Biology 325:  Advanced Genetics

University of Indianapolis Spring 2005

 

Instructor:     Dr. Sandra Davis                  Phone: 788-3289                              

                        Lilly Hall 130C                      Email:  sdavis@uindy.edu  

 

Office Hrs:    Mon. 11:00-12:00pm, Tues. & Thurs. 9:00-10:00am, Wed. 2:00-3:00pm or by appt.  Feel free to drop by my office, if the door is open, I will be most likely willing to talk to you.

 

Textbooks:    Concepts of Genetics, 7th Edition, by William Klug and Michael Cummings, 2003, Prentice Hall, Inc. (or any other general genetics textbook)

 

                        A Primer of Population Genetics, 3rd Edition by Daniel Hartl, 2000, Sinauer Associates, Inc.

 

                        Essentials of Genomics, Philip Benfey and Alexander Protopapas, 2005.  Prentice Hall, Inc.

 

Locations/Times:     Lecture: MWF 1:00-1:50pm; Lilly Hall 026

Lab: Tuesday 12:00-1:50pm; Lilly Hall 023

 

Course Objectives: This course is an extension of Biology 225: Introduction to Genetics. The goal of this course is to build on knowledge gained in Bio 225 and to introduce students to special topics in genetics that cannot be covered in an introductory genetics course because of time restrictions. As genetic information is growing exponentially, our emphasis will be on developing the ability to solve problems using genetic ideas and methods, to understand the nature and reliability of genetic inference, and to apply genetic reasoning to biological research.

 

Topics include:

♦ The molecular anatomy of the gene

♦ Regulation of gene expression

♦ Genetics of Cancer

♦ Functional Genomics and Bioinformatics; current paradigms and methods

♦ Developmental genetics

♦ Genetics of Quantitative

♦ Evolutionary genetics

♦ At least some time per week will be reserved for a discussion of problems or research papers taken from the current literature.

 

Prerequisite: BIOL 225 or equivalent. All students should have a working knowledge of basic concepts of genetics and molecular biology. If you are uncertain of your preparation, I urge you to review by reading and, more importantly, solving the problems in, a good undergraduate genetics textbook.

 

 

Course components:

            Lecture:  Class periods will consist of lecture, discussion, and group work.  Attendance will be taken according to University policy, but will not be counted in your grade.  Although attendance is not strictly required for you to pass this course, you are responsible for all material covered in lectures, whether or not it is covered in the textbook.  In addition, some time will be devoted to discussing worksheets, which will be collected during the class period (see below).  Therefore, it is very important and expected that you attend all lectures.

 

            Worksheets:  There will be a total of 10 worksheets consisting of various types of problems that you will be expected to complete during the course.  You will be given worksheets in class or you may print them out from the web.  You are expected to try all the problems and complete the worksheet as fully as you can.  If needed, some time in class will be spent with the students in small groups or as a class discussing some of the more complex problems.  At the end of this time, worksheets will be collected.  NO WORKSHEETS WILL BE ACCEPTED AFTER THIS POINT.  If you do not hand in your worksheet at this point you will receive 0 points.  Each worksheet is worth 10pts for a total of 100pts.  In addition, the format of worksheet questions will be very similar to exam questions, so it is very important to complete the worksheets.  NOTE:  the time devoted in class to discussing the worksheets is inadequate to complete a worksheet from scratch, so you must work on it before coming to class.  Also, although we will sometimes be working on these worksheets in groups and hence I encourage co-operation and discussion, the final product should be an individual effort (I donÕt want 25 xeroxed copies of the same thing).  If 2 individuals have identical answers on their worksheets, both will receive a 0. The time given in class is to discuss different ways to solve problems, helping each other understand concepts, etc., not to copy answers to the questions you didn't finish from your friends.

 

            Exams:  Dates of the exams are listed on the course schedule. There will be 4 exams worth 100pts each.  The fourth exam will be given during finals week, but will NOT be comprehensive.  The format of all exams will be a mixture of some short answer, maybe matching or multiple choice, and mostly problems.  The questions on the exams will be similar in format to the questions on the worksheets and the problems at the end of textbook chapters. I curve only in one case: if the exams have been, in my opinion, too difficult, I will curve the class accordingly. I will NOT use a curve if I feel that people just didn't try. I have no problem with giving everyone in the class an A if they all score above 90%, but I've yet to see it happen. Since you are not being curved, it will be of benefit to you to study with your peers. Being able to logically explain a concept to another student equates with at least partial understanding of the topic. I frown deeply upon missed exams.  Unless I am notified of an appropriate excuse in advance, any make-up exams will be of the format all problems and essay type questions.  I will not give makeup exams in cases of oversleeping, personal problems, work schedules, etc.  If you come to me with such an excuse you will receive a 0 on that exam.  In cases of illness, death in the family, etc.  I require appropriate documentation: doctorÕs note, obituary, etc.  This is not personal so do not be offended when asked.  I do call to verify such excuses.  Furthermore, you must notify me within 24 hrs. of a missed exam or you will not be allowed to make it up. If you feel I have erred in grading, please let me know, and I will regrade your entire paper. You might get points back, but then again, I might see something I missed before...

Lab component: As labs provide hands-on experience with the topics covered in lecture and discussion, it is vital that students attend all lab sessions.  As such, if a student misses more than one lab session, that studentÕs lab grade will be reduced by 5% for each additional lab missed, and that student will receive a zero on all associated assignments for that lab.  If you have a legitimate and verifiable excuse for missing a lab, as with exams, you must notify me within 24hrs. of the missed lab, and we will attempt to allow you to make up the missed lab if possible.  As many of the labs require extensive set up, this may not be possible.  It is the studentÕs responsibility to arrange his or her schedule to accommodate the lab schedule, not the instructorÕs.  You will be required to keep a lab notebook in which you will make notations, record results, make diagrams, etc.  You should purchase a composition notebook for this purpose.  You will turn in your lab notebook twice during the semester to be evaluated.  Each turn in will be worth 50 pts.

 

 

Grading:  your grade for the course will be based on the points you earn on the following:

 

Assignment

Points Possible

Lecture exam I

100

Lecture exam II

100

Lecture exam III

100

Lecture exam IV

100

Worksheets

100

Lab notebook turn-in (50 pts. Each)

100

Total

600

 

 

 

 

Letter grades will be assigned according to the percentage of points accumulated out of the total possible using the following scale:

 

98-100%

588-600 pts.

A+

93-97.9

558-587

A

90-92.9

540-557

A-

87-89.9

522- 539

B+

83-86.9

498- 521

B

80-82.9

480- 497

B-

77-79.9

462- 479

C+

73-76.9

438- 461

C

70-72.9

420- 437

C-

67-69.9

402- 419

D+

63-66.9

378- 401

D

60-62.9

360- 377

D-

Below 60

0- 359

F

 

 

Web page:  In order to make study materials and myself more accessible, I have put together a web page for the course.  You can find the page at:  pages.uindy.edu/~sdavis

Here you will find important announcements, worksheets, lecture outlines, study materials, etc.

 

Finally, CHEATING: If I suspect cheating, I WILL pursue it according to University policy.  I have a ZERO TOLERANCE POLICY on this subject.  Nuff said.

 

Lecture Schedule

 

Week

Monday

Wednesday

Friday

Text Readings

1

01/17-Intro to course

MLK Day-special schedule

01/19- Review: Structure of DNA and RNA

01/21- Review: DNA replication

K&C- Chap. 9: pp 226-244; Chap. 11: pp 283-292

2

01/24- DNA sequence organization and chromosomes

01/26- Anatomy and Function of a Gene: Dissection through mutation

01/28- Anatomy and Function of a Gene: Dissection through mutation

K&C- Chap. 10

K&C- Chap. 13: 334-340

3

01/31- Review: Central Dogma

02/02- RNA splicing

02/04- Overlapping genes and exon shuffling

K&C- Chap. 12,13;

K&C- Chap. 12: pp 306-318

4

02/07- Extranuclear Inheritance

02/09- Catch-up / Review

02/11- Exam I

K&C- Chap. 15

5

02/14- Introduction to Genomics

02/16- Technical Foundations of Genomics

02/18- DNA sequencing

K&C- Chap. 14

B&P- Chap. 1, 2

6

02/21- Fundamentals of Mapping and Sequencing

02/23- Genome sequencing

02/25- Genome sequencing

B&P- Chap. 3, 4

7

02/28- RNA Expression Analysis

03/02- RNA Expression Analysis

03/04- Proteomics

B&P- Chap. 5;

B&P- Chap. 7

8

03/07- Proteomics

03/09- Catch-up / Review

03/11 – Exam II

B&P- Chap. 7

9

03/14- Spring Break: No Classes!!

03/16 – Spring Break: No Classes!!

03/18– Spring Break: No Classes!!

 

10

03/21– Gene Regulation in Prokaryotes

03/23- Gene Regulation in Prokaryotes

03/25- Gene Regulation in Eukaryotes

K&C- Chap. 17

K&C- Chap. 21

11

03/28- Gene Regulation in Eukaryotes

03/30- Developmental Genetics

04/01- Developmental Genetics

K&C- Chap. 21

K&C- Chap. 22

 

12

04/04- Genes and Cancer

04/06- Catch up/ review

04/08- Exam III

K&C- Chap. 23

B&P- Chap. 9

13

04/11- Video: Genes & Cancer

04/13- Population Genetics

04/15- Population Genetics

K&C- Chap. 25

Hartl- Chap. 1

14

04/18- Evolutionary Genetics

04/20- Evolutionary Genetics

04/22- Comparative Genomics

K&C- Chap. 26

Hartl- Chap. 2

B&P- Chap. 8

15

04/25- Quantitative Genetics

04/27- Quantitative Genetics

04/29- Catch up/ review

K&C- Chap. 5

Hartl- Chap. 4

16

Final Exam: TBA

 

This schedule is tentative, and lecture subjects may change.  Dates of Exams however are fixed, and will only change with regards to the subject matter covered.  Additional outside readings are not listed, but will be assigned in class.

 

 

Lab Schedule

 

Week

Tuesday

Readings

1

01/18- Human DNA

K&C- Chap. 9

2

01/25- Molecular Biology of HIV Replication

K&C- Chap. 10

3

02/01- Molecular Biology of HIV Replication

K&C- Chap. 12, 13

4

02/08- Amylase Activity

K&C- Chap. 12, 13

5

02/15- Human Mitochondrial DNA

K&C- Chap. 15

6

02/22- DNA sequencing & the Human Genome Project

K&C- Chap. 14

B&P- Chap. 1, 2

7

03/01- DNA/RNA Microarrays

B&P- Chap. 5

8

03/08- Bioinformatics

B&P- Chap. 6

9

03/15- Spring Break: No Classes!!

 

10

03/22– PCR analysis of genetically modified food

B&P- Chap. 7

11

03/29- Gene Regulation in E. coli

K&C- Chap. 17

12

04/05- In Search of the Cancer Gene/ Morphology of Cancer Cells

K&C- Chap. 23

B&P- Chap. 9

13

04/12- Determination of Alu frequency in Genetic Students

K&C- Chap. 25

Hartl- Chap. 1

14

04/19- Comparative Genomics

K&C- Chap. 26

B&P- Chap. 8

15

04/26- Calculating Heritability

K&C- Chap. 8

Hartl- Chap. 4

 

 

This a TENTATIVE LAB SCHEDULE:  It is subject to change as the semester progresses.