San José State University
Chemistry Department
CHEM 130A, Biochemistry I, Section 01, Spring 2014
Instructors:
Prof. Marc d’Alarcao
Dr. Elizabeth Pollom
Office Location:
MD: Duncan Hall 607
EP: Duncan Hall 605
Email:
marc.dalarcao@sjsu.edu (preferred method of contact)
epollom@stanford.edu (preferred method of contact)
Office Hours:
Class Days/Time:
Classroom:
GE/SJSU Studies Category:
Prerequisites:
Tue and Thu at 2:30 - 3:30 PM, and by appointment
Tuesdays and Thursdays at 10:30 – 12:20 PM
Duncan Hall 135
Partial Fulfillment of Area R: Earth & Environment
CHEM 55 (with grades of "C" or better; "C-" not accepted).
CHEM 112B (with grades of "C" or better; "C-" not accepted).
Course Web Page
Instructions: http://www.sjsu.edu/at/ec/canvas/
Login: https://sjsu.instructure.com/
Course Description
Chemistry of amino acids, carbohydrates, lipids and nucleotides. Studies of protein
structure and function, protein isolation, enzyme kinetics and enzyme mechanisms.
This course also contains content that overlaps with Area R learning objectives.
Course Goals and Learning Objectives
Course Learning Outcomes
Upon successful completion of the course, students will be able to describe and solve
problems related to:
CLO (1) the structure and function of the major classes of biomolecules,
CLO (2) the chemical and physical mechanisms of their action, and
CLO (3) the experimental basis by which these mechanisms are deduced.
GE Area R (Earth and Environment) Goal
Biochemistry I, CHEM 130A, spring 2014
Page 1 of 10
Students will cultivate knowledge of the scientific study of the physical universe or
its life forms. Students will understand and appreciate the interrelationship of science
and human beings to each other.
SJSU Studies Area R Learning Outcomes addressed by Chem 130A:
Upon successful completion of this course, students will be able to:
Area R GELO (2): distinguish science from pseudoscience.
Area R GELO (3): apply a scientific approach to answer questions about the earth
and environment.
Additional this course addresses the following GE Content Objectives:
Diversity: Issues of diversity shall be incorporated in an appropriate manner.
Civic Learning: Courses shall address the civic relevance of the topic in an
appropriate manner.
“A minimum aggregate GPA of 2.0 SJSU Studies (R, S, & V) shall be required of all
students as a graduation requirement.” To see full text, review University Policy S11-3 at
http://www.sjsu.edu/senate/docs/S11-3.pdf.
Program Learning Objectives Covered in CHEM 130A
Upon successful completion of the course, students will be able to:
PLO (5) - Demonstrate understanding of core concepts and to effectively solve
problems in biochemistry.
Required Texts/Readings
Textbook
Donald Voet and Judith Voet Biochemistry, 4th Edition (ISBN: 978-0-470-57095-1)
Other Readings
Occasionally papers from the scientific literature will be suggested for additional
information on certain topics covered.
Dropping and Adding
Students are responsible for understanding the policies and procedures about add/drops,
academic renewal, etc.
Instructions for adding or dropping a class are available at:
http://my.sjsu.edu/students/student_tutorials/index.html.
The deadlines for adding or dropping a class are available at
http://www.sjsu.edu/registrar/calendar/2144/index.html.
Biochemistry I, CHEM 130A, spring 2014
Page 2 of 10
Information about late drops is available at:
http://www.sjsu.edu/aars/policies/latedrops/
Students should be aware of the current deadlines and penalties for adding and dropping
classes.
Assignments and Grading Policy
Requirements:
Graded work will include a total of three in-class exams, one comprehensive final
exam, and three in-class quizzes. Homework problems from the text will be suggested, but
not graded. It is assumed that students will do all suggested homework. Working the
homework problems is an excellent way to prepare for exams and quizzes.
Course Grade:
There are five equally weighted scores that will determine the final grade in the
course: Exam I, Exam II, Exam III, Final Exam, and Quiz Average. Each will be given a
raw score and a scaled score. The raw score will simply be the number of points earned for
correct answers on a particular exam or quiz, while the scaled score will reflect your
performance on that material as compared with your classmates. Scores will never be scaled
down. Generally, the average score on an exam will be scaled to the C+/B- range, though I
reserve the right to adjust this in either direction if, in my estimation, the class overall
performed differently than a “typical” class.
The final grade for the course will be determined by averaging five scaled scores:
those from in-class Exams I, II, and III, the comprehensive Final Exam, and the quiz average
(all five weighted equally). The course grade will be determined from the resulting average
as follows:
Scaled Score Average
Final Course Grade
97-100
94-96
90-93
A+
A
A-
87-89
84-86
80-83
B+
B
B-
77-79
74-76
70-73
C+
C
C-
67-69
64-66
60-63
< 60
D+
D
DF
Biochemistry I, CHEM 130A, spring 2014
Page 3 of 10
Missed Exams and Quizzes
If an exam or quiz is missed without a legitimate excuse a scaled score of 0 will be
entered for that exam. If an acceptable excuse is provided then the exam grade will be
prorated. In no case will a make-up exam or quiz be given.
Exam Regrades
If you feel that an error was made in the grading of your exam you may submit the
exam, together with a written description of the error, to me for regarding not later than one
week after the graded exam is returned to the class. However, I will not entertain requests
for more partial credit on a problem unless the posted partial credit scheme was not properly
applied to your exam. Be aware that students who submit frivolous regrade requests may
become ineligible to receive future letters of recommendation from me.
University, College, and Department Policies
Students in this course are expected to be familiar with and follow various policies
developed by the University and the Chemistry Department. The important policies are:
Consent for Recording of Class and Public Sharing of Instructor Material
University Policy S12-7, http://www.sjsu.edu/senate/docs/S12-7.pdf, requires students to
obtain instructor’s permission to record the course.

“Common courtesy and professional behavior dictate that you notify someone when
you are recording him/her. You must obtain the instructor’s permission to make
audio or video recordings in this class. Such permission allows the recordings to be
used for your private, study purposes only. The recordings are the intellectual
property of the instructor; you have not been given any rights to reproduce or
distribute the material.”

“Course material developed by the instructor is the intellectual property of the
instructor and cannot be shared publicly without his/her approval. You may not
publicly share or upload instructor generated material for this course such as exam
questions, lecture notes, or homework solutions without instructor consent.”
Academic Integrity
“Your commitment as a student to learning is evidenced by your enrollment at San
Jose State University. The University Academic Integrity Policy S07-2 at
http://www.sjsu.edu/senate/docs/S07-2.pdf requires you to be honest in all your
academic course work. Faculty members are required to report all infractions to the
office of Student Conduct and Ethical Development. The Student Conduct and
Ethical Development website is available at http://www.sjsu.edu/studentconduct/.”
[From the SJSU Accessible Syllabus template, updated Jan. 13, 2014]
Campus Policy in Compliance with the American Disabilities Act
“If you need course adaptations or accommodations because of a disability, or if you
need to make special arrangements in case the building must be evacuated, please
make an appointment with me as soon as possible, or see me during office hours.
Presidential Directive 97-03 at
Biochemistry I, CHEM 130A, spring 2014 Page 4 of 10
http://www.sjsu.edu/president/docs/directives/PD_1997-03.pdf requires that students
with disabilities requesting accommodations must register with the Accessible
Education Center (AEC) at http://www.sjsu.edu/aec to establish a record of their
disability.” [From the SJSU Accessible Syllabus template, updated Jan. 13, 2014]
Emergencies and Evacuations
"If you hear a continuously sounding alarm, or are told to evacuate by Emergency
Coordinators (colored badge identification), walk quickly to the nearest stairway
(end of each hall). Take your personal belongings, as you may not be allowed to
immediately return. Follow instructions of Emergency Coordinators. Be quiet so
you can hear. Once outside, move away from the building. Do not return to the
building unless the Police or Emergency Coordinators announce that you may."
From Addendum to all Chemistry Department Greensheets – revised August 2006
Chemical Safety
Chem 120S is a required course for all chemistry majors and minors and a
prerequisite for all Chem 180/298 research. (From Addendum to all Chemistry
Department Greensheets – revised August 2006)
Workload Expectation
“Success in this course is based on the expectation that students will spend, for each
unit of credit, a minimum of forty-five hours over the length of the course (normally
3 hours per unit per week with 1 of the hours used for lecture) for instruction or
preparation/studying or course related activities including but not limited
to internships, labs, clinical practica. Other course structures will have equivalent
workload expectations as described in the syllabus.” From SJSU Academic Senate
Policy S12-3
Biochemistry I, CHEM 130A, spring 2014
Page 5 of 10
CHEM 130A, Biochemistry I, Spring 2014, Course Schedule
The schedule is subject to change. Changes will be noted in class.
Class
Date
Lecturer Readings and Topics
1
Jan. 23
MD
Chapter 1 – Intro, cells, basic energetics, intramolecular forces
2
Jan. 28
MD
Chapter 2 - Water, pH, electrolytes, buffers
3
Jan. 30
MD
Chapter 3 - Thermodynamics
4
Feb. 4
MD
Chapter 4 - Amino acids
5
Feb. 6
MD
Chapter 6 - Intro to proteins, purification
6
Feb. 11
MD
Quiz 1; Chapter 7 - Proteins, primary structure
7
Feb. 13
MD
Chapter 7 - Proteins, AA analysis, chemical synthesis
8
Feb. 18
MD
Chapter 8 - Proteins, secondary structure
9
Feb. 20
MD
Chapter 8 - Proteins, secondary and tertiary structure
10
Feb. 25
MD
Chapter 8 - Proteins, tertiary, quaternary structure
11
Feb. 27
MD
Chapter 9 - Protein folding
12
Mar. 4
MD
Chapter 10 - Hemoglobin
13
Mar. 6
14
Mar. 11
MD
Chapter 11 - Carbohydrates
15
Mar. 13
MD
Chapter 11 - Carbohydrates
16
Mar. 18
MD
Chapter 11 - Carbohydrates
17
Mar. 20
MD
Quiz 2; Chapter 12 - Lipids
18
Apr. 1
MD
Chapter 12 - Lipids
19
Apr. 3
MD
Chapter 12 - Lipids
20
Apr. 8
MD
Chapter 12 - Lipids
21
Apr. 10
EP
Chapter 13 - Introduction to enzymes
22
Apr. 15
23
Apr. 17
EP
Chapter 14 - Enzyme kinetics
24
Apr. 22
EP
Chapter 14 - Enzyme kinetics
25
Apr. 24
EP
Chapter 14 - Enzyme inhibition
26
Apr. 29
EP
Quiz 3; Chapter 15 - Enzyme mechanisms
27
May 1
EP
Chapter 15 - Enzyme mechanisms
28
May 6
EP
Chapter 15 - Enzyme mechanisms
29
May 8
30
May 13
Final
May 16
9:45-12:00
Exam I
Exam II
Exam III
MD & EP Comprehensive Review
Comprehensive Final Exam
APPENDIX 1:
CHEM 130A – Biochemistry I
Examples of Specific Content Related to Area R GELOs
Diversity Issues
1. Biochemistry was discovered and developed by a diverse group of scientists.
a. Class activities: When their discoveries are discussed in lecture,
underscore the triumphs and challenges of scientists with diverse
backgrounds in the development of modern biochemistry. Examples
include Maud Menten (as in Michaelis-Menten equation), G.N.
Ramachandran (as in Ramachandran plot), Gerty Cori (as in the Cori
cycle), etc.
b. Assessment activities: Exam and quiz questions. Please see sample
question 1.
2. The two sides of sickle-cell trait.
a. Class activity: Discuss sickle cell disease including the specific
mutation involved and the biochemical and medical consequences.
Discuss the resistance to malaria that is conferred to those who are
heterozygous in sickle-cell trait. Point out that while 1 in 90,000
Americans has sickle cell disease, the prevalence among African
Americans is 1 in 500. Discuss the issues related to research equity,
treatment quality, and the role of legislative action in addressing this
disparity. Note that despite the fact that cystic fibrosis affects fewer
than half as many people as sickle cell disease, the NIH spends 1.4
times as much on the former than the latter (see Pediatrics 2006,
117, 1763-70.)
b. Assessment activities: Exam and quiz questions. Please see sample
questions 2, 3.
3. Lactose intolerance.
a. Class activity: Discuss the evolutionary advantage of having infants
lose the ability to digest lactose as they get older. If this is indeed
advantageous, why do certain populations retain the ability to digest
lactose throughout their life? Discuss possible reasons that lactose
intolerance roughly correlates with latitude.
b. Assessment activities: Exam and quiz questions. Please see sample
question 4.
4. Dietary fish and heart health.
a. Class activity: Discuss the epidemiological studies showing very low
incidence of coronary heart disease among Greenland Inuit
populations despite high fat diets, and the hypothesis that a diet high
in cold water (fatty) fish is responsible. Discuss the relationship
between omega-3 fatty acids, prostaglandins, clotting times, and
heart health. What is the role of low dose aspirin in improving heart
health?
b. Assessment activities: Exam and quiz questions. Please see sample
questions 5, 6, 7.
5.
6.
Civic Content
7. An essential vitamin that shaped the world: the role of scurvy in history.
a. Class activities: Discuss the biochemistry, pathology, and history of
scurvy. Discuss the role of scurvy in shaping the modern world,
including the consequences of the rescue of Jacques Cartier’s crew
from scurvy by the St. Lawrence Iroquoian Chief Donnacona, the
death of Vitus Bering from scurvy because he ignored the advice of
his naturalist Georg Steller to eat the curative scurvy grass that was
abundant on their route, and the role of lime juice in British naval
grog in establishing the British navy as the dominant sea force in the
16th-19th centuries.
b. Assessment activities: Exam and quiz questions. Please see sample
questions 8, 9, 10.
8. Altitude adaptation and culture
a. Class activities: Discuss the evolutionary advantages of hemoglobin
binding to bisphosphoglycerate (BPG), including the ability to adapt
to high altitude. Ask the class to name the highest elevation national
capital. Use this as an opportunity to point out that the answer is
different depending on your political opinions. (i.e. Lhasa is higher
that La Paz, but is only a “national capital” if you believe Tibet is a
country). Discuss the fact that more than half a million people live in
each of these cities and explain the biochemical mechanisms by
which they can do so despite the rarefied air. Mention the interesting
phenomenon that unlike in many sea-level cities, in La Paz, the poor
neighborhoods are located at higher elevation than the affluent
neighborhoods. Also, discuss the relationship of this topic to blood
doping in bicycle racing.
b. Assessment activities: Exam and quiz questions. Please see sample
question 11.
Distinguishing Science from Pseudoscience
9. How are biochemical discoveries made?
a. Class activity: Discuss why it took so long to establish that vitamin C
deficiency causes scurvy, including the lack of controlled
experiments, the changing content of vitamin C in foods over time
because of oxidation upon exposure to heat or metals such as copper
and iron, and the prevalence of ineffective “snake oil” cures.
b. Assessment activities: Exam and quiz questions. Please see sample
questions 9.
10. Weight loss fads.
a. Class activity: Discuss the actual biochemical and physiological
consequences of certain diet fads and aids that claim to lead to
weight loss. Focus on how experiments would be designed to confirm
an effective method for weight loss.
b. Assessment activities: Exam and quiz questions. Please see sample
question 12.
APPENDIX 2:
Sample test and/or quiz questions used to assess GE Area R LOs in CHEM
130A
1. Identify a person mentioned in lecture who was responsible for advancing
the field of biochemistry and who had to overcome some personal
challenges to do so. Please a) name the person, b) identify her/his
achievement in biochemistry, and c) describe the personal challenge he/she
faced and how it was overcome.
2.
3. Sickle cell disease is a destructive condition that can significantly reduce life
expectancy. The disease is hereditary. Please a) describe the biochemical
change that results in the disease, and b) explain how the sickle cell gene has
be maintained in the gene pool despite the destructive disease it causes.
4.
5.
6. Describe a situation where, in your opinion, research funding for a human
disease with biochemical components has been inequitably allocated. Why
do you think the allocation is not equitable? Are there public policy solutions
that could be applied to redressing the inequity?
7.
8. Lactose is -4-D-galactopyranosyl-D-glucopyranose. Please draw the
chemical structure of lactose. Do you expect any humans to be able to digest
lactose’s beta glycosidic linkage? If so, please describe the evolutionary
advantages that may have made this possible.
9.
10.
11. Describe ways in which increasing the ratio of -3 to -6 fatty acids in the
diet can affect heart health.
12.
13. Describe a possible biochemical basis for the observation that Greenland
Inuit populations have lower incidence of heart disease than other
populations consuming high-fat diets.
14.
15.
16. Why do physicians advise their patients to avoid taking aspirin before
surgery? What is the biochemical and biological reason for the effect that
leads to this advice?
17.
18. Describe, in detail, the cause of scurvy and the biochemical process affected
in scurvy. How does altering this process lead to the symptoms of the
disease?
19.
20.
21. Why did it take so long for the cause of scurvy to be unequivocally
established?
22. How did cultural differences among the navies of France, England, Spain,
and Portugal affect the incidence of scurvy in their sailors? Give an example
of a historical consequence of these differences.
23.
24. As one of the favorites to win the La Paz, Bolivia marathon, you have trained
there for the several weeks it requires to become adapted to its 3700-m
altitude. A manufacturer of running equipment who sponsors an opponent
has invited you for the weekend to a prerace party at a beach house near
Lima, Peru, with the assurance that you will be flown back to La Paz at least
a day before the race. Is this a token of respect for you or an underhanded
attempt to handicap you in the race? Explain your answer using your
knowledge of the biochemistry of altitude acclimation.
25.
26.
27. An eat-all-you-want nostrum, which was touted as a “starch blocker” [and
which the Food and Drug Administration ultimately banned], contained an
-amylase-inhibiting protein extracted from beans. If this substance had
really worked as advertised, what unpleasant side effects would have
resulted from its ingestion with a starch-containing meal? Discuss why this
substance, which inhibits -amylase in vitro, would not do so in the
intestines after oral ingestion.