Dynamic Syllabus Genetics and Genomics BI319, Fall 2014,

(update 090314)
Class Meetings

Lectures
Tuesday and Thursday 9:00am - 10:15am, Cushing Hall 001
Discussion Sections
Monday
4:00pm 4:50pm, Higgins 260
Monday
5:00pm 5:50pm, Higgins 265
Tuesday
5:00pm 5:50pm, Higgins 265
Wednesday
4:00pm 4:50pm, Higgins 265

Professor

Tim van Opijnen, Ph.D.

Office: Higgins Hall 420A
Office hours:
Friday 08:30 10:30am
Email: tim.vanopijnen@bc.edu

Teaching Assistant Adam Jenkins:

adam.jenkins@bc.edu

Peter Johansen:
johansep@bc.edu

Text and Materials Concepts of Genetics, Tenth Edition Klug, Cummings, Spencer and
Palladino (Bookstore Text)
Mastering Genetics Access via Concepts of Genetics purchase (Online website) http://www.masteringgenetics.com/ - COURSE ID:
BI319VANOPIJNEN2014
Pre-/Co-requisite

Biology 204, Investigations in Molecular Cell Biology

Course Overview
Biology is the most exciting and important discipline among the natural sciences. Genetics,
which studies the heredity and the variation of inherited characteristics, is an essential
discipline within Biology. Our understanding of genetics is deepened with increasing speed
by the field of genomics, which partially concerns itself with sequencing sets of genes and
complete genomes preferably by using high-speed and high-throughput methods.
Ultimately genetics and genomics have as a goal to understand what genes are used for
and how they work together to generate an organism or for instance trigger a disease.
Discoveries in genetics and genomics continue to advance our understanding of ourselves
and of the biological world. The overall goal in this course is to help you to establish a
conceptual understanding of genetics and genomics, which is important for at least two
reasons: 1) for those who major in the life sciences, genetics and genomics will become part
of your everyday life; 2) for those majoring in another area, genetics and genomics will
become part of your everyday life, for instance due to the advent of personal medicine, the

BI319 Dynamic Syllabus Fall 2014

loss of biodiversity in the world, and the increase in the use of GM-food.
To make a long story short there are two specific goals for the course this semester:
1. Understand the importance of genetics and genomics in many aspects of our lives
today.
2. That G&G is incredibly dynamic and under constant scrutiny and pressure to
adapt and rise to new challenges that society faces.

Course Structure
During the fall semester of 2014 we will meet twice a week for lectures on Tuesdays and
Thursday and one discussion section.

Lectures
For the first two and half weeks (5 lectures) Dr. van Opijnen will lecture on and discuss
basic but essential topics from Genetics by Klug et al. Starting from Thursday September18
(Lecture 6) the course structure will change and require a substantial contribution from
you, the student. The lecture will be split into two parts, the first 30-40 minutes Dr. van
Opijnen will lecture on topics from Genetics, while the second part of each lecture will be
filled with a PK15 presentation and a discussion with the class led by one group on one of
the assigned current topics in G&G (for more information on CTG&G see below).

Discussion Sections
Students in the course must enroll in one of the discussion sections associated with the
lecture. Discussion sections are directed by a TA and will provide additional opportunity to
ask questions regarding content from lectures and current topics in G&G. TAs will present
ungraded practice quizzes and discuss outcomes from the previous mastery quiz, and help
you prepare for the next mastery quiz. TAs will explain the oral presentation (PK15), and
the written assignment (News and Views popular science essay) associated with the class.

Mandatory?
Because you are all (close to being) grown-ups, the lectures nor discussion section
is mandatory. But do note that current topics in G&G are an important part of each
lecture and of the exams: not only does your teams presentation and the way it handles the
discussion contribute significantly to your grade, your contribution to each in-class
discussion (i.e. when youre not part of the presenting team) is appreciated and noted.
Additionally, attendance will be taken for the discussion sections. Although this does not
directly affect your grade it may be used to determine your involvement in the course and
could affect your grade in case of any borderline issues. Thus, although nothing is
mandatory, it will be hard to do well if you are not present.

BI319 Dynamic Syllabus Fall 2014

Course Readings
1. Readings from Klug et al., Tenth Edition are listed in the lecture schedules. You
should use the contents of lectures as a guide for what to focus on when studying the
material in the textbook.
2. Starting from Thursday September 18 (Lecture 6) each lecture will be accompanied
by a current topic in G&G. Each topic is accompanied by 3 to 8 (news) articles that
present the current scientific state and often the importance of the topic to society.
CTG&G will form a major part of each lecture as well as the exams.

Laboratory Considerations
BI204 has been defined as a prerequisite or co-requisite. This has been done so that the
instructors can assume that you have mastered the topics (concepts, processes and
procedures) covered by that laboratory course. These include but are not limited to:
micropipetting, microscopy, sterile technique, microbial genetics, selective media,
databases, plasmids, restriction endonucleases, restriction mapping, polymerase chain
reaction, gel electrophoresis, immmunochemistry, genetic transformation and genetic
complementation.

Course website
There is a Canvas website for the course lecture, which you can access via your Agora
account. The syllabus, current topics in G&G-content, lecture slides, answer keys and
descriptions of assignments and your grades for quizzes, assignments and exams will be
available for you from this site.

Meeting in person and office hours

Dr. van Opijnen and his TAs have made it their goal to make this a course that will give
you essential insight into what is happening in G&G today and show you the impact it has
on our lives. To achieve this depends on a cooperative effort between all of us. Both our and
your consistent engagement with the course meetings and course content is essential for
this.
If there is anything unclear or there is something you want to discuss that comes up after
class or the discussion sections feel free to meet with Dr. van Opijnen during his office
hours. If you have time conflicts during his office hours, you can arrange a meeting by
contacting Dr. van Opijnen preferably before or after lecture. Meetings with the TA outside
of discussion sections can be arranged before or after the discussion section or by sending
an e-mail inquiry to your TA.
Because office hours are sometimes a bit too restrictive Dr. van Opijnen will be available in
person for short and simple questions, for concerns, pressing issues, problems or just a
simple chat most anytime you want. You can drop by his office @ Higgins Hall 420 or his
lab @ Higgins Hall 400. But keep in mind it either needs to be incredibly life saving
important, a very simple question that only requires a handful of neurons to answer or a
conversation in which you express how wonderful the class is.

BI319 Dynamic Syllabus Fall 2014

Peer Learning
We encourage you to study the course material with peers. Talking with other students is
for many the best way to clarify what they do and do not understand, and then work to
improve their understanding. To do this, try to get to know others in your residence
hall/apartment building/house who are taking the course, and arrange a regular time when
you can meet to go over material from the course. Alternatively, make it a point to get to
know a couple of people who sit near you in lecture, and arrange to meet some time outside
of class.

Examinations
There will be four hour-long examinations ("hour exams") scheduled during the semester,
plus an hour-long comprehensive final examination. Examination grades will be returned
to you within one week after the date of the examination.
The first three hour-long exams will be given during class time on:
Tuesday September 30; Tuesday October 28; and Tuesday November 18.
The fourth hour exam, covering material presented during the last portion of the course,
will be given during the second hour of the final examination period, which begins at 9am
on Tuesday, December 16. The comprehensive final examination will be given during the
first hour of the final examination period. On the evening preceding each examination, we
will do our best to be available electronically until 8pm, if you have any last-minute
questions.
The textbook and supplementary materials we employ in this course are very rich in facts,
concepts and information. When considering the content of the course on which to focus as
you study for examinations, concentrate your efforts on the contents of the lectures,
discussion section meetings, quizzes, and study problems assigned from the text. We will
emphasize for you the content in the course that we consider most important for you to
master.
Each examination will consist of short answer and problem-solving questions. You will
have 60 minutes to complete each examination. Quizzes and study problems will provide
you with examples of the types of questions you will see on examinations and the ways in
which we will assess your understanding of the course material. Examination grades will
be provided to students within one week after each examination is given.
Because conceptual understanding and problem solving is emphasized in the
course, you are allowed to bring one 8.5 x 11inch piece of paper, with any content
you wish, on one side, typed in font Arial 12, with 1.0 line spacing into every
examination. If you wish to avail yourself of the use of such supporting material, bring
the paper with your name on it to the TA in class before the beginning of the examination,
and s/he will mark it with colored ink to certify your preparation of a single sheet of
supporting information.
Three of the four hour-long examinations plus the comprehensive final examination will be
used in determining your course grade (see Course Grading below). In other words, the

BI319 Dynamic Syllabus Fall 2014

lowest grade among your four hour-long examinations will be dropped before course grades
are calculated.
If you are a student with a documented disability seeking reasonable
accommodations in this course, please contact Kathy Duggan, (617) 552-8093, at the
Connors Family Learning Center regarding learning disabilities, or Paulette Durrett, (617)
552-3470, in the Disability Services Office regarding all other types of disabilities.
If you require an accommodation for taking written examinations, you must
contact Dr. van Opijnen during the first two weeks of classes. There are some
arrangements we need to make, and these cannot be completed immediately before an
examination.
If you will miss an examination due to your involvement in intercollegiate
athletics, you must contact Dr van Opijnen during the first two weeks of classes.
This will provide sufficient time to determine whether the examination will be considered
as your dropped exam grade.

Missed Exams
If you do not take an examination at the announced date and time, you will receive a zero
for that examination. If you miss an examination because of illness or an emergency, you
must present written documentation from a health professional or a Deans excuse to Dr.
van Opijnen within one week of the missed examination. There will be no make-up
examinations given in this course, in order to avoid the inequities associated with make-up
examinations. Because only three of the four hour-long examinations will be used to
calculate your course grade, the first examination you miss will be the examination that is
dropped. If you miss two of the hour examinations without appropriate documentation, the
first missed hour examination will be your dropped examination and the second missed
hour exam will be assigned a grade of 0. If you miss the comprehensive final examination
and document your reason as noted above, we will use the average of your three best hourlong examinations as your final examination grade in the determination of your course
grade. If you should be unfortunate enough to miss two of the hour examinations because
of documented illnesses and/or emergencies, we will consider your situation on a case-bycase basis.

Questions Regarding Re-grading

If you want to request re-grading of questions on a problem set or examination, you must
make this request in writing to one of the course instructors within one week after
receiving the grade in question. Your written request must provide the reason why you
believe you should have received a higher grade. Requesting re-grading regarding a portion
of a quiz, problem set or examination opens the entire quiz, problem set or examination to
re-grading. A response will be provided within one week of the receipt of your written
request.

Mastery Quizzes
These quizzes will enable you to demonstrate your understanding of genetic concepts and

BI319 Dynamic Syllabus Fall 2014

processes, and to refine your genetic problem-solving skills. In general the quizzes are not
very difficult but it partially serves the purpose to keep you on track with content. Topics
for each quiz are indicated on the course schedule (below). Quiz grades (maximum grade of
15 points each) will be returned to students within one week after quizzes are
administered. Quizzes will be administered via the MasteringGenetics web site, for which
you should register yourself. During the weeks indicated in the syllabus, Quizzes 1-8 will
be available for 30-minute intervals (for 45- minute intervals for students with extendedtime accommodations) from Thursday @ 12-noon until Sunday @ 12-midnight.

Current topics in Genetics & Genomics - written and oral assignment (working in
groups of 5):
Starting from lecture 6 one representative of a team of 5 students will present an assigned
topic in a highly structured oral format called Pecha Kucha (15 slides, 25 seconds/slide = 6
minutes and 15 seconds). After the PK15 the team presents three statements that relate to
the presented topic and should fuel a class discussion (Part I). By the end of the semester
your team is expected to have written an exciting and engaging popular science essay on
the assigned topic (Part II).
The goal of the CTG&G assignment is two-fold:
1. To get an understanding of what is actually happening in G&G research today
and how it affects our lives.
2. To be able to take a current scientific G&G related topic and transform it into an
exciting story that is clear and understandable for someone that is not an expert and
supplies enough information to trigger an interesting discussion.
Part I PK15 oral presentation and discussion
The first part of this assignment requires you to work in a team of 5, present your topic in
an oral format called Pecha Kucha and lead a class discussion. For details on this
assignment see the current topics in Genetics & Genomics explanation document. The
presentations will be graded for a maximum of 100 points. PowerPoint files are due and
should be delivered to Dr. van Opijnen the day before the presentation at 12-noon.
Turning in PowerPoint files late will result in 0 points.
Forming and working in groups of 5 - You will get the chance to pick your own group
and you should register online on the Canvas website no later than Thursday
September 4 @ 12-noon. Those who have not picked a group by then will be assigned to a
group randomly. Each group is connected to a topic, the first group/topic presents during
Lecture 6, group 2/topic 2 presents during Lecture 7 and so on (also see the schedule at the
end of this document).
Part II - News and Views style popular science essay
Part II of this assignment is focused on writing about your assigned topic in an exciting

BI319 Dynamic Syllabus Fall 2014

and understandable way directed at a non-expert audience. For details see the current
topics in Genetics & Genomics explanation document part II. The assignment will be
graded for a maximum of 100 points and will be due by 12-noon on Monday November
24, as an e-document in Word format. Assignments turned in late will earn 0 points.

Course Grading
Assessment of your understanding of the course material and your grade in the course will
be based on problems sets, the CTG&G assignment, and hour and final examinations.
Four hour-long exams (top 3 of 4)

100 each =

300

Comprehensive final exam (1)

100 total =

100

Mastery quizzes (8)

15 each =

120

PK15 presentation and discussion (1) 100 total =

100

News and Views essay (1)

100

100 total =

Course total (maximum)

720

A+ (100-97%); A (96-93); A- (92-90); B+ (89-87); B (86-83); B- (82-80); C+ (79-77); C

(76-73); C- (72-70); D+ (69-67); D (66-65); F (below 65)

Academic Integrity
On the examinations, quizzes and other assignments, your work must be your own. We
encourage you to study in groups, but examinations and quizzes are to be taken
individually. As it states in the university policy on academic integrity, which can be found
at http://www.bc.edu/integrity: Students [at Boston College] have a responsibility to
maintain high standards of academic integrity in their own work, and thereby to maintain
the integrity of their degree. It is their responsibility to be familiar with, and understand,
the University policy on academic integrity. Any student determined to be in violation of
these standards of academic integrity with respect to conduct in our course will receive a
grade of zero for the examination or quiz in question. A letter of notification describing the
incident and the penalty will be forwarded to the appropriate Associate Dean, and to the
Chairperson of Biology. A second violation will result in dismissal from the course and
assignment to the student of a failing grade in the course.

BI319 Dynamic Syllabus Fall 2014

Dynamic Lecture, Assignment and Examination Schedule Genetics and

Genomics BI319, Fall 2014
Chap. refers to chapters from Concepts of Genetics, 10th Edition by Klug et al.
Week

Date

Topic

Readings

Tue, Sept 2 Lecture 01

Course introduction

Chap 1

Thurs, Sept 4 Lecture 02

Mendelian genetics

Tue, Sept 9 Lecture 03

Extensions of Mendelian genetics

Thurs, Sept 11 Lecture 04

DNA structure, replication and recombination

Chap 10, 11

Tue, Sept 16 Lecture 05

Genetic code, transcription and translation.

Chap 13, 14

Thurs, Sept 18 Lecture 06 /

CTG&G Topic 1

Gene mutation, DNA repair and transposition

Chap 15

Fri, Sept 19

Mastery Quiz 1: Mendelian genetics:

Chap 4, 10

Tue, Sept 23 Lecture 07/

CTG&G Topic 2

Population and evolutionary genetics

Thurs, Sept 25 Lecture 08/

CTG&G Topic 3

DNA organization in chromosomes

Epigenetics

Chap 12, ST III

Fri, Sept 26

Mastery Quiz 2: Central dogma

Chap 11, 13, 14

Tue, Sept 30

Exam I

Lects 1-7,

Thurs, Oct 2 Lecture 09/

CTG&G Topic 4

Variation in chrom. number and arrangement

Chap 7, 8

Tue, Oct 7 Lecture 10/

CTG&G Topic 5

Genetic mapping in prokaryotes and

eukaryotes

Chap 5, 6

Thurs, Oct 9 Lecture 11/

CTG&G Topic 6

Extranuclear inheritance

Fri, Oct 10

Mastery Quiz 3: Pop/evol genetics:

Tue, Oct 14 Lecture 12/

CTG&G Topic 7

Transposons and viruses

Chap 22/9E

Thurs, Oct 16 Lecture 13/

CTG&G Topic 8

Recombinant DNA technology

Chap 20

Fri, Oct 17

Mastery Mastery Quiz 4: Genetic mapping:

Chap 5, 6, 9

2 Disc.
Mtgs

3 Disc.
Mtgs

4 Disc.
Mtgs

6 Disc.
Mtgs

7 Disc.
Mtgs

Chap 3 (Chap 2)

Chap 4

Chap 25

Chap 9
Chap 25, 12, 7, 8

BI319 Dynamic Syllabus Fall 2014

Week
8 Disc.
Mtgs

10 Disc.
Mtgs

11 Disc.
Mtgs

12

13 Disc.
Mtgs

14 Disc.
Mtgs

15

Date

Topic

Tue, Oct 21 Lecture 14/

CTG&G Topic 9

Genomics, bioinformatics and proteomics

Thurs, Oct 23 Lecture 15/

CTG&G Topic 10

Omics and Human genetics I

Fri, Oct 24

Mastery Quiz 5: Recombinant DNA

Readings

Chap 21
Chap 21

Exam II

Lects 8-13

Thurs, Oct 30 Lecture 16/

CTG&G Topic 11

Omics and Human genetics II

Chap 7, ST II

Tue, Nov 4 Lecture 17/

CTG&G Topic 12

Prokaryotic gene regulation

Chap 16

Thurs, Nov 6 Lecture 18/

CTG&G Topic 13

Eukaryotic gene regulation

Fri, Nov 7

Mastery Quiz 6: 'Omics and bioinformatics

Tue, Nov 11 Lecture 19/

CTG&G Topic 14

Dissection of gene function

Chap 23/9E

Thurs, Nov 14 Lecture 20/

CTG&G Topic 15

Genetic engineering

Chap 22

Fri, Nov 14

Mastery Quiz 7: Gene regulation

Tue, Nov 18

Exam III

Lects 14-18

Thurs, Nov 21 Lecture 21/

CTG&G Topic 16

Developmental genetics

Chap 18

Mon, Nov 24 @ 12-noon

deadline: News and Views essay

Tue, Nov 25 Lecture 22/

CTG&G Topic 17

Cancer genetics

Thurs, Nov 27

Thanksgiving

Tue, Dec 2 Lecture 23/

CTG&G Topic 18

TBD

Thurs, Dec 4 Lecture 24/

CTG&G Topic 19

TBD

Fri, Dec 5

Mastery Quiz 8: Develop./cancer genetics

Tue, Dec 9

CTG&G essay and presentation reward

ceremony

Dec 11 - 12

Study Days

Tue, Oct 28

Chap 17

Chap 19

BI319 Dynamic Syllabus Fall 2014

16

Tue, Dec 16 9:00 am

Final Examination

Comprehensive

10:00 am

Exam IV

Lects 19-22,

10