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General Biology 111
Fall 2013
Lecturer & Coordinator:
Jill Penn, Ph.D.
office: W-2-074
e-mail: jill.penn@umb.edu
office hours: After lecture, Fridays 2:30 - 4:00 pm, or via appointment
Required Materials:
1. Textbook: Biology by Campbell & Reece, 9th edition. In course handouts etc., this will be
referred to as Campbell. This is available in two versions; you should be sure to get one:
• The “Full Campbell”. This is the entire 1,300+ page book. It is comprehensive and
expensive. We will use the first part of this book in Bio 111; we will use the second part
in Bio 112. You should get this version of the book if you will be taking Bio 112. This is
available at the UMB Bookstore & some on-line bookstores like amazon.com. Note that
the page numbers in the 8th edition are very similar, but not identical to the 9th.
• The “Skinny Campbell”. This includes only the parts of the book that are relevant to
Bio 111. It includes Chapters 1 - 20, the CD-ROM, access to the Campbell website, the
index, and the Table of Contents. It is substantially less expensive. You should get this
version of the book if you will not be taking Bio 112. This is available at the UMB Bookstore
only.
2.
Lab Manual & A Problems Approach to Introductory Biology (APAIB): The Lab Manual is
essential for performing the lab activities; the lab manual also contains pre-labs,
worksheets, etc. APAIB contains practice problems (both on paper and computer-based)
that will be used in lab and provide essential practice with the material for the exams. You
can purchase a 3-ring binder of both from Quinn Reprographics (Quinn LL-024). Both are
also available for free download via a link on the course blackboard page. I strongly advise
you to buy the printed versions. You must bring your lab manual to every lab session
3.
111 Materials: This is a folder of software and documents that are required to complete
many of the course assignments. You can download this for free from the course
blackboard site. Please note that there may be other versions of this on the web; you must
get the version available on the course blackboard site.
4.
iClicker Transmitter: All students must have an iClicker transmitter (see later for details)
and bring it to each lecture. These are available from many sources including the UMB
Bookstore. Please note that you will need to be able to read the serial number of your
iClicker in order to register it; so, if you buy a used iClicker, be sure that you can read the
character serial number on the back of it. Any iClicker model will work fine (e.g. iClicker,
iClicker +, iClicker 2).
Course Blackboard site: In Bio111, we will be using the course blackboard site frequently.
This site has links for the warm-ups, homework, handouts, etc.. It also has links to the lab
discussion boards and data blogs.
You should be sure to check it regularly for
announcements.
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Course Policies:
Lectures: Lectures meet in Lipke Auditorium: Mon and Wed, 7:00 to 8:15; regular attendance is
expected.
Lab Sections: Lab sections meet in W-2-030, -031, and -032. Some labs involve hands-on
activities; others involve problem-solving exercises. Lab sections will be assigned before the
first week of class; you may not switch sections after that time. Attendance in lab is expected.
In an emergency, you may make up a missed lab by attending another section that
meets during the same week with the permission of the TA; TAs may refuse entry to students
once the section is full. You may attend only one make up lab section per semester; after that,
if you attend a lab other than the one to which you have been assigned, you will be allowed to
attend that lab but your pre-lab and any other materials due in that lab will not be graded.
You must read the lab manual before lab. Some labs have pre-lab exercises based on the
lab manual; these are due at the start of lab and will not be accepted late. You will not be
admitted to lab unless you have a copy of the lab manual with you.
The lab sections are as follows:
Section Time
20
Tu 6:30 PM - 9:30 PM
21
Tu 6:30 PM - 9:30 PM
22
Th 9:30 AM - 12:30 PM
23
Th 6:30 PM - 9:30 PM
25
Fri 8:30 AM - 11:30 AM
Room
W-2-030
W-2-032
W-2-032
W-2-031
W-2-030
Note: lab sections are very full - if you do not fill out and sign a student information sheet
at the first lecture, your space in lab will be given to another student even if you are
registered for the class.
Exams:
- There will be eleven exams: ten 30-minute exams given in class during the semester and
a comprehensive 3-hour final exam
- There will be no make-up exams. No conflict exams will be given.
- The lowest grade of the first five 30-minute exams and the lowest grade of the last five
30-minute exams will be dropped when calculating your final grade.
- The final exam will be scheduled during the semester. The final exam score cannot be
dropped.
- You may bring a single 8.5 x 11 sheet of paper with whatever you want on it to each
exam and four such pages to the final exam.
Exam Re-grades: Occasionally, we make mistakes when grading. If you feel that your exam
was graded in error, you can request a re-grade. Instructions and notes for re-grading:
• Re-grades must be in writing; because different TAs graded different questions, neither
I nor your TA can re-grade your exam “on the spot”.
• When asking for a re-grade, you should include the following:
o Your whole exam. Do not mark on it in any way. In order to prevent cheating,
we xerox or scan some or all of the exams; any marks made on your exam after it
was graded and given to you in lab may be interpreted as cheating. Students
who alter their answers and submit these altered answers for a re-grade will
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•
•
receive a grade of “F” for the course and a letter will be sent to the Dean of
Undergraduate Education notifying him/her of the incident.
o A note on a separate piece of paper (attached to your exam) explaining what
needs to be re-graded. Don’t simply say, “Re-grade question 3”; you should
explain why your answer deserves more credit that we gave. If it is an addition
error, explain which numbers were added up incorrectly.
o Re-grade requests that do not follow these rules will be returned without review.
Re-grade requests must be turned in to your TA within 2 weeks of the date the exam
was handed back in lab.
Re-graded exams will be returned in lab about 2 weeks later.
Snow/hurricane/emergency days: If class is cancelled due to an unforeseen emergency, check
the course blackboard site for announcements. In general, an emergency before an exam will
not cause the exam to be moved; if class is cancelled on a day of a scheduled exam, the exam
will be held in the next lecture period.
Grades: Your final grade will be calculated on the basis of 600 points as follows:
100 points for your best four of exams 1-5 (25 points each)
100 points for your best four of exams 6-10 (25 points each)
100 points final exam
150 points Lab: Your lab grade will be totaled (max = 375) and scaled to a maximum of
150 points (multiplied by 150/375); see breakdown that follows.
100 points warmups and homework: Your grade in this category will be totaled
(max = 145) and scaled to a maximum of 50 points; see breakdown that follows.
50 points iClicker. Your iClicker points will be totaled and scaled to 50 points.
Lab Grades
Done at home & handed in at start of lab
Pre-labs
11 x 10 pts = 110
Chromatography Report
25
Amylase Report
25
Aipotu I Report
25
VGL Electronic Report
20
Aipotu III Report
30
Work done entirely in lab
Pre-survey
Small Molecules Worksheet
Protein Structure Checkoff
Aipotu I Checkoff
Aipotu II Checkoff
VGL Challenges Checkoff
GFP I Checkoff
PTC I Checkoff
Aipotu III Checkoff
GFP II Checkoff
PTC II Checkoff
Pre-survey
10
20
20
10
10
10
10
10
10
10
10
10
Total: 375
Warmup and Homework Grades
Done and turned in on-line (Blackboard)
Warm-ups (7 out of 8) x 10 pts
70
Homework (3 out of 4) x 25 pts
75
Total: 145
All individual grades as well as your final grade will be determined using the following
breakdown: 86-101 = A; 71-85 = B; 56-70 = C; 41-55 = D; 0-40 = F.
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Lecture, Homework, & Lab Schedule
Date
W 4-Sep
M 9-Sep
W 11-Sep
M 16-Sep
W 18-Sep
M 23-Sep
W 25-Sep
M 30-Sep
W 2-Oct
M 7-Oct
W 9-Oct
M 14-Oct
W 16-Oct
M 21-Oct
W 23-Oct
M 28-Oct
W 30-Oct
Topic
Introduction: Course
Overview; Atoms
Chemistry 1:
Molecules and Bonds
Chemistry 2:
Hydrogen Bonds
Chemistry 3:
Reading Molecules
Biochemistry 1:
Macromolecules
Biochemistry 2:
Protein Structure
Biochemistry 3:
Protein Structure cont.
Biochemistry 4:
Enzymes &
Thermodynamics
Biochemistry 5:ATP,
Glycolysis, Respiration
Photosynthesis
Genetics 1:
Basic Genetics
Genetics 2:
Sex-linkage
University Holiday
Genetics 3:
Pedigrees I
Genetics 4:
Pedigrees II
Genetics 5:
Genetics Limitations
Molecular Biology 1:
The link between
Genes and Proteins
Molecular Biology 2:
DNA Structure and
Replication
Exams
Warm-up & Lab & [Due Date]
Homework
NONE
(30 min)
(1) Build a
Molecule 1
(2) Build a
Molecule 2
Exam 1
01: Chemical Structures
02: Chromatography
(3) Build a
Protein
Exam 2
[Lab report due week of 9/23]
03: Protein Structure
(4) Break a
Protein
Exam 3
04: Amylase
[Lab report due week of 10/7]
(A) Proteins
Exam 4
(5) VGL 1
05: Aipotu I: Biochemistry
(6) VGL 2
[Lab Report due week of 10/14]
06: Aipotu II: Genetics
Exam 5
(B) VGL 1
07: VGL Challenges
(C) VGL 2
[Electronic Lab Report due in class]
08: GFP I: Transformation
Exam 6
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Lecture, Homework, & Lab Schedule, continued:
Date
M 4-Nov
W 6-Nov
M 11-Nov
W 13-Nov
M 18-Nov
W 20-Nov
M 25-Nov
W 27-Nov
M 2-Dec
W 4-Dec
M 9-Dec
W 11-Dec
Topic
Molecular Biology 3:
Transcription &
Translation
Molecular Biology 4:
Introns
Veterans’ Day
Molecular Biology 4:
Mutations
Molecular Biology 5:
Lac Operon
Cell Biology 1:
Prokaryotes and
Eukaryotes
Cell Biology 2: Cell
Cycle & Mitosis
Happy Thanksgiving
Cancer 1: Growth
Factors & Cell Signals
Cancer 2: Oncogenes
& Mutations
Cancer 3: Genetics &
Treatment
Overview
Exams
Warm-up & Lab & [Due Date]
Homework
(7) Build a
09: PTC/PCR I: DNA extraction & PCR
Gene
(30 min)
Exam 7
10: Aipotu III: Integration
(8) Break a
Gene
(D) Genes
[Lab Report due in class]
11: GFP II: Purification
Exam 8
NONE
12: PTC PCR II: Gel Electrophoresis
Exam 9
NONE
Exam 10
Warm-up Problems
These are designed to give you practice with the material before the lectures. These are an
essential part of the course. They are due at 6:00 PM before the lecture listed above; they will
not be accepted late for any reason. They will be very challenging but you do not have to get
them right; you only have to try. You will get full credit for trying. You will complete each of
these assignments individually; they must be in your own words. They are designed to help
you come to class prepared and help me to target my lectures to the difficulties you are having
with the material. Your answers must be submitted online through the Bio 111 Blackboard
site; details about each of the Warm-ups can be found on the Bio 111 Blackboard site. You need
only complete 7 of the 8 warm-ups; that is, you can miss one with no loss in credit.
Homework
These are designed to give you graded practice with the material after lectures. They are due at
11:00 PM on the day listed above; they will not be accepted late for any reason. In order to get
full credit, you must give the correct answers to these problems; partly correct answers may
receive partial credit. Your answers must be submitted online through the Bio 111 Blackboard
site; details about each of the Homeworks can be found on the Bio 111 Blackboard site. You need
only complete 3 of the 4 homeworks; that is, you can miss one with no loss in credit.
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Readings and Practice Problems
The readings in Campbell are intended to be read before the lecture listed. Because the
readings do not always go in the order found in the book, it may be useful to review by
reading all the sections in page order rather than the order on the reading list.
The practice problems in APAIB are designed to be worked after the lecture listed. You
will notice that some lectures have many problems while others have none. In general, by the
end of the lecture listed, you have all the information necessary to solve the problems listed.
Some of these problems will be worked each week in lab to show you problem-solving
strategies. You do not have to do all the listed problems after each lecture; you should be sure
to have done them all before the exam on that material. Note: the solutions to the practice
problems in APAIB are an essential part of the book. You should read them over carefully
after you have written out answers to the problems in the book. Solutions can be found via a
link on the course blackboard site.
Software from A Problems Approach to Introductory Biology will run on almost any
computer, Mac or PC. It is also set up to run on some of the computers in the Library. In the
Red lab (Healey Library UL), it is set up on the PCs only. You can access the programs from
the programs menu; look in the “B. White APAIB” sub-menu. The software is also available
on the PCs on the 4th floor of the Library and on the 2nd floor on the computers behind the Cafe.
The software can be found in the Software folder of the 111 Materials.
Reading & APAIB Problem List
Readings in
Campbell
APAIB Problems
{except these}
Ch2: 1.1.all*; C1
Ch2: 1.2.all
Ch2: 2.1.all, C3
Ch2: 2.3.all; C5; 2.4.all; 2.5.all; C6
Ch2: C8
Ch2: 3.1.1; 3.1.3, 3.1.4; 3.1.7; C7
Ch2: 3.1.2; 3.3.1-3.3.7
Genetics 1
30-37
38-43; 46-47; 58-66
50-51
68-81
81-84
142-149; 152-155; 326-327
149-151; skim 163-179 &
184-189
264-267; 269-273
Genetics 2
Genetics 3
Genetics 4
Genetics 5
Molecular Biology 1
Molecular Biology 2
Molecular Biology 3
Molecular Biology 4
Molecular Biology 5
Cell Biology 1
Cell Biology 2
Cancer 1
Cancer 2
Cancer 3
228-234; skim 248-257
286-292; 297-300
269-270; 275-281
279-281; 300-302
86-89; 305-318; 325-334
337-343; 356-362
334-336
344-346
381-390
94-101; 125-129
206-211; 242-243; 373-376
376-377
-
Lecture
Introduction
Chemistry 1
Chemistry 2
Chemistry 3
Biochemistry 1
Biochemistry 2
Biochemistry 3
Biochemistry 4
Biochemistry 5
Ch1: 1; 1.1.all 1.1.2; V1; V2; 1.3.all
1.3.4-1.3.7; V3
Ch1: 1.4.all; V4
Ch1:1.2.all; 1.5.all
Ch1: 3.8; 3.9
Ch3: 1.all; 2.all; C1
Ch3: 3.diagnostic only; 4.1.all
Ch3: 4.2.all
Ch3: C2
Ch4: all
-
* Note that “1.1.all” means “all problems that start with number 1.1”;
in this case, it is 1.1.1 through 1.1.3.
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Due dates: Lab reports are due as indicated in this syllabus or as modified by your TA. In
cases where there is a conflict between when the Lab Manual says that a report is due and
when the syllabus or TA says so, your TA is the final source; the syllabus is next. In certain
cases, and only with the permission of your TA, lab reports may be turned in to the TAs
mailbox in the Biology office (W-3-021) by 5:00 PM on the day that they are due. In ALL other
cases, late reports will NOT be accepted* – do not assume that we will grant you an exception.
I have very limited flexibility; if you need an exception, it can only be granted if you come to
me in advance.
* Each student will be allowed to turn in one and only one lab report one week late for a
maximum of ½ credit. Specifically, if the lab report is turned in between 1 and 7 days late
(relative to the student’s assigned lab section meeting time), the student’s lab report will be
graded; the score received will be ½ of the grade earned. Each student may do this only once
per semester.
⇒ If you have computer problems with your lab report, you have several options for turning it
in on time (in each case you are responsible for making sure that your TA receives your
report):
1. Turn in a partially-complete report on time.
2. Bring your report to your TA on disk (only with your TA’s permission).
3. E-mail your report to your TA as an attachment (only with your TA’s permission).
4. Fax your report to the Biology office (617 287-6650); attention: your TA (only with your
TA’s permission).
It is always good practice to keep backup copies of lab reports on other disks to guard against
hard drive crashes. Another option is to save your lab report to a cloud service (eg. Dropbox).
Incompletes: Incompletes will only be granted under certain special conditions. To receive an
incomplete, you must be passing the course and the work to be completed must be a welldefined unit of the course. An incomplete must be arranged in advance of your absence at a
meeting in person with Jill Penn.
Academic Conduct: Students are required to adhere to the Code of Student Conduct,
including requirements for the Academic Honesty Policy, delineated in the University of
Massachusetts Boston Graduate Studies Bulletin and relevant program student handbook(s).
http://media.umassp.edu/massedu/policy/3-08%20UMB%20Code%20of%20Conduct.pdf
In this course, penalties for academic misconduct, including plagiarism (copying from
another student, a book, or the internet), are strictly enforced. It is my policy to make the
consequences of being caught cheating on a given exercise much more severe than the
consequences of not turning in that particular exercise.
iClicker Throughout the semester I will ask short multiple-choice question during lecture
(note that the exams will not be multiple-choice); these questions are designed to see if you
have understood a major point from my lecture.
You will submit your answer as described below; you will receive credit for each
answer you submit, whether it is correct or not. Answers are due during the lecture on the
day the question was asked; no late answers will be accepted; there are no make-ups for
missed iClicker questions. After all the answers have been logged in, I will announce the
correct answer.
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Using an iClicker This looks like a small TV remote control. You transmit your answer
to the receiver in Lipke and your answer is logged by the computer. You will need to register
your iClicker serial number so you can get credit. This will be done with your TA during the
first laboratory section. You should not register through iClicker.com. You can miss up to
three iClicker questions without losing any credit.
Accommodation for Students with Disabilities
Section 504 and the American with Disabilities Act of 1990 offer guidelines for
curriculum modifications and adaptations for students with documented disabilities. If
applicable, you may obtain adaptation recommendations from the UMass Boston Ross Center
617-287-7430. You need to present and discuss these recommendations with me within a
reasonable period, prior to the end of the Drop/Add period.
If you are using adaptive software with Blackboard Vista, please contact the instructor
for information regarding the software’s interface with the LMS.
Studying For Bio 111 One successful strategy is to read the introduction to APAIB; it gives a
productive way to use that book. You should read over the sections in Campbell; don’t try to
memorize it all, just get a sense of what’s there and what it says. Then, start working through
the assigned problems in APAIB and use Campbell as a reference when you work through the
problems in APAIB.
Tips for success in Bio 111:
Succeeding in Bio 111 will require a substantial effort on your part. The keys to success are:
(1) Come to every lecture. More so than many courses you have taken, the course is primarily
based on lecture, not the book. The readings are designed as background and to help you
understand what you didn’t get in lecture. Other peoples’ lecture notes are better than
nothing, but there is no substitute for attending lecture.
(2) Come to lab prepared. The TAs will assume that you have read the lab manual and/or
looked over the practice problems.
(3) Participate in lab discussions. Lab is designed to have you practice with the material from
lecture. Lab sections are designed to allow your questions to be answered; be sure to take
advantage of this opportunity.
(4) Do the practice problems and write out your answers before looking at the solutions. The
hardest part of problem-solving is the start and if you look at the solutions, you will never
get the practice starting that you will need for the exams.
(5) Connect with your TA and the tutors early. They are there to help you; don’t wait until it’s
too late.
Tips from past Bio 111 Students
(1) “Go to lecture! Go to lab! Pay attention!”
(2) “Read questions on exams VERY CAREFULLY!”; “Really explain yourself on exams.”
(3) “Be prepared to solve questions, not just learn facts. Pay a lot of attention because when it
comes to exams you’ll need to know everything (hard exams).”
(4) “Keep up in lecture, review your notes, and do all the practice problems in the lab manual.
They are really helpful.”
(5) “Go to every lecture. Make good use of Lab TA for information and questions on problem
solving.” “Don’t fall behind. Get a tutor.”
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(6) “Chill out and don’t stress. It’s not as hard as you might think. If you keep up with the
work, you’ll be fine. Do the practice problems (that’s what the exams are about).”
(7) “Use all the tools you have at your fingertips ie: lecture notes, extra question problem sets,
the text… All together, they provide you with everything you need for success.”
(8) “Best prep: read labs, lecture material prior to class. This aids in comprehension and
allows you to ask informed, useful, questions in class.”
(9) “Don’t neglect the textbook. It isn’t emphasized but helps fill in the gaps for non-science
folks like me.”
(10) “You must be absolutely certain that you want to take Biology 111 because it’s hard! It
requires a lot from you. You can’t afford to “goof off” in this class; everything taught in
lecture and lab counts.”
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