San José State University
Department of Biological Sciences
Biol 115, General Genetics, Spring 2018
Instructor:
Rachael French, Ph.D.
Office Location:
Duncan Hall 237
Telephone:
408-924-4894
Email:
Office Hours:
biology115.french@gmail.com (preferred method of
communication)
Th 11 to 1
Class Days/Time:
Lecture: M/W/F 10:30 – 11:20 a.m.
Classroom:
WSH 109
Prerequisites:
BIOL 30 and BIOL 31 (with grade of "C" or better in
each); CHEM 001A and CHEM 001B (with a grade of
"C-" or better in each)
Biochemistry majors: BIOL 30 (with grade of “C” or
better); CHEM 001A and CHEM 001B (with a grade of
“C-“ or better in each)
Canvas
Copies of course materials such as the syllabus, lecture slides, discussion materials, and problem sets can be
found on the Biol 115 Canvas page. You are responsible for logging on each week to download any course
materials. You can access Canvas at http://sjsu.instructure.com. If you have any problems logging in, contact
the help desk at (408) 924-2377 or visit them on the first floor of Clark Hall. If you do not have a computer, see
“Student Technology Resources” below.
Information will be presented in class that is not available on Canvas. Students are not required to come to
class; however, they are responsible for all information given during lectures.
Course Description
Biology 115 is a challenging upper division class that is the prerequisite for many other upper division classes.
It will cover the principles and methods of microbial, plant, animal and human genetics. The broad areas of
Mendelian (classical) genetics, cytogenetics, molecular genetics, recombinant DNA, genomics, mutagenesis
and population genetics will be included in the course.
Course Goals and Student Learning Objectives
GE Area R Learning Outcomes (GELO)
Upon successful completion of this course, students will be able to:
Biology 115, General Genetics, Spring 2018
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Area R Student Learning Objectives
1. Demonstrate an understanding of the
methods and limits of scientific
investigation.
Assignments that address this SLO
• Discussion topics, including Science Literacy, Gene
Therapy, Genetically Modified Organisms, and
Forensic DNA Analysis
• Assessed in Group Project Conference-style Oral
Presentations as well as occasional short written
assignments
Three content requirements for the Area R will also be addressed in this course: diversity, civic learning, and
the scientific study of life forms.
Content
Assignment that addresses this content requirement
• Discussion of the discovery that a single nucleotide mutation is
responsible for 30% of the pigmentation differences between
people of Caucasian and Asian descent. (Exam 1)
• Discussion of contributions to the field by biologists who are
women and people of color. (Exam 2, 3)
• Discussion of the genetic similarity between all people – 99.9%.
(Exam 3)
This course shall address the • Discussion of how genetic engineering affects crops and the
recent voter initiative in California to label all GMO foods.
civic relevance of topics in
(Exam 3)
genetics in an appropriate
•
Discussion of how genome sequencing has the potential to
manner.
affect medicine, individuals, and society. (Exam 3)
• Discussion of eugenics and the related topic human germline
gene editing (Final Exam and oral discussions in activity
sections)
Issues of diversity shall be
incorporated in an
appropriate manner.
This course will focus on
the scientific study of life
forms, based on knowledge
and skills established in
Core GE Science.
• This course will focus on the scientific study of life forms
including a discussion of the genetic model organisms: A.
thaliana plants, E. coli bacteria, C. elegans nematodes, D.
melanogaster flies, D. rerio fish, M. musculus mice, as well as
H. sapiens humans. (Exam 1)
“A minimum aggregate GPA of 2.0 SJSU Studies (R, S, & V) shall be required of all students as a graduation
requirement.” To see full text, review at http://www.sjsu.edu/senate/docs/S11-3.pdf.
Program Learning Goals (Biological Sciences)
BIO LO1 Students will demonstrate the ability to formulate hypotheses and design experiments to address a
scientific question using the scientific method.
BIO LO2 Students will demonstrate an understanding of relevant content in their discipline.
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BIO LO3 Students will demonstrate laboratory or field skills in their discipline.
BIO LO4 Students will demonstrate proficiency in scientific writing skills.
BIO LO5 Students will demonstrate proficiency in oral presentation skills.
BIO LO6 Students will demonstrate the ability to work effectively in groups.
BIO LO7 Students will demonstrate the ability to perform literature searches using relevant tools.
Course Learning Outcomes (CLO)
CLO1: Students will learn to perform genetic analysis by solving quantitative and qualitative problems (BIO
LO2; Exams and weekly problem sets)
CLO2: Students will learn the basic vocabulary of genetics and become familiar with the model organisms
utilized in contemporary genetics research (BIO LO2, exams and discussion section activities)
CLO3: Students will strengthen critical thinking skills and acquire the ability to interpret societal issues
involving genetics
CLO4: Students will demonstrate the ability to work in groups to solve activity problems (BIO LO6, BIO LO7;
discussion section activities)
Required Texts/Readings
Textbook
Pierce, BA, Genetics: A Conceptual Approach. 6/e. WH Freeman & Co.
It also acceptable to use the fifth edition of the Pierce text instead of the sixth edition; however, you will be
responsible for determining the corresponding reading assignments.
Recommended
Pierce, BA, Genetics: Problem Solving Manual. 6/e. WH Freeman & Co.
Other Readings
Additional reading materials will be provided on Canvas.
Other Materials
- For all exams bring #2 pencil and scantron form 882-E.
Lectures
Course lectures will include material the instructor feels is most important in a general genetics course. Do not
ask the instructor what will be on the exam! If information is covered in class, if it is on a problem set, or if
it is mentioned in a discussion section, it could be on an exam.
Discussion Sections
The discussion sections will be used for review, and for additional activities that are meant to strengthen or add
to your learning. Material from these activities will also be on exams.
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Classroom Protocol
Students should be punctual, and if you must be late, enter silently from the back entrance, to avoid disturbing
the other students. Students should at all times be respectful of other students and the professor. Those who are
not may be asked to leave the class. Participation in class is strongly encouraged and will add to your learning
experience. Participation will help you and other students develop not only a deeper understanding of the
material, but an ability to articulate your thoughts in a scientific context.
Attendance in lectures and discussions is not mandatory, but past experience suggests that it is unlikely that
students who miss more than four classes (including lectures and discussion sections) will succeed in and pass
the class. I strongly recommend that students who will need to miss more than three classes drop the course and
take it another semester when they can attend all of the classes.
Electronic devices can be distracting to other students who are sacrificing time, energy and money to
accomplish their educational goals. Therefore, a very strict policy will be enforced. All cell phones, PDAs, and
other electronic devices must be put on silent (not vibrate) and placed inside a purse or backpack for the
duration of the class. If the device makes any noise or if a student uses or views it during class (even below the
desk), it will be confiscated and the student may be asked to leave the class. The student will still be
responsible for the information provided in class that day. Students are allowed to use laptop and tablet
computers in class; however, similar rules apply if the computer makes any noise or if they are used for
purposes other than viewing the lecture presentation or taking notes.
Exam Protocol
Students must sit in a seat for exams and must put all materials except a pencil and scantron in a zipped bag or
backpack underneath their desk. Earpieces are not allowed, and neither are hats or hoods that could conceal
earpieces. If any other materials or earpieces are found, you will receive a 0 on the exam and be reported for
academic dishonesty, for which you could be expelled. Students must remain quiet from the time the exam is
displayed or passed out until ALL quizzes or exams are collected. The only exception to this policy is questions
asked directly to the professor or teaching assistants.
Exams will begin promptly; any student arriving more than 20 minutes late for an exam or after other
students have finished and left the exam will not be permitted to take the exam and will receive a 0.
Email Policy
Send all class-related e-mails to biology115.french@gmail.com. Student e-mails will be answered once per
day, M-F, and not on weekends. If you e-mail me after 5:00 p.m., it is very unlikely that you will get a
response before the next day.
Respect For Your Professor and TA’s Time
Your instructors (both your professor and your TAs) are very busy, and our time is valuable. Please respect our
time by: 1) attempting to attend office hours when possible, rather than request individual meetings. 2) If you
must request a meeting outside of office hours, please be aware that it will be at least a week before such a
meeting will be possible.
Remember, your successful interactions with your instructors will be maximized if you plan ahead; neither your
professor nor your TAs are obligated to accommodate you if you fail to do so.
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Dropping and Adding
Students are responsible for understanding the policies and procedures about add/drop, grade forgiveness, etc.
Refer to the current semester’s Catalog Policies section at http://info.sjsu.edu/static/catalog/policies.html.
Add/drop deadlines can be found on the current academic year calendars document on the Academic Calendars
webpage at http://www.sjsu.edu/provost/services/academic_calendars/. The Late Drop Policy is available at
http://www.sjsu.edu/aars/policies/latedrops/policy/. Students should be aware of the current deadlines and
penalties for dropping classes.
Information about the latest changes and news is available at the Advising Hub at
http://www.sjsu.edu/advising/.
Assignments and Grading Policy
Your grades will be determined in the following way:
Assignment/Exam
Lecture Exams (3)
Percent of Final Grade
50%
Online Quizzes
33%
In-Class Activities and Participation
17%
Total
100%
The final (letter) grades for this course will be assigned as follows, unless the average class grade is below a
C:
100 – 98%
93 – 97%
90 – 92%
89 – 88%
83 – 87%
80 – 82%
79 – 78%
73 – 77%
70 – 72%
60 – 69%
0 – 59%
A+
A
AB+
B
BC+
C
CD
F
Final grades will be scaled only if the average class grade is below a C, but this cannot be determined until all
assignments and exams are completed including the final exam.
Biology 115, General Genetics, Spring 2018
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Exams
There will be four in-class exams, for a total of 50% of your final grade. All exams will be closed-note and
closed-book. No electronic devices may be used during examinations, with the exception of calculators (NOT
housed within your smartphone). Bring a scantron form (Form 882) and a #2 pencil to exam sessions.
Exam dates are on the course schedule. There will be no make-up exams – the lowest exam score will be
dropped for each student, and this is intended to accommodate illness and other conflicts. If you miss a second
exam for any reason, that score will be recorded as a zero. If your life circumstances are such that you have to
miss a larger proportion of the course, please see the instructor about taking an incomplete or late drop. (Of
course, accommodations for students with a disability are available through the Accessible Education Center;
the instructor will work with you and the AEC to make appropriate arrangements).
Final Examination or Evaluation
There will be a comprehensive final exam that will be all multiple choice and true/false questions with
approximately a proportionate number of questions per lecture. The final exam will be 1.5 hours in length and
will be administered during the first 1.5 hours of the scheduled final exam period only.
Your score on the comprehensive final exam will only be used to increase your point total. Your percent
score on the final must beat your average percent on the midterm exams. If it does not, then you will receive the
grade based only upon your three (3) midterm exams and other forms of evaluation. If you do beat your
midterm exam average, then half the difference between your final exam percentage and your average midterm
score will be added to your total exam grade.
Online Quizzes
You will take weekly online quizzes via Canvas, except during exam weeks. These quizzes will be worth 33%
of your final grade. The quizzes will require a lockdown browser. The quizzes will be available for a 24-hour
period, and, once you begin, will be available for a set amount of time, from 15 to 60 minutes, depending on
length. Do not click on a quiz unless you are ready to take that quiz.
Quiz dates are on the course schedule. There will be no make-up quizzes – the lowest quiz score will be
dropped for each student, and this is intended to accommodate illness and other conflicts. If you miss a second
quiz for any reason, that score will be recorded as a zero. If your life circumstances are such that you have to
miss a larger proportion of the course, please see the instructor about taking an incomplete or late drop. (Of
course, accommodations for students with a disability are available through the Accessible Education Center;
the instructor will work with you and the AEC to make appropriate arrangements).
Participation
Attendance is not required and will not affect your grade. However, participation does count, and 17% of your
grade will depend on your contributions to in-class discussions and other activities during and related to activity
sections. These points will be awarded by the TAs for participation in that week’s discussion section
activity. Points will not be awarded simply for participation - you must also demonstrate that you are familiar
with the material and have thought out your contributions to the activity. The assignments will not be onerous,
but it will be insufficient to try and “fake” your way through them. To maximize your participation grade you
Biology 115, General Genetics, Spring 2018
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should attend activity sections; while in class, you should ask questions, share (relevant) comments, help
maintain an open and respectful environment for discussion and learning, and participate in any assigned group
activities. There is no way to make up participation points; however, the lowest participation score will be
dropped for each student and this is intended to accommodate illness and other conflicts.
Extra Credit
Extra Credit is not typically available; however, on rare occasions, the professor may offer in-class extra credit.
These points will be available only to students who are present, and there will be no way to make them up.
Late Work Policy
Late work will be accepted (with the exception of in-class participation activities, where no late work is
accepted). However, there will be penalties for work submitted late, as follows: For online quizzes, late
submissions will be accepted for 8 hours, and the penalty for late submission will be 10% of the total points
available. For all other assignments: If the assignment is turned in within 12 hours of the deadline, there will be
a 5% penalty. 12 - 24 hours: 10%. An additional 10% will be deducted for each 24 hour period after that, and
no work will be accepted more than 5 days after the deadline.
Appealing Assignment Grades (Requesting Regrading)
The instructor will gladly explain or review the grade you receive on any assignment. If you would like an
assignment regraded, you must make your request in writing within one week after the assignment is
returned. Your written request should NOT begin with the question “Why is my answer wrong?” You must
begin your grievance by writing “My answer is correct because…” You must submit the original assignment
(not a copy) with your request. You will be notified of my decision in writing within one week of submitting
your request. When you make a request for regrading you should understand that your grade may be raised,
lowered, or remain the same after regrading. I reserve the right to regrade the entire assignment.
University Policies
Academic integrity
Your commitment as a student to learning is evidenced by your enrollment at San Jose State University. The
University’s Academic Integrity policy S07-2, located at http://www.sjsu.edu/senate/S07-2.htm, requires you to
be honest in all your academic course work. Faculty members are required to report all infractions to the office
of Student Conduct and Ethical Development. The Student Conduct and Ethical Development website is
available at http://www.sjsu.edu/studentconduct/.
Instances of academic dishonesty will not be tolerated. Cheating on exams or plagiarism (presenting the work of
another as your own, or the use of another person’s ideas without giving proper credit) will result in a failing
grade and sanctions by the University. For this class, all assignments are to be completed by the individual
student unless otherwise specified. If you would like to include your assignment or any material you have
submitted, or plan to submit for another class, please note that SJSU’s Academic Integrity Policy S07-2 requires
approval of instructors.
Campus Policy in Compliance with the Americans With Disabilities Act
If you need course adaptations or accommodations because of a disability, or if you need to make special
arrangements in case the building must be evacuated, please make an appointment with me as soon as possible,
or see me during office hours. Presidential Directive 97-03 at
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http://www.sjsu.edu/president/docs/directives/PD_1997-03.pdf requires that students with disabilities
requesting accommodations must register with the Accessible Education Center (AEC) at
http://www.drc.sjsu.edu/ to establish a record of their disability.
Student Technology Resources
Computer labs for student use are available in the Academic Success Center at http://www.sjsu.edu/at/asc/
located on the 1st floor of Clark Hall and in the Associated Students Lab on the 2nd floor of the Student Union.
Additional computer labs may be available in your department/college. Computers are also available in the
Martin Luther King Library.
A wide variety of audio-visual equipment is available for student checkout from Media Services located in IRC
112. These items include DV and HD digital camcorders; digital still cameras; video, slide and overhead
projectors; DVD, CD, and audiotape players; sound systems, wireless microphones, projection screens and
monitors.
SJSU Peer Connections
Peer Connections, a campus-wide resource for mentoring and tutoring, strives to inspire students to develop
their potential as independent learners while they learn to successfully navigate through their university
experience. You are encouraged to take advantage of their services which include course-content based tutoring,
enhanced study and time management skills, more effective critical thinking strategies, decision making and
problem-solving abilities, and campus resource referrals.
In addition to offering small group, individual, and drop-in tutoring for a number of undergraduate courses,
consultation with mentors is available on a drop-in or by appointment basis. Workshops are offered on a wide
variety of topics including preparing for the Writing Skills Test (WST), improving your learning and memory,
alleviating procrastination, surviving your first semester at SJSU, and other related topics. A computer lab and
study space are also available for student use in Room 600 of Student Services Center (SSC).
Peer Connections is located in three locations: SSC, Room 600 (10th Street Garage on the corner of 10th and
San Fernando Street), at the 1st floor entrance of Clark Hall, and in the Living Learning Center (LLC) in
Campus Village Housing Building B. Visit Peer Connections website at http://peerconnections.sjsu.edu for
more information.
Biol 115/Genetics Spring 2018 Course Schedule
•
This schedule is subject to change. Any changes will be announced in class.
Week
1
Dates
Jan 24 –
30
Topics, Assignments, Deadlines
Course Introduction
How is genetic information transmitted?
• Meiosis
• Mendel
• Sex Linkage and the Chromosome
Theory of Heredity
Biology 115, General Genetics, Spring 2018
Readings
Pierce, Chapters 3 and 4
(If you need to read Chapters 1
and 2 for review, do so)
Suggested problems:
Chapter 3: 14, 16, 19, 22, 25, 28,
Page 8 of 12
31, 34, 38, 41, 43
Chapter 4: 15, 18, 21, 24, 27, 30,
34, 37, 40, 41, 44, 45
January 26: Discussion 1
(introduction/registration)
2
Jan 31 – Feb
6
Pierce, Chapters 4 and 5
How is genetic information transmitted?
• Sex Determination
• Dosage Compensation
Suggested problems:
Chapter 5: 13, 16, 19, 22, 25, 28,
31, 34, 38, 42, 44, 47
How do genes affect phenotypes?
• Dominance interactions
February 2: Discussion 2 (Science
Literacy)
February 5: Quiz 1
3
Feb 7 – 13
How do genes affect phenotypes?
• Genetic Interactions and their effects
on Mendelian ratios
• Complementation
Pierce, Chapters 5 – 7
Suggested problems:
Chapter 6: 19, 22, 25, 28, 31, 34,
37
Chapter 7: 13, 16, 19, 22, 25, 28,
35, 38
How is genetic information transmitted?
• Inheritance patterns and pedigrees
• Twin and adoption studies
• Genetic counseling and testing
• Linkage and genetic recombination
February 9: Discussion 3 (Genetic
Screening, I)
February 12: Quiz 2
4
Feb 14 – 20
How is genetic information transmitted?
• Linkage and genetic recombination
• Genetic and physical mapping
• Chromosome rearrangements
Pierce, Chapters 7 – 8
Suggested problems:
Chapter 8: 21, 24, 27, 30, 33, 39,
42, 45
February 16: Discussion 4 (Exam Review)
February 19: Exam 1 (in class)
Biology 115, General Genetics, Spring 2018
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5
Feb 21 – 27
How is genetic information transmitted?
• Chromosome rearrangements
• Aneuploidy
• Polyploidy
Pierce, Chapter 8
Suggested problems:
See last week
February 23: Discussion 5 (Genetic
Screening, II)
February 26: Quiz 3
6
Feb 28 –
March 6
How is genetic information transmitted?
What is a gene?
• DNA Structure
• Chromosome Structure and genome
organization
• Organelle Inheritance
• DNA Replication
Pierce, Chapters 10 – 12
Suggested problems:
Chapter 10: 19, 24, 28, 31, 34, 39
Chapter 11: 19, 22, 25, 28, 31,
35, 38
Chapter 12: 20, 26, 29, 32, 35, 37
March 2: Discussion 6 (Personal
Genomics, I)
March 5: Quiz 4
7
March
7 – 13
How is genetic information transmitted?
• DNA Replication
How is genetic information expressed?
• Transcription
Pierce, Chapters 12 – 13
Suggested problems:
Chapter 13: 14, 17, 21, 25, 30, 34
March 9: Discussion 7 (Personal
Genomics, II)
March 12: Quiz 5
8
March
14 – 20
How is genetic information expressed?
• RNA processing and posttranscriptional modifications
• One gene, one enzyme?
March 16: Discussion 8 (Exam Review)
Pierce, Chapters 14 – 15
Suggested problems:
Chapter 14: 21, 25, 29, 33, 38
Chapter 15: 16, 18, 21, 24, 27,
35, 41
March 19: Exam 2 (in class)
Biology 115, General Genetics, Spring 2018
Page 10 of 12
9
March 21 –
April 3
How is genetic information expressed?
• The genetic code
• Translation
How are genes regulated?
• Gene regulation in bacteria
Pierce, Chapters 15 – 16
Suggested problems:
Chapter 16: 11, 14, 17, 19, 23,
26, 29, 31
March 23: Discussion 9 (Genetically
Modified Organisms)
No class March 26 – 30 (Spring Recess)
April 2: Quiz 6
10
April 4 – 10
How are genes regulated?
• Gene regulation in bacteria
• Gene regulation in eukaryotes
• Epigenetics
Pierce, Chapters 16 – 17, and 21
Suggested problems:
Chapter 17: 17, 18, 28
Chapter 21: 21, 24, 27, 31, 34
Where does genetic variation come from?
• Mutation
April 6: Discussion 10 (CAS/CRISPR)
April 9: Quiz 7
11
April 11 – 17
Where does genetic variation come from?
• Mutation
• Transposable elements
• DNA repair
• The physical basis of recombination
Molecular genetic analysis
• Recombinant DNA Technology
Pierce, Chapters 18 – 19
Also Chapter 12.5
Suggested problems:
Chapter 18: 17, 20, 23, 28, 32,
34, 38, 41, 44
Chapter 19: 26, 29, 33, 36, 39, 42
April 13: Discussion 11 (Exam Review)
April 16: Exam 3 (in class)
Biology 115, General Genetics, Spring 2018
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12
April 18 – 24
Molecular genetic analysis
• Recombinant DNA Technology
• Cloning and transgenic animals
• Gene Therapy
Pierce, Chapter 19
April 20: Discussion 12 (Bioinformatics,
I)
April 23: Quiz 8
13
April 25 –
May 1
Molecular genetic analysis
• Genomics and Proteomics
• Epigenetics
April 27: Discussion 13 (Bioinformatics,
II)
Pierce, Chapters 20 – 21
Suggested problems:
Chapter 20: 25, 28, 34, 39
April 30: Quiz 9
14
May 2 – 8
Molecular genetic analysis and complex
regulation of gene expression
• Developmental Genetics
• Cancer Genetics
May 4: Discussion 14 (Eugenics)
Pierce, Chapters 21 – 23
Suggested problems:
Chapter 22: 10, 13, 16, 19
Chapter 23: 21, 24, 31, 34
May 7: Quiz 10
15
May 9 – 15
Complex regulation of gene expression:
• Cancer Genetics
Genetics and evolution:
• Population genetics
Pierce, Chapters 23 and 25
Suggested problems:
Chapter 25: 16, 19, 22, 25, 32,
35, 40
May 11: Discussion 15 (Final Exam
Review)
May 14: Exam 4 (In Class)
Monday, May
21
9:45 – 11:15
Comprehensive Final Exam
•
Biology 115, General Genetics, Spring 2018
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