Genetics - PCB3063 Spring 2009 Home Page
Section 4462- TR 9:35-11:30pm (periods 3 and 4)

Contents:

For course postings, scroll down to the course schedule. You can download Adobe Acrobat Reader (free) to read pdfs.  Likewise, to view powerpoint presentations if you do not have powerpoint you can download a powerpoint viewer (also free).

Lecturer: 

Dr. Edward Braun
Office: Carr 514
Phone: 846-1124
Email: ebraun68-AT-ufl.edu
Office Hours: Tues, 5th period (11:45am-12:35pm) and Wed, 7th period (1:55-2:45pm)

Graduate Teaching Assistants: 

Kin Han, 317 Carr
Email: hankin-AT-ufl.edu
Office Hours: Thurs, 6th period (12:50pm-1:40pm)

Matt Salomon, 619 Carr
Email: msalomon-AT-zoo.ufl.edu
Office Hours: Thurs, noon - 1pm 

Undergraduate Teaching Assistant: 

Cara Capitena

Email: caracap-AT-ufl.edu

Schedule:

Room: Text: Concepts of Genetics, 9th edition, by Klug, Cummings, Spencer, and Palladino

Exam Schedule:

Grading: Grades will be determined from the three exams, homework, and the papers. There will be NO extra credit.

Determination of grades:

Regrades must be requested in writing, within 7 days of the return of the exam. There will be absolutely no discussion of any grading issues without a written request. Regrades may forfeit any curve that might have been applied to the test, and they should include a detailed explanation - with specific citations (e.g., specific pages in the textbook or specific portions of the class notes) - of why the grade originally given is being contested. Make up exams will not be given except under exceptional circumstances (such as illness or injury); should such circumstances arise, the nature of the exam will be at the discretion of Dr. Braun.

Grading will be on a percent scale (90%+, A; 86-90%, B+; 80-86% B; 76-80%, C+; 70-76%, C; etc.). A curve may be applied at the discretion of Dr. Braun. This curve will only be applied to increase grades, never to decrease grades.

Honor Code: You are expected to follow the University of Florida honor code. Academic dishonesty of any form will not be tolerated. If we are certain that you were cheating or plagiarizing on an assignment, all persons involved WILL receive a zero for the relevant problem set or exam.

Anybody showing up more than 30 min. late to exams MAY be denied the right to take exams. It is your responsibility toknow when exams are scheduled. Any changes in the day of an exam willbe announced at least 7 days ahead of time.

Web Page: The class website is http://people.biology.ufl.edu/ebraun/PCB3063. Class notes will be posted on this site weekly (usually by Friday).

Attendance is not required, but material covered only in the lecture WILL appear on exams.

What material am I responsible for? You will be responsible for ALL material covered in class and for all readings assigned on the schedule (in the "Readings and Problem Sets" section of the scedule). We have included a substantial amount of material that is not in the book. You are expected to master this material as well as material in the book. Material that I expect you to master that is not in the book will be made available in a clear manner (e.g., we will post it on the web page). Readings that are listed as "pp. XX-YY" refer to the Klug et al. textbook.

The material listed under "Supplementary Material" is NOT explicitly assigned - you will not have to turn it in and it will not be graded. However, it represents practice material for you to work on, so I would recommend you do that work..

Since we are covering material in a different order than in the text, the chapters (and chapter sections, listed as "CHAPTER.SECTION") used as sources for some of the information in the lecture are presented. The chapter reading should be done to HELP you understand the lecture, and they are NOT assigned independently of the lecture. Likewise, the problems are chosen to resemble material on the quizzes. Thus, problems listed in the "Supplementary Material" column are likely to be helpful, but we will not grade them.

TENTATIVE SCHEDULE


 
Week of Topic  Supplementary
Material:

 Chapters
and Problems		 Readings and Problem Sets
5 Jan
Introduction to Genetics - What is a gene?

[lecture set 1 ppt] [lecture set 1 pdf]

 Chapter 1 is a brief summary of the field of Genetics - is can help remind you of previous courses

 Assigned reading: 

Mitosis and Meiosis
Chapter 2, all (don't worry about memorizing the subdivisions of the prophase of meiosis I)

Mendelian Genetics
Chapter 3, pp. 43-54

Complete this reading by 13 Jan
12 Jan Extensions of Mendelian Genetics

[lecture set 2 ppt] [lecture set 2 pdf] 		Chapter 4

Work through problems 22-24 in Chapter 3 (p. 67)
19 Jan Genetic Mapping

[lecture set 3 ppt] [lecture set 3 pdf]		 Chapters 5 & 6

Work through problems 14, 24, 40, and 46 in Chapter 4 and work through problems 10, 13, 17, 28 and 32 in chapter 5
26 Jan Genetic Mapping

[Focus on mapping ppt]

[Focus on mapping pdf]		 Chapter 5
2 Feb
 Genetic Mapping

[lecture set 4 ppt] [lecture set 4 pdf]
 Chapter 5 & 6
 Take the Practice Quiz for the upcoming Test [available at e-learning] on Thurs 5 Feb 2009.

Remember, this is a practice quiz - don't worry if you get questions wrong. IF you have problems seeing the figure on the quiz, you can download the [quiz figure pdf].

If you have problems, email Kin.

If you have not taken the quiz yet, I recommend that you download a copy for practice:

[quiz pdf]

[quiz answers pdf]

Cara will be available Sunday 8 Feb from 5pm-7pm on the 3rd floor (at one of the group table overlooking Turlington)
9 Feb TEST 1 - Tues. 10 February 2009

Bacterial and Phage Genetics

[lecture set 5 ppt] [lecture set 5 pdf] 		Chapter 6
 Review Session - Mon. 9 Feb 2009
at 5:10pm (10th period) in McCarty A G186 (the same room as the class)
16 Feb Sex Chromosomes, Dosage Compensation


[lecture set 6 ppt] [lecture set 6 pdf]		 Chapters 7
23 Feb Organelles, Extranuclear Inheritance

[lecture set 7 ppt] [lecture set 7 pdf]		 Chapters 9 
2 Mar Extranuclear Inheritance, Prions

Chromosomal Abberations		 Chapters 8 & 9

I recommend that you read chapter 10, pp. 247-250 for additional coverage of bacterial transformation.
9 Mar Spring Break
16 Mar TEST 2 - Thurs. 19 March 2009

DNA Replication, Gene Regulation

[lecture set 8 ppt] [lecture set 8 pdf]		 Chapters 11 & 12

(some examples from chapter 10) 		You should look at the following problems:

Chapter 6:
2, 6, 7, 10, 11, 19, 26, 27

Chapter 7:
5, 6, 7, 10, 11 (what should we call the chromosomes if the male is the heterogametic sex), 17, 19, 22, 29, 30, 34, 35, 36, 37 (don’t memorize all of the specific examples, just make sure you understand the mechanisms of sex determination)

Chapter 8:
Just focus on some of the terminology I introduced briefly in class. For example, know what euploidy vs aneuploidy is, be able to explain why sex chromosome aneuploidy is generally less problematic in humans than autosomal aneuploidy, understand what a Robertsonian translocation is.

Chapter 9:
3, 4, 8, 17, 23 (also make sure you can desecribe the process of secondary endosymbiosis)

I will be doing a Review Session:

Wednesday

NPB 1001 for 3/18/09 from 5:15 pm to 7:00 pm (NPB is the Physics Building)
23 Mar Transcription, Translation


[lecture set 9 ppt] [lecture set 9 pdf]
Chapter 14
(Chapter 15 also has material on translation - but only use the reading to help you understand notes)
 
30 Mar

Mutagenesis 

[lecture set 10 ppt] [lecture set 10 pdf]		 Chapters 21
6 Apr Cancer

[lecture set 11 ppt] [lecture set 11 pdf]

 Chapters 16 & 20 (along with some material from Chapter 22)
13 Apr Population Genetics

powerpoint slides will be available from the e-learning site on Monday

Transcriptional Regulation

[lecture set 12 ppt] [lecture set 12 pdf]		 Chapter 27

Chapters 17 & 18		 Remember the first two tests -- just like those tests, the focus will be on the material presented in the LECTURE. So use the lecture notes to guide your studying. Use the book to help you understand the lectures, and don't worry about sections that were not covered in the lecture.

The following problems should be especially helpful:

Chapter 10:
5, 6, 17, 18, 24, 32

Chapter 11:
2, 3, 20, 24, 37

Chapter 14:
1, 2, 3, 8, 16, 20, 24, 30

Chapter 15:
3, 23, 32

Chapter 16:
7, 9, 11, 16, 29

Chapter 17:
3, 5, 6, 11

Chapter 18:
6

Chapter 20:
6, 7, 8, 15, 17, 19, 22

Chapter 27:
1, 2, 10, 13, 14, 15, 27, 28, 29, 30
20 Apr TEST 3 - Tues, 21 April 2009
I will be doing a Review Session:

Monday, 20 April

NPB 1002 from 5:15 pm to 6:00 pm (NPB is the Physics Building)

Choosing a topic for your short paper:

You should search the “OMIM” database with terms that interest you. Choose five terms that you want to use as queries. For example, if you are interested in cancer, simply search with the term “cancer”. Obviously, simply using the term “cancer” as a search term will find more records than a more limited search term (e.g., “kidney cancer”). Choose one gene from the set of records that you retrieve – remember, you don’t have to pick the first record you see.

The first paper:

The first paper is simply list the search terms you used and the record you chose. You should choose records associated with specific genes. Note – there are records in OMIM that focus on inherited conditions that are not associated with specific genes (e.g. search with “BRACHYDACTYLY, COMBINED B AND E TYPES” to find a record is not associated with a specific gene). The information you should list is:

The search term you used (e.g., “kidney cancer”)
The accession number of the record you chose for that search term (e.g., “*611731”)
The description of the record you chose for that search term (e.g., “APC GENE”)
The map location of the gene for that search term (e.g., “5q21-q22”)
A one or two sentence description of the gene you chose for that search term.

So, you should have 5 search terms; present this information for each.

This first paper is DUE by Tuesday, 14 April 2009

The second paper:

Choose one topic (of the 5 you tried) and write a one-page paper about the gene. The OMIM records include references, and you can find additional papers by searching the “Gene” division of Entrez (choose “Gene” from the same pop-up menu that you used to select “OMIM”) using the gene name. Indicate the papers you read and summarize the results of those papers. When you summarize, try to integrate material from the sources you are using. In other words, don't write two paragraphs -- with paragraph 1 describing only paper 1 and paragraph 2 describing only paper 2.

To summarize -- you need to write a single coherent summary about the gene of interest using information from at least two papers.

Do not simply reiterate the OMIM record -- in other words, if you chose the Androgen Receptor (*313700) you would see a record with many subtopics (Description, Cloning, Gene Function, etc.). If you tried to cover all of these you would need many sources and would not be writing a focused paper. Focus on something specific within a subtopic (e.g., something within gene function).

For the purpose of this exercise you can define the word "gene" broadly. What I mean by that is that you can write about any aspect of a specific OMIM record that interests you, as long as that record is focused on a specific gene (if this is not clear, see above for an example of an OMIM record that does not focus on a single gene). In other words, don't worry about fine distinctions within the gene -- you should write about any aspect of the gene that you are interested -- this includes (but is not limited to) the regulation, the coding region, the splicing, the encoded protein, phenotype of mutations, clinical tests, etc. associated with a gene. However, you should focus on a single gene. It is ok to mention other genes (e.g., the product of gene X forms a complex with gene Y) but ultimately, you should focus on a single gene.

You should read and summarize at least two papers. Two papers is a minimum -- it may actually be easier to use more than two sources (it depends upon the topic you have chosen). Even if you only focus on two papers, it may help to read additional papers to help understand the two you have chosen. You should read the whole OMIM record and choose your papers carefully. If you cannot find two papers that interest you in the OMIM record, you should do addtional searches as described above (e.g., of the Entrez Gene division) or simply choose a different OMIM record.

Along with the 1 page paper, you should include references in the following:

   * Journal articles: Authors listed as Last Name, Initials. Year of Publication. Title. Journal Volume:Pages.

For example:
    * Journal articles: Pensole G, Gissi C, Lanave C, Saccone C. 1995. Glutamine synthetase gene evolution in bacteria. Mol. Biol. Evol. 12:189-197.
    * (>10 co-authors): Wilson R, Ainscough R, Anderson K, et al. (55 co-authors). 1994. 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans. Nature 368:32-38. (Please note that 55 includes all authors of the article.)
   
In the text, indicate your sources using (Name Year) if the paper has a single author, (Name1 and Name2 Year) if the paper has two authors, and (Name et al. Year) if the paper has three or more authors. e.g., you would use (Pensole et al. 1995) for the paper listed above.

The paper should be single-spaced and use a standard font (e.g., Times or Times New Roman, Helvetica, Geneva, etc.) and a font size of 11 or 12.
The paper should have margins of 1 to 1.5 inches.

This second paper is DUE by Monday, 27 April 2009

You should turn the papers in to elb.PCB3063@gmail.com