BIOL 215 – Cells and Proteins

Spring 2020

Instructor: Dr. Valerie Haywood Email: vxh20@case.edu

Office: 506C Millis
*Note: You must use the middle stairs/elevator to reach the 5 th floor of Millis
(the elevators or stairs at either end of Millis Hall only reach the 4 th floor…if you use one of
those, you will not be able to get to my office…and I will be sad …)
Office Hours: W: 2-3pm, or by appointment

Major Goal of this course:

In this class, we will explore and understand the “inner life” of a cell. Topics include:
biological molecules (focus on proteins, carbohydrates, and lipids); cell structure (focus on
membranes, energy conversion organelles and cytoskeleton); protein structure-function;
enzymes, cellular energetics, cell communication and cell motility.
This course is the second in a series of four courses required for Biology majors.
Prerequisites: BIOL 214 AND either CHEM 105 or CHEM 111.  Coreq –OR- Prereq: CHEM
106 or ENGR 145 (i.e. you are either currently enrolled in –OR- already took Chem 106 or
ENGR 145).
*Please note: 215 and 215L are two separate courses. It is strongly recommended
that students take them together, however students are not required to enroll in 215L if
enrolled in 215.

Required Materials:
1) Becker’s World of the Cell. 9th ed. by Hardin, Bertoni and Kleinsmith.
*Older editions are not recommended.
Note: I am not including an ISBN, because the ISBN will vary depending on
where/how you purchase the book (i.e. alone or as part of a package). Below is a link
to the text on the publisher’s website.
http://www.mypearsonstore.com/bookstore/beckers-world-of-the-cell-9780321716026?xid=PSED
You will also have the option to purchase an e-text along with your MasteringBiology
access code. I have placed a copy of the text on reserve in the Kelvin Smith Library.

2) iClicker
Note: Any version of the iClicker will work in our class (i.e. iClicker, iClicker+,
iClicker2). Applications on your smart phone are NOT compatible.
We will use the iClicker the first day of class. Register your clicker no later
than 5pm on the first day of class (instructions further below).
3) Register for MasteringBiology - **A detailed handout outlining the registration
process can be found on our course Canvas site under ‘Modules’  ‘Course
Documents’  ‘How to Register for MasteringBiology’
*Please note: the codes in the front of the ‘World of the Cell’ textbook are for a different
website and do NOT work for MasteringBiology.
4) Four-function calculator – e.g. Sharp EL, available in the campus bookstore (~$5).
This is the only type of calculator permitted for exams (Graphing/scientific
calculators are NOT permitted).

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Optional Materials:
1) Solutions Manual for World of the Cell. ISBN-13: 978-0-321-68961-0

In-Class ELECTRONICS POLICY

Aside from the iClicker, other electronic devices of any kind (e.g. laptops, cell phones) are
not permitted in class. Such items are distracting to you, to those around you and to your
instructor. Recent studies have demonstrated that in-class electronics lower student
engagement, encourage “multitasking” (aka splitting attention away from the material at
hand), and provide a distraction for neighboring students (Fried 2008; Sana, Weston, and
Cepeda, 2013; Wurts, Smarkola and Gaffney, 2008). As such, they are not permitted under
any circumstance, not even to take class notes. Recent studies have demonstrated that
taking notes by hand increases retention rates compared to taking notes on a computer
(Mueller and Oppenheimer, 2014). I apologize in advance for any inconvenience.
Please be sure to turn off your phone prior to the start of class. Not only is using
your phone in class unacceptable, it is also very unprofessional.
Failure to comply with these rules will result in a 1% grade reduction of your final
course grade (i.e. your weighted total) each time a violation of this rule occurs. I also
reserve the right to confiscate your electronic device for the duration of class time if you
are caught violating this policy. Please consider this as your warning.
During an exam, if you are found using a cell phone or if you have a cell phone in your
line of vision, it will be considered an Academic Integrity Violation and treated accordingly.
You will receive a zero for that exam and may possibly fail the course.

MediaVision:
The course lectures will be available on MediaVision. Please note, MediaVision’s policy is to
post lecture videos within 48 regular business hours from the time of recording (although
usually available the same day). If there are any problems with the videos, please contact
MediaVision: support@case.edu, 368-1020.

Lecture Materials:
Lecture slides will be posted on Canvas after class. You should review the slides after class
that day along with your notes. Please note: slides ARE NOT posted before class. I like to
ask MANY questions in class in order to engage students. Having the lecture slides in front
of you would defeat the purpose of me asking questions, as you would already have the
answers. Thank you in advance for your understanding!
The textbook is meant to serve as mainly a reference guide for the material
presented in lecture. Chapters and page numbers where relevant information can be found
are provided on the syllabus. *Students are not responsible for topics found in the text
that were not covered in lecture or referenced in the learning objectives.
The iClicker is a REQUIRED course material. The iClicker serves several purposes.
It is designed to actively engage students in the class and it also provides feedback: it tells
you how well you understand a particular concept; it allows the instructor to gauge the level
of understanding of the entire class. For example, if a student answers most of the
questions on a given topic incorrectly, that lets the student know that they should review
that topic in more depth. From the instructor’s perspective, if most students answer a
clicker question incorrectly, that lets the instructor know to review the material again with

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the class, but perhaps in a different way. The iClicker is used in BIOL 214, 215 and 216, as
well as CHEM and PHYS courses. So hold onto your device and take good care of it. You will
use it in many science classes.

Learning objectives:
A confirmed list of learning objectives for each lecture will be posted on Canvas after
class. These are meant to serve as a guide to the lecture material so you will understand
the instructor’s expectations. LEARNING OBJECTIVES ARE USED BY THE
INSTRUCTOR TO WRITE EXAM QUESTIONS. You should also use these as your main
study guide to assess your understanding of the course material.
A tentative list of learning objectives for the first week is now posted. These are
meant to serve as a guide for you as you browse through the reading assignments. A
confirmed list of learning objectives for each lecture will be posted on Canvas after class,
verifying what we covered in class that day. Until confirmed, the learning objectives are
tentative and are subject to change based on the pace of the course and the instructor’s
discretion.
In past classes, the most successful students have indicated that they complete the
learning objectives as soon as possible after class that same day. They do not wait until a
later date to complete them. Rather, they complete them on the same day as they are
posted, and then use them as a guide to repeatedly reinforce the course material.

Grading:
Course grades consist of four midterm exams and MasteringBiology assignments. There is
no ‘Final Exam’ during finals week. Exams are comprehensive in the sense that knowledge of
previous material is needed to answer questions covering new material. Midterm exams will
be held in class for the entire class period. No lecture will be given on exam days. Midterm
exams will consist of multiple choice and True/False questions worth two points each. Exam
questions will be drawn from material covered in lecture and referenced in the learning
objectives. Please note: you are responsible only for topics covered in 1) lecture, AND 2)
referenced in the Learning Objectives. *Students are NOT responsible for topics found
in the text that were not covered in lecture or referenced in the learning objectives.

The point values and weights are listed below and can also be found on Canvas.
PLEASE NOTE: SCORES ARE WEIGHTED.

Midterm Exam 1 50 questions @ 2 pt each = 100 pts x 20% weight

Midterm Exam 2 50 questions @ 2 pt each = 100 pts x 20% weight
Midterm Exam 3 50 questions @ 2 pt each = 100 pts x 20% weight
Midterm Exam 4 50 questions @ 2 pt each = 100 pts x 20% weight
MasteringBiology Assignment #1 = 25 pts of extra credit
assignments Will be included in total mastering point, for a maximum
possible of 350pts. i.e. students cannot earn more than 350 points
for MasteringBiology
Assignments #2-15 @ 25 pt each = 350pts x 20% weight
TOTAL 750 pts / 100% possible

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The ‘Grade Center’ on Canvas is automatically set up to calculate the weighted total for you.
This is the ‘Weighted Total’ column. If you do not know how to calculate a weighted average,
a good tutorial can be found at:
http://www.blacksdomain.com/files/Notes/Calculating_WA.php
Occasionally, grading errors occur and/or students have legitimate complaints about
graded materials. All grading questions regarding the MasteringBiology assignments and
midterm exams must be initiated via email within two days of the date the material
was graded and/or returned. Otherwise, you forfeit your right to dispute the grade at a
later date. For example, if the material was returned February 2 nd, you must submit your
concern in email to the instructor no later than February 4 th. I will respond to your
request within two business days.
Please note: There is an overwhelming litany of information available online on
almost any subject. Students should focus on the material provided in class as a resource.
If you find conflicting or confusing information on a topic, you should resolve this with me
prior to the exam, otherwise I will not accept any such outside information as a valid
dispute. Students should focus on the material presented in class when answering the exam
questions or disputing exam questions.

Course grading scale:

90.0 – 100 % A
80.0 – 89.99 % B
70.0 – 79.99 % C
60.0 – 69.99 % D
Below 60.0 % F

The grading scale is firm. There is no rounding-up or extra credit.

MasteringBiology Assignments:
MasteringBiology is an online tutorial, homework, and assessment system developed by
Pearson Publishing to accompany their biology texts. Note: the system was originally
designed for the ‘Campbell Biology’ book. Thus, some of the chapter references in
MasteringBiology refer to Campbell Biology. Please do not get confused by the chapter
references if they don’t match our textbook.
Working with Pearson Publishing, I have developed a series of online assignments
relevant to the Biol 215 class in order to provide an additional set of learning activities for
Biol 215 students to help you reinforce the material. The MasteringBiology assignments are
weighted at 20% of your final course grade, i.e. equivalent to an exam score.
**A detailed handout outlining the registration process can be found on our course
Canvas site under ‘Modules’  ‘Course Documents’  ‘How to Register for
MasteringBiology’
There will be 15 assignments total. Assignment #1 is designed to familiarize you
with the MasteringBiology program and the course syllabus. Assignment #1 is worth 25 pts
of extra credit, to be added to your total MasteringBiology score. This will also serve as a
buffer in case you miss any of the mastering assignments. The remaining 14 assignments (2-
15) are each worth 25 pts, for a total of 350 pts maximum, i.e. students cannot earn more
than 350 points for MasteringBiology. Each assignment will be due every Friday (see

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‘Lecture & Exam’ schedule at end of syllabus). MasteringBiology assignments are designed to
cover: 1) material that will be discussed in lecture that week, 2) review material from
previous lectures, 3) material that will be presented in the upcoming weeks. Students
should expect to read ahead in the book to find information not yet covered in lecture.
Note: MasteringBiology assignments will not be a comprehensive coverage of all
lecture material. They will touch on most topics, but will not cover everything. In
other words, being able to complete the MasteringBiology assignments will not
guarantee you an ‘A’ in the course. Students should refer to the Learning Objectives
for a comprehensive list of lecture items.
The due date will be 5pm each Friday after the assigned date. For example, if an
assignment was given on Monday 1/13, it will be due on Friday 1/17 at 5pm. After that time,
the assignments will be closed and no longer available for points. Assignments will be
available to rework for additional practice after the due date, but this work will not be
saved and will not affect your grade. Students will be notified on Canvas when each
assignment becomes available. There will not be an extension of the due date for any reason.
Again, assignment #1 is built in just in case students miss one assignment for any reason
during the semester.
For each MasteringBiology question, students will have 2 attempts to answer each
question correctly. For the first incorrect attempt, 75% is deducted. If the question is
answered correctly on the second attempt, 25% will be awarded. If the question is not
answered correctly on the 2nd attempt, no credit will be given for that question. For
example, on a given question, it takes a student 2 tries to answer the question; i.e. first
attempt is unsuccessful, second attempt is correct. The student will earn 25% on that
question (75% deducted for the incorrect attempts). The grading scheme is designed to
ensure that students are making a legitimate attempt at answering the questions, and not
simply guessing. Some questions only have two answer choices, hence the two attempt limit.
Answers are graded automatically on a central server run by MasteringBiology (i.e.
your instructor is not manually grading your work). Students will be able to view their
MasteringBiology scores via the MasteringBiology site. Note: these scores will not be
added to our Canvas site until the end of the semester.
If you are having problems with registration or any other aspect of
MasteringBiology, please contact the Pearson Support Team:
email: http://247pearsoned.custhelp.com/app/ask
live chat: http://247pearsoned.custhelp.com/app/chat/chat_launch
Please note: Data for each student using MasteringBiology is saved on FOUR different
platforms within in the Pearson Publishing system (gradebook answer recording, gradebook
time display, diagnostic student time, user activity report). In other words, there are four
separate systems that collect and monitor data. Pearson Publishing is able to track the ‘click
path’ for each individual user. Loss of data does not occur for a single student. Any such
claims will be thoroughly investigated. False claims will be reported to Academic Integrity
and will result in loss of ALL MasteringBiology points (i.e. 20% of your final course grade),
not just the assignment(s) involved.

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iClicker: (software = iClicker Classic; Learning Management System = Canvas)
We will be using the iClicker classroom response system. This is a required material. This is
an invaluable assessment tool that provides feedback to both the student and the
instructor. This item is also used in the Biol 214 and 216 courses.
The iClicker serves several purposes. It is designed to actively engage students in
the class, provide examples of exam questions, and it also provides feedback: it tells you
how well you understand a particular concept; it allows your instructor to gauge the level of
understanding of the entire class. For example, if a given student answers most of the
questions on a given topic incorrectly, that lets the student know that they should review
that topic in more depth. From the instructor’s perspective, if most students answer a
clicker question incorrectly, that lets the instructor know to review the material again with
the class, but perhaps in a different way.
To register your iClicker, visit http://www.iclicker.com/registration/. For your
'Student ID' use your Case Network ID (e.g. abc123). DO NOT use your 7-digit student
ID or your SS#. We are using iClicker Classic and Canvas. It is recommended that you
write down the clicker code (looks like a UPC code on the back of the clicker) and keep that
information in a safe place. This will be useful in case you lose your clicker or the numbers
wear off and you need to use the clicker for another class. Your instructor does not keep
records of clicker numbers once the class is over.
If you registered your iClicker for a previous course (e.g. Biol 214), you should still
re-register this semester.  If you are purchasing a used iClicker, the iClicker company
requires a one-time registration fee of $6.99. This fee is required only when registering a
used remote.
If you are having difficulty registering, please contact the company directly
(1.866.209.5698). If your remote ID is worn off, you can use this link:
http://www.iclicker.com/registration/lookup.aspx. If either of those fail, you need to
purchase a new clicker as there is no other way to identify your clicker.
Clicker registration will be analyzed after the drop/add deadline = after 5pm
that day. I kindly request that you do not ask me to check if your iClicker is properly
registered. I will analyze the iClicker registrations after drop/add and will notify those
students who DO NOT have a clicker registered to their name. If you are NOT notified, you
can safely assume your clicker is registered.

Communication:
Class information (e.g. announcements) will be posted to Canvas and/or sent via email to
students using the course mailing list provided on Canvas (your Case email address). All
students are expected to check the Biol 215 Canvas site regularly and check their Case
email daily and to ensure that they are able to receive email, i.e. that they are not over
quota and that their default email address in the university system is valid.
Emails sent to the instructor will be answered within 2 business days (i.e. weekends
and holidays NOT included). In general, emails sent after 5pm will not be read until the
next business day. Please note, Dr. Haywood does have a family and a life outside of CWRU.
Evenings and weekends are devoted to family/personal time. As such, you should not expect
an immediate response to an email sent on the weekend or after 5pm during the week. You
can expect a response within two business days.

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Attendance:
Please read the established university guidelines regarding attendance:
http://students.case.edu/handbook/policy/conduct/attendance.html
Students are expected to attend classes regularly and actively participate in the class.
Distracting/disrespectful behavior (e.g. sleeping, reading the newspaper) will not be
tolerated. If you engage in such behavior, you will be asked to leave and your grade will be
reduced (see below). Please see “In-Class Electronics Policy”
While sometimes absences cannot be avoided, your grade will be adversely affected
if you do not attend class regularly: you may miss in-class activities and you will miss
valuable information presented in lecture. Excessive absence will result in failure of the
course. This is the University Attendance Policy.

Missing an Exam or Homework:

Exams can be made-up only under extenuating circumstances. Makeup exams will be in essay
form and questions will vary from the regularly scheduled exam. There are no makeups for
the MasteringBiology assignments.
If you need to miss an exam due to illness or other emergency, you must email the
instructor by the day of the exam. This discussion must occur via email for
documentation purposes. Verbal discussions are NOT valid. If you have a valid reason for
missing an exam, you must take a make-up exam before the next class period. For example,
if the exam was on Monday, 9/30, you must take the exam sometime before class starts on
Wednesday, 10/2. You may not take a make-up exam if you already took the regularly
scheduled exam. Exams cannot be returned until everyone has completed one, so any delay
affects the entire class. If the reason is medical, you must provide a doctor’s note which
explains the reason for your absence. The doctor's note must state the reason for your
absence. It cannot simply state that you were seen that day. It is your responsibility
to obtain a proper doctor’s note. Failure to do so will result in an unexcused absence.
If you need to take a makeup exam, it is YOUR responsibility to arrange a
makeup exam in a TIMELY manner. You must contact me before the exam to notify me of
your absence. Then you must make arrangements with me for a makeup exam no later
than 5pm on the day of the regularly scheduled exam. This may take several email
correspondences or a phone call. Regardless, it is your responsibility to make sure that we
make arrangements for your makeup exam. “Oh, sorry, I didn’t check my email…” …is not an
excuse for not making proper arrangements. You will not be allowed to take a makeup
exam if you fail to make proper arrangements by the specified deadline.
An excuse from the Dean will be required from anyone missing an exam without
prior consent of the instructor and may be required in other circumstances . You may not
make up an exam if you do not have prior consent of the instructor. The exam schedule is
available at the beginning of the term so make your vacation/travel plans accordingly. “But
I didn’t check the schedule until now, and I have to go to XYZ”…this is not a valid excuse.

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Tardiness:
Please be on time. As a courtesy to your fellow students and to your instructor, please be on
time to each scheduled meeting. Directions and other important information will be
discussed at the beginning of each class meeting. If you are more than 10 minutes late for
an exam, you will be penalized 10% per each 10-minute increment (i.e. % will be deducted
from total possible points, not points earned). Please note that a late arrival will not extend
the examination period.

Secure testing: 
Once the first student leaves the exam, no further late students will be permitted into the
exam. Such students will not have their exam rescheduled and they will receive a zero.   No
student will be permitted to leave the testing room during their exam time – this includes
using the restroom.  All personal items, including cell phones and other communication
devices are to be stored at the front of the classroom.   NO ear pieces are to be permitted
during the exam (iPods etc.).  Students must keep their hands above their desks at all
times. You may be asked to stand if you are seen with your hands below your desk so
that your seating area can be examined. Your writing utensils may be examined by the
testing staff to insure they are free from any questionable information.  No sharing of
items (pens, pencils, calculators, erasers etc.) during the exam. 

Academic Integrity:
Any evidence of dishonesty will be reported to the Academic Integrity Board. Please review
the following website: http://studentaffairs.case.edu/office/handbook/policy/integrity.html

In-class announcements:
Announcements promoting any sort of event are not permitted. Our class time is valuable
and we need every minute for class-related items. As such, no announcements are
permitted. My apologies for the inconvenience.

Course materials:
ALL course materials are the intellectual property of the instructor. Students are
prohibited from posting ANY Biol 215 course materials to a 3 rd party website, e.g. Course
Hero, etc. Such a violation of course policy will result in a letter grade reduction of your
final course grade.

Study Suggestions:
Please see ‘Course Documents’ on the course Canvas site for Study Suggestions.

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LECTURE & EXAM SCHEDULE
**Tentative**- Topic dates may change depending on the pace of the class, but all exam
dates are firm. Readings are from “Becker’s World of the Cell” 9th ed. by Hardin, Bertoni
and Kleinsmith.
Week 1 (MasteringBiology Assignments #1 and #2 available)
1/13 – lec 1
Introduction, “Inner Life of a Cell”, Brief History of Cell Biology, Phylogenetic
1/15 – lec 2
Organization of Cells , - pp 1-17; pp 18-25 (through ‘Water’ section); 27-32
(‘Polymerization’ …stop at ‘Self-assembly’); 34 (‘Noncovalent bonds ‘);
Limits to Cell size, “Tour of the Cell” - pp 75 - 105; 324 – 341 (stop at
‘Exocytosis’ section); 352 – 364; 254 – 258 (‘Mitochondrion’ section); 295 – 297
(‘Chloroplast’ section); Box 11A pp 298 – 299; 536 – 548

*Chemistry Review Worksheet (found under ‘Course Documents’ on BB)

*Measurements Worksheet (found under ‘Course Documents’ on BB)

1/17 DUE by 5pm - *MB Assignments #1 and #2

Week 2 (MB #3 available)
1/20 NO CLASS – MLK JR. DAY

1/22 - lec 3 “Tour of the Cell”, cont…

Chemistry Review; Types of Bonds; Functional Groups; Macromolecules: Lipids,
Carbohydrates and Proteins; - pp 41-54 (stop at ‘Nucleic Acids’); pp 60-74; 178 –
180 (SDS-PAGE section); 696 – 705; 32 – 40; 679 – 696 (‘Gene expression’…
stop at Protein Targeting’)

1/24 DUE by 5pm - MB Assignment #3

Week 3 (#4 available)
1/27 - lec 4 Macromolecules, cont.; Amino Acids; Protein Structure/Function
1/29 – lec 5

1/31 DUE by 5pm - MB Assignment #4

Week 4 (#5 available)
2/3 - lec 6 Protein Structure/Function, cont…
2/5 – lec 7

2/7 DUE by 5pm – MB Assignment #5

Week 5 (#6 available)
2/10 – lec 8 Energy Flow in the Cell – Ch 5: all pages, Ch 9: 224 – 228

2/12 EXAM 1

2/14 DUE by 5pm – MB Assignment #6

Week 6 (#7 available)

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2/17 – lec 9 Enzymes Ch 6: all pages
2/19 – lec 10

2/21 DUE by 5pm – MB Assignment #7

Week 7 (#8 available)
2/24 – lec 11 Lipids; Membrane Structure and Function – Chapter 7: all pages; pp 65-74; 163-
2/26 – lec 12 169 (stop at ‘The Lipid Bilayer is Fluid’)

2/28 DUE by 5pm – MB Assignment #8

Week 8 (#9 available)
3/2 – lec 13 Membrane Transport - Chapter 8: all pages, 341 – 352 (‘Exo- & Endocytosis’ up
to ‘Lysosome’ section)
3/4 – lec 14

3/6 DUE by 5pm – MB Assignment #9 (#10 available early due to upcoming break)
Week 9
3/9 – 3/13 NO CLASS – SPRING BREAK

Week 10 (#11 available)

3/16 DUE by 5pm – MB Assignment #10 (extra time given due to Spring Break)

3/16 – lec 15 Chemotrophic Energy Metabolism: Glycolysis and Fermentation – pp 229 – 238
(Stop at ‘Alternative Substrates….” section)

3/18 EXAM 2

3/20 DUE by 5pm – MB Assignment #11

Week 11 (#12 available)
3/23 - lec 16 Chemotropic Energy Metabolism: Aerobic Respiration, ATP Synthesis- pp 252-
3/25 – lec 17 263 (stop at ‘Fats’ section), 267 – 292 (omit Box 10A, ‘Glyoxylate Cycle’)

Regulation of Chemotropic Energy Metabolism - pp 238-247, 263-267 (‘Several

TCA Cycle Enzymes…’ stop at ‘Electron Transport), Box 10A pp 268-269

3/27 DUE by 5pm – MB Assignment #12

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 Week 12 (#13 available)
3/30 – lec 18 Phototropic Energy Metabolism (Photosynthesis) – pp 293 – 312 (stop at
‘Regulation of Calvin Cycle’) +

4/1 – lec 19 Signal Transduction - Chapter 14: all pages

4/3 DUE by 5pm – MB Assignment #13

Week 13 (#14 available)
4/6 EXAM 3

4/8 – lec 20 Signal Transduction, cont. - Chapter 14: all pages

4/10 DUE by 5pm – MB Assignment #14

Week 14 (#15 available – last MB assignment)

4/13 – lec 21 Cellular Movement, Motility and Contractility - pp 449 – 460 (stop at ‘Muscle’
4/15 – lec 22 section), 471-476

4/17 DUE by 5pm – MB Assignment #15

Week 15
4/20 – lec 23 Beyond the Cell: Extracellular Structures, Cell Adhesions and Cell Junctions –
4/22 – lec 24 Chapter 17: all pages
“Inner Life of a Cell”, revisited

4/27 EXAM 4

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