Cell Biology

BIOL 2085C –Spring 2023

Lecture: M-W-F (12:20 pm –1:15pm, Zimmer 400)

Professor: Maria F. Torres, PhD.

Email: maria.torres@uc.edu
Phone: 513-566-9732
Office Hours: Will be held via Zoom

Office Hours: I am available to discuss class material and class-related issues most days of the week,
usually in the afternoons. Students can sign up for office hours using my bearcat network
(https://www.uc.edu/aas/mybearcatnetwork.html). To meet with me connect to my Zoom personal
room: https://ucincinnati.zoom.us/j/3555445091

Professional Communication: Emails received without professional formatting will not be answered. I
will only reply to official UC email accounts. Emails to me, the lab coordinator or TAs must be
formatted with a greeting, body, and a closing signature.

Textbook: Karp’s Cell and Molecular Biology, Ninth Edition, by Janet Iwasa and Wallace Marshall.
Wiley Publishing. You also need to purchase access to WileyPlus, in order to complete the weekly
assignments. Additional instructions on how to purchase access to WileyPlus can be found in Canvas.
This video that will help you with more detailed instructions if needed: https://bcove.video/2KkILqu

Turning Technologies Personal Response App: We will make extensive use of the TurningPoint PRS
system for real-time class quizzes and questions. If you have never used TurningPoint before, you will
need to register and acquire a license. Here is the video on how to register: https://turningtechnologies-
5.wistia.com/medias/nrmqd3cag9. More detailed instructions can be found on Canvas and will be
provided on the first day of class.

Prerequisites: Minimum grade of C- in BIOL2083.

Course Format
Research on different learning methods has recently shown that an active learning approach, where
students have the opportunity to engage with the material and are able to discuss it and share it with
other students, makes the learning process more efficient. On regular work environments, people are
required to work in teams, and a similar structure is used in this class. On the very first day, students
will be assigned to groups of 4 individuals that will work together during lectures and laboratory
sessions throughout the semester.

1
Before each lecture, a set of Learning Outcomes will be posted on Canvas. The Learning Outcomes are
designed to emphasize the most relevant points of the assigned readings, but by no means they will
delimit the extend of the material covered and discussed in class. Students need to work on achieving
these outcomes before coming to class, as a basic understanding of these concepts will be assumed. The
majority of the lecture time will be spent unifying and clarifying concepts and students working in their
groups to discuss and build upon the learning outcomes. Learning outcomes will not be collected,
however each class will start with an individual quiz based on the assigned readings and learning
outcomes.

Learning Outcomes

By the end of this course, students will be able to:

• Identify the major interactions between biological macromolecules and how these interactions
define and affect different cellular processes.
• Explain how cells utilize and acquire energy under a constantly changing environment.
• Characterize the molecules and signal-transduction pathways that mediate interactions between
cells and their environment.
• Describe how different cellular components are synthesized, modified and sorted to their
destinations inside and outside of the cell.
• Explain how specific cellular mechanisms are affected when external and/or internal stimuli
interfere with cellular homeostasis, and how these alterations lead to disease.
• Analyze and interpret laboratory data and present and discuss experimental results.

Basis for grades

The lecture portion of the course is worth 70% of the final grade, and the lab portion is worth 30%.

1. The lecture grade is broken down in the following way:

A. 60% from four equally weighted exams. There are 4 midterms and one final. The lowest
midterm exam score is dropped*. The final exam cannot be dropped.

B. 17.5% will be derived from the daily in-class questions using PRS transmitters. The lowest 4
scores are dropped*. Daily PRS questions will be mostly based on assigned reading material and
Learning Outcomes for that day.

C. 12.5% will be based on problem sets and worksheets solved together in student groups. This
includes individual quizzes based on worksheets developed on previous classes. The lowest two
scores are dropped*.

2
 D. 10% will be based on weekly online WileyPlus assignments and “short summary videos” that will
be posted to describe the goals and objectives of each class module. There will be one weekly
Wiley Plus assignment posted on Friday after class, which will be due the following Monday by 8
pm. The short videos will be announced on Friday and will follow the same deadlines. The lowest
score is dropped.

2. The laboratory grade is broken according to specifications in the lab schedule.

Scale for Letter Grades

A = 89.5-100% B+ = 86.60-89.49% B =79.50-86.59% C+ = 76.60-79.49 %

C = 69.50-76.59% D+ = 66.60-69.49% D = 59.50-66.59% F = <59.50%

W (Withdrawal): The last day to withdraw from class is April 7. The deadline to withdraw without a W
on your record and with a full refund is January 23. If you are thinking about dropping this course, I
suggest that you arrange a meeting with me first. It is likely that your grade is higher than you think and
my goal is to help you succeed and we can make a plan to help you do that.

X (Non-attendance): Assigned for students who never attended any classes and did not submit any
assigned work

WX (Official withdrawal, non-attending). Assigned for those students who officially withdraw from
the class but who never attended any classes and did not submit assigned work

UW (Unofficial withdrawal): Assigned when a student participates in class and misses too much
coursework to allow a grade to be assigned, but fails to withdraw or make arrangements for an
incomplete.

I (Incomplete): Assigned only when a student fails to submit all required coursework by the end of the
semester, has made prior arrangements to complete the missing work (and it is possible for students to
complete the work without class attendance), but cannot make up the work before grades are to be
submitted.

There will be no makeup exams or assignments, or any kind of “extra credit”/ I offer a variety of
office hours and opportunities to answer questions and clarify terms, throughout the semester. I
will refer you to the syllabus if you ask us about this.

3
Lab Coordinator
The Laboratory Coordinator, Jose Barreiro (barreijm@ucmail.uc.edu), will manage the lab portion of
this class. The Lab Coordinator is the most appropriate person to contact if you have questions related
to the lab.

Supplemental Instruction
Supplemental Instruction (SI) is offered for this course by the Learning Commons.
These sessions are facilitated by your SI leader, Lucas Klaus (klauslr@ucmail.uc.edu) who will be
attending class and preparing SI sessions based on the class content. SI sessions utilize a collaborative
learning model to aid in comprehension and synthesis of course material and development of effective
study techniques. On average, students who regularly participate in SI sessions earn a higher final
course grade, as well as higher exam grades, than students who do not participate in SI. More
information about SI sessions will be provided during the first day of class.

Classroom Procedures and Policies

Safety guidelines
All UC members must follow safety measures and health practices, as specified by the university
(https://www.uc.edu/publichealth.html). In this class, students will be free to decide if they want or not
wear facial coverings, and any updates on this matter or any additional changes in University
regulations will be announced in class.

Weekly Assignments
WileyPlus assignments and “short summary videos” will be available through the weekend and are due
on Mondays at 8p.m. The assignments will not be available online after this time, and other submission
forms will not be accepted.

Exams
All students have the option of dropping one exam in the semester. This policy is implemented so that if
you have a personal commitment, family issue, accident or emergency, you can miss the exam without
it affecting your grade. You do not need to present documentation because there are no makeup exams
offered. I will be available to go over your tests up to 7 days (exactly one week) after they are returned
to you. If you do not come to discuss your grade within that time, it is assumed that you agree with it
and no further changes need to be made.

4
In-class PRS questions and assignments
Only PRS questions, assignments and worksheets filled during class, by students present in lecture will
be accepted. Exceptions include those assignments that are developed and due outside of class time.
*The lowest scores are dropped to account for occasional technology issues or malfunctions and/or
allow students to miss a few classes without impacting their grades.

Diversity and Inclusion Statement

Diversity and inclusion are important, in both school and work environments diverse groups have been
shown to improve decision making and problem solving. To that end we have the goals for the class as
a whole and for your individual group are: everyone is allowed to feel they can work and learn in a
supportive and safe environment; everyone respects varied races, ethnicities, classes, genders, physical
and mental abilities, and sexualities; everyone matters and therefore all individuals are to be respected
and treated with dignity and civility; and everyone shares the responsibility for making our class a
positive and better place to be, work and learn.

Academic Integrity Policy

The university rules, including the Student Code of Conduct (https://www.uc.edu/campus-
life/conduct/student-code-of-conduct.html) and other documented policies of the department, college,
and university related to academic integrity will be enforced. Any violation of these regulations,
including acts of plagiarism, fabrication or cheating, will be dealt with on an individual basis according
to the severity of the misconduct. Sanctions range from receiving a zero for the specific assignment
involved to failure for the course.

Special Needs and Accommodation policy

If you have any special needs related to your participation in this course, including identified visual
impairment, hearing impairment, physical impairment, communication disorder, and/or specific
learning disability that may influence your performance in this course, you must register with the
Student Disabilities Office (http://www.uc.edu/disability.html) and meet with me to arrange for
reasonable provisions to ensure an equitable opportunity to meet all requirements of this course.

Counseling Services
Students have access to counseling and mental health care through the University Health Services
(UHS), which can provide both psychotherapy and psychiatric services. In addition, Counseling and
Psychological Services (CAPS) can provide professional counseling upon request; students may receive
five free counseling sessions through CAPS without insurance. Students are encouraged to seek
assistance for anxiety, depression, trauma/assault, adjustment to college life, interpersonal/relational
difficulty, sexuality, family conflict, grief and loss, disordered eating and body image, alcohol and
substance abuse, anger management, identity development and issues related to diversity, concerns
associated with sexual orientation and spirituality concerns, as well as any other issue of concerns. After
hours, students may call UHS at 513-556-2564 or CAPS Cares at 513-556-0648. For urgent physician
consultation after-hours, students may call 513-584-7777.
5
Title IX
Title IX is a federal civil rights law that prohibits discrimination on the basis of your actual or perceived
sex, gender, gender identity, gender expression, or sexual orientation. Title IX also covers sexual
violence, dating or domestic violence, and stalking. If you disclose a Title IX issue to me, I am required
forward that information to the Title IX Office. They will follow up with you about how the University
can take steps to address the impact on you and the community and make you aware of your rights and
resources. Their priority is to make sure you are safe and successful here. You are not required to talk
with the Title IX Office. If you would like to make a report of sex or gender-based discrimination,
harassment or violence, or if you would like to know more about your rights and resources on campus,
consult the website www.uc.edu/titleix or contact the office at 556-3349.

Electronic Communication
The course website is on Canvas (https://canopy.uc.edu/). All course announcements will be sent via
Canvas so make sure that your correct email address is correctly registered with Canvas.

Technology use during class

Technology is fully integrated into our daily lives and being in constant communication has proven
many benefits. However, cellphones, texting and social media can become intrusive. You are welcomed
to bring electronic devices to class and use them only for academic purposes. Be respectful of your
instructor and your peers and limit your use of electronic devises for class-related work only. Repetitive
disruption of class by the use of cellphones or computers will be dealt with on an individual basis.

6
Course Calendar

Week Date Topic Assigned Reading

Introduction to cell and molecular 1.1-1.3; Experimental Pathways:
Mon Jan 9
biology “The origin of eukaryotic cells”
1 Wed Jan 11 Basic Chemistry 2.1, 2.3- 2.5
Carbohydrates, lipids and proteins;
Fri Jan 13 2.7 (until p65)
structure and chemistry
Mon Jan 16 Martin Luther King Jr. Holiday
2.7 (pp 65-73 - "primary structure"
Wed Jan 18 Higher order protein structure
2 to "quaternary structure")
2.7 (p74-83 - "protein folding" to
Fri Jan 20 Protein conformation and chaperones
"experimental pathway")
Mon Jan 23 Thermodynamics and free energy 3.1 (until p 106: coupling reactions)
3.2 (until p114: inducing strain in
3 Wed Jan 25 Enzymes I
the substrate)
Fri Jan 27 Enzymes II 3.2 (from 117: enzyme kinetics )
Mon Jan 30 Midterm Exam 1 Material from Jan 10 to Jan 27
4.1-4.3 (until p150: Lipid anchored
Wed Feb 1 Lipid Membranes and proteins
membrane proteins)
4
4.3-4.5 (p151-162- From "studying
Fri Feb 3 Membrane fluidity and transport protein structure" to "control of
membrane protein mobility")
Mon Feb 6 Transport across Membranes 4.6 (skip p172-179)
5 Wed Feb 8 Membrane potential 4.7
Fri Feb 10 Introduction to metabolism 3.3
Mon Feb 13 Cellular Respiration I 5.1-5.2
5.3, 5.5-5.6 (skip "types of electron
6 Wed Feb 15 Cellular Respiration II
carriers"
Fri Feb 17 Photosynthesis 6,1, 6.3, 6.6
Review LO's, class notes,
Mon Feb 20 Overview of metabolism
worksheets
7 Wed Feb 22 Midterm Exam 2 Material from Feb 1 to Feb 20
Fri Feb 24 Cells and their environment 7.1
Mon Feb 27 Integrins and cell-cell interactions 7.3
7.4, 7.6 (skip "adherens junctions
Wed Mar 1 Cell-cell interactions and junctions and desmosomes" and "the
8 experimental pathway")
8.1-8.3 (until p322: "synthesis of
Fri Mar 3 Endomembrane system I secretory, lysosomal or vacuolar
proteins" )

7
Week Date Topic Assigned Reading
Mon Mar 6 Endomembrane system II 8.3-8.4 (from p321-332)
9 Wed Mar 8 Targeting vesicles and exocytosis 8.5
Fri Mar 10 Midterm 3 Material from Feb 24 to Mar 10
University of Cincinnati Spring
Mar 13-17
Break
9.1-9.2, 9.4-9.5 (skip "experimental
Mon Mar 20 Microtubules, kinesin and dynein
pathway")
10 Cilia, flagella and Intermediate
Wed Mar 22 9.6-9.7
filaments
Fri Mar 24 Actin and muscle contraction 9.8-9.9
Mon Mar 27 Cell Cycle and Cell Cycle Control 14.1
14.2 (until p667- the "spindle assembly
Wed Mar 29 Mitosis
11 checkpoint")
Cell signaling and G-protein coupled
Fri Mar 31 15.1, 15.3 (until p707. Skip p698-703)
receptors
15.3, 15.5 (from p707 – 717: "GPCRs in
Sensory perception and Receptor
Mon Apr 3 sensory perception" to "adapting to
Tyrosine kinases
transmit different types of information”
12
The Ras pathway and the insulin 15.5, 15.8 (from 717 – signaling by the
Wed Apr 5
receptor insulin receptor)
Fri Apr 7 Review session Review LO's, class notes, worksheets
Mon Apr 10 Midterm 4 Material from Mar 21-Apr8
16.1-16.3 (until p748. Skip
13 Wed Apr 12 Cancer overview
"experimental pathways"
Fri Apr 14 Tumor suppressor genes 16.3 - (from p749-757)
Mon Apr 17 Oncogenes and the cancer genome 16.3 (from p757)
14 Wed Apr 29 Strategies for combating cancer 16.6
Fri Apr 21 Techniques in molecular biology 18.7, 18.9, 18.10
15 Tue Apr 25 Final Exam: 12-2 pm Material from Jan 9 to Apr 21

I reserve the right to update this syllabus as class needs arise. Be assured that I will
communicate to you any changes to our schedule, syllabus or policies quickly and efficiently
through Canvas