’re welcome to drop by. I also occasionally post links via my Facebook account (Nina Rojas, current profile picture is of a Lego lady chemist).