Introduction,
Policies, & General Education (HUB) for Biochemistry I & II
Fall 2021/Spring 2022
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
interfaces both chemistry and biology, as well as psychology, physics,
mathematics, astronomy, bioinformatics, and of course, medicine. Yet, it's a stand-alone discipline. The student studying biochemistry needs a
background in both chemistry and biology.
A high-school level of understanding of the principles and nomenclature
of cell and molecular biology are essential; however, an understanding of
biological molecules most importantly requires a solid foundation based on the
chemical principles learned in freshman chemistry and organic chemistry.
Another
purpose of these courses (421/422) is to provide an introduction to
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, 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 (Biochem I & II)
be taken. 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. 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 building of organelles, and how energy is
derived from them to power these and other processes. This course is a good preparation for
advanced courses such as Physical Biochemistry (CH525), Membrane Biochemistry
(BI556), Protein Chemistry (CH722), Chemical
Biology (CH423), Enzymology (CH625), Epigenetics (CH626), Metallobiochemistry
(CH 634), RNA Structure and Function (CH427), Molecular Biology Laboratory (BB522), Molecular Biology
I & II (BI552 & BI553), and Advanced Biochemistry (MB722).
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 and first-year master's students, in particular
those majoring in Biochemistry and Molecular Biology (BMB) or Chemistry:
Biochemistry. Students are enrolled in
BI421, CH421, BI621, CH621, BI527, or CH527, depending on their program of
study. In the fall (421), students will
attend lectures in person or remotely and take exams (in person) in one of two
parallel lecture sections (A1; MWF or A2, TR) (except those in 527). These two sections will cover the same material. However, the A1 and A2 lectures do not share
common exams, with perhaps the exception of the Final Exam. 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 BI/CH621) 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, all students perform the same basic laboratory experiments, but
those in CH 421 will have a slightly different emphasis. The precise differences will be outlined in
the respective lab syllabi. In the
spring (422), all students will perform the same laboratory experiments, attend
the same lectures, and take the same exams.
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, there will be a supplementary lecture sections held after
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.
Likewise,
while the four semesters of chemistry are required, the levels at which this
chemistry was taught (or learned) will vary drastically. For EVERYONE, we will mention material in cell
and molecular biology, and general and organic chemistry, available in the
textbooks and/or Sapling, that comprises required prerequisite material for the
class. Regardless, 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 two textbooks for the
entire two semesters. (1) The main textbook for the lecture material
will be “Lehninger’s Principles of Biochemistry 8th
edition” by Nelson and Cox. (2) The laboratory will utilize
“Biochemistry Laboratory Manual 5th edition” by Tolan & Medrano. This laboratory manual has introductory
material for each laboratory exercise that describes the theoretical background
of each experiment and problems for study.
There is also the option of enrolling in “Achieve,” which offers the e-text, supplemental materials and problems,
as well as answers to all the problems in the textbook.
These courses have
multiple web sites. The A1 course (those in BI 421, CH 421, BI 621, or CH 621
from CAS, GRS, or MET) has had a web site since before wordpress, dreamweaver, blackboard, etc.
(http://www.bu.edu/aldolase/biochemistry). It was designed and is managed by
Prof. Tolan and does not require Kerberos passwords for access. There are also
separate Blackboard web sites for the A2 course (BI/CH
421 A2 Biochemistry 1 (Fall 2021)), and one each for the BI
Laboratory (BI421/527/621 Labs - Biochemistry 1 (Fall 2021)) and the CH Laboratory (CH421-F21-Biochemistry
LAB). Those registered in BI 527 or CH 527
should use the BI Laboratory Blackboard site.
In addition, because a problems approach is
essential for learning biochemistry, students can purchase access to Achieve, which provides more problems,
as well as access to an interactive e-Book with adaptive learning quizzes,
interactive metabolic maps, animated figures for biochemical techniques and
enzymatic mechanisms, problem solving videos, and other resources. Instructions as to how to access the Achieve site for this course will be
posted on the A1 web site. Achieve
access is not required for the course and Drs. Tolan and Whitty do not actively
manage the Achieve site. All readings, suggested problems,
announcements, examples of old exams, course outlines, etc. will be available
on the A1 web site. Each lecture section
will have a different web site containing information appropriate for each
section. The laboratory sections will
also have their own web sites. Access to
these sites is listed on the appropriate syllabus.
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
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). Due to the nature
of recent events, an attempt to ease into therenewed
person-to-person teaching mode, 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. In
addition, students should be familiar with the textbook by the second semester
and as such reading assignments will be left up to the student.
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.
We
can’t over emphasize the power of doing the Suggested Problems. The syllabus lists some relevant
problems associated with each lecture. Completion of these ungraded problem
sets will enhance your understanding of the material and help you to identify
concepts that you might need additional help mastering. You are encouraged to
work these problems 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 me for
help: My open office hours are Mondays 2:00-3:00 PM and Wednesdays
11:00 AM–12:00 noon & 4:30-5:30 PM, which were determined from the class
matrix as times most students can attend.
If you cannot attend at this time, or students looking for individual
appointments with me, you can book them by sending me 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. I can also be reached
by email with quick questions that you don’t think require face time. For these
emails, please include in the subject, “Biochemistry Class.” I will generally respond to emails within 24
hours.
ACCOMODATIONS
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 17th. 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, bring the exam to Drs. Tolan, Perlstein, or Whitty. 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 your lab coordinator, Dr. Jose Medrano or Dr.
Vardar-Ulu (CH-labs only).
Regardless of what you are
disputing, you must bring it to the attention of the appropriate staff 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!”
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.
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 ten sections doing the
laboratory exercises each week this semester, with about 14-20 students, and
two-three TFs responsible
for the instruction, preparation, equipment, grading, and safety procedures for
their section. Three of the sections
will be for those enrolled in CH 421. 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.
You
should purchase a pair of approved safety eye goggles and a spiral laboratory notebook with perforated carbonless
copy pages and square grids (CH labs may be using an alternative).
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.
If any laboratory issues are not resolved by your TFs, have them contact
the lab coordinator (Dr. Jose Medrano (for BI 421) or Dr. Vardar-Ulu (for CH
421)) to help resolve the issue. In addition, the
laboratory coordinator, the laboratory curator (Ms. Jenna Lafleur), and/or Drs.
Tolan, Whitty, or Perlstein may be in attendance at various times during each
of the laboratory periods.
Assignment
to, and attendance of, laboratory sections is required, except as outlined below in case of a need to isolate. 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). Late assignments will be
penalized up to 10-20% per day. 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. In addition, due to the ongoing pandemic, the following
policies will be in place:
o
As
per BU policies, students, faculty and TFs must complete a COVID symptom survey
each day before coming to class, and must take frequent COVID tests. DO not
come to lab if your COVID status is NOT GREEN, regardless of the reason. If anyone
sees your status is red, you will be sent home, and your violation of BU COVID
policies will be reported..
o
COVID: What to do if you test
positive or are required to isolate: Most importantly, (1) if you are
sick, make sure you seek proper medical care; (2) DO NOT COME TO CLASS; and (3)
notify both your lecture and lab instructors so we can help support
you through your isolation period. We will work with you, to the extent
possible, to ensure that you can continue with your studies to the extent your
health permits, and that you do not lose credit for assignments that you are
forced to miss due to your illness/isolation. Prolonged absences (i.e. more
than 1-2 weeks) due to illness with COVID will be handled according to the
“Absences due to illness” policy outlined above.
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.
WELL-BEING
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.
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.
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.