Chemistry 4150L Syllabus
Spring 2015
Course Information
Genomics and Proteomics Lab (CHEM 4150L)
2 credit hours
Course Meetings
Section 01
TR 7:50 - 10:40 am
NCF 316
Instructors
Dr. Tasha Toro
NCF 276
x 5358
ttoro@xula.edu
Office Hours
M 1:00 pm - 3:00 pm
Textbooks
Fundamental Laboratory Approaches for Biochemistry and Biotechnology, 2nd
edition. Ninfa, Ballou, & Benore, 2009 (Wiley).
Essential Biochemistry, 3rd edition. Pratt & Cornely, 2013 (Wiley).
Course Description
This course is designed to introduce students to the laboratory and
computational methodologies used in analyzing DNA and proteins using
modern molecular biology, chemistry, and bioinformatics techniques. A student
completing this course will have better insight into the theoretical and practical
aspects of the structure and function of DNA and proteins.
Course Prerequisites
Grade of C or better in CHEM 3130/3130L
Dr. Terry Watt
NCF 314
x 5271
tjwatt@xula.edu
T 10:45 am - 11:45 am
W 2:00 pm - 5:00 pm
R 4:15 pm - 5:15 pm
F 9:00 am - 10:00 am
You may also request appointments outside of these scheduled times.
Course Objectives
Genomics & Proteomics Lab will explore experimental and computational methods for determining
biomolecular structure and function. The goals of this course are: 1) to build your skills in critical thinking
and analytical reasoning; 2) to enhance your knowledge of biomolecular structure and function in
preparation for professional school, graduate school, and careers; and 3) to develop familiarity with common
molecular biology, chemical, and bioinformatic techniques relevant to the study of genomes and proteins. At
the end of the semester, you should be able to describe these techniques, explain the principles behind how
they work, and be able to apply them in appropriate contexts. In addition, you will develop and execute an
independent project for the second half of the semester, and you will communicate the results of that project
in both written and oral form.
Course Structure
Blackboard
Your instructor will use Blackboard throughout the semester to distribute modules and supplemental
reading assignments, grade written assignments, post copies of handouts, and contact students by email.
You should make a habit of checking Blackboard for course materials on a regular basis and should verify
that your account is set up to receive emails from Blackboard. You will also be expected to upload all written
assignments (module assignments, outline assignments, and the final paper) to Blackboard. You should plan
to complete these assignments with enough time to spare in case of computer issues. Late assignments will
not be excused due to computer issues unless the University Blackboard system is down for an extended
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period of time (i.e., more than 12 hours). If you are having difficulties accessing your Blackboard account or
uploading documents, please see ITC to resolve the issue. Your instructor will not be able to provide
technical assistance.
Class Attendance and Practical
You should attend each class and be on time. You are responsible for all notes, assignments,
handouts, instructions, etc. given during your absence. If you need to miss a class for a legitimate reason
(severe illness, university sponsored event, etc.), you must notify your instructor before the missed class
period. Missed class work may be made up in the next class session, as time permits, or in some cases at an
alternate time arranged with your instructor. However, due dates will generally not be extended. You are
expected to be prepared for lab (which includes wearing appropriate attire and completing all reading
assignments), pay attention and participate during class discussions, remain engaged during the entire lab
period (e.g., no use of social media or texting during a lull in activity), and clean up before leaving lab. Your
instructor may deduct points if you fail to meet expectations. You must wear closed-top shoes (no part of the
top of the foot or sock visible) have a lab coat or other protective clothing, and have protective eyewear.
Appropriate clothing and lab behavior applies regardless of whether or not reagents are being used on any
particular class day. Lab coats must be worn at all times in the lab if your clothes do not completely cover
your legs to your knees and completely cover your torso (sleeveless is acceptable). Extensively ripped
clothing is not appropriate without a lab coat. You should also bring a USB drive to every class so that you
can save any data generated during class. A portion of your grade will depend on your preparation,
participation, and lab technical skills demonstrated in each class meeting; unexcused absences will result in
an automatic deduction of practical points (4 pts per unexcused absence or excused absence that is not made
up). Although many classes and independent project days may involve primarily computational analysis, you
are still expected to be present, on time, and actively participating in class each day.
Lab Notebooks
You are required to maintain a laboratory notebook. The notebook is a place where all your data and
calculations are recorded along with any relevant observations. This notebook is not to be used for class notes
– only information about the experiments should be recorded in your notebook. You should have this notebook
with you during every class session, and should write in it during experiments to ensure that you have a
record of what you did. A composition notebook or a notebook from a previous class can also be used, but
not a notebook concurrently in use for any other purpose or course. The notebook should include a purpose
for the lab and outline of the procedure, including all relevant calculations and any changes made during the
experiment. Pasting a printed copy of the protocol in the lab notebook is not an acceptable substitution for
the purpose or method, nor is copying the protocol word-for-word from the module information on
Blackboard. The notebook should also include a summary of the results (including any tables and/or figures
generated as part of the data analysis). This summary should be handwritten in your notebook. While it is
acceptable and encouraged to paste in copies of graphs, charts, and extensive tables, it is not acceptable to
simply staple in the entire typed results or any other typed analysis completed as part of an assignment.
Please consult your assigned textbook or ask your instructor if you have questions about how to keep a lab
notebook. All notebook entries must be written in pen. The notebook will be checked by your instructor
during the semester. If you do not have your notebook in class during a notebook check, you will receive a zero
for that check.
Modules
Experimental protocols will be available on Blackboard prior to the scheduled lab date, and you
should look at the protocols well in advance of each lab. Protocols contain details about necessary pre-lab
preparation and often contain important background information. It is your responsibility to be prepared
and understand the relevant background each day. Failure to prepare for experiments may result in the
inability to complete experiments within the allotted class time. Some experiments are “dry labs” that will be
done primarily on a computer, and so bringing a laptop computer regularly is recommended. Assigned
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readings are given in the modules, and should be completed before the indicated class period so that you are
prepared for the discussion.
In-class Discussions
Many classes will begin with a discussion of the assigned reading. You are expected to actively
participate in these discussions, and to have completed the assigned reading before class. You may wish to
bring your textbooks to class on discussion days, especially if you had specific questions on the assigned
material.
Module Reports
Details of each module report will be provided within each module. Each module assignment will
require you to prepare a short report covering the activities of the module, usually based in part on
additional work performed outside of class. The specific requirements for each module report will be
described within the module. All module reports are to be submitted online using the designated
Blackboard/TurnItIn link. Module reports will not be accepted by email or on hard copy. All assignments must
be your own work; it is never acceptable to copy any work from another student or other sources. All
module assignments are due at the beginning of the class indicated on the course schedule.
Your instructor will grade your work online and provide comments if appropriate; it is your
responsibility to look at the graded work for any comments by your instructor using the TurnItIn interface.
Your instructor may leave comments in the grade report for the assignment and/or on the document itself
within the TurnItIn interface. If you do not understand how to view these comments, please seek help early
in the semester. (Two hints: placing your mouse cursor over a comment will expand it to show more detail,
and you can click-and-drag comments to more clearly determine which text a particular comment refers to.)
Note that the TurnItIn interface for mobile devices, including tablets, does not provide full functionality and
may restrict your ability to view feedback. It is your responsibility to view feedback with an appropriate
computer.
Note that assignments may be submitted multiple times until the time they are due. The last version
uploaded will be the one graded. You can take advantage of this feature to ensure that a draft is uploaded
well in advance of the due date, and then upload a final version later if necessary. This will help you avoid
late penalties in the event of technical difficulties uploading close to the beginning of class. However, be
aware that revised versions cannot be uploaded after the time the assignment is due, even though it is still
possible to upload a first version (with a late penalty).
Additional Assignments
At several points in the semester, you will be asked to turn in smaller assignments, based on in-class
activities, development of your independent project, or preparation for your final paper. Specific
expectations for each outline assignment will be provided. Please note that the comments above concerning
the uploading and grading of module assignments also apply to these additional assignments.
Independent Project
The second half of the semester is devoted to independent projects. These projects will be developed
during the first half of the semester in collaboration with your instructor. It is important that you meet
deadlines for the development of your project, or else required reagents may not be available in time.
Projects will address some scientific question using a selection of the genomics and proteomics techniques
discussed during the semester. Although most projects will involve a combination of lab experiments and
computational analysis, the methods used will depend on the question being asked, available resources, and
your interests. Upon completion of your project, you will prepare a final paper and presentation.
Final Paper
You will write up the results of your independent project as a manuscript using the format for the
journal Biochemistry (http://pubs.acs.org/journal/bichaw). You will be given many opportunities
throughout the semester to complete and receive feedback on portions of this manuscript via the outline
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assignments. As with other written assignments, this paper is to be submitted electronically by the time
given in the course schedule. The shorter, incremental assignments due throughout the semester are your
opportunity to get feedback from your instructor on your final paper, and are designed to encourage you to
work on the final paper in stages throughout the second half of the semester.
Presentation
You must prepare a presentation of 10-15 minutes on your independent project, which will be given
in class following the last class period dedicated to working on the independent project. Following your
presentation, your classmates and instructor will have the opportunity to ask questions. Specific guidelines
for this presentation will be provided.
Exam
There will be a single mid-semester exam given, covering the major techniques used during the first
half of the semester, the key ideas covered during class discussions, and material from reading assignments.
The format of the exam will be several open-ended questions. The exam will take approximately half of a
class period, and will be closed to all materials.
Course Grading
Course component
Module reports
Exam
Additional assignments
Lab Notebook
Practical
Presentation
Final paper
Total points
Letter Grade
A
B
C
D
F
Midterm points
150 (3 reports @ 50 pts each)
100
60 (4 assignments @ 10 pts each
& 1 assignment @ 20 pts)
20 (1 check)
330
Final points
300 (6 reports @ 50 pts each)
100
100 (8 assignments @ 10 pts each
& 1 assignment @ 20 pts)
50 (2 checks)
100
100
250
1000
Midterm Points
297
364
231
198
< 198
Final Points
900
800
700
600
< 600
The Blackboard gradebook will be updated periodically so that you can confirm that your grade
record is correct; please bring discrepancies to your instructor's attention.
Course Policies
Late assignments. All assignments are due by the beginning of the class indicated on the course
schedule and must be submitted electronically by that time. Late module reports and additional assignments
will be penalized 10% per day (excluding weekends and holidays). Once a report is five days late, it will be
treated as a resubmission (see below) with a maximum possible score of 50%. Other assignments will be
accepted until the late penalty reaches 100%. If you have an emergency that prohibits you from turning in
work on the due date, you must immediately notify your instructor and provide the appropriate
documentation within one week of the original due date. Late final papers will have a deduction of 1% per
hour and will not be accepted once the total possible points reaches zero. For graduating seniors, late final
papers will not be accepted after 10 am on quiet day.
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Resubmission of module reports. All module reports can be revised and resubmitted after your
instructor has graded them. A resubmitted assignment may earn up to half of the points deducted based on
the initial submission, or 50% of the maximum if it was not submitted at all before the assignment was
graded. All resubmissions are due exactly 14 days (2 weeks) after the original due date. Resubmitted
assignments must show substantial evidence of improvement to earn any additional points; minor edits will
not significantly affect your original grade. When resubmitting an assignment, include an additional page (as
the first page) that describes the changes that you made. Failure to include this page will result in a
resubmission not being graded. It is recommended, but not required, that you discuss plans to resubmit with
your instructor prior to doing so. Late resubmissions will not be accepted. A report that is not submitted for
the first time by the resubmission deadline will receive a score of zero.
Collecting your graded work. Your instructor will return all graded work as quickly as possible.
Assignments submitted electronically will also be graded electronically, and may be viewed using the
TurnItIn interface in Blackboard.
Laptops. Most of the classes during the first half of the semester will require the use of a computer. If
possible, bring a laptop to all classes. Tablets and smart phones are not adequate for the purposes of the
class. A limited number of computers are available for shared use. Computers should be used only for
classwork while in class.
Electronic devices. Silence cell phones for the duration of the class period. If there is a situation that
requires that you be able to answer your cell phone during a class, please inform your instructor before the
class. If you use your phone during class (including text messaging), you may be asked to leave; an exception
will be made if the phone is used strictly as a timer or clock during appropriate experiments.
Regrade requests. Grades on assignments and the exam may be disputed up to one week after being
returned or 11 am on Quiet Day, whichever comes first. Regrade requests must be in writing with a detailed
explanation for the request. Regrades may result in a grade higher or lower than the original grade. It is
your responsibility to keep track of your grades and notify your instructor immediately if you feel that you
are missing an assignment grade. Note that regrades are not the same as resubmissions (see above); a
regrade request is a challenge to a grade given to the original submission without any modifications.
Instructor communication. As needed, you are strongly encouraged to attend office hours, talk to your
instructor after class, or set up an appointment. Your instructor will answer email questions, although some
questions may be difficult to answer in email. Replies to email may take 24 hours, so plan accordingly. Phone
conversations about course material are inefficient and will generally be avoided; phone messages will not
be responded to. Your instructor will occasionally communicate with the entire class via Blackboard
announcements and email, so check your xula.edu email at least once a day.
Evacuation. If classes are canceled due to a hurricane evacuation, assignments and course materials
will be posted to Blackboard. Please log on to the Blackboard site as soon as possible after the evacuation.
Health or disability concerns. If you have special needs, please make an appointment to speak to your
instructor to discuss any appropriate accommodations.
Academic Misconduct
The CAS Academic Integrity Policy will be followed in this course. According to the policy, academic
misconduct includes, but is not limited to, the following:
1. Using unauthorized materials in completion of an exam, quiz, or assignment.
2. Assisting or gaining assistance from an unauthorized source during an exam, quiz, or assignment.
3. Providing assistance to another student in a manner not authorized by the instructor.
4. Obtaining an examination or assignment in an unauthorized manner.
5. Using material from a source without giving proper citation.
6. Fabricating or altering data.
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7. Submitting work to one class that is substantially similar to work submitted for another class
without prior approval from the instructors involved.
8. Submitting written work that is not completely one’s own or allowing others to submit one’s work.
9. Destroying or altering the work of another student.
10. Committing any other violation of academic integrity as described in this syllabus.
Specific examples of academic misconduct include:

the use of a cell phone during an exam for any reason (even as a calculator);

talking during an exam;

using anything other than explicitly authorized materials on an exam;

attempting to read from another student's exam;

copying class assignments, including sharing files to analyze or present data;

using data that you did not collect in a report without proper attribution;

using written or graphical material that is not your own without proper attribution.
You are responsible for arriving on time for the exam, as you will not be permitted to begin after any
other student has left the room. You are responsible for all written materials on, under, and near your seat
during the exam, so it is in your best interest to ensure that the desk surface is clear of writing and that no
extraneous papers are within your line of sight (both when you begin and finish). Cell phones should always
be off and inside a bag during an exam; your instructor will not give you the benefit of the doubt if a cell
phone is used or visible. The CAS policy makes no distinction between the person receiving unauthorized
assistance (copying an assignment) and the person providing the assistance (allowing work to be copied);
both actions are academic misconduct.
All cases of academic misconduct will be reported to the CAS Dean's Office per Xavier's Academic
Integrity Policy. Any case of academic misconduct on assignments will result in a grade of zero for the
assignment and may result in a grade of F for the entire course. Premeditated academic misconduct during
an exam (for example, using a cell phone to text or preparing a “cheat sheet”) will result in the student being
asked to leave immediately and in a failing grade for the course.
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Course Schedule
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Date
Tues
Thurs
Tues
Thurs
Tues
Thurs
Tues
Thurs
Tues
Thurs
Tues
Thurs
Tues
Thurs
Tues
Thurs
Jan 13
Jan 15
Jan 20
Jan 22
Jan 27
Jan 29
Feb 03
Feb 05
Feb 10
Feb 12
Feb 17
Feb 19
Feb 24
Feb 26
Mar 03
Mar 05
Tues
Thurs
Tues
Thurs
Tues
Thurs
Tues
Thurs
Tues
Thurs
Tues
Thurs
Tues
Thurs
Mar 10
Mar 12
Mar 17
Mar 19
Mar 24
Mar 26
Mar 31
Apr 02
Apr 07
Apr 09
Apr 14
Apr 16
Apr 21
Apr 23
Mon
Apr 27
Class Activity
Module 1
Module 1
Module 2
Module 2
Module 2
Module 3
Module 4
Module 4
Module 4
Module 4
No class: Mardi Gras break
Module 4
Module 4
Module 5
Module 6
Exam
Notebook check
Project workshop
Independent project
Independent project
Independent project
Independent project
Independent project
Independent project
No class: spring break
No class: spring break
Independent project
Independent project
Independent project
Independent project
Independent project
Project presentations
Notebook check
Assignment Due
Genomics tools summary
Module 1 report
Module 2 report
Module 3 report
Project question list
Project ideas
Project proposal
Proteomics tools summary
Module 4 report
Module 5 report
Module 6 report
Introduction draft
Materials & methods draft
Results draft
Discussion draft
Project presentation
Project final paper (at 5:00 pm)
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