Introduction, Policies, & General Education (HUB) for Biochemistry I & II
Fall 2025/Spring 2026
Welcome to Biochemistry!!! These courses were designed as a 2-semester
series, and both semesters should be taken for a complete picture of this
important and foundational field. Both
courses are not required and many opt for just the fall course, which offers a
foundation in understanding the molecules that make life possible. The second semester offers a foundation in
understanding the energy and chemical principles under which these molecules
interact.
The field of biochemistry
encompasses a large and diverse field of inquiry. It obviously interfaces with both chemistry
and biology, but
as well psychology,
physics, mathematics, astronomy, bioinformatics, and of course, medicine all seek a
level of biochemical understanding. Yet, Biochemistry is its own stand-alone
discipline. The student studying biochemistry essentially needs a
high-school level of understanding of the
principles and nomenclature of cell and molecular biology; however, understanding biological molecules
most importantly requires a solid foundation
in the chemical principles learned in general and organic chemistry. Without this background, a student will
struggle to grasp
the concepts and
significance of biochemistry.
Another purpose of these courses
(421/422 & 621/622) is to introduce biochemistry
in a way that lays a foundation for further study; be that in elective courses here at BU, in
graduate school in virtually any biology
or chemistry discipline, or in professional schools; including medicine, dentistry, nursing, and
even law. For example, this two-semester course, along with the
two-semester Molecular Biology courses
(BI 552/553), covers all the material one would confront in the Graduate Record Subject Examination
in Biochemistry, Cell and Molecular Biology,
and in particular for the MCAT5 examination with its emphasis on biochemistry. The competencies listed for the MCAT5 exam
will require that both semesters
(Biochemistry I & II). The course
will primarily take a problem-solving
approach, integrated with a certain amount
of memorization that is required to become fluent in the language of biochemistry. As mentioned above, this two-semester series
is considered an integrated whole
course, although there are distinct flavors
in each semester. The first semester
describes the molecules of
life and the chemical
principles under which they operate to maintain life. The
second semester describes how these molecules are utilized and inter-converted, from small
molecules to macromolecules and the function
of organelles, and how energy is derived from them to power life as we know it. This course is a good preparation for
advanced
courses such as
Physical Biochemistry (CH525), Protein Chemistry (CH722), Chemical Biology (CH423), Enzymology (CH625),
Epigenetics
(CH626), Metallobiochemistry (CH 634), RNA Structure and Function (CH427), Molecular Biology
Laboratory (BB522), Chemical Biology Laboratory
(CH 524), and Molecular Biology I & II (BI552 & BI553).
ENROLLMENT
As alluded to above, this course
constitutes the first of a two-semester course in introductory
biochemistry. It is designed for
undergraduate science majors, in particular those majoring in Biochemistry and
Molecular Biology (BMB) or Chemistry: Chemical Biology, as well as and
first-year master's students. In the
fall, students are enrolled in BB 421, BB 527, or BB 621, depending on their
program of study. Students will attend
lectures in one of two parallel lecture sections (Section A1; MWF or Section A2,
TR) (except those in BB 527, which is the lab only). These two sections will cover the same
material at roughly the same pace and order.
However, the A1 and A2 lectures do not share common exams. Therefore, students should attend the lecture
in which they are registered to ensure they have all of the section-specific
information for the midterm exams.
Graduate students (those in BB 621) will have a scholarly research
topic/project and will meet at various times during the semester to discuss
topics and other issues related to this assignment. For the laboratory (Section B), all students
perform the same basic laboratory experiments and attend either one of two
pre-lab discussion sections (Section C).
In the spring, the courses are BB 422, BB 622, and BB 528. All students will attend the same lectures,
take the same exams, and perform the same laboratory experiments.
PREREQUISITES
All students are REQUIRED to have
passed two semesters of Organic Chemistry
with a C or better to take Biochemistry I & II. While this is the only prerequisite, students who have not had any biology
since high school will find that in
certain portions of the course they will need
to work harder. Likewise, while the four
semesters of prerequisite
chemistry are
required, the levels at which this chemistry was taught (or learned) will vary drastically
among students. For EVERYONE, we will provide material in cell and
molecular biology, and general and organic
chemistry, available on /Achieve/, that comprises required prerequisite material for the
class, as well as reading from Chapter 1 of
the textbook. Students may find study of
this material in the first
week or two of the
class will allow you to assess your preparedness for this course. Because of the structure of the curriculum
here at BU, a
majority of students
who take biochemistry have also had BI 108 (Intro Biology 2) and perhaps BI 203/206 (Cell Biology/Genetics). For those who
have not taken such courses, or need a refresher, we have included Pre-requisite Material (available
on the Lab Blackboard (Bb) site (see below)). This material includes a list of expected
prior knowledge in
both chemistry and
biology, a video on basic molecular biology (It will review essential fundamental concepts required
for successfully
mastering the material
related to the biochemistry of information transfer
(how the information in DNA is stored and utilized)), and a quiz on the video material. This quiz and 1-2 questions on Exam 1 will comprise 2% of your final grade and
is a great incentive to get up to speed
at the beginning of the course. Others
may prefer independent
study of one of the
many textbooks used in these courses (e.g., Albert's “Biology of the Cell‚” or Cooper
& Hausman's, “Cell‚”, or you could form a study group with some of your classmates who have had
this course to
help you review some
of the essential biology concepts you should have been exposed to in your high-school biology
course. For those of you who have had BI 203, you may
recognize some of the biochemistry and molecular
biology to which you were exposed.
TEXTS & WEB SITES
The course uses two
textbooks for the entire two semesters:
(1) “Lehninger‚ “Principles of Biochemistry
8th edition“ by Nelson and Cox. The textbook is generally offered as an ‚
“e-book “ through enrolling in ‚ “Achieve “ This resource also has
required homework and quizzes to assist in your study, as well as supplemental
materials and problems, as well as answers to all the problems in the
textbook. (2) The laboratory will
utilize ‚ “Biochemistry Laboratory Manual 6th edition “ by Tolan, Medrano, and Low. This laboratory manual has introductory
material for each laboratory exercise that describes the theoretical background
of each experiment and problems for study.
For the Fall Laboratory, many of
the exercises have been updated, so the details of the weekly procedures will
be provided online each week or so on the Lab Blackboard (Bb) site (see
below). These courses have multiple web
sites. The A1 course (those in Section A1 in BB 421 & BB 621 from CAS or
MET) has its own website and will NOT use Blackboard. It
was designed and is managed by Prof. Tolan and does not require Kerberos
passwords for access. The Blackboard site for A1 is only for FirstDay. There are separate Blackboard sites for the A2
course, BB421/621
A2 Biochemistry 1 (Fall 25) and the Laboratory, BB421/527/621
A1/A2/C1/C2 Biochemistry 1 (Fall 25).
Those registered in BB 527 should use the Laboratory Blackboard site. For the A1 section, all readings, problems,
announcements, examples of old exams, course outlines, etc. will be available
on the A1 web site.
For the Spring course (Section A1
in BB 422 & BB 622 from CAS or MET), there is only one section. This course will have its own website and NOT use
Blackboard.
In addition, because a problems
approach is essential for learning biochemistry, students will use the
companion Web site for the textbook: Achieve.
The site has the homework assignments
and assigned quizzes, as well as access to an interactive e-Book and other
resources for key concepts encountered in the course, such as interactive
metabolic maps, animated figures for biochemical techniques and enzymatic
mechanisms, problem solving videos, and other resources.
For those who are going on to
graduate study in chemistry or biochemistry, a more advanced text such as
Mathews, van Holde, and Ahern's ‚ “Biochemistry, “ or Garrett & Grisham's ‚
“Biochemistry, “ are recommended. For
those who are premed, another text, Devlin's ‚ “Textbook of Biochemistry with
Clinical Correlations “ could be purchased.
In addition, a subscription to the American Chemical Society journal, ‚
“Biochemistry, “ and/or the American Association for the Advancement of Science
journal ‚ “Science “ are both available at drastically reduced prices for
students and are useful for those going on in biochemistry.
GRADES
We don't wish anyone to be overly ‚
“grade conscious,“ but this can’t be helped.
Therefore, it is important to understand at the very outset exactly how
you will earn your grade. Depending on
which course you have enrolled, the exact grading process will be different
(see syllabus). All the courses (except
BB 527) have FOUR common aspects; the lecture examinations, the homework, the
Pre-requisite quiz, and the laboratory.
In the first semester for Section A1 there will be 4 one-hour exams and one two-hour
comprehensive final exam, which will be held at the scheduled times denoted on
the syllabus: schedule. For both
sections, the Final Exam is mandatory and no make-ups will be given, so make
your plans accordingly. For the five
exams, each of which will cover roughly the same amount of new material, from
7-9 lectures. The final exam will be
part new material and part cumulative.
The exams will be of a more problem-oriented nature, although due to the
size of the class and the amount of material, multiple-choice and matching type
questions cannot be eliminated. The
examinations will cover material from lecture only, but pedagogical
concepts from the laboratory might creep in.
In addition, several of the homework problems could re-appear on the
examinations.
For the A1 section, because
everyone makes mistakes, only your best 3 of the 4 one-hour exams will be used
for computation of your grade. As such, no
make-up exams will be given. If
you miss an exam for ANY reason, it will count as your lowest exam. If you miss more than one exam (which
must be for a legitimate reason (due to a serious illness, a personal or family
emergency, or a religious observance; see below)), your two remaining exams
will be averaged to give you the third score. If you miss the Final exam, you
will be given an Incomplete (I) (see below).
We don't wish anyone to be overly “grade conscious,”
but it is important to understand at the very outset exactly how you will earn
your grade. Depending on which course
you have enrolled, the exact grading process will be different (see
syllabus). All the courses (except CH/BI527)
have two common aspects; the lecture examinations and the laboratory. In the first semester, each lecture section
will have 3-4 one-hour exams and one two-hour final exam, which
will be held at the scheduled times denoted on the appropriate syllabus. The Final Exam is mandatory and no make-ups
will be given, so make your plans accordingly.
Each of the THREE-FOUR one-hour exams will cover roughly the same amount
of new material and the final exam will be at least partially cumulative. The exams will be of a more problem-oriented
nature, although due to the size of the class and the amount of material,
multiple-choice and matching type questions cannot be eliminated. The examinations will cover material from
lecture and may include some of the basics concepts from the laboratory
(not specific analytical problems). Only
those parts of the laboratory for which you will have already turned in a lab
write-up, and had in returned for feedback will be included on the exam. In addition, several of the “suggested”
problems could appear on the examinations (see below).
Because
everyone makes mistakes and the possibility of isolation, only your best 3 of
the 4 one-hour exams will be used for computation of your grade. As such, no
make-up exams will be given. If you
miss an exam for a legitimate reason (due to a serious illness, a personal or
family emergency, or a religious observance; see below), it will count as your
lowest exam. If you miss more than one exam (the second must be
for a legitimate reason), your two remaining exams will be averaged to give you
the third score. If you miss the Final exam, you will be given an Incomplete
(I) (see below). An attempt to ease into the course,
the first exam will cover less material than subsequent exams.
The exams during the second
semester will be organized slightly differently. The details will accompany the course
schedule to be given out in January.
Homework Policy:
On the ACHIEVE website, each semester there will be 30-50
problem-sets assigned as homework. In the
A1 sections in both semesters, there will be about 15–20 Adaptive Quizzes from
the chapters in the assigned reading designed to help study for each exam. All homework and quizzes are due at midnight
on Sundays (1–4 per week). In the
Spring, the Quizzes are due by 4 pm on Tuesdays right before the exams. These are hard deadlines, there
will be no makeup opportunities on the homework or quizzes regardless of any
reason. The entire set of 45–60
assignments of homework and quizzes will comprise 7-8% of your overall grade,
mostly as incentive because doing them will help prepare yourself for the
exams. Because no makeups are allowed,
approximately your lowest 20-33% of all the homework and quizzes will not
count. For example, for Fall 2025, which
will have 36 homework assignments, only your top 25 homework scores (of 34) and
top 15 quiz scores (of 20) will be used for calculating your overall homework
score. Each quiz and/or homework is potentially
worth the same (0.2%) fraction of your grade despite differences in the number
of questions and/or problems in each assignment. For Spring 2026, which will have 33-36
homework assignments, only your top ~75% homework scores and quiz scores will
be used for calculating your overall homework score.
COURSE SCHEDULE, GETTING HELP, AND SUCCESS STRATEGIES
All of the listed lectures and labs
have required attendance. Much of the
material presented in the lecture and lab discussion sections is not found in
any of the textbooks. We will attempt to
follow the accompanying schedule denoted in the syllabi, which have been
prepared with some degree of optimism.
It must be remembered that this is a difficult course, both in content
and in the time required, particularly with the inclusion of the laboratory and
its necessary theoretical background.
While this in an introductory biochemistry course, it isn't a ‚ “survey
“ course since, as noted above; biochemistry is an interdisciplinary science
that requires background, formal and informal, in several aspects of chemistry
and biology. This is the rationale
behind providing students with a list of terms and topics with which they should be familiar before tackling
this course.
PLEASE don't hesitate to approach an instructor or
teaching fellow if the course pace is too slow or too fast for you, or if you
have difficulties. ANY difficulties
should be solved whenever they occur rather than be allowed to pile up
to the end of the semester. This chiefly
applies to your understanding of the material.
If you have difficulties in comprehension, please ask for the available
help during office hours or at another arranged time. All members of the teaching staff, professors
and teaching fellows, check their email regularly and will normally respond
within 24 hours. Due to the
interdisciplinary nature of the biochemistry field, bear in mind that the
educational background of students in this course is different. Areas in which we seem to be “creeping” to
the biologist may seem like a jet flight to the chemist, and in other areas, of
course it will be exactly the opposite.
This course offers you the opportunity to form multidisciplinary study
groups with other students not in your major who have different diverse
backgrounds. If there are persistent
difficulties, see Dr. Tolan who can refer you
to outside tutors in biochemistry.
Through years of experience, we have learned from
successful students that one is advised to recopy one's notes daily or
weekly. You would be surprised at how
well this helps for the comprehension and review of important points and
"jogging" your memory. The
reading for each lecture is set out in the syllabus. It is also available on the class web
site. It is best to read the textbook
prior to lecture and work through the “suggested” problems. Following the lecture is a good time to
recopy notes and work through the problems.
Although the answers to all the homework problems are on Achieve, it is best to work
through each problem before looking at the answer. Do not hesitate to attend office hours to ask
questions about lecture material or the assigned problems, especially those for
which your answer and the provided answers differ.
Workload: You should expect to spend at 4-8 hours per week
outside of class studying for the lecture portion of BB 421/621 or BB 422/622 (i.e.
~2 hrs per lecture). The required work includes (i) reading the textbook
in preparation for class,
(ii) rewriting your lecture notes
after class, and (iii) working on the
homework problems. In addition, the work associated with the laboratory portion of the course
is constant and includes preparation of the weeks protocols and notebook
entries, then analysis of the data from each week’s lab and preparation of the
report. You are encouraged to work with
your lab partner, or a group, for all of this except the report. You should expect to spend 3-6 hours per week on
the laboratory assignments. The success
students have in this course is strongly
linked to how much time and effort they put into it,
so if you want to succeed be prepared to consistently do the necessary work.
You should feel free to ask questions during the lecture. That is part of what the lecture is for, and we strongly encourage it. If you are attending lecture in person and wish to ask a question, raise your hand and the instructor will get to you as soon as they reach a suitable break. We feel very strongly that there is no such thing as a stupid question. If, after some thought, you’re still unsure about something, then you can bet that a lot of your classmates are too. We expect each of you to listen respectfully, as we will, to any questions your classmates ask in class, even if the answer seems obvious to you, as you should expect other people to be appropriately respectful when you have a question.
We can’t over emphasize the power of doing the Homework. The syllabus lists some relevant problems associated with each lecture, which will comprise the bulk of the homework questions. Completion of these homework assignments will enhance your understanding of the material and help you to identify concepts that you might need additional help mastering. You are encouraged to do the Homework independently or in small study groups. Any questions you have about these problems or concepts from lecture or assigned reading should be addressed at office hours. You can expect ≥10% of the points on each exam to come directly from these suggested problems.
Office hours and finding help: Open office hours are posted for Dr. Tolan as well as the other instructors and ALL the teaching staff on the Staff page of the web site. If you cannot attend the office-hour time of your instructor or teaching fellows, there is a matrix of office hours for the entire teaching staff on the web site. As well, individual appointments can be made by sending an email with several suggested times. Office hours are not just for discussion of course material, but are intended for personal matters such as grade discussions. Dr. Tolan, and the entire staff can also be reached by email with quick questions that may not require face-to-face time. For these emails, please include in the subject, “Biochemistry Class.” If that term is in the subject line, I will generally respond to emails within 24 hours. If not, it might go to the spam folder and replies could be delayed or not occur.
ACCOMODATIONS
Students with
documented disabilities, including learning disabilities, may be entitled to
accommodations intended to ensure that they have integrated and equal access to
the academic, social, cultural, and recreational programs the university
offers. Accommodations may include, but are not limited to, additional time on
tests, limiting distractions, and note-taking assistance. If you believe you
should receive accommodations, please
contact the Office of Disability & Access Services (25 Buick
Street, Suite 300, 617-353-3658) to discuss your situation. This office can
give you a letter that you can share with instructors of your classes outlining
the accommodations you should receive. The letter will not contain any
information about the reason for the accommodations. If you already have a
letter of accommodation, you are encouraged to share it with your instructor as
soon as possible. If you need
any special accommodations for this course, lecture or lab, such as extra time
to complete assessments, specific room requirements during exams, etc., you
need to notify Prof. Tolan and the appropriate lab coordinator about your needs
as soon as possible but no later than
a week before the first exam of the semester. This includes providing a letter from the Office of
Disabilities and Access Services stating
the precise nature of the accommodation.
Time is needed to plan for these requests, and last-minute requests may
not be honored. Even if you do not yet have documentation, let us know about
your needs as soon as possible. Attending office hours or even a quick email
during the first week or two of class are good ways to communicate your needs
to the teaching staff.
DIFFERENCES OF OPINION
If you believe that an error was made in correcting
any exam, regrade requests are done exclusively through GradeScope.
If you believe that an error was made in correcting any laboratory
notebook, report, quiz, or write-up, bring it to the attention of your
TFs. If any unresolved issues remain
after consulting with your laboratory TF, please bring the issue to the
attention of the lab coordinator.
Regardless of what you are disputing, you must bring it to the attention of the appropriate staff member or otherwise deal with it within one week of its distribution, and the staff will thoughtfully consider the problem. Any mistakes in the grading of exams, quizzes, etc. will be corrected quickly and happily. Please be aware that re-grading may need to consider a fresh look at the entire assignment. However, changes in marks and grades will not be considered after the one-week “review” period. Likewise, if there is a concern about anything in the lecture, you have the responsibility to bring that problem to the attention of your professor before the next lecture or at the very least within one week. We value your feedback and we will try to help anyone and everyone as much as we can.
ACADEMIC CONDUCT
Integrity is the foundation of all academic
endeavors. In this regard, lack of
integrity is a severe violation of the spirit of inquiry and search for
truth. It is expected that every aspect
of your performance and behavior will abide by this academic honesty. The College of Arts and Sciences Academic Conduct site offers online resources for those who need
reminding of these principles and the policies developed to ensure academic
honesty. If you are caught cheating on
an examination, you will be awarded a “zero” for that exam and the incident
will be reported to the Academic Conduct Committee in accordance to the Boston University Academic Conduct Code. For
specifics on cheating or plagiarism in the laboratory, see below. The URL for Boston University’s undergraduate
Academic Conduct Code: https://www.bu.edu/academics/policies/academic-conduct-code/. The basic
rule of thumb is “DON’T DO IT!”
LAB SECTIONS
The biochemistry laboratory is designed to introduce you to modern
techniques used in biochemical research and give you hands-on experience “at
the bench.” It is aimed to help you
appreciate how biochemists design and conduct experiments to test their
hypotheses, and how to analyze your data and present your results. This part of the course has the greatest
potential for securing jobs and post-graduate academic opportunities. The more you can say in an interview about
the types of experiments you performed in this lab and your understanding of
the theoretical underpinnings of the techniques, the more desirable you will be
as a candidate for your potential employer or for a position in a past-graduate
program.
Throughout the semester you will be working in pairs in your lab sections using extensive resources including expensive equipment, costly materials, and experienced teaching fellows (TFs), who are committed to making your lab experience as valuable as possible. We hope that you will all appreciate this collective effort and be proactive about making the best use of this opportunity.
We will have 11 sections doing the laboratory exercises each week in the Fall semester, with about 13-18 students, and two TFs responsible for the safety, instruction, preparation, equipment, grading, and procedures for their section. In the Spring, there will be 6-7 such sections. Please keep in mind that just as you would appreciate a clean work area and functional equipment when you come into the lab to do your experiments, the same is true of everyone in the section that follows yours. PLEASE clean up after yourselves as not doing so will negatively affect your grade.
You should purchase a pair of approved safety eye goggles and other items defined in the lab syllabus and described to you by Dr. Szymczyna. All pre- and in-lab work will be done in a proper laboratory notebook. In addition, any written lab reports that may be required, will use electronic automated checks for plagiarism (see below). As mentioned above, all questions and difficulties should be brought to the attention of your TFs. If you miss either of your TFs’ office hours, go see one of the other TFs in the course. An office-hour matrix will be posted on both the Lab and Lecture websites (see COURSE SCHEDULE, GETTING HELP, AND SUCCESS STRATEGIES above). If any laboratory issues are not resolved by your TFs, have them contact the lab coordinator Dr. Blair Szymczyna to help resolve the issue. In addition, the laboratory coordinator, the laboratory curator (Ms. Arisdelsy Cervantes), biochemistry-lab work-study students, and/or Drs. Tolan or Liu may be in the lab for help at various times during each of the laboratory periods.
Assignment to, and attendance of, laboratory sections is required. Most laboratory exercises will be done with a lab partner. Partners and final laboratory sections will be arranged during the first week of classes. Your laboratory grade will be determined based on your attendance, the written accounts of your work, and overall laboratory performance as evaluated by the teaching staff as defined in the laboratory syllabus. Attendance and punctuality, preparation, effort, laboratory skills, quality of experimentation, ability to work in a group, fully analyzed data, and adherence to safety regulations will all be factored into this evaluation. The lab write-up assignments are DUE and should be available at the times requested (For Fall see Laboratory Syllabus). You should not wait until the last minute to start analyzing data and discussing results with your partner, especially those labs that extend over two or more weeks.
Since you will be working in pairs, you will be sharing data. It is your responsibility to have the complete data set for each experiment before you leave. The write-up/analysis for each laboratory should be your own work. Students are allowed, and encouraged, to talk and discuss the experiment and the results with each other. You can expect to have a greater understanding when you collaborate on understanding the material. However, ALL work in preparing and writing the assignment, including the generation of graphs and tables, that is turned in for grading should be done individually. No joint preparation of lab write-ups is allowed. Failure to adhere to this policy in the laboratory will be considered a violation of the Academic Code of Conduct and treated accordingly. Any violation of the Academic Code of Conduct will result in failure of that laboratory, possibly resulting failure of the course, without a chance to withdraw.
EXCUSED ABSENCES
We affirm
the Policy on Religious Observance. For other students who must be absent for legitimate reasons (besides religious observations: validated
medical issue or serious personal reasons), you will be given an opportunity,
if possible, to make up missed work, which applies mostly to the laboratory.
The policy on missed exams is stated above under GRADES.
INCOMPLETES
The use of incompletes will adhere to the College of
Arts and Sciences rules. This is generally for and circumstances
prevent the student from completing remaining requirements by the conclusion of
the course. A substantial amount of work
must have been satisfactorily completed before approval of such a grade is
given. The instructor and student must
sign the Incomplete Grade Agreement indicating the nature of the work and a date by
which all course requirements must be completed.
STATEMENT ON COPYRIGHTED
COURSE MATERIALS
The syllabus, course descriptions, text slides, and
handouts created by the Professors of this course, and all class lectures, are
copyrighted by Boston University and Professor Tolan. Except with respect to
enrolled students as set forth below, the materials and lectures may not be
reproduced in any form or otherwise copied, displayed or distributed, nor
should works derived from them be reproduced, copied, displayed or distributed
without the written permission of the Professors. Infringement of the copyright
in these materials, including any sale or commercial use of notes, summaries,
outlines or other reproductions of lectures, constitutes a violation of the
copyright laws and is prohibited. Students enrolled in the course are allowed to share with other enrolled students course materials,
notes, and other writings based on the course materials and lectures, but may
not do so on a commercial basis or otherwise for payment of any kind.
Please note in particular that selling or buying class notes, lecture notes or
summaries, or similar materials both violates copyright and interferes with the
academic mission of the College, and is therefore prohibited in this class and
will be considered a violation of the student Academic Conduct Code of
responsibility that is subject to academic sanctions.
CLASSROOM
BEHAVIOR
Students and faculty each have responsibility for
maintaining an appropriate learning environment. Those who fail to adhere to
such behavioral standards may be subject to discipline. Professional courtesy
and sensitivity are especially important with respect to individuals and topics
dealing with differences of race, color, culture, religion, creed, politics,
veteran’s status, sexual orientation, gender, gender identity and gender
expression, age, disability, and nationalities.
This policy is
outlined on the BU website (see below).
Class
rosters are provided to the instructor through MyBU with the student's legal name. The teaching staff will gladly honor your
request to address you by an alternate name or gender pronoun. Please advise
Prof. Tolan of this preference early in the semester so that appropriate
changes can be communicated to the staff and the course records.
DISCRIMINATION AND HARASSMENT
Boston University is committed to maintaining a
positive learning, working, and living environment. The University Policy states that the University and its entities does not discriminate on
the basis of race, color, national origin, sex, age, disability, creed,
religion, sexual orientation, or veteran status in admission and access to, and
treatment and employment in, its educational programs and activities. Students
who believe they have been discriminated against should contact the Equal
Opportunities Office or if harassment under Title IX,
contact Title IX Team. Although Boston University requires sexual misconduct prevention
training, incidents and experiences occur.
We care about student well-being and are committed to maintaining a
healthy campus community and awareness and resources are available for anyone
who may feel discriminated against or harassed.
There are also online reporting mechanism
you can use to report an issue or incident.
Predecessors in this course have described it as one of the most time consuming and challenging courses in the College. After graduation, these same predecessors describe the course as one of the most valuable and rewarding. In taking on this challenge, students should be mindful of their physical and mental well-being. One of the things that biochemistry has taught us is that long-term memory requires sleep. Therefore, staying up all night to memorize amino-acid structures is usually not effective. In fact, sleep is one of the most important aspects to physical and mental well-being. Although lectures start early in the morning, plan ahead and get to class. It’s often stated that 80% of success is just showing up! (the other 20% is being able to follow directions). If you have difficulties in any aspect of maintaining physical and mental health due to circumstances in the course or beyond the course, there are resources available.
The Institute for Excellence in Teaching and Learning has a clearing house of resources available. Among these is the Educational Resource Center’s staff is there to work with students who need time management, study skills or academic planning assistance. They hold weekly workshops for students to assist them with test preparation, anxiety, time management, etc. The ERC offers Peer Tutoring, Writing Assistance, Language Link conversation groups, and Workshops; although, resources for tutoring in biochemistry are limited, they have excellent tutors in the basics of chemistry and biology. The ERC professional staff is also available to meet with students individually to develop a personalized plan for academic success and/or to assist them in developing specific skills. These services are free and can benefit all students who are interested in improving their academic performance.
The most important aspect of well-being is your mental state. Often during the course of the course life happens and students may feel overwhelmed. If circumstances occur in your life, please do not hesitate to ask for help. As a start, student health services offers a variety of mental health resources for you.
GENERAL EDUCATION:
THE BU HUB
HUB
Units earned in the Fall:
Quantitative Reasoning II (QR2)
Quantitative II Outcome 1
Students will frame and solve complex problems using
quantitative tools, such as analytical, statistical, or computational
methods. Both the lecture and the lab include calculations of
force, free energy, entropy, pH, product and reactant concentrations,
activities, buffer capacity, calibration curves, normalization, errors and
error propagation, inhibition, equilibrium constants. Algebra and calculus, as
well as graphical tools are used too solve problems
posed in class lecture and data from the laboratory. By the completion of this course, all
students will be adept at use of spread sheets such as Excel for data analysis.
Quantitative II Outcome 2
Students will apply quantitative tools in diverse
settings to answer biochemical questions.
Both statistics and graphs
are used in a variety of laboratory exercises, as well as in-lecture quizzes,
to answer questions about macromolecular size and purity, enzyme action and
kinetic parameters, membrane transport and chemiosmosis, etc. Nearly every week
in either lecture or laboratory, new tools and ways of analysis to answer
biochemical questions are learned. Communicating quantitative data using graphs
and tables supporting various models and communicate this quantitative
information visually and numerically is part of many laboratory reports.
Quantitative II Outcome 3
Students will formulate, and test an argument by
marshaling and analyzing quantitative evidence.
For most of the quantitative
calculations and tools involved in the course are used to answer a question or
formulate an argument, such as what is the relative size of these
macromolecules consistent with the argument, or what is the dissociation
equilibria for a molecule from the enzyme, and what kind of inhibition is being
exhibited?
Quantitative II Outcome 4
Students will communicate quantitative information
symbolically, visually, numerically, or verbally. Visual
and numerical communication of quantitative information is an essential part of
written lab reports; within which questions are formulated and tested by properly
displaying data, including the use of statistical analysis. Furthermore, many
test questions require answers that communicate of quantitative information in
the answer, often reiterating and reinforcing what was done in the lab reports,
such as draw the shape of a curve indicating some kind of behavior (binding,
allostery, state-transition, etc.) along with proper labeling of axes, etc.
There are explicit questions coming from laboratory pedagogy included in the
lecture exams.
Quantitative II Outcome 5
Students will recognize and articulate the capacity
and limitations of quantitative methods and the risks of using them improperly. Recognition
of the limitations of quantitative methods, such as extrapolation versus
interpolation from a calibration curve, are constantly taught. Direct feedback on a weekly basis comes from the
return of lab reports where these limitations are expected as part of the
analysis. In particular, the limitations
of significance when doing calculations on spreadsheets like Excel are learned. Lecture emphasizes instances where the
correct application of an equation, theory, or calculation is to be used and
why.
Critical Thinking (CRT)
Critical Thinking Outcome 1
Students will be able to identify key elements of
critical thinking, such as habits of distinguishing deductive from inductive
modes of inference, recognizing common logical fallacies and cognitive biases,
translating ordinary language into formal argument, distinguishing empirical
claims about matters of fact from normative or evaluative judgments, and
recognizing the ways in which emotional responses can affect reasoning
processes. Building on formal teaching in distinguishing the
inductive and deductive parts of the scientific method, students in
biochemistry will put these forms of logic to work by developing hypotheses in
laboratory write-ups and deducing the conclusions from data in lecture
exams. The 421 course will amplify these
skills by weekly or daily interrogations about data presented in class or measured
in the laboratory. Students will have to
describe the questions being tested and deduce from the data the answers to
those questions. In several instances, common fallacies and evaluation judgements
that can bias conclusions will be taught.
Critical Thinking Outcome 2
Drawing on skills developed in class, students will
be able to evaluate the validity of arguments, including their own. How to evaluated and think critically about the
validity of their own data in all the laboratory modules, as well as examples
from the literature of scientific dogma presented in lectures (and included on
examinations) are taught. In particular, students will be taught how to read
(from the literature) and create graphs and tables of data, including how that
presentation of the arguments provides evidence for supporting or refuting a
given hypothesis. In lecture, students will engage in
several critical thinking points throughout the semester such as the
hyperventilating patient, the sequence analysis puzzle, comparisons regarding
structure and function, the interpretation of kinetic data to get modes of
inhibition and deducing what that means for enzyme structure and function, as
well as the effect of the nano-environments inside of proteins and how these
change the chemistry.
Teamwork
& Collaboration (TWC)
The
teaching and implementation of teamwork and collaboration is key, actually
critical, to BOTH semesters of the laboratory.
Both semesters will teach the skills of proper teamwork and
collaboration, and then allow students to act it out week after week, thus
seeing the value in this skill. In the first semester, the basics of 2-3 person
teams in constant support in performing the laboratory exercises are taught,
performed, and evaluated. This skill is also taught in the first weeks and
evaluated as a group at the end of the semester.
Teamwork Outcome 1
As a result of explicit training in teamwork and
sustained experiences of collaborating with others, students will be able to
identify the characteristics of a well-functioning team. In the first
lecture each semester, and the first pre-lab discussion sections, successful
teamwork strategies will be taught and emphasized as the only way to get
through the laboratory exercises.
Aspects of a well-functioning team are described and identified, as well
as the lessons teamwork teaches; innovation, leadership development, and
fostering knowledge of one’s own strengths and appreciation for those of
others. In addition, there it’s
explained that success in the laboratory will rely on effective collaboration
with others, most importantly is the sustained interactions with their lab
partner. All lab exercises are performed
with a lab partner(s). Partners work
closely the entire semester in preparation, performance, and analysis. The
biochemistry laboratory aims to mimic a real-world situation wherein you have
several overlapping objectives that all must be completed in the allotted four
hours. This can only be accomplished if
there is cooperation. Moreover, there are several exercises that require the
cooperation among the pairs, so teams and tasks expand and contract during the
semester. During the end of the
semester, in the prelab discussion sections, an evaluation of how well the
partners and teams worked together and what worked for success and what
interfered with success will be included.
Teamwork Outcome 2
Students will demonstrate an ability to use the tools
and strategies of working successfully with a diverse group, such as assigning
roles and responsibilities, giving and receiving feedback, and engaging in
meaningful group reflection that inspires collective ownership of results. How well teams function are assessed on a regular
basis, as well as how well everyone functions as a member of that team. Teamwork
is learned by performing all data collection and analysis working with a lab
partner throughout the semester and with other groups at various points when
data comparisons warrant. The ability to work successfully with diverse groups
in which everyone may have different roles are integral to the laboratory’s
function. Final assessment of achieving this teamwork learning outcome, will
include submission of both a self-evaluation and team-evaluation to their
instructor at the end of the semester. The instructor will consider these
evaluations in the context of the team contract when assigning final grades for
teamwork, attitude, attendance, safety, and communication, all of which
comprises 10% of their lab grade.
HUB Units earned in the Spring:
Teamwork
& Collaboration (TWC)
The
teaching and implementation of teamwork and collaboration is key, actually
critical, to BOTH semesters of the laboratory.
Both semesters will teach these skills of proper teamwork and
collaboration, and then allow students to act it out week after week, thus
seeing the value in this skill. In the second semester, larger groups of teams
are brought together in organized efforts to get complementary experiments
accomplished. In addition, the group
project for the spring semester for solving problems of biosynthesis,
metabolism, or enzyme mechanisms will be done in groups of 6-8 students, which
will foster working together in an intellectual context outside the laboratory.
This skill is also taught in the first weeks and evaluated as a group at the
end of the semester.
Teamwork Outcome 1
As a result of explicit training in teamwork and
sustained experiences of collaborating with others, students will be able to
identify the characteristics of a well-functioning team. In lecture and
pre-lab discussion sections, successful teamwork strategies will be taught and
emphasized as the only way to get through the laboratory exercises. Aspects of a well-functioning team are
described and identified, as well as the lessons teamwork teaches; innovation,
leadership development, and fostering knowledge of one’s own strengths and
appreciation for those of others. In
addition, there it’s explained that success in the laboratory will rely on
effective collaboration with others, most importantly is the sustained interactions
with their lab partner. All lab
exercises are performed with a lab partner(s).
Partners work closely the entire semester in preparation, performance,
and analysis. The biochemistry laboratory aims to mimic a real-world situation
wherein you have several overlapping objectives that all must be completed in
the allotted four hours. This can only
be accomplished if there is cooperation. Moreover, there are several exercises
that require the cooperation among the pairs, so teams and tasks expand and
contract during the semester. During the
end of the semester, in the prelab discussion sections, an evaluation of how
well the partners and teams worked together and what worked for success and
what interfered with success.
Teamwork Outcome 2
Students will demonstrate an ability to use the tools
and strategies of working successfully with a diverse group, such as assigning
roles and responsibilities, giving and receiving feedback, and engaging in
meaningful group reflection that inspires collective ownership of results. Students are assessed on a regular basis on how well
they are functioning as a team and as a member of that team. They learn
teamwork by performing all data collection and analysis working with a lab
partner throughout the semester and with other groups at various points when
data comparisons warrant. Students will demonstrate an ability to work
successfully with diverse groups in which they may have different roles. Final
assessment of achieving this teamwork learning outcome, will include submission
of both a self-evaluation and team-evaluation to their instructor at the end of
the semester. The instructor will consider these evaluations in the context of
the team contract when assigning final grades for teamwork, attitude, attendance,
safety, and communication, all of which comprises 10% of their lab grade.
Research Information Literacy (RIL)
The
teaching of Research Information Literacy is a year-long process in the
biochemistry for majors courses.
Throughout the course, the lectures refer to various publicly available
biochemical and molecular data bases and analytical resources. At various times, the class is lead to those
sites on the Internet, and lessons proceed using them. Moreover, during a continuous laboratory
exercise that begins in the fall and finishes in the spring, students get
hands-on training in using several of these publicly available databases for
asking a basic research question: How do
pharmaceutical companies analyze targets for drug development? For this, several hypotheses are posed and students
are lead to the information sources to help test these ideas. They finally communicate their findings in
the lab write-ups for these two exercise, call bioinformatics exercises.
Research Outcome 1
Students will be able to search for, select, and use
a range of publicly available and discipline-specific information sources
ethically and strategically to address research questions. This
HUB unit is one taught and earned throughout the two-semester course and
awarded with successful completion of 422.
For teaching literacy in information technology in biochemistry, there
are rich and varied collections of data about which students will be introduced
in lectures. Furthermore, through
constant reference and attribution in the lectures, as well as a purposefully
sequenced laboratory exercise for hands on use of many of these information
databases in the laboratory sections of both 421 and 422, students will learn
of the content and sources of such biochemical information. Furthermore,
students will learn how to use primary literature sources to support and report
their findings as they write their lab reports.
Research Outcome 2
Students will demonstrate understanding of the
overall research process and its component parts, and be able to formulate good
research questions or hypotheses, gather and analyze information, and critique,
interpret, and communicate findings. Again, throughout the two-semester course, both in
lecture and laboratory, students learn the use of these databases as tools in a
laboratory setting; learning the quality and analyze the validity of data from
many of these informational databases; report and communicate what they know
about informational databases in their laboratory write-ups; and apply such
information for addressing the problem posed, culminating with a discussion
section in the laboratory write up that requires students to formulate a
subsequent hypothesis based on their observations, specifically using
informational databases as a tool.
Writing Intensive (WIN)
The
teaching of scientific writing in several genres is a major thread throughout
the laboratory sections of BOTH semesters.
Both semesters will teach these writing skills to different degrees in
each semester. In the fall semester, the
emphasis will be on composing and writing a proper laboratory notebook.
In the second semester, the emphasis will be on composing and writing proper tables, figures, and legends
needed for scientific reports, publications, and proposals. These two major skills are taught throughout
the two-semester series, but emphasized accordingly. This part of the course is
often cited anecdotally from graduates as a key aspect to their attaining
employment or admission to their post-graduate endeavors.
Examples of proper scientific
writing in lecture, either protocols from notebooks or data from publications,
are used in lecture. Moreover, the nature
of the laboratory manual guides students from data collection and analysis that
begin with “cook-book”-like recipes and data tables, through generation of flow
charts and data tables, through conversion of raw data to analyzed data, to
extraction of procedures and analysis from the manual and conversation into a
properly written protocols in the Notebook and polished presentation of
analyzed data in Tables and Figures, with footnotes and legends, respectively,
in the write-ups. Written and analyzed
data allow students to gauge how well such data to stand on its own and can be
understood by the reader without reference to another source like the manual.
Each week pre-lab notebook assignments teach the basic skills of writing
protocols and flow charts. The end-of-chapter write-ups get progressively more
sophisticated teaching how to present raw versus
analyzed data, then to write a stand-alone figure legend polished for a
presentation. Write-ups are due following
the completion of the laboratory, but are not due until feedback is received
from the prior writeups.
Writing Intensive Outcome 1
Students will be able to craft responsible,
considered, and well-structured written arguments, using media and modes of
expression appropriate to the situation.
Writing is fundamental for
communication of scientific discoveries. The assignments in these courses will
introduce students to biochemical writing. These assignments will introduce the
form and function of formal and informal scientific writing, and allow the
honing of skills in this writing style. How to construct a convincing arguments
based on data collected will be taught, and all for seeing new ways of
evaluating evidence collected in the laboratory.
It is expected that students can already
read the primary literature, and recognize the structure and important features
common to publications in the primary literature. in biology and chemistry. This
course will teach throughout each semester the more informal, but equally
valuable, form of scientific intensive writing:
keeping a scientific notebook and reporting scientific data.
In the first, the basic tenants and
importance of keeping a scientific notebook will be taught. The lab manual is designed to progress from
exercises where the procedure and data collection are spelled out explicitly,
to exercises wherein the procedures are merely described in essence and the
data to be collected is discerned from the questions being asked. Every week, this information in the manual is
transposed into a lucid and sound set of procedures for their weekly
protocol. This includes assigning roles
between them and their partners.
In the second, how to write scientific
reports will be taught. Such reports are
part of any laboratory presentation, grant proposal, manuscript, or formal
presentation in the biochemical sciences.
As such the reports required in these courses lay the foundation for all
of these genres of scientific writing. Lab reports will teach how to make: a proper figure, with figure legend, a proper
Table with footnotes, and a proper conclusion & discussion.
All writing assignments are evaluated each
week by the Teaching Fellows, who will give feedback for the following weeks
assignments. The final product, as well as the ability to synthesize and
improve following feedback, will be assessed. These writing assignments
comprise the majority of the points for grading the laboratory, 70% of the lab
grade, which is 21% of the final course grade coming from the writing
components.
Writing Intensive Outcome 2
Students will be able to read with understanding,
engagement, appreciation, and critical judgment. Both
genres of writing derived from information in the laboratory manual, literature
articles, and information in pre-lab discussion sections to understand and
appreciate how to extract such details from these sources and create a logical
protocol, flow chart, and/or data table for their notebook and for their
reports. This skill is required for
any scientist who has to develop protocols suited to their questions and
situation derived from previously published literature.
Writing Intensive Outcome 3
Students will be able to write clearly and coherently
in a range of genres and styles, integrating graphic and multimedia elements as
appropriate. As mentioned above, the two major genres of
scientific writing honed by the completion of this course, keeping a scientific
notebook and reporting scientific data, require intelligible writting. This
importantly includes integration of graphical and tabular data and analysis. Logical
and lucid writing of conclusions and opinions deduced from collected data are taught. The graphical presentation of the
analyzed data, with proper footnotes and legends, are key elements of what
students will learn to write.
Creativity
and Innovation (CRI)
The Metabolism Project, allows students to use their considerable knowledge attained after over 5-8 semesters of gaining knowledge in biology and chemistry. Based on the subject matter of the Spring, which is biological energy transfer and metabolism, an explicit project is undertaken that teaches and encourages creativity. The pedagogy of creativity is taught early in the semester in the discussion sections and working in teams of 4-5 students (which also allows students to use and hone skills in teamwork), students devise and write three progressive assignments tackling a problem or disease that involves metabolism.
Creativity Outcome 1
Students will demonstrate understanding of creativity as a learnable, iterative process of imagining new possibilities that involves risk-taking, use of multiple strategies, and reconceiving in response to feedback, and will be able to identify individual and institutional factors that promote and inhibit creativity. This two-semester course will accomplish the goals in Creativity and Innovation in three manners. The first will be through a thorough grounding in the principles governing the underlying chemistry and physics of biological systems. Without these tools and information, there is no palate or foundation for thinking creatively in biochemistry. These principles are the focus of 421 wherein all four major classes of biological macromolecules and complexes are described and explained. In addition, this information is integrated with the laboratory wherein students learn how to measure and manipulate these molecules. The second, the students will learn the basic principles involved as well as the major pathways for energy production and utilization in the lectures in 422, as well as the details of enzyme mechanisms through examples. In the integrated laboratory section in 422, students will participate in an iterative process of inquiry as they learn in more detail the intricacies of the enzyme’s active site and the structure of the plasma membrane. Moreover, throughout lectures in both semesters multiple stories are told embodying examples of the creative process, including deciphering the structure of the alpha helix of proteins, the double helix of DNA, the sequence of proteins, the ATP synthesis via chemiosmosis, membrane structure, etc. The third and most critical component of learning Creativity and Innovation is a distinct project, The Metabolism Project, wherein students will participate in the creative process themselves using the information they have from the underlying chemistry and physics of biological systems and from the metabolic pathways to propose a solution to proposed problems of biosynthesis, metabolism, or enzyme mechanisms. Students will discuss and brainstorm solutions to metabolic disease or metabolism use in a creative open-ended project to solve some problem involving metabolism. The first assignment is to brainstorm a number of possible projects. Feedback on which lends itself to the most creativity and limiting overlap with other projects in the class is provided. The second assignment involves devising a new or creative modification in a method for diagnosis of a metabolism disease of outcome of some metabolism. Feedback is provided on scholarship and the degree of creativity. The third and final assignment is to submit a creative summary of some treatment of a metabolic disease or some other use of metabolism.
Creativity Outcome 2
Students will be able to exercise their own potential for engaging in creative activity by conceiving and executing original work either alone or as part of a team. The Metabolism Project allows students to use their own creative ideas based on their own interests and background. Then as part of a team, and including feedback, a creative proposal for a solution involving metabolism is composed. Students will work in groups of 4-6 with group discussions helping to advance the project. A preliminary proposal is turned in wherein feedback would be on the soundness and feasibility and be sent back for refinement or re-thinking. In this iterative fashion, pathways leading to dead ends can be eliminated. Students are encouraged to undertake targets that are not well understood, but which build on the knowledge they’ve accumulated over the two semesters of biochemistry. The delivery of the final assignment can take the form of a written report, a slide show, a poster or other work of art (but well annotated), or a video.