BIO 311: Biochemistry

Fall 2015
Prerequisite: CHEM 242. Organic Chemistry II
Recommended Bio 201 Human Physiology
Class meetings:
Lecture on Mon-Wed-Fri, 2:00- 2:50 pm in PISB106
Recitations on Friday: (Except for special notice)
Section 001: 10:00-10:50 am in PISB 108
Section 002: 11:00-11:50 am in PISB 108
Instructor:
Nianli Sang, M.B., M. Surgery., Ph.D.
Office: PISB 417
Phone: 215-895-6885
email: ns448@drexel.edu
Office Hours:
Fri: 3:00- 5:00 pm
Teaching Assistant:
Chengqian Yin, Ph.D. Candidate
PISB 401: 215-895-1436
Textbook (required):
Nelson and Cox, "Lehninger Principles of Biochemistry", 6th Ed., 2012
Or
Nelson and Cox, "Lehninger Principles of Biochemistry", 5th Ed., 2008
.
Suggested other textbooks for reference:
Berg, "Biochemistry", 6th edition, Freeman, 2007
Devlin, "Biochemistry with Clinical Correlations", 6th edition, Wiley, 2005

Website:
Course related materials will be posted in Bb-LEARN. Use your DrexelOne account and select
"My Courses" to access the BIO311 site. Included in these materials will be the PowerPoint
slides used in class in .pdf, assignments, review guidelines, back exams and announcement of
any changes in time and place of meetings. Slides used in lectures will be posted one day
before the meetings, and should be used for the purpose of studying this course only.

Goals
The overall goal of this course is for you to develop a thorough understanding of
how animals, including human beings, obtain energy and materials from the
environment to maintain life. We will discuss: 1) what are the major components that we
need and obtain from our diet; 2) how they are utilized to release energy; 3) how they
are utilized to synthesize other molecules we need to maintain life; and 4) the relevance
of these procedures in major human diseases. A numerous metabolic pathways formed
by sequential or coupled reactions and enzymes catalyzing these reactions will be
studied. In addition, how these pathways are regulated and their relevance to normal
cell physiology and human health will be discussed. You are expected to participate in
the discussion of enzymes and metabolic diseases, to develop critical, logical thinking
skills, and to integrate yourself an encompassing view of metabolic reactions and
pathways. A combination of knowledge and skills of thinking will hopefully lay a solid
foundation for your future careers in modern medical practice, biomedical research,
pharmaceutical development, biomedical education and other professions involving
biomedical sciences.

Outcomes
At the completion of this course you are expected to understand how animals
obtain energy and matter from the environment. This begins with understanding how the
dietary components carry the energy and fundamental elements and cofactors into
animal cells, how and where enzymes and cofactors work together to catalyze the
chemical reactions, and how these sequential or coupled reactions are linked together
to form metabolic pathways. Particularly, you are expected to know the basic energyproducing and energy-utilizing pathways (catabolism and anabolism) and how ATP links
these pathways. You are expected to understand the central roles of key molecules
(e.g. glucose, lipids, amino acids, molecular oxygen, acetyl-CoA, NAD(P)H, vitamins,
trace elements) in the pathways and how the pathways are regulated. These key
molecules and enzymes will be most intensely studied with regard to carbohydrate, lipid
and amino acid metabolism. Finally, examination of metabolism of nitrogenous
molecules will round out the major metabolic pathways. This composite knowledge will
lead to a better understanding of biochemical basis of human diseases (particularly
those common diseases such as diabetes, obesity, cardiovascular disorders and tumor)
and the benefits of good nutrition and healthy life-style.
Special requirement for each lecture will be posted in review
guidelines immediately after the lecture.

Course Outline
Module I: Foundations of Biochemistry
Week 1: Overview & Foundations of Biochemistry
Week 2: Bioenergetics, Reactions, Enzymes and Cofactors
Week 3: Cellular Machinery for ATP Biosynthesis
Week 4: Review and Mid Exam I
Midterm I
_______________________________________
Module II: Utilization of Carbon Sources
Week 5: Utilization of Glucose and Dietary Fat for ATP
Week 6: Storage of Glucose as Carbon Source Reserve
Week 7: Regulation of Glucose and Energy Homeostasis
Review for Mid Exam II
Midterm II (1st meeting of week 8)
_________________________________________
Module III: Biosynthesis and Disposal of Important Biomolecules
Weeks 8: Biosynthesis of Important Lipids and Lipid Transportation
Weeks 9: Biosynthesis of Important Nitrogenous Molecules
Week 10/11: Disposal of Nitrogenous Metabolic Wastes
Week 12: Final Exam: Date and location to be scheduled by University
__________________________________________
Please see schedule for more details!

Assessment: 100 + Extra = Total Points

1)

Weekly Quizzes: (25.0 points)

There will be 6 closed-book quizzes, each on an assigned Monday prior to lecture.
Each 5.0 point-quiz will be comprised of 6 questions relevant to the materials
presented during the previous weeks. You are expected to answer 5 and 5 only of
those 6 questions. If you answer all of them, only the first 5 answers will be graded,
wrong or right. The results of the best 5 quizzes of each student will count toward the
final score. Make-ups will not be regularly offered for weekly quizzes. Students with
justifiable excuses have the option to take a make-up quiz at the end of the term (see
schedule).
2) Midterm: (40.0 points)
There will be two midterm exams, 20.0 points each. The second midterm exam
may cover contents learned earlier, but emphasizing on the new materials discussed
after the first Midterm exam. The exams may contain multiple choice questions or short
questions or both. The answers to the questions should be concise but conceptually
clear.
3) Final exam: (35.0 points)
There will be a final exam given in week 12, date to be announced by the University.
It will be comprehensive, with an emphasis on the materials not covered in the midterms
I and II.

5) Optional Extra Points (8 points): There are three ways to get some extra points:
a) A pre-course test will be carried out in the first meeting. Your participation,
and a clear demonstration of your best effort will earn 2 extra points, no matter your
answers are wrong or right.
b) Optional assignments: (4 extra points) Assignments will be posted on BbLearn. The maximal one can receive are 4 extra points from these assignments. You
may finish the assignments and submit them electronically at anytime during the course
for extra points, but no later than 12:00 noon, November 30. These assignments are
optional, but if you decide to do them, you should do so independently and submit them
on time in order to get credits.
c) Extra for attendance: 2 extra points: Attendance is strongly recommended.
Sign-in sheets will be provided for each lecture. Those who signed in at least 25
lectures will get 2.0 extra points. Those who missed 4 or less meetings will receive 1.0
extra credit. Those who missed more than 4 lectures will not receive extra points for
attendance.

6). Make-up Exams:

Midterm and final examinations are mandatory. Absence from major examinations
(Midterms and Final) without pre-approval from the Instructor will receive zero for the
missed examination. For emergency that preapproval cannot be requested, sufficient
proof must be presented to request for an arrangement (eg: make-up examination).
Specially arranged make-up examination usually is different from, and may be slightly
more difficult than the regular one. Only one make-up will be arranged for each exam. If
you need special arrangement for the major exams, let me know as early as possible.
Please note: make-up exams are to be arranged for students who miss the
examinations with proper, justifiable excuses that are acceptable and approvable by
both the Instructor and the Department. According to university policy, no make-up
exam is allowed for students who fail the exam, or miss the exam without a
proper, justifiable excuse.
Due to busy schedule during the final week, make-up for final exam may be
arranged at the beginning of next term.
7) Academic honesty is extremely important.
All quizzes and exams are closed-book ones, and neither cheat-sheet nor study
material is allowed to be used during tests. Cheating and academic misconduct are
serious breaches of academic integrity and will be dealt with according to University
policy set up by the Office of Judicial Affairs. Cheating will not be tolerated.
8) Final grade: The final scores will be calculated by adding up all scores from the
above. To be fair with everyone, I take a firm stand that no change of grade will be
made.
>=97.0 =A+;
93.0-96.9=A;
90.0-92.9=A87.0-89.9=B+;
83.0-86.9=B;
80.0-82.9=B77.0-79.9=C+;
73.0-76.9=C;
70.0-72.9=C66.0-69.9=D+;
60.0-65.9=D;
55.0-59.9=D-

< 55.0=F.

Bio 311: Biochemistry

Weeks
One

Two

Three

Four

Prerequisite: Chem 242

Credit 4:00
Instructor: Nianli Sang, M.B., Ph.D.
(Schedule may change from time to time)
Lecs Topics
Weekly Reading
1 Introduction & Course Overview
TOC, Syllabus
2 Chemical Foundations : Bio-elements & Bio-molecules Chap 1.1-1.3, Chap 2
3 Biological Foundations: Nutrients, Digestion & Absorption
Chapters 13 and 6
4 Thermodynamics and Reaction Equilibrium
5 Reactions, Energy Transfer and ATP
6 Enzymes, Cofactors & Biological Redox
7 Acetyl CoA and TCA (Krebs) Cycle
Chapters 16 and 19
8 Mitochondrion & Electron Transfer Chain
9 Oxidative Phosphorylation
Happy Columbus Day-NO meeting
Review for Exam I, Q & A

Exam I
Five

Six

Seven

10
11
12
13
14
15
16
17

Glucose & Glycolysis

Fates of Pyruvate: Acetyl CoA, Lactate or other?
Dietary Lipids & Oxidation of Fatty Acids
Glycogen Synthesis
Pentose Pathway & Biosynthesis of Fatty Acids
Triacylglycerol and Amino Acids in Energy Metabolism
Regulation of Glucose Homeostasis
Regulation of Energy Homeostasis
Review for Exam II, Q & A

Chapter 14.1-14.2
Chapter 14.3
Chap 10, Chap 17
Chapter 14.4
Chap 14.5, Chap21.1
Chap 15, Chap 21.2
Chapter 21.1-21.2
Chapter 17.3, 18.3

Exam II
Eight

Nine

18
19
20
21
22
23

Ten

Eleven
Twelve

24
25

Biosynthesis of Cholesterol & Lipoproteins

Biosynthesis of Phospholipids and Eicosanoids
Biosynthesis of Amino Acids & One Carbon Units
Biosynthesis of Nucleotides
Biosynthesis of Other Nitrogenous Molecules
Metabolic Fates of Amino Groups and Urea Cycle
Thanksgiving eve-no class
Post Thanksgiving-no class
Catabolism of Special Amino Acids
Catabolism of Heme and Nucleotides
Review for Final Exam, Q & A. Make-up quiz

Chapter 21.4
Chapter 21.1
Chapter 22.2
Chapter 22
Chapter 22.3-4
Chapter 18.1-2

Chapter 22.4
Chapter 22.4

Final exam to be scheduled by UNIVERSITY

12/4/2015: Optional makeup quiz