Download Syllabus BIO 152 – Spring 2015

Syllabus BIO 152 – Spring 2015
Instructor: Dr. Corinne Pierce
Office: Barnum 111
Email: [email protected]
Office Hours
Monday: 1:30 PM – 2:30 PM
Tuesday: 2:00 PM – 3:00 PM
Other times by appointment
Teaching Assistant: Michael Babokhov
Office: 20 Dana
Email: [email protected]
Office Hours
Friday: 2:30 PM – 3:30 PM
Other times by appointment
Open Door Policy: If my door is open, please feel free to stop in (and I will do my best to see you). If my
door is closed, it means that I am unavailable. My door will always be open during office hours.
Class Time and Location
Block I+: Monday & Wednesday, 3:00-4:15 PM in Barnum 008.
Optional Recitation
A recitation time is reserved on Tuesdays from 4:30-5:45 PM in Barnum 008. This will mainly be used to
hold review sessions on Tuesdays before exams (all scheduled for Wednesday) but additional
recitations may be held if we feel there is a need. These recitations are optional and no new material
will be covered during this time.
Course Description
Biochemistry is the study of the chemical processes of living things. The course is an in-depth
examination of the structure and function of biomolecules: chemical and physical properties of proteins,
carbohydrates, and lipids; enzyme kinetics and mechanisms; metabolism of carbohydrates, lipids, and
amino acids and the metabolic relationships of organ systems. At the end of the course, students will
understand how the chemical and physical properties of biological molecules influence their function.
Furthermore, they will be able to use this knowledge to describe how chemical changes alter the
function of biological systems. The student will master new vocabulary and demonstrate an
understanding of the molecular structure and function of biological molecules.
Prerequisites
Prior to taking BIO 152, students must have completed BIO 13 and CHEM 50 or CHEM 51
• If you are considering a major in Biochemistry, you should enroll in the year-long biochemistry
course offered through the chemistry department (Chem 171/172 – cross-listed as Bio 171/172). Bio 152
will not fulfill course requirements for the biochemistry major.
• Since we focus on the central energy-yielding pathway, we will not be covering nucleic acid
structure or function; the phosphogluconate shunt; photosynthesis; amino acid metabolism; or the urea
cycle. If you need to know this material for standard exams, you will have to review it on your own.
Required Text
Moran, Horton, Scrimgeour, & Perry. Principles of Biochemistry, 5th Edition, Pearson Publishing © 2011.
This text is also available as an ebook at a reduced price and can be rented for the semester from both
the bookstore and other 3rd party sites.
http://www.amazon.com/Principles-Biochemistry-5th-Edition-ebook/dp/B008UFWMTE/ref=ktr_rin_dp
Course Objectives
At the end of this course students should be able to:
• understand acid/base chemistry as it applies to biological molecules.
• use the first and second law of thermodynamics to predict the direction of chemical reactions that
occur in biological systems.
• understand the basic molecular properties of 3 of the 4 classes of biological molecules (proteins,
carbohydrates, and lipids) and the subunits from which they are formed. (Nucleotides are covered
more in depth in other courses).
• explain how the structure of biological molecules dictates function and how changes in structure
direct biochemical reactions.
• describe the catalytic functions of enzymes, and perform enzyme kinetics calculations.
• describe the network of chemical reactions that make up central metabolism.
• explain how regulatory systems maintain homeostasis in biological systems and how disease and
trauma disrupt these systems.
• read and understand scientific literature pertaining to subject matter in biochemistry.
• apply knowledge & concepts to novel problems
Evaluation
Grading will be determined by four in-class exams and homework/in-class assignments. All of these
items are voluntary (you can choose to hand them in or not based on your own priorities) – but please
be aware that opting out of graded assignments will result in a grade of zero for that assignment.
Exams
There will be four exams given during normal class time over the course of the semester. There will be
no final exam. Dates for the exams are listed in the course schedule. Each exam will cover assigned
lectures. Although the four exams are not cumulative, later material does tend to build on concepts
taught earlier in the semester. Exams will be weighted when determining final grades such that:
Exam
% of final grade
Best exam score
25%
2nd best exam score
25%
3rd best exam score
15%
Worst exam score
10%
Excluding verifiable illness or serious family emergency, all students are expected to take tests on the
days that they are given. Illness must be verified in writing by Health Service or a licensed physician (on
letter-head stationery); a family emergency must be verified in writing by the Dean. If you need to miss
an exam for a valid reason, your other three exam scores will be used in the calculation of your final
grade – with the best two exam scores counting for 30% each, the 3rd best score counting for 15%, and
the missed exam not being included. There will be no makeup exams.
Errors in marking of exams (including addition errors) must be brought to the instructor’s attention
within four school days of the test’s return to class. To expedite review of potential errors in grading, all
exams will be scanned. To request an error correction, email Dr. Pierce with the specific questions you
are contesting. Keep in mind, if a reevaluation of an exam is requested, we reserve the right to re-grade
the entire exam.
Homework & In-class assignments
There will be at least 10 graded homework/in-class assignments. The ten best scores will make up the
remaining 25% of your final grade. All homework assignments will be submitted through Trunk (unless
explicitly stated otherwise) and late assignments will be assessed a 20% per day penalty and will not be
accepted more than 2 days after the due date. If you are not present for an in-class assignment you will
receive a grade of zero for that assignment.
Grading scale
The following is a minimum grading scale. The instructor reserves the right to curve the scale upward (so
that the average class grade is at least a C), but will not curve the scale to grades below the following:
A+ : 99-100%
A : 93-98%
A- : 90-92%
B+ : 87-89%
B : 83-86%
B- : 80-82%
C+ : 77-79%
C : 73-76%
C- : 70-72%
D+ : 67-69%
D : 63-66%
D- : 60-62%
F : <60%
Trunk site (http://trunk.tufts.edu)
If you are registered for this course you can gain full access to this site. Trunk will contain information
including the syllabus, course schedule, grades, old exams, and lecture slides. Additionally, the Trunk
Forums should be used for general questions regarding the content of the course.
Slides – PowerPoint slides will be posted to Trunk no less than 12 hours prior to lecture. Slides
prior to lecture may not contain complete information, as some information will be filled in
during the discussion. In these instances, lecture slides will be updated after lecture.
Previous Exams – The material on exams from 2013 (plus answers) will be available on Trunk.
These exams can be used to test your comprehension but the old exams were written by a
different professor and covered the material in a slightly different order.
Forums – General questions about course schedule or content should be posted to the Forums
on the Trunk site so that information from the instructors can then be transmitted to everyone.
We will attempt to answer these questions as quickly as possible and post the replies to this
site. In this way, everyone can benefit from these discussions. Emails sent directly to the
professor or TA about course content or the course schedule may not receive an immediate
response. However, questions of a private nature should never be posted to the Forums and
should be directly sent to the professor or TA (see below).
Course Policies
Each class period will begin and end on time. Please arrive on time so that disruptions are kept to a
minimum. As research on learning shows, unexpected noises and movement automatically divert and
capture people's attention, which means you are affecting everyone’s learning experience if your cell
phone, pager, laptop, etc. makes noise or is visually distracting during class. For this reason, please turn
off your mobile devices (cell phones, MP3 players, etc.). You may take notes on your laptop, but please
turn the sound off so that you do not disrupt other students' learning. If you are doing anything other
than taking notes on your laptop, please sit in the back row so that other students are not distracted by
your screen.
Classroom activities may be recorded by a student for the personal, educational use of that student only
with written permission from Dr. Pierce. Recordings may not be further copied, posted online,
distributed, published or otherwise used for any other purpose. All students are advised that classroom
activities may be taped by students for this purpose and should act accordingly.
Email Procedures
When emailing the instructor, students should send email from tufts.edu accounts or through Trunk.
Email addressed from other sources (for example: hotmail, gmail, or yahoo accounts) may not make it
through junk mail filters. The instructor will answer all emails within 24 hours during the week and
within 48 hours on weekends. Any emails sent after 7pm will not get a definite answer before 9am the
following morning. This includes the evening before the exam.
Students with Disabilities
If you need special accommodations because of a disability, you must provide the instructor written
documentation at least two weeks prior to the first exam. Questions should be directed to the
instructor or the Office of Disability Services (617-627-4539)
Academic Integrity
Science is a collaborative field. Therefore, you are encouraged to work together when learning and
studying the material. All exams and assignments are intended to measure an individual’s
understanding of the material and therefore collaboration is prohibited (unless explicitly stated
otherwise by the instructor). Do not share computer files of work (including text, graphs, tables, etc.) to
be submitted for grading. We expect all students to know and abide by the University’s policy on
academic integrity. To find the pdf document “Academic Integrity for graduate and undergraduate
students, 2010-2011” go to the student services site –
http://uss.tufts.edu/studentaffairs/judicialaffairs/index.asp – and follow the hotlink under Academic
Integrity. Plagiarism and/or cheating will be handled harshly. Students will be referred to the Dean of
Students for disciplinary action and will receive a grade penalty following the University disciplinary
guidelines.
Course Schedule
On the following page is a tentative schedule of classes with the corresponding reading in the Moran
textbook. Note, the color-coding highlights what material will be covered on which exam (blue = exam
1, pink = exam 2, green = exam 3, and orange = exam 4). We have one “Tufts Monday” where we have
class on a day other than Monday and it is in bold and highlighted. Also, remember that this course
follows Block I+: Monday & Wednesday, 3:00-4:15 PM.
* denotes there will definitely be an in-class assignment on these days (Lack of a * does not mean an in
class assignment will not be given)
Class
Date
Day
1
14-Jan
Wed
2
19-Jan
21-Jan
Mon
Wed
3
26-Jan
Mon
Topic
Reading
Introduction to Biochemistry/Water, Buffers,
and pH
Martin Luther King Day
Amino Acids & Physical Properties of Proteins; 2o
Structure
Proteins 3o and 4o Structure; Hemoglobin and
Myoglobin, and Antibodies and Antigens
Purification and Analysis of Proteins
Enzyme Kinetics
Enzyme Kinetics & Enzyme Regulation
Six Classes of Enzymes
Exam 1
President’s Day
Enzyme Catalysis
Membrane Structure, Fluidity & Transport
Introduction to Metabolism; Thermodynamics
and ATP
Literature Paper*
Carbohydrate Structure
Exam 2
Glycolysis and Fermentation
Citric Acid Cycle
SPRING RECESS!
Ch 1 pg. 1-16, Ch 2
Mon
Wed
Metabolic Engineering and Biofuels
Gluconeogenesis; Glycogen Metabolism
19 30-Mar
20 1-Apr
21 6-Apr
Mon
Wed
Mon
22 8-Apr
Wed
Metabolomics
Exam 3
Reduction Potential, ETC and Oxidative
Phosphorylation
Fatty Acid Oxidation
Review article
Ch 12 pg. 355-362; Ch 12
pg. 368-377
TBA
23 13-Apr
24 14-Apr
25 15-Apr
20-Apr
26 22-Apr
27 27-Apr
Mon
Tues
Wed
Mon
Wed
Mon
Hormone signaling
Caloric Restriction and Aging
Warburg Effect
Patriots’ Day
Exam 4
Literature Paper*
4
5
6
7
8
28-Jan
2-Feb
4-Feb
9-Feb
11-Feb
16-Feb
9
18-Feb
10 19-Feb
11 23-Feb
Wed
Mon
Wed
Mon
Wed
Mon
Wed
Thurs
Mon
12
13
14
15
16
25-Feb
2-Mar
4-Mar
9-Mar
11-Mar
Wed
Mon
Wed
Mon
Wed
16 & 18
M&
W
Mar
17 23-Mar
18 25-Mar
No Classes
Ch 3 pg. 55-68; Ch 4 pg.
85-99
Ch 4 pg. 99-119; Ch 4 pg.
122-130
Ch 3 pg. 68-79
Ch 5 pg. 139-148
Ch 5 pg. 148-159
Ch 5 pg, 134-138
No Classes
Ch 6
Ch 9
Ch 10 pg. 294-305; pg.
308-315
Ch. 8 pg. 227-244
Ch 11 pg. 325-342
Ch 13 pg. 385-394
No Classes
Ch 14
Ch 16 pg. 475-483, 493500
TBA
TBA
Ch 13 pg. 408 and TBA
No Classes
TBA
NOTE: We will do our best to follow the course syllabus – however, we reserve the right to make
modifications as needed during the semester.