Introduction,
Policies, & General Education (HUB) for Biochemistry I & II
Fall 2024/Spring 2025
Welcome to Biochemistry!!! The two-semester series of Biochemistry I and
II were designed as a single course of study, and both semesters should be taken
for a complete picture of this important and foundational field of biochemistry. 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 energy transformations and
the 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) 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), and Molecular
Biology I & II (BI552 & BI553).
ENROLLMENT IN THE FALL
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. Students
are enrolled in BB 421, BB 527, or BB 621, depending on their program of
study. In the fall, 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 (BB 422), 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. Because of the structure of the curriculum
here at BU, a majority of students who take biochemistry have also had BI 108
and/or BI 203/206 (Intro Biology 2 & Cell Biology/Genetics). For those who have not taken such courses, or
need a refresher, we will include a supplementary on-line lecture/review
session around midterms that 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). 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. However, you
are also welcome to attend the supplemental lectures to ensure you are
prepared. There will be a quiz as well,
which s part of the Homework, but not one that will
be dropped (see below).
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.
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.
TEXTS
& WEB SITES
The course uses one textbook for the
entire two semesters: “Lehninger’s
Principles of Biochemistry 8th edition” by Nelson and Cox. (2) 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.
The
laboratory will utilize weekly exercise documents provided online each
week or so on the Lab Web site (see below).
This material for each laboratory exercise will describe the theoretical
background of each experiment and procedures for each week..
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 web site (http://www.bu.edu/aldolase/biochemistry). It was designed and
is managed by Prof. Tolan and does not require Kerberos passwords for access.
There is NO Blackboard site for A1. There is a separate Blackboard site for the
A2 course is BB421/BB621 A2 Biochemistry 1 (Fall
2024), and that for the Laboratory is Biochemistry 1 Laboratories (Fall 2024). Those registered in BB 527 should use the Laboratory Blackboard
site. All
readings, problems, announcements, examples of old exams, course outlines, etc.
will be available on the A1 web site.
In
the Spring, BB 422/622 has only one web site. Grading will be done on GradeScope
and Homework will be done on the Achieve
site that comes with your textbook (see below).
In
addition, because a
problems approach is essential for learning biochemistry, students will use the
companion Web site or the textbook: Achieve. The site has the homework
assignments and assigned quizzes, as well as access to an interactive e-Book. It also has 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 would be
useful.
GRADES
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 BB
527/528) have three common aspects; the lecture examinations, the homework, and
the laboratory. In the first semester,
each lecture section will have 3-4 one-hour exams and one two-hour
comprehensive 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. For the A1 section, there
are FOUR one-hour exams, each of which will cover roughly the same amount of
new material, and the final exam, which 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 and may include some of the basic 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 homework problems
could re-appear on the examinations.
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). To help ease
into the semester, the first two exams 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. Similar to
the Fall, there will be five exams and one will be dropped.
Homework Policy for the Fall:
Using the ACHIEVE website,
there will be 35 problem-sets assigned as weekly homework. Most will come from the end-of-chapter
questions, which are mostly due weekly.
In addition, there will be about 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 (average of 3 per week). These will be hard deadlines, there
will be no makeup opportunities on the homework or quizzes regardless of any
reason. The entire set of 55 assignments
of homework and quizzes will comprise only 10% 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 forth of all the homework and quizzes will not
count. In other words, only your top 25
homework scores (of 35) 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 (0.25%) fraction
of your grade despite differences in the number of questions and/or problems in
each assignment.
Homework Policy for the
Spring: The homework and quizzes for the Spring
2025 course (BB 422/622) will be similar.
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.
PLEASE
don't hesitate to approach the instructor or teaching fellows 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.
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 problems are
given in the textbooks (more detailed answers to the textbook 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 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.
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, staggered homework assignments, 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 and no
later than Friday Sept 13th.
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, short
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, Dr. Szymczyna.
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, marks and grades will not be changed 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 the
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!”
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 this semester, with about 13-18
students, and two TFs responsible for the safety, instruction, preparation,
equipment, grading, and procedures for their section. 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 a spiral laboratory notebook with perforated carbonless
copy pages and square grids.
All pre- and in-lab work will be done in this 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 the website. 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 (Mr. Joe Salzo),
and/or Drs. Tolan or Liu may attend 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. 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
(see 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 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 CAS Advising. 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
Center for 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.