Biology 111A (Spring 2016)
Unity of Life: Cells, Molecules, and Systems
COURSE SYLLABUS
Instructor:
Office:
Office Phone:
Email:
Mark O. Martin (“Doc Martin” is my preferred
nickname)
Thompson 257A
(253) 879-2747
momartin@pugetsound.edu and for our class
DocMartinUPS@gmail.com
Research Lab:
TH 275
Office Hours:
Monday 3PM to 4PM
Wednesday 8AM to 9AM
Friday 9AM to 10AM
or by appointment (I’m often here on weekends)
Texts:
Biology: How Life Works, 1st ed., Morris et al., 2013
A Student Handbook for Writing in Biology, 4th ed.,
Knisely, 2013
LaunchPad online learning tool for How Life Works
Biology 111 Laboratory Manual, Fall 2016: distributed
weekly on Moodle.
Readings and articles on Moodle
Lecture notes (as PDFs) available on Moodle after
class.
Laboratory manual:
Other resources:
INTRODUCTION
Biology 111 is an introductory–level course in the biological sciences designed for
students intending to major in biology or a related science. In Biology 111 we will focus
on structure, function, and systems at the cellular and molecular levels. These
characteristics are true of all living things, hence the title: the unity of life! You will find
that the information provided in not simply interesting to your professor, but relevant to
everyday and the news.
COURSE OBJECTIVES
The primary objective of this course is for you to develop an understanding of how
structure and function in biological systems is connected to the composition and
organization of those systems at the cellular and molecular levels---again, for all living
things. Through this course you will develop confidence in your ability to think logically
and critically and to communicate ideas effectively. Writing clearly is one of the most
important skills you will develop in college. One of the goals of this course is to help you
recognize the elements of good scientific writing and allow you to develop your
scientific writing skills.
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Course Syllabus
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Within this framework, by participating in this course you should be able to meet the
following objectives:
• Understand the basic concepts of the evolution of cellular and molecular
biological systems
• Apply the basic concepts of biology to new problems
• Relate biological principles to your own experience as an individual and as a
member of society
• Develop your power of reasoning and analysis through application of scientific
methods
• Develop research skills such as data collection, analysis, and interpretation
• Develop writing skills for effective communication
In addition, I would like to remind you of some overarching concepts that occur
throughout this course. Keeping these concepts in mind---fitting in what you are
learning about each lecture into this framework---can only help organize your thinking
and improve student outcomes. These concepts are:
1.
2.
3.
4.
5.
Evolution
Structure and function
Information flow, exchange, and storage
Pathways and transformations of energy and matter
Systems
STRATEGIES FOR SUCCESS IN THIS COURSE
Please consider employing the following proven strategies to help meet the objectives
of this course:
1. Attend all classes and laboratories; please arrive on time.
2. Prepare for each class by reviewing notes from the previous class(es) and reading
the assigned pages of text(s).
3. Come to class prepared to think about the material, participate in discussions, take
detailed notes, and ask questions about the material.
4. Study the material after each class. Information and ideas will be most fresh in your
mind at this time. Integrate current class information with material from previous
classes, readings, and laboratories. Use the online LaunchPad tool to support your
study sessions and assess your learning.
5. Use each class session and your study time to prepare for quizzes and exams.
Breaking up the topics into small packages is a successful strategy. No matter what
you may think, last minute cramming is not only bad for your heath, but
demonstrably does not lead to retained learning, good scores, or a pleasant
experience! I know all this from painful experience; be wiser than I was!
6. Prepare for lab well in advance by reading lab instructions, notes, and text. Think
about and prepare well-thought out answers to the pre-lab questions. Do not wait
until just before lab to do this. Arrive at the lab on time, informed about what you
will be doing, and prepared to efficiently use the time available.
7. Seek help from the professor and course assistant.
Biology 111A (Spring 2016)
Course Syllabus
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Another very effective mechanism that will enhance your learning in this course is to
work with other students to master the subject matter. Organize or join a small study
group. Use the group to review information and test each other’s knowledge and ability
to explain the material. The more you intellectually engage your mind with the topic
materials, the more you will learn and the better prepared you will be for the quizzes
and exams.
Make sure your class, lab, and study time is specific and focused. PLEASE turn off
electronic devices and minimize distractions. A shorter amount of focused study time is
more productive than a longer period of time filled with distractions.
COURSE MECHANICS
Moodle:
Moodle is the Learning Management software used here at Puget Sound. The Moodle
site for this class will contain essential material for the course, such as readings, as well
as announcements and reminders. I will post course outlines and my PowerPoint slides
after each lecture. I may have you submit some assignments via Moodle—I will provide
more information about this in class. You can access Moodle
(moodle.pugetsound.edu) using your Puget Sound username and password. You
should already be enrolled in BIOL 111A on Moodle.
Please note:
1.
Our course Moodle site should be up and running by Wednesday evening.
2.
Lab “chapters” for the coming week will be available on Moodle, the Friday
before that week’s lab. Thus, next week’s lab will be available on Friday.
LaunchPad:
Launchpad is the online system for the How Life Works text. We will discuss LaunchPad
in class and will use the system throughout the semester. LaunchPad has a number of
self-assessments, interactive modules, and other helpful tools to facilitate your learning.
In addition, there is an electronic version of the text on LaunchPad. Explore!
Class Sessions:
Biology 111, section A, meets Monday, Wednesday, and Friday at 11:00 AM in TH 193.
Class topics are listed on the attached schedule. Your time in class will be most
productive if you:
1.
2.
3.
4.
5.
6.
Prepare for class by studying the reading assignment before the class.
Come to class on time.
Engage in thoughtful, effective note taking during class.
Ask for a restatement or clarification of statements you do not understand.
Contribute to class discussions.
Following each class, devote 2-3 hours to carefully rereading the text
material and integrating it with your lecture notes.
I encourage you to ask questions at any time during the class. I would much rather
“get behind” in my lecture than leave students behind! My goal is to be an effective
instructor, and that is a collaborative effort between us. Plan to use opportunities to ask
Biology 111A (Spring 2016)
Course Syllabus
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questions by writing down questions that come to mind during your reading and study
or if I say something you do not understand or seems confusing. I am also available
during my office hours or through an appointment.
Readings:
Biology: How Life Works, by Morris et al., is an excellent introductory biology text
organized around the underlying principles of evolution and systems thinking. The
textbook, the accompanying LaunchPad site, provide coverage of key concepts in
multiple ways. The approach works well for such an integrated subject as biology. You
will also use this textbook and tools for Biology 112, the other (organismal and ecology
based) semester introductory biology course. The schedule for this course identifies the
chapter(s) appropriate to read in preparation for each topic. The accompanying
materials for each chapter are designed to enhance your thinking about the topics
being considered in this course. I encourage you to use these resources.
A Student Handbook for Writing in Biology, 4th ed., by Knisely, is a guide for writing
papers in all biology courses. Use this handbook as a resource and a guide for the
various writing assignments and constructing figures, tables, and legends in this course.
It will also be useful for writing review and research papers in other courses and will help
you organize poster presentations.
You will be reading several examples of primary literature in this course. Primary
literature is so-named because it is the original source of data on a specific topic. In
the sciences, most primary literature is in the form of an article in a peer-reviewed
scientific journal. The articles usually provide some introductory material then outline
the methodology used, the results of the research, and a discussion of how the results
add to current understanding. Reading these articles will allow us to apply the
concepts we have learned and to critically analyze scientific work. We will discuss and
analyze the articles in class so make sure you have read the articles prior to the class
session listed. All readings will be available on Moodle well before our discussions.
Laboratory:
This course includes an integrated laboratory component. Laboratory topics are
designed to complement and extend topics covered in class. Therefore, laboratory
topics are appropriate material for quizzes and exams. Be sure to include lab activities
in your study and review sessions. Again, the laboratory manual will be available
weekly, in chapters, on Moodle.
You must be registered for a laboratory section associated with Biology 111A and
attendance is mandatory. You must attend the lab for which you are registered. In
extenuating circumstances, it may be possible to attend a different lab section,
provided you make arrangements with me in advance. Labs cannot be made up after
the last lab section of the week has met.
You must come to lab PREPARED. Carefully read the appropriate section in your lab
manual before coming to lab. Most of the lab exercises contain pre-lab questions that
must be completed before your lab meets and must be submitted at the beginning of
the lab session (late pre-lab questions will not be accepted). Careful preparation
before the lab will (1) allow you to get more out of the lab, (2) make it much more likely
Biology 111A (Spring 2016)
Course Syllabus
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that you will enjoy the lab, and (3) increase the probability that you will finish the lab on
time. In addition, you have control over how you accrue points on these assignments!
It is essential that you write clear, concise, and well-documented papers and reports. All
laboratories will include some form of written assignment. These are designed to
strengthen your understanding of lab topics and develop good writing skills.
Academic Integrity:
The university’s academic integrity policy is clear and comprehensive. It is available
online as part of the Academic Handbook (http://www.pugetsound.edu/studentlife/personal-safety/student-handbook/academic-handbook/academic-integrity/ ).
You are responsible for understanding what constitutes plagiarism and other forms of
academic dishonesty. Academic integrity is vital to your work as a student. All
assignments must be written individually. Cheating, plagiarism, and other forms of
academic dishonesty will NOT be tolerated. Contact me with any questions regarding
academic integrity.
Late Assignment Policy:
Unless indicated otherwise, all assignments are due, in paper form, at the beginning of
the class or lab period on the identified due date. Assignments turned in late on the
same day it is due will be assessed a penalty of 5% of the total points possible. After
the due date, all late assignments will be assessed a penalty of 10% per day for up to
one week only (including weekends and holidays). After one week, no credit will be
given.
Please note: extra-curricular activities, travel, employment, work in other courses, etc.,
are not valid excuses for late work. If you must miss class, it is your responsibility to
determine what assignments may be due in your absence and to turn those
assignments in on time. Please check with me if you are unsure about assignment due
dates. Looking ahead to problems, and solving them ahead of time, is a vital life skill.
Please work with me on this.
Absences for medical or family emergencies may be exempt from the late assignment
policy. Written documentation of the nature of the emergency may be required.
Please consult with me in these circumstances.
Bereavement Policy:
Upon approval from the Dean of Students’ Office, students who experience a death in
the family, including parent, grandparent, sibling, or persons living in the same
household, are allowed three consecutive weekdays of excused absences, as
negotiated with the Dean of Students. For more information, please see the Academic
Handbook.
Biology 111A (Spring 2016)
Course Syllabus
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Assessment of Learning:
There will be eight short quizzes (10 points each) given over the course of the semester
(see schedule). Quizzes will be given during the first 10 minutes of class on the
designated Wednesdays and will cover topics from previous classes, labs, and current
reading assignments. Quizzes will ONLY be administered during the first 10 minutes of
class; no additional time or make-up quizzes will be given. Your lowest quiz grade will
not be included in the course grade calculations.
The three in-class exams (see schedule) will each be 50 minutes in length. Exams will
consist of objective (multiple choice, matching, and completion) and short essay
based questions (definitions, explanations and problems). The topic coverage for each
exam will be indicated in class and on the Moodle site; exams will include material from
readings, laboratories, and classes.
Please note: there will be several optional opportunities for all students to earn
additional points. These assignments are at my discretion. I do this because not every
student learns in the same fashion.
The final exam is scheduled for Friday, May 13th , from 12PM – 2PM. This exam will focus
on material following the third exam, will include much cumulative material from topics
covered earlier in the course, and will require you to integrate the important topics
covered throughout the semester. In accordance with university policy, the final must
be taken at the scheduled time.
THERE WILL BE NO MAKE-UP OF EXAMS OR QUIZZES. Absence for medical reasons or
family emergencies will require written evidence and MAY (OR MAY NOT) be
considered in your course grade.
If you wish to dispute a grade on any course assignment, quiz, or exam, please follow
the following procedures. Return the graded document directly to me with a typed
appeal attached to the front of assignment. This appeal should indicate (1) what
portion of the assignment you would like re-graded and (2) why you are disputing the
grade you received, based on information appearing in the assignment key, presented
in class, in the outlines, or PowerPoints. I will accept appeals up to one week from the
date that the assignment/quiz/exam was returned to you, with a detailed key.
Behavioral Expectations:
I expect you to behave in an appropriate manner while attending this class. Here are a
few guidelines:
• Be punctual—be on time for both class and lab.
• During class and lab time I expect you to be working on materials for this course
only.
• Personal technology; please be respectful of others in class:
o Turn your phone OFF before coming to class
o You may use a laptop or tablet in class as long as it is not a distraction to
others
o Refrain from using email or text messaging during class
o You may not touch or use your phone/laptop/tablet in any way during an
exam
Biology 111A (Spring 2016)
Course Syllabus
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You may not listen to a phone, iPod, or similar device during an exam or
quiz
You may not make audio recordings of our class or lab sessions without
permission.
If you leave the room during a test or quiz without permission, your paper will be
collected and will not be returned to you.
Lack of respect for others will not be tolerated in the class. Respect everyone
regardless of age, life experiences, profession, race, religion, gender, nation,
lifestyle, social class, learning style, philosophy of life, sexual orientation,
personality, mental and physical challenges, customs, or values, among others.
You may bring food and/or drinks to class as long as the consumption of food
and/or drinks is not a distraction to others
ABSOLUTELY NO FOOD OR DRINK is allowed in the laboratory. Drinks can be kept
outside the lab door. Wash your hands prior to consuming food or drink.
Wear closed-toed shoes while in the laboratory.
Telephones located in classrooms and labs are for staff use and medical/safety
emergencies only.
Student access to the lab prep areas is prohibited unless authorized by an
instructor.
o
•
•
•
•
•
•
•
•
Contacting Me and Class Correspondence
You may contact me by telephone, e-mail, or in person. I check my e-mail periodically
throughout the day but usually not in the evenings. I will use e-mail and/or Moodle to
provide information about the class and/or lab. Make sure you routinely check your
Puget Sound e-mail.
Grading
Here are the assignments in this course, and their point totals (note, there will be several
optional extra credit assignments for ALL students):
Assignment
Quizzes (10 pts each) x 8 (lowest score
dropped)
Exams (100 pts each) x 3
Laboratory Pre/Post questions
Final Exam
Biofilm Lab Report
Lab Practical
Cell and Molecular Biology in the News
Collaborative Learning Exercises x 2
Total points for YOU to earn
Points
70
300
165
150
50
20
20
60
835 points
Biology 111A (Spring 2016)
Course Syllabus
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Final letter grades for this course will be based on your total accumulated points at the
end of the semester based on the percentages below:
Grading Scale:
Average Percentage
93-100
90-92
87-89
83-86
80-82
77-79
70-76
68-69
66-67
60-65
0 - 59
Grade
A
AB+
B
BC+
C
CD+
D
F
ACCESSIBILITY AND ACCOMMODATION
If you have a physical, psychological, medical or learning disability that may impact
your course work, please contact Peggy Perno, Director of the Office of Accessibility
and Accommodation, 105 Howarth, 253.879.3395. She will determine with you what
accommodations are necessary and appropriate. All information and documentation
is confidential.
EMERGENCY RESPONSE PROCEDURES
Please review university emergency preparedness and response procedures posted at
www.pugetsound.edu/emergency/. There is a link on the university home page.
Familiarize yourself with hall exit doors and the designated gathering area for your class
and laboratory buildings.
If building evacuation becomes necessary (e.g. earthquake), meet your instructor at
the designated gathering area so she/he can account for your presence. Then wait for
further instructions. Do not return to the building or classroom until advised by a
university emergency response representative.
If confronted by an act of violence, be prepared to make quick decisions to protect
your safety. Flee the area by running away from the source of danger if you can safely
do so. If this is not possible, shelter in place by securing classroom or lab doors and
windows, closing blinds, and turning off room lights. Lie on the floor out of sight and
away from windows and doors. Place cell phones or pagers on vibrate so that you can
receive messages quietly. Wait for further instructions.
Biology 111A (Spring 2016)
Course Syllabus
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SOME FINAL THOUGHTS FROM DOC MARTIN
I love the field of biology---constantly changing and improving. There is something new
and exciting nearly every day related to what we will be learning in lecture and lab.
Thus, I adore talking about it. Ours is a large class, but keep in mind that our labs are
small, and I do my level best to be available to students a great deal. Also, I tend to be
a little less flamboyant one on one than in class or lab.
Obviously, grades are only a snapshot of how life and learning are going for a student
on a given day. I work hard to be EVERYONE’s professor. I will work hard to be YOUR
professor---if you work with me. So come see me, and let’s collaborate on your learning
experience.
I want the grade you earn in this course--- as well as the experience and information
you take away from it---to reflect the time and effort you put into the course.
Ownership, once again.
If you do well, it will be because YOU worked hard. YOU earned it. If you are not
putting the time and effort into this class---well, you can guess the result. And you must
own that, too.
The choice is, as always, yours. I want to help each of you reach your goals for this
course. But you are the one studying, asking questions, and taking exams. All I can do
is meet you half way---and I will. I will be as available and helpful as I can manage--again, I want every student in my classes to do well.
Good luck to all of you---and talk with me often. I genuinely care about the students
here at the University of Puget Sound. And that includes YOU.Let’s work hard together,
laugh a little, and learn a lot. I’m here to help---but it is up to you!
BIOLOGY 111A
Lectures: MWF 11 – 11:50AM, Thompson 193
Lab section AA: Th 9:00 – 11:50AM
Lab section AB: Th 1:00 – 3:50PM
Lab section AC: F 1:00 – 3:50PM
All Labs held in Harned 251
Dr. Mark O. Martin
Phone: X2747; Office: Thompson 257A
Research lab: Thompson 275
Email: momartin@pugetsound.edu and
DocMartinUPS@gmail.com
Office hours: M 3-4PM, W 8-9AM F 910AM, or BY APPOINTMENT.
COURSE SCHEDULE
“The Unity of Life: Cells, Molecules, and Systems.”
Spring 2016
Please note: the lecture topics are subject to modification and change as the semester
progresses---each handout will include reading for the next lecture!
WK
DATE
M
Jan
18
MLK DAY – NO CLASS
Course introduction, philosophy, and
overview
The “Molecules of Life”
The “Molecules of Life” and
Tinkertoy Biochemistry.
QUIZ #1 and More Tinkertoy
Biochemistry
Nucleic Acids and Transcription
Nucleic Acids and Transcription
1
W
20
2
F
M
22
25
W
27
F
M
W
29
1
3
3
4
5
6
7
Feb
TOPIC
F
5
M
8
W
10
F
12
M
W
15
17
F
19
M
22
W
24
F
M
26
29
QUIZ #2, Translation and Protein
Structure.
Special topic and class discussion:
crazy cool collagen, a good example
of structure/function
Lipids, Membranes, and
Compartmentalization (The
“Tupperware of Life”).
Quiz #3 , Lipids, Membranes, and
Compartmentalization.
An Overview of Metabolism: the
biochemical context of life.
Exam #1
Harvesting cellular energy, Part I: the
sugary goodness of glycolysis.
Harvesting cellular energy, Part II:
the circular logic of the Krebs cycle.
Harvesting cellular energy, Part III:
waterfalls of protons and making
ATP.
QUIZ #4, then Photosynthesiscapture of light energy
Photosynthesis-fixing carbon
Cellular Communication
TEXT
READING
LAB
NO LAB
Chapter 1
Chapter 2
Chapter 2
CELLS AND TISSUES
Chapter 2
Chapter 3
Chapter 3
Chapter 4
BACTERIAL BIOFILMS-PART I
TBA
Chapter 5
MEMBRANE TRANSPORT
Chapter 5
Chapter 6
BACTERIAL BIOFILMS-PART II
Chapter 7
Chapter 7
Chapter 7
CELLULAR RESPIRATION
Chapter 8
Chapter 8
Chapter 9
PHOTOSYNTHESIS
W
F
M
8
Mar
W
F
2
4
7
QUIZ #5, Cellular Communication.
Paper Discussion
Cell Form and Function
Chapter 9
TBA
Chapter 10
9
11
Cell Form and Function
Exam #2
Chapter 10
Mar 14 - 18 S P R I N G B R E A K – N O C L A S S
9
10
M
21
W
23
F
25
Dividing things up, Part I: mitosis,
the cell cycle, and cancer
Dividing things up, Part II: meiosis
and reduction division.
Overview of the Central Dogma of
Molecular Biology
NO LAB
Chapter 11
TBA
28
DNA Replication in Context
Chapter 12
W
F Apr
30
1
QUIZ #6, Genomes.
More About Genomes
Chapter 13
Chapter 13
11
M
4
DNA Mutation and Repair
Chapter 14
12
W
F
M
6
8
11
QUIZ #7, Genetic Variation
Mendelian Inheritance
More About Mendel
Chapter 15
Chapter 16
Chapter 16
W
13
F
M
W
F
15
18
20
22
QUIZ #8, Special Topic: Human
Genetic Disease
Beyond Mendel
Exam #3
Genetic and epigenetic regulation
Gene transfer and gene expression in
prokaryotes
14
M
25
15
W
F
M May
27
29
2
Collaborative learning exercise exploring
the rise of antibiotic resistant bacteria,
and what we can do about it.
Weird and Wonderful Viruses.
Regulation of expression in eukaryotes
Genes and Development
W
4
Overview of course
13
FINAL EXAM ON FRIDAY (yes,
Friday the 13th)…
12 – 2 PM (comprehensive)
F
May
MITOSIS AND HUMAN
GENETICS, PART I
Chapter 11
M
13
NO LAB
MEIOSIS AND HUMAN
GENETICS, PART II
FROM GENOTYPE TO
PHENOTYPE, PART I
FROM GENOTYPE TO
PHENOTYPE, PART II
TBA
Chapter 17, 18
BIOETHICS
Chapter 19
Chapter 26.4
& Chapter 19
Prior
Handouts
Chapter 13.5
Chapter 19
Chapter 20
Chapter 20
LAB PRACTICAL
NO LAB