| Biology
111 Molecules, Genes, and Cells Spring 2012, Davidson College |
MWF 10:30-12:20 in Chambers 1003 Lab Wed 1:30 or Thurs 1:40 in Watson 147 |
Dr.
Karen Hales Dana 201A, x2324 |
Science news web sites: |
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Course objectives: Cellular and molecular biology is a vast discipline that encompasses a number of sub-fields, each of which is growing extremely rapidly. In this course, instead of trying to learn every detail, you will develop an understanding of the unifying principles of life at the molecular and cellular level through exploration of illustrative examples. You will become familiar with how scientists think in the laboratory, and you will learn to design, execute, and analyze experiments. Finally, you will practice communicating biological ideas with clarity and precision in your written and oral laboratory reports.
Textbooks:
Life: the Science of Biology, 9th edition,
by Sadava, Heller, Orians, Purves, and Hillis.
Study Guide and Lab Manual by Campbell, Lom, Hales, Bernd, Sarafova, and Wessner, Spring 2011 version (in the bookstore).
A Short Guide to Writing About Biology, 7th edition, by Jan Pechenik.
Web reading mentioned in the study guide can be found at http://www.bio.davidson.edu/bio111.
Additional handouts and WWW reading to be announced.
Office hours: Please always feel free to email me 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 stop by whenever my office door is open. My door is open most of the time when I am not in class, though I do step out for meetings and errands. I will guarantee my presence in the office Thursdays 1:00-1:30 PM and Fridays 11:30-12:10 PM.
Email: I will regularly send important announcements via email. You are responsible for any information/assignments/instructions I send by email, so check your messages each day.
Grading: Your final grade for the course will be calculated as follows:
Three reviews |
One short test |
Lab reports, both written
and oral (details) |
Final exam |
Participation and daily preparation, both lecture and lab |
36% (12% each) |
8% |
25% |
20% |
11% |
% |
94-100 |
90-93.9 |
87-89.9 |
83-86.9 |
80-82.9 |
77-79.9 |
73-76.9 |
70-72.9 |
66-69.9 |
60-65.9 |
0-59.9 |
Final grade |
A |
A- |
B+ |
B |
B- |
C+ |
C |
C- |
D+ |
D |
F |
Participation: Your participation/daily preparation grade depends upon the extent to which you participate in classroom and laboratory dialogue over the course of the semester as well as upon your responses to written and verbal quizzing at the beginning of class and lab.
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.
Laptops and recording devices: You may not use a laptop or recording device in class. If you would like to request an exception, you must come see me with sufficient justification.
Lectures: PowerPoint files to accompany each lecture will be posted online by the evening before each class. I use PowerPoint only to provide illustrations and 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.
Daily homework: Reading assignments to complete before each lecture are indicated below. The page numbers refer to the Study Guide. Within the Study Guide reading, you will be directed to read particular sections of your textbook. Some textbook reading is designated as "overview reading," meaning you should read for the general ideas only. When the textbook reading is designated as "focused," you should read carefully for detail. Come to class prepared to answer questions on any aspect of the material from the previous lecture. There will be regular quizzes at the beginning of class on the previous day's material; quiz grades make up a portion of the "participation and daily preparation" portion of your grade.
Reviews: Some reviews will be entirely take-home, closed book, and closed notes, while some reviews will also have in-class portions. The take-home portion will be posted on the web from links on this syllabus. You may access a take-home review only when you are ready to start it. You may 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 and a half to two hours, but you will have twelve waking hours from when you start until when you must finish. The final exam will be offered through the Exam Center in Chambers, and it will be designed to take two to three hours. I strongly recommend using old reviews as a primary way to study. Old reviews are here: Rev#1, Short Test, Rev#2, Rev#3, Final exam.
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.
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 new Center for Teaching and Learning, in the library. Drop-in hours are Sunday through Thursday, 8:00 PM-11:00, and Sunday/Tuesday/Thursday 4-6 PM, starting January 29th. Appointments are available at other times. For more information, visit www3.davidson.edu/cms/x39569.xml, or contact Dr. Mark Barsoum (mabarsoum or 704 894 2796).
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 of the 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. Paraphrasing (taking another person's sentences and changing a few words here and there) is NOT equivalent to writing something in your own words, and it is considered plagiarism unless proper citation is made. Please see the Davidson Department of Biology statement on plagiarism for comprehensive information.
Lecture schedule |
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Date |
Lecture
topic Click lecture 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. |
Reading Page numbers refer to the Study Guide (SG) unless otherwise noted. SG assignments normally end with the study questions on the appropriate page. Reading assignments accompany the indicated day's lecture. Quizzing on that material may occur on the subsequent lecture day. Additional reading TBA. |
Notes |
| W
1/18 return to top |
Read the whole syllabus. You are responsible for knowing all the information/requirements detailed therein. |
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| Special assignment to be fulfilled by Thursday January 26th at noon: everyone must come see me in my office for a least a few minutes. If you want, you may come by in pairs or groups of three, but no more than that. It's best to make an appointment ahead of time, but you are welcome to drop by any time I am in the office. This visit will be worth 3 points on the first review. A visit must take place for me to record your grade on the first review. The purpose is to familiarize you with the location of my office and to help me get to know you. | |||
| F 1/20 | Unit
1 introduction: Your body's cellular and molecular response to fear. What role does the liver play? |
1-5 (Note that all Study Guide readings will refer you to more extensive readings in the textbook) |
Beginning of Unit 1: Cellular communication |
| M 1/23 | How does your liver "know" when you're scared? | 5-7 |
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| W 1/25 | Connecting epinephrine to glucose release in the liver: enzyme cascades and second messengers |
7-12 |
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| F 1/27 | 12-18 |
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| M 1/30 | How
does your heart muscle contract? |
18-20 |
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| W 2/1 | How does your brain
tell your legs to run away? |
20-29 |
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| F 2/3 |
Another
example of cellular communication-- how does an egg know when it's been
fertilized? |
29-35 |
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| M 2/6 return to top |
Interactive catch-up day and question/answer session with teaching assistant Sarah P. |
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| W 2/8 | Cellular communication in bacteria |
Watch the first ~18 minutes of Part 1 of this lecture by Bonnie Bassler and write a paragraph summarizing what you learned. Don't worry if you don't understand all the terminology--just do your best. Note that you can also get this video free through iTunes. |
End of Unit 1. |
| F 2/10 | Review #1 in-class portion today; take home portion due Monday. |
Take-home portion of review #1 available today. | |
| M 2/13 | Unit
2 introduction: genetics Mitosis and meiosis |
39-41 |
Take-home portion of review #1 due at class time.Beginning of Unit 2: Genetics |
| W 2/15 | Mendel
and his monohybrid crosses |
41-45 |
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| F 2/17 | Analyzing
patterns of inheritance |
41-45 again; also 87-88 |
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| M 2/20 | Dominance
and recessiveness at the molecular level |
45-48 |
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| W 2/22 | More on DNA replication |
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| F 2/24 | Genes and chromosomes The genetic code; mutations and diseases The steps of gene expression: transcription |
48-54 (through study questions in second column) |
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| M 2/27 | The steps of gene expression: RNA processing, translation and beyond |
54-59 also see one translation animation and another translation animation here |
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| W 2/29 | Catch up day; question and answer session | Take-home short test available today. | |
| F 3/2 |
Finding
the sickle cell anemia gene, then cystic fibrosis gene mapping: dihybrid crosses |
55-58 again; also 59-62 |
Take-home short test due at class time. |
| M 3/5 | SPRING BREAK | ||
| W 3/7 return to top |
SPRING BREAK | ||
| F 3/9 | SPRING BREAK | ||
| M 3/12 | More on gene mapping: independent assortment and linkage, RFLPs and VNTRs |
62-66 |
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| W 3/14 | Side
topic: DNA fingerprinting |
66-68 (stop at "So, how do you locate..") |
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| F 3/16 | Recombination & mapping the CF gene via linkage to RFLPs and VNTRs |
68-72 |
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| M 3/19 | Mapping the CF gene via linkage
to RFLPs and VNTRs, continued |
72-74 |
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| W 3/21 | When
you've mapped a disease to a chromosomal region, how do you find the exact
gene? |
74-76 |
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| F 3/23 | Confirming
you've found the right gene; analyzing the defect at the molecular level |
76-81 | |
| M 3/26 | 81-83; skim 83-86 | End of Unit 2. | |
| W 3/28 | Review #2 in-class portion today; take home portion due Friday. |
Take-home portion of review #2 available today. |
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| F 3/30 | Unit 3 intro: bioenergetics and energy conversions Reactions of photosynthesis: why was paraquat sprayed on Mexican marijuana? |
89-94 |
Take-home portion of review #2 due at class time. Beginning of Unit 3: Bioenergetics. |
| M 4/2 |
Energy conversions in chemical reactions; role of enzymes; more on light reactions of photosynthesis | 94-99 |
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| W 4/4 | More on light reactions of photosynthesis no powerpoint today! |
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| F 4/6 return to top |
Finishing photosynthesis: synthesizing food via the Calvin Benson cycle | 99-103 |
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| M 4/9 | EASTER BREAK |
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| W 4/11 | Releasing energy from food: glycolysis, pyruvate oxidation, and the Krebs cycle; also fermentation | 103-108 |
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| F 4/13 | Releasing energy from food, continued. Why is cyanide a good poison? |
109-112 |
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| M 4/16 | Interactive catch-up day and question/answer session with teaching assistant Sarah P. |
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| W 4/18 | Why update vaccinations after a flood? Anaerobic metabolism: bacteria that cause tetanus and botulism |
112-115 |
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| F 4/20 | Nitrogen metabolism: why is tofu a good source of protein? Unit 3 question and answer session in any remaining time |
115-117 |
End of Unit 3. Take-home review #3 available today. |
| M 4/23 | 118-122 |
Beginning of Unit 4: miscellaneous topics | |
| W 4/25 | Cancer continued |
123-131 |
Take-home review #3 due at class time. |
| F 4/27 | HIV: statistics, viral anatomy, how the virus invades cells |
131-139 |
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| M 4/30 | How is HIV infection detected and treated? Could vaccines work? |
139-151 |
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| W 5/2 | Cloning and genetic engineering | 151-156 |
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| F 5/4 | More on cloning and genetic engineering (no new ppt) | ||
| M 5/7 | Even more on cloning and genetic engineering; wrap-up; course evaluations | ||
| W 5/9 | Optional question and answer session. Ames test lab reports due today by 2 PM. Please email the file. Put your last name at the beginning of the file title (NOT the subject line of the email, but the title of the file you attach). | ||
| 5/11- 5/16 | Self-scheduled final exam | ||
Laboratory schedule |
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Date |
Topic |
Reading Page numbers refer to the Lab Manual unless otherwise noted. In the Lab Manual, you will also be referred to particular textbook pages. |
| Jan 25-26 | Preliminaries: Introduction to lab. Lab safety. How to measure very small volumes with a pipetman. Main activity: Introduction to spectrophotometry |
1-16 |
| Feb 1-2 | IDH enzyme activity | 17-35 |
| Feb 8-9 | Parameters that affect IDH activity: independent experiments | 36-44 Also, in Pechenik, read "Introduction and General Rules" |
| Feb 15-16 | Introduction to data presentation For reference: sample lab report 1, sample lab report 2 (PDF files). |
45-49, also Appendices C and D Read the Pechenik chapter entitled "Preparing Oral Presentations" Read the Pechenik chapter entitled "Writing Laboratory and other Research Reports" |
| Feb 22-23 | Group oral presentations on
IDH lab results. |
50-52 through "D1S80 factoids" |
| Feb 29-Mar 1 | PCR results; Using microscopes; introduction to Chlamydomonas |
52-61 |
| Mar 7-8 | NO LAB: SPRING BREAK | |
| Mar 14-15 | Chlamydomonas flagellar regeneration | 62-72 |
| Mar 21-22 | Varying parameters affecting Chlamydomonas flagellar regeneration: independent experiments | 73-75 |
| Mar 28-29 | A beginner's guide to statistics and graphing | 76-81 Skim the Pechenik chapter entitled "Reading and Writing about Statistical Analyses," focusing on the information related to the lab manual material. Read the Pechenik chapter on preparing Lab Poster presentations. Poster template file is here. |
| Apr 4-5 | Group oral presentations on Chlamydomonas lab results. (Written lab report on the Chlamydomonas experiments due at lab time.) **Special note: Bring potential mutagens to lab today!! |
82 |
| Apr 11-12 | NO LAB |
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| Apr 18-19 | Introduction to the Ames test (remember to return Fri-Sun to move plates to the refrigerator). | 83-91 |
| Apr 25-26 | Quantitating a mutagen: Ames test independent experiments (remember to return Fri-Sun to move plates to the refrigerator). | 92-96 |
| May 2-3 | NO OFFICIAL LAB. However, you have access to the room to count colonies (if you haven't done so already) and to work on your individual lab reports/posters. There are no oral lab reports expected this time. I will be present for the first half hour to answer any questions. Ames test lab reports due by Wednesday May 9th at 2 PM. Please email the file. Put your last name at the beginning of the file title (NOT the subject line of the email, but the title of the file you attach). |
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More information on laboratory write-ups and presentations
Written lab reports:
You will be writing group reports for the first two lab report assignments. For a given report, a different person within your lab group should be in charge of each of the major sections (introduction, materials and methods, results, discussion). Once a first draft of each section has been written, a separate person in the group should be in charge of editing that section, using input from all members of the group. Editing involves more than fixing typos; rework the order of ideas, the language, and the logic to achieve maximal precision, completeness, and clarity. Work collectively to construct the title, abstract, and references.
You must be in charge of a different section each time and must edit a different section each time. At the end of each report, make a chart indicating who was the primary author and who was the primary editor of each section.
See the appropriate appendix in your Study Guide & Lab Manual, as well as the appropriate Pechenik chapter, for instructions on the organization and content of your lab reports. Pay special notice to this additional requirement regarding the reference section: you should cite the lab manual, AND you must find at least two additional relevant print sources and one additional online source for each report. Proper formatting of citations is described at the Biology Department statement on plagiarism.
In addition to the grading criteria listed below, correct spelling, grammar, and syntax are essential. It is in your best interest to focus my attention on the meat of your report instead of on messy mechanics.
Signing the pledge on your lab report signifies (among other things) that everyone in the group has contributed his or her fair share of the work.
Lab posters: For the second lab report, you will also adapt your data into a lab poster presentation.
Third lab report: At the end of the semester you will prepare an individual write-up on the Ames test experiments. You may choose either a written report or a lab poster format. .
Oral presentations:
Each
group will have 15 minutes for their oral presentation, with a few additional
minutes for questions afterwards. You will have access to all the audiovisual
equipment in the lab, including the computer and document camera. Each presentation
should be divided into four sections: Introduction, Materials and Methods, Results, and Discussion. Each member of your
lab group must speak, with everyone contributing roughly equally. See the appropriate appendix in your Study Guide & Lab Manual
for what kinds of information to put into each section.Your classmates will critique your presentations,
but their comments will not determine your grade.
Grading:
I will evaluate your written and oral reports
based on the following criteria:
1. Clarity and organization of presentation
2. Whether you show an understanding of your experiments and results
3. Completeness, especially in your discussion section
4. Conciseness
Grading rubric for final lab report or poster (note that on the poster some sections can be combined, but the content will be graded as if these elements were separate components):
Title/authors/affiliation 4 pts
Abstract 5 pts
Introduction 12 pts
Methods 10 pts
Results 12 pts
Discussion/conclusions/future directions 12 pts
References and acknowledgments 5 pts
Quality/organization of writing (lab report) or formatting/aesthetics/balance of text and graphics (poster) 10 pts
The lab grades are apportioned as follows:
IDH lab report |
Chlamydomonas lab report |
Ames test lab report |
Total lab grade |
|
oral component |
4% |
4% |
(none) |
25% of course grade |
written component |
4% |
3% written report, 3% lab poster (group) |
7% written report OR lab poster (done individually, choose either option) |