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# System prepended metadata

title: BI163D Syllabus

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# ![](https://hackmd.io/_uploads/HyMed2X0n.jpg) BI163D *The Cellular Basis of Life* 
### *Colby College* - *Fall 2023*
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## Instructor
Dr. Christina D. Cota 
cdcota@colby.edu
### BI163D Learning Assistants (LAs)
AJ	Held	ajheld26@colby.edu
Nick	Levinson	nglevi25@colby.edu
Jacqueline	Ortiz Lopez 	jortiz25@colby.edu

## Course description
An examination of cells as the fundamental unit of life. Aspects of evolutionary biology, cell biology, molecular biology, and genetics are discussed. A major objective is development of the intellectual tools to be able to ask and answer interesting biological questions. The objectives of the laboratory are to allow each student to design and conduct experiments, to analyze and present data, to write accurate scientific papers, and to critically evaluate the scientific literature. 
***Four credit hours.  N,Lb.***

###### **Course Image (top of page): "HeLa Cell" by National Institutes of Health (NIH) is marked with Public Domain Mark 1.0.*
## Learning Objectives
Through this course you will develop an appreciation of cells as the fundamental structural unit of all living organisms. You will be able to recognize and describe the macromolecular building blocks (proteins, lipids, carbohydrates, nucleotides) cells are composed of, and how these molecules function together to drive cellular processes. Through active participation in the both the lecture and lab you will learn how scientists apply this information to ask and answer interesting biological questions.

## Meetings Times
BI163D lecture will meet M-W-F, 12-12:50pm, Olin 001
(BI163 Lab sections will meet as scheduled)

## Office Hours: 
Tuesday 9-10am and Friday 9-10am in Arey 401
*Individual meetings are available on request @ https://doodle.com/bp/christinacota/book-a-meeting

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## Course Requirements:
## Readings:
### Biological Science; Scott Freeman, 6th Ed. (Textbook)
***<u>Reading assignments will be posted by 9am on Mondays</u>***.
The textbook readings are intended to support the material presented and discussed in class. You will learn more if you do the readings. Moreover, while I may not assign readings from certain chapters of sections in the book, you may find the material in these sections useful in understanding other material covered in the course. I strongly suggest that you review the material covered in each chapter of the textbook and refer to it as needed. Additional readings may be assigned throughout the semester to supplement the material covered. These readings will be provided and made available on the course Moodle site.

### Class Meetings:
To compliment the readings in the textbook, course material will be presented via a series of in person lectures and discussions. Accompanying powerpoint slides will be posted on the course Moodle page immediately after the lecture.
### <u>Attendance</u>
This is a participation-based course therefore, **failure to attend class meetings will result in grading penalties and/or dismissal from the course with a failing grade**. Excuses may be granted at the instructor's discretion for the following reasons:
* critical emergencies (verified by the Office of the Dean of the College)
* college-sponsored activities or events (e.g. musical performances or athletic competitions)
* Religious Holidays

For the latter (college sponsored activities or events), you must notify the course instructor by e-mail at least 7-days in advance of the date in question. Failure to do so may result in unexcused absences.

If you are sick and cannot come to class, you must notify the course instructor by e-mail as soon as possible. If you must miss more than a single class due to a prolonged illness (typically verifyed by the College Health Center) please contact the Office of the Dean of the College. The course instructor will work with both the student and the Dean's office to provide appropriate support and/or accommodations on a case-by-case basis.

### Lecture Topics and Textbook Reading:

#### *Topics will be covered generally in this order:*
Cell Theory: Ch 1: pp 1-4
Evolution & Tree of Life: Ch 1: pp 4-11
Chemical Basis of Life: Ch 2: pp 55-60
Protein Structure & Function: Ch 3: pp 78-91, Ch 8: pp 179-184
Nucleic Acids & DNA: Ch 4: pp 93-104, Ch 15: pp 316-320
Lipids & Cell Membranes: Ch 6: whole chapter
Cytoskeleton: Ch 7: pp 163-168
Cell Respiration & Fermentation: Ch 9: pp 189-208
Photosynthesis: Ch 10: pp 210-229
Cell Cycle: Ch 12: pp 253-263
DNA Replication: Ch 15: pp 320-326
DNA Damage & Repair: Ch 15: pp 329-332
Transcription & Translation: Ch 17: pp 348-363
Bacteria & Archaea: Ch 26: pp 518-528 
Viruses: Ch 33: pp 682-692
## Assessment and Grades:
Your grade will be based on lecture (75%) plus laboratory (25%). The specifics of your laboratory grade, and a lab syllabus, will be provided by your lab instructor on the first day of lab.
### Exams
There will be three exams total for the semester: two mid-term exams and one final
comprehensive (cumulative) exam covering the whole semester. For these exams you will
be responsible for all material covered in class and in the assigned readings. The tentative dates and locations for the exams* are:

**Exam 1: 7pm, October 3rd; Bixler Auditorium
Exam 2: 7pm, November 9th; Bixler Auditorium**
Final Exam: TBA (Final exams are scheduled by the Colby Registrar)

*The times, dates and locations for these exams are subject to change based on classroom availability. Any changes will be announced in advance in class and via the course Moodle site.
### Graded Assignments and Quizzes
Assignments and quizzes will be administered from time to time throughout the semester via Moodle. Failure to complete assignments by the due date will lower your grade.

**Assignments and problem sets will be posted by <u>9am on Mondays</u>** on the course Moodle site and will be due by midnight on Sunday. You may work through these assignments throughout the week as your schedule permits.

### Problem Sets
Problem sets will be ungraded. They are meant to familiarize you with the level of knowledge expected and the types of questions you may see on an exam. You will not turn these in.

### Laboratory:
The lab will give you hands-on experience exploring the principles of biology discussed in class. You will learn about the practical aspects of the way that scientists do biology: experimental techniques, proper use of equipment, methods of data analysis, and abundant scientific writing.
These concepts serve as a foundation for more advanced courses in the biology major. All aspects of laboratory (communication, assignments, instruction) will be managed by your lab instructor. Laboratory attendance: Unexcused absence from the laboratory will result in your being dropped from the course. Please attend the laboratory section assigned to you. Only in the case of a family or medical emergency can you switch to a different laboratory
section in a given week, and only with the permission of both lab instructors. 

*Extracurricular activities that conflict with regularly scheduled academic classes are not considered to be emergencies.*


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### Lecture grade components:
Exam 1: 17%
Exam 2: 22%
Exam 3 (final): 26%
Graded assignments/activities/quizzes: 10%
#### Final Grade = Lecture Grade (75%) + Lab Grade (25%)
**>90 A (most likely <93 A-, >93 A, A+ for exceptional performance)
80-90 B (most likely <83 B-, 83-87 B, >87 B+)
70-80 C (most likely <73 C-, 73-77 C, >77 C+)
60-70 D (most likely <63 D-, 63-67 D, >67 D+)
<60 F**
 


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## Additional Course/College Policies and useful links:
### Academic Honesty & Consequences for Academic Dishonesty:
Honesty, integrity, and personal responsibility are cornerstones of a Colby education and provide the foundation for scholarly inquiry, intellectual discourse, and an open and welcoming campus community. These values are articulated in the Colby Affirmation (Below) and are central to this course. You are expected to demonstrate academic honesty in all aspects of this course. If you are clear about course expectations, give credit to those whose work you rely on and submit your best work, you are highly unlikely to commit an act of academic dishonesty.
#### <u>*The Colby Affirmation*</u>:
##### *Colby College is a community dedicated to learning and committed to the growth and well-being of all its members. As a community devoted to intellectual growth, we value academic integrity. We agree to take ownership of our academic work, to submit only work that is our own, to fully acknowledge the research and ideas of others in our work, and to abide by the instructions and regulations governing academic work established by the faculty.*
##### *As a community built on respect for ourselves, each other, and our physical environment, we recognize the diversity of people that have gathered here and that genuine inclusivity requires active, honest, and compassionate engagement with one another. We agree to respect each other, to honor community expectations, and to comply with college policies.*
##### *As a member of this community, I pledge to hold myself and others accountable to these values.*

 #### Academic dishonesty includes, but is not limited to:
* violating clearly stated rules for taking an exam or completing an assignment; plagiarism (including material from sources without a citation and quotation marks around any borrowed words)
* claiming another’s work or a modification of another’s work as one’s own
* buying or attempting to buy papers or projects for a course
* fabricating information or citations; knowingly assisting others in acts of academic dishonesty
* misrepresentations to faculty within the context of a course, on an academic assignment, or an academic record
* submitting the same work, including an essay that you wrote, in more than one course without the permission of the instructors for those courses.

**Academic dishonesty is a serious offense against the college.** 
Sanctions for academic dishonesty are assigned by an academic review board and may include failure on the assignment, failure in the course, or suspension or expulsion from the College for multiple academic dishonesty findings.

Additional information regarding Colby’s policies pertaining to Academic Dishonesty can be found in 2023-2024 student handbook which can be accessed [here](https://life.colby.edu/your-safety/community-values-conflict-resolution-and-restorative-practice/student-handbook/).

For more information on recognizing and avoiding plagiarism, see the [library guide](https://libguides.colby.edu/avoidingplagiarism).


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### Academic Accommodations:
If you believe you need academic accommodations, please contact Colby’s Dean of Studies Office (email: accommodations@colby.edu, Ph: (207)859-4000) to discuss your needs or visit their website: https://life.colby.edu/get-support/access-disability-services/ to submit a request for accommodations.

<u>***All accommodations must be arranged through the Dean of Studies Office who will issue formal Accommodation Letters as deemed appropriate.***</u> 

Accommodations require early planning. If you have any questions or concerns you may contact me, however, all disability-related accommodations must be arranged through the Dean of Studies Office.


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### Academic Support Services:
Colby offers a number of useful academic support services to students including Financial support for purchasing textbooks; the Farnham Writers Center for help with all aspects of writing; the Olin Science Library for assistance with searching and acquiring literature; and Counseling Services (x4460) at the Health Center. A list of these services can be found here:
https://life.colby.edu/get-support/advising-academic-success/resources/. 
*Please review these resources and reach out as necessary.*


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### Athletics:
Colby College is supportive of athletic participation by its students, however, academics take priority over athletics. Both NCAA and Colby rules prohibit missing class for practices, thus students should never miss class or lab for an athletic practice. In the case of overlapping commitments between class and athletic competitions, the student <u>**must**</u> meet with the professor as soon as possible to discuss these overlaps. The student may request
permission to miss class and make up the missed work; however, the instructor has final authority either to grant or to withhold permission. Students on academic probation may not be excused from any class because of extracurricular or athletic activities.

***<u>It is the responsibility of the student to communicate directly with their instructors during the first week of class to resolve scheduling conflicts</u>.***

Athletic schedules are available [here](https://www.colby.edu/athletics).


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### Religious Holidays:
Colby College is supportive of the religious practices of its students, faculty, and staff. The College is committed to ensuring that all students are able to observe their religious beliefs without academic penalty. The College will enable any student to make up any course requirements scheduled during a religious holiday that is observed by that student. 

***<u>Students are expected to inform course instructors within two weeks of the beginning of the term of any religious observance that will conflict with coursework</u>.*** 

If you observe a religious holiday that will impact your work in this course, please see me at the beginning of the term. We will then work to find a reasonable accommodation that will allow you to complete the academic work.


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### Covid-19:
Students are required to abide by Colby’s [Covid-19 Health and Safety Protocols](https://covid19.colby.edu/covid-19-health-and-safety/) at all times.

Noncompliance with Covid-19 Health and Safety Protocols may also result in sanctions including warnings, probation, restorative justice measures, campus or community service, loss of or restrictions upon social or travel privileges, or loss of the opportunity to attend College activities or events in person, removal from College housing, loss of
student employment or off-campus study opportunities, suspension and expulsion (https://my.colby.edu/ICS/COVID-19_Student_Policy.jnz).