Biology 201: Genetics
Fall 2013, Davidson College

MWF 10:30-11:20 in Chambers 1006
Lab Wed 1:30 or Thurs 1:40 in Dana 256

Dr. Karen Hales
Dana 201A, x2324


lab syllabus
lab manual contents page
course schedule
(Go to Aug, Sep, Oct, Nov, Dec)
genetics links

Course objectives: 1) You will build a precise understanding of the physical nature and metabolism of the genetic material, patterns of inheritance of traits, and basic approaches of recombinant DNA technology; 2) You will learn to approach genetic issues in society with a critical mind and educated perspective; and 3) You will learn first hand via original laboratory experimentation how research works and how classical and molecular genetics intertwine.

Required textbooks:
iGenetics: A Molecular Approach, 3rd edition by Peter Russell (Pearson/Benjamin Cummings, 2010).
http://wps.aw.com/bc_russell_igen_mol_3. The web site contains the same activities and animations as the textbook CD-ROM.
A Short Guide to Writing about Biology, 8th edition, by J. Pechenik, Addison-Wesley, 2012. (If you already own an earlier edition, that's fine).

Office hours: Email me in advance to make an appointment for any mutually acceptable time; list three possible dates/times in your email and I'll get back to you. Or, you are welcome to stop by any time my door is open, which is most of the time when I am not in class or other meetings. Generally, right after class or lab, Tuesday afternoons, and Thursday mornings are good time frames for appointments.

Email: You are responsible for all information I send by email, so check your messages each day.

Grading: Your final course grade will be calculated as follows:

Three reviews
Daily quizzes
Paper proposal
Term paper (see below)
Lab (see lab syllabus for breakdown)
Final exam
Participation, effort, initiative
30% (10% each)
5%
2%
10%
25%
20%
8%

%
94-100
90-93.9
87-89.9
83-86.9
80-82.9
77-79.9
73-76.9
70-72.9
67-69.9
60-66.9
0-59.9
Course grade
A
A-
B+
B
B-
C+
C
C-
D+
D
F

Attendance and Participation: In lecture I do not record attendance, but I usually notice if you are not there. Absences are also apparent from daily quiz results. Laboratory sessions are mandatory. Each unexcused absence from lab will result in a full letter grade deduction from your course grade. Your participation grade depends upon the extent to which you participate in classroom and laboratory dialogue.

Classroom etiquette: Please do not get up and leave the classroom in the middle of class unless it is a true emergency. Use the restroom before coming to class. Turn cell phones completely off during class. Do not use a laptop in class unless you have asked for and received my permission.

Policy on recording of class: Davidson College policy prohibits audio and video recording of classes by students without permission of the instructor. I will consider permission requests on a case-by-case basis. For students with a disability, permission will always be granted when the accommodations authorized by the Dean of Students Office include recording. Authorized recordings are for the sole use of the individual student and may not be reproduced, sold, posted online, or otherwise distributed.

Disabilities: I will do my best to provide accommodations for students with learning or physical disabilities. If you have a learning disability documented by Davidson College, please let me know during the first week of class so that arrangements can be made. I encourage students with other disabilities to self-identify (confidentiality guaranteed) so that we may explore ways to enhance your learning.

Lectures: PowerPoint files to accompany each lecture will be posted online by the evening before each class. I use PowerPoint to provide illustrations and sometimes outline topics but not to write out every idea; viewing a PowerPoint file therefore does **not** substitute for attending lecture. Click the link from the lecture schedule below to download the file. Log in using the same information as for email, and for the domain name type davidson. To print the file, please first set printer options to include multiple slides per page.

Reading/listening/viewing assignments and problem sets: Each assignment and problem set on the syllabus relates to the topic of that day. Normally, you may choose whether to read and do the problems before or after you encounter the material in class. A few assignments are specifically designated to be completed before class, however. Problem sets will not be collected. You may work together on the problem sets; solutions are available in the solution manual on informal reserve in our lab (Dana 256).

Math and Science Center: The MSC offers free assistance to students in all areas of math and science. Trained and highly qualified peers hold one-on-one and small-group tutoring sessions on a drop-in basis or by appointment. Emphasis is placed on thinking critically, understanding concepts, making connections, and communicating effectively, not just getting right answers.  In addition, students can start or join a study group and use the MSC as a group or individual study space.  The MSC is located in the Center for Teaching and Learning in the library.  See the website for hours or contact Dr. Mark Barsoum (mabarsoum or 704 894 2796).

Quizzes: On some days there will be a short written quiz on the material covered on the previous class day. Other times there will be informal verbal quizzing. You may have two "pass" days for which your written quiz grade does not count.

Reviews: Reviews will be take-home, closed book, and closed notes. They will be posted on the web from links on this syllabus, and a review is typically due on the second class meeting after is posted. You may view/print a review only when you are ready to start it. You can choose whether to hand write or type your answers; however, since I sometimes ask for word counts, typing is more efficient. Each review is designed to be completed in roughly one to two hours, but you will have eight waking hours from when you start until when you must finish. The final exam (also take home) will be designed to take two to three hours. I strongly recommend using old reviews as a primary way to study. Last year's reviews are here: #1, #2, #3, Final

Paper: You will complete a term paper for which you may choose from among several formats. You will submit a detailed proposal ahead of time. See the bottom of the syllabus for details, and see the course schedule below for due dates. This project is separate from and unrelated to our laboratory research project.

Lab notebook and poster summary: You will maintain a laboratory notebook, and you will turn in a short lab summary at the end of some lab sessions. You will create a virtual poster at the end of the semester to summarize the lab project. See lab syllabus for details.

Penalty for late assignments: Ten percent per day or part thereof. The full ten percent penalty applies starting at the beginning of each day that the assignment is late; for example, an assignment that is one hour late will have a ten percent penalty applied.

Honor Code: You are to affirm your respect for and compliance with the Davidson Honor Code on every review and paper. The full Honor Pledge reads as follows: "On my honor I have neither given nor received unauthorized information regarding this work, I have followed and will continue to observe all regulations regarding it, and I am unaware of any violation ofthe Honor Code by others." Plagiarism is an Honor Code violation and is defined as representing another person's words and ideas as one's own. Please carefully read the Davidson Department of Biology statement on plagiarism for comprehensive information on what constitutes plagiarism and how to avoid it.

 

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Course schedule
Go to Oct, Nov, Dec

Date

Lecture topic
Links will become active by the evening before each class.

Reading/listening/viewing
(occasional additional assignments may be added later)

Assignments accompany the indicated day's lecture. Quizzing on that material may occur on the subsequent lecture day.

Suggested study questions/problems
Will not be collected. The listed problems relate to that day's lecture and are fair game for quizzing at the beginning of the subsequent class.

M 8/26

What is genetics, and how does it relate to other areas of biology? How was it shown that DNA is the hereditary material?

Click title to download powerpoint file for printing. Use email credentials to log in. You may need to type davidson\username. Please conserve paper by printing double sided, with multiple slides per page.

Read the entire syllabus. You are responsible for all the information and requirements detailed therein.

Russell Chapter 1: Read pp.1-8
Chapter 2: Read pp.9-14
Browse (skim for main points, don't read in depth) the following online selections on common genetic model organisms: yeast, worms, flies, zebrafish, mice, mustard plant

2: 1-5
Special assignment to be fulfilled by Thursday afternoon September 5th, worth 3 pts on the first review if completed on time: come see me in my office for a least a few minutes. You may arrive in pairs or groups of three, but no more than that. You may make an appointment beforehand--email me with some possible times. The purpose is to familiarize you with the location of my office and to help me get to know you. A visit must take place for me to record your grade on the first review.

W 8/28

The structure of DNA, chromosomes, and genomes

2: 15-27; stop at end of Keynote box.

Explore the following web tutorials:

DNA Structure -- do the animated interactive tutorial sections, A, C, D.
Exploring DNA -- Follow all three links under "Contents."

Also view the DNA packaging animation

2: 8, 10, 11, 13, 15, 16, 17, 20, 32-35
F 8/30 Intro to gene function 6: 102-106 through Keynote box
4: 60-65; skim 65-72
6: 1, 2
4: 7, 11, 14-16, 20

M 9/02
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Transcription and RNA processing

Review figures 2.8-2.9
5
: 81-97
View a transcription animation
View an mRNA processing animation
View an mRNA splicing animation

5: 1-5, 7, 8, 11, 13, 14, 16, 17, 18, 23

W 9/04

The genetic code and translation

6: 108 (Characteristics..)-122
View a prokaryotic translation animation
(may ask you to login twice; use email credentials)
View a eukaryotic translation animation

6: 17, 18, 22, 23, 24, 26, 29, 30, 32, 33

F 9/06

More on translation; how the genetic code was deciphered.
Intro to DNA replication

6: 106-108
For fun: view this film from the early 1970's. Note that the term "T factor" refers to the elongation factor EF-Tu.
3: 36-39
6: 6, 8, 9
3: 1, 3

M 9/9

More on DNA replication;
Cell division: mitosis and meiosis
3: 39-54
12: 326-339
View a replication animation
View the mitosis and meiosis animations.
Do this meiosis self-test, and if necessary, click the meiosis link at the top to review the concepts.
3: 5, 13, 14, 16, 17, 18
12: 1-9, 11, 13, 15, 17, 18

W 9/11

Monohybrid crosses; intro to Mendel; rediscovery of Mendel; chromosome theory of inheritance 11: 297-307 (through Keynote at top), also p. 312 (section on "Rediscovery")
12: 339-344 (stop at "Bridges tested his hypothesis further...") Be sure to read box 12.1 on p. 343.
11: 1, 3, 4, 5, 6, 10, 11
12: 22, 23
**take home review #1 on material up through mitosis and meiosis:
available W 9/11 by noon, and due M 9/16 at class time.

F 9/13

Patterns of inheritance and probability assessments

4: 72-74
11
: 314-317
12: 351-353
13: 385 (Extranuclear..)-388 (top of second column).
11: 7, 32, 33, 36
12: 24, 25, 30, 31, 32, 33, 42-50
13: 47, 48
M 9/16

Interactions among alleles of a single gene; connections between genotype, phenotype, and the environment

13: 363-378

13: 2, 4, 5, 6, 7, 12, 23, 28

Special assignment in preparation for project proposal: Read the chapters called Locating Useful Sources and Citing Sources and Listing References in the Pechenik book. In the chapter with guidelines on specific tasks, find the information most relevant to the paper option that you choose. Also read the Department of Biology statement on plagiarism.

W 9/18

Dihybrid crosses and independent assortment

11: 307-314 11: 2, 9, 15,18-20, 24, 27

F 9/21

Crossing over and linkage mapping

14: 401-403 (through Keynote), 405-418 14: 2, 3, 6, 7, 10, 11

M 9/23

Crossing over and linkage, part 2
14: 403-405
14: 4, 8, 9, 26

W 9/25

Gene interactions: multiple genes

13: 378-385
Read supplementary info on nonsense suppressors

13: 33, 36, 37, 38
**Paper proposal due as email attachment by 5 PM Friday 9/27. See instructions below for naming files.

F 9/27

NO CLASS    
M 9/30

Gene mutation and repair

7: 130-143 through keynote, 146 ("Repair of..") to 148 (stop at "Translesion..") 7: 2, 5, 11, 14, 15, 17, 20

W 10/02
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More mutation and repair

7: 150-158; skim 158 ("The Ac-Ds..) through 161.

7: 4, 29, 30, 34, 35, 36, 40

F 10/04

Transposable elements; chromosomal mutation: chromosome structure

16: 463-476
View animations: inversion formation, paracentric inversion in meiosis, translocation formation, reciprocal translocation in meiosis

16: 2, 4, 13, 14, 15-17

M 10/07

Chromosomal mutation: chromosome number

16: 476-483
12: 346 ("Sex Chromosomes..")-350 (stop at "Sex Determination in..")
4: review 72-74
16: 24-28, 34, 36-39
**take home review #2 on material through chromosomal mutation:
available W 10/09 by noon, and
due F 10/11 at class time.

W 10/9

Unit 2 catch-up day in preparation for review    

F 10/11

Bacterial genetics
15: 429-445 15: 1-4, 12-16, 26

M 10/14

FALL BREAK    

W 10/16

Genetics of bacteriophage and viruses

15: 445-452
15: 18, 20, 31

F 10/18

Recombinant DNA and genome sequencing projects: isolating and sequencing DNA

8: 170-189
Read Asilomar and Recombinant DNA, Nobel lecture by Dr. Paul Berg
Optional supplement: see a video of Dr. Berg speaking about these events.

8: 1, 3, 4, 5, 8, 9, 10, 13, 21, 22

M 10/21

Recombinant DNA and genome sequencing projects: assembling the genome and identification/annotation of genes

8: 189-191, 193-206
Browse Quick Guide to Sequenced Genomes


8: 28, 29, 31, 33, 34

W 10/23

Structural genomics and DNA fingerprinting

10: 269-273 (through Keynote), 277 (DNA typing)-280 (through Keynote)
2
: 27("Centromeric..")-30.
7: 160 (Human Retrotransposons)-161.
13: 387, box 13.1
View PCR animation; also see Figure 9.3 and associated text, pp, 221-223
Read the research article from 1994 on Romanov DNA analysis and a summary of a 2004 controversy on the matter.
Skim Thomas Jefferson and Sally Hemings

9: 8-11
10
: 37, 38, 41-44, 46, 47
13
: 50, 51
**Paper due via email by 10 AM on Fri 10/25. See instructions below for naming files.

F 10/25

Using DNA technology to connect genes, proteins, and functions (part 1) 10: 249-252 (section on expression vectors), 255 (Cloning a...)-top of 258, also box 10.1 p.259.

10: 3-7, 15, 17, 18, 24, 25

M 10/28

Using DNA technology to connect genes, proteins, and functions (part 2)
9: 220 (Assigning...)-229 (through Keynote). Focus on gene knockouts in the mouse and on RNA interference.
10: 267-273 through keynote.


9: 13, 15, 16

W 10/30

Using DNA technology to connect genes, proteins, and functions (part 3)

10: 260-261 (Identifying Genes...), 261-263 (section on Southern and Northern blots), SKIM 263-265 (Wide Range of Uses of PCR), review 269-273
Read About the International HapMap Project from the Human Genome Project
14:
416-418

10: 16, 20, 21, 26, 39, 40
14: 36-38

F 11/01
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Larger scale analysis: functional genomics and proteomics 9: 230-234 9: 21-23, 25

M 11/04

DNA testing for disease
Gene therapy

10: 273-277, 280-281
Read personal accounts of genetic testing for Huntington's and breast cancer
Read Targeting DNA a gene therapy overview by Jef Akst from The Scientist
Find and read one recent gene therapy news item at either Science Daily or The Scientist.

10: 35, 36, 48

W 11/06

Genetically modified prokaryotes, fungi, and animals

10: 281-282
Browse the news story links at New Scientist GM Organisms Guide, focusing on stories about bacteria, fungi, and animals

Read "The Wipeout Gene" (November 2011) by Bijal Trivedi from Scientific American. Search on the article titles and download the PDF from this index site.

 

F 11/08

Genetically modified plants

10: 282-285

Read the following articles from Scientific American. Search on the article titles and download the PDFs from this index site.
"Does the World Need GM Foods?" December 2006
"Edible Vaccines" December 2006
"Sowing a Gene Revolution" September 2007
"Are Engineered Foods Evil?" September 2013

10: 49, 50

M 11/11

Cloning, reproductive and therapeutic
Induced pluripotent stem cells

19: 550 (Cloning animals..)-552

Read Cloning Fact Sheet and browse its links.

Read "New Life for Ancient DNA" (August 2012) and "Your Inner Healers" (May 2010) from Scientific American. Search on the article titles and download the PDFs from this index site. Regarding the second paper, is therapeutic cloning becoming a moot point? Look up the latest news on iPS cells in various online science news sources.

 
**take home review #3 on material up through cloning and iPS cells:
available W 11/13 by noon, and due M 11/18 at class time.

W 11/13

Gene regulation in prokaryotes

17: 491-503, skim 503-509 to determine main differences among the lac, trp, and ara operons.
18: 518-529
17: 1-12, 14, 15
18: 1, 2, 4

F 11/16

Gene regulation in eukaryotes: transcriptional control

18: 529-534

Read "Hidden Switches in the Mind" from Scientific American, December 2011. Search on the article title and download the PDF from this index site.

Watch all the features at NOVA Science NOW's "Epigenetics"

18: 9-12

M 11/18

Gene regulation in eukaryotes: post-transcriptional control
Sex determination as an example of gene regulation

18: 534-541
Read "The Alternative Genome" by Gil Ast from Scientific American, April 2005. Search on the article title and download the PDF from this index site.
View this RNAi animation
19
: 557-564

18: 14-17, 20
19: 17, 19-21

W 11/20

Quantitative genetics and the genetics of behavior

13: Reread 375-376 ("Nature vs Nurture")
22: 650-661
22: 1, 2, 4-9, 11

F 11/22

More quantitative genetics
22: 661-674
Read What Makes People Gay? by Neil Swidey (Boston Globe, August 2005).
22: 16, 18, 19, 20, 21-27

M 11/25

Population genetics 1

21: 603-614 21: 1-12, 13-18, 37

W 11/27

THANKSGIVING BREAK    

F 11/29

THANKSGIVING BREAK    

M 12/02  

Population genetics 2
21: Skim 614-621; read 621-641 21: 22, 23, 26, 27, 38-42

W 12/04

At normal class time today:
Population genetics 3
Molecular evolution

Link to Excel spreadsheet on selection is here

Today and tomorrow in lab: lecture and ethics discussion on "Genetics up to the present: filling in the timeline, including the history of the eugenics movement" (no powerpoint posted; instead refer to the Timeline of Genetics History)

21: 641-642
23: 683-702 (read for the main ideas only)
Read "The Real Life of Pseudogenes" from Scientific American, August 2006. Search on the article title and download the PDF from this index site.

For our history and ethics discussion in lab this week: Read Engineering American Society: the Lesson of Eugenics (PDF file) by David Micklos and Elof Carlson. This article summarizes much of what is found at Eugenics Archive. Browse the links ( "Social Origins" through "Immigration Restriction") at the Archive to see supplementary photographs and additional information. You will need the Flash Player plugin to look at the archive.

21: 28
23:
7, 8, 9, 17

F 12/06

Genetics in today’s literature, art, and pop culture
(no powerpoint)
Browse Center for Genetics and Society's film section.  
** lab posters are due at 10:00 AM on Fri 12/06. Please email me the properly-named file.  

M 12/09

The promises and dilemmas of genetics in the future

9: 232-233

Read FAQs about Pharmacogenomics from the Human Genome Project

Read Marathon mouse keeps on running from the HHMI and "Gene Doping" from Scientific American, July 2004 (search on the article title and download the PDF from this index site).

 

W 12/11

Question and answer session in preparation for final. (Note that Dr. H will be off campus at a conference the evening of 12/13 through 12/18.)    

F 12/13- Th 12/19

Take home final exam, due at 3:00 PM on Thursday December 19th.

 

Paper instructions return to top

Choose from among the following three formats.

1. Summarize and synthesize recent original research on a genetics topic of your choice, using papers from academic journals. Pick this option if you're interested in learning about a particular genetic disease or the genetic basis of any phenomenon, in humans or another organism. This assignment is essentially to write a "review" paper. Use PubMed to find at least three recent (i.e. 2011 or later) original research papers on your topic. Use interlibrary loan to obtain journal articles for which the library does not already provide online or print access. Be sure to distinguish between research papers and review papers as sources. "Review" papers (like the one you will be writing) are often included in journals but do not contain original results; they just summarize other people's work. You can read older review papers to give you background information, but the bulk of your paper should be focused on explaining original research papers. Your paper should be 1200-1800 words, not including references. Your explanations should reflect your own internalization and intellectual synthesis of the concepts, making it clear that you have a full understanding of the information. A simple paraphrasing of each paper would not be acceptable. Follow guidelines in Pechenik ("Writing essays and term papers"), and use the citation style described therein.

2. Write a critical analysis of depictions of genetics in a fiction book. Choose a novel you have not read before that was originally published in 1993 or later (must be approved by me in advance) and whose plot centers heavily on genetics topics. Read the book, taking notes as you go, and write a critical review (1200-1800 words) exploring the accuracy of the depiction of genetics, the use of genetics ideas as literary devices (and the meaning thereof), and the potential effects on how the general public perceives genetic issues. Among the background sources you read should be peer-reviewed articles from scientific journals--you are expected to incorporate such information into your analysis. You must have read every source you cite. Discuss reasons (valid or not) for the author's diverging from scientific accuracy. You should follow MLA citation style, using direct quotations from the work of fiction in the text of your paper, along with page number references.

3. Write a critical analysis of an ethical issue related to genetics, as illustrated in a recent news item. Pick a news story from 2011 or later from the New York Times, BBC, or other reputable news source whose articles typically go into some depth. Critically analyze the specific issue in detail and how it fits within a broader context. Among the background sources you read should be peer-reviewed articles from scientific journals--you are expected to incorporate such information into your analysis. You may not use Wikipedia or other online or print encyclopedias as cited sources, though you may refer to them initially to point you to primary sources. You must have read every source you cite. For web sources and non-peer reviewed sources, consider carefully their reliability.You are expected to state your position on the issue and support it appropriately with the information you have found. Your paper should be 1200-1800 words not including references. Follow guidelines in Pechenik ("Writing essays and review papers"), and use the citation style described therein.

A project proposal and annotated bibliography is due in late September, and the paper itself will be due in late October (see course schedule above). For the proposal, write at least 250 words explaining your chosen format, your general topic, your thesis (where applicable), and your overall approach. Then list your sources, and include a few sentences for each to explain specifically how that source will contribute to your project. You must demonstrate that you have spent significant time reading your sources. Your grade will be based on the specificity and novelty of your proposed project, the breadth and quality of the sources you have found, and the depth with which you have read and understood your sources.

Citing sources: Proper citations of sources is your responsibility! Paraphrasing (taking another person's sentences and changing a few words here and there) can be considered plagiarism under some circumstances, even when the source is cited. Study carefully the appropriate sections of Pechenik as well as the following web page for detailed information on paraphrasing and citing sources: Davidson Department of Biology statement on plagiarism.

Naming files for electronic submission: When submitting assignments by email, please title the file with your last name and the nature of the assignment (e.g. Halesproposal.doc). This instruction refers to the file itself that you are attaching to the email, NOT to the subject line of the email. Following this instruction is worth two points of your grade.

Grading: Your initial proposal counts as 20 points, or 2% of your course grade. The proposal grade is based on the cohesiveness and appropriateness of your topic, the quality of your sources, and your familiarity with those sources. Your paper counts as 100 points, or 10%, of your course grade. For the paper, the grading rubric is as follows: originality, 15 pts; scientific accuracy and completeness, 35 pts; scope/depth within topic, 20 pts; organization of ideas, 15 points; quality of writing, 13 points; proper naming of emailed file, 2 pts.

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last modified January 7, 2014 by K. Hales