BIOL 116 Information in Living
Systems
|
UNDER CONSTRUCTION! Last
modified 11/30/2009 MWF 10:10- 11:00 a.m.
(Period 3)
M, W, F 7:45- 8:00, 9- 10:00;
11:00-11:45 a.m.
Course outline
How to do well in this class:
How
to contact the instructor: Office hours, the weekly review session, and e-mail
are the best ways to make contact with me. Also, you may call me at home before
9:00 p.m.
Grading scale 90-100 A range, 79-89 B range, 67-78 C range, 56-66 D range, 55 or below F. NOTE ON EXAMS AND QUIZZES: Exams or quizzes missed due to unexcused absences (e.g. my alarm didn't go off) will count as a zero. Exams missed due to an excused absence can be made up. It is the responsibility of the student to make arrangements to do so with the instructor. When an exam conflicts with a scheduled excusable event, the student must contact the instructor one week before the exam is scheduled to arrange for an alternate time. Ordinarily, this will be before the rest of the class takes the exam. Therefore, athletes should check the syllabus and their athletic contest schedules closely and make note of any conflicts. There will be no make up quizzes. If you miss a quiz due to an excused absence, it will not count as a zero and the two lowest grades of the remaining quizzes will be dropped.
Academic Honesty. Do not lie, cheat, or plagiarize. This class will follow the official Kenyon College position on academic honesty. It is your responsibility to review and observe the official College policy on academic honesty. Special Needs. College policy provides for reasonable accomodations for documented physical, psychological or learning disabilities that may impact your ability to participate fully in the course. Please speak with me and with Erin Salva, Coordinator of Disability Services (PBX 5453; salvae@kenyon.edu). All information and documentation of disability is confidential. Please see the Disability Services web site for more information. Logistical details of any approved accomodation (e.g. extended exam time) must be arranged with the instructor in advance. |
If particular pages or a section number follow a chapter you are responsible for
just those pages or sections.
DATE | TOPIC & WEBNOTES links | READING second edition-- Color coded | Reading third edition |
Aug. 31 M
|
The Central Dogma Ch. 15 (section 15.3, pp. 334-336) |
The Central Dogma Ch. 15 (pp. 320-322). | |
Sep. 2 W |
DNA
structure(optional), Chromosomes |
Ch. 4 (4.1, 4.2); pg. 130; essay pg. 87 |
Ch. 4 (4.1, 4.2); pg. 120-121; Box 4.1 pg. 75 pg 124 (the nucleus) |
Sep.4 |
histone code: Gel electrophoresis
|
Ch. 18 (18.2), Box 4.1 pg. 78, box 19.2 pg. 412 | Ch. 18 (18.2), Bioskills 7 pg B12-B13, box 19.1 pg. 398 |
Sep. 7 M |
DNA as the genetic material;
centrifugation Quiz 1 |
Ch. 14 (303-310), Box 7.1 pg. 140, Box 19.1 pg. 404 |
Ch. 14 (295-302), Box 7.1 pg. 133, Box 12.2 pg. 256 |
Sep.
9 W |
DNA
replication, telomeres Paper discussion |
Ch. 14 pp. 310-318 tissue
engineering paper |
Ch. 14 (sections 3 and 4) tissue
engineering paper Guided reading for paper on Moodle |
Sep.11 F |
Mitosis |
Ch. 11 (start through 11.2) Also readings on Moodle with guided reading. |
Ch. 11 (start through 11.2) Also readings on Moodle with guided reading. |
Sep.
14 M
|
Ch. 12 (all except section 12.3), Fig 25.9 pg. 547 |
Ch. 12 (all except section 12.3), Fig 26.8 pg. 535 | |
Sep. 16 W | Mendelian inheritance
|
Ch. 13 pp. 269-281; Optional Dihybrid Cross (#'s 1-10) | Ch. 13 pp. 265-276; Bioskills 9 Optional Dihybrid Cross (#'s 1-10) |
Sep. 18 F | Sex
linked traits, recombination Quiz 3 take home due Monday |
Ch. 13 pp 281-286; Linkage More Practice | Ch. 13 pp 276-281; Linkage More Practice |
Sep. 21 M | Gene mapping, pedigrees | Ch. 13 (sec. 13.6), Ch. 19 (sec. 19.3) | Ch. 13 (sec. 13.6), Ch. 19 (sec. 19.4) |
Sep. 23 W | Exam
1
|
Bring Klinger paper, 8.5 x 11 cheat sheet and calculator. | Bring Klinger paper, 8.5 x 11 cheat sheet and calculator. |
Sep.
25 F
|
Ch. 13 (sec. 13.5) Download Flowers(optional)
|
Ch. 13 (sec. 13.5) Download Flowers(optional) | |
Sep. 28 M |
How Genes Work
E. coli as model organism (optional) Nobel Prize for cracking genetic code (optional) |
Chapter 15, Box 27.1 pg 588
Beadle and Tatum animation- click on test tubes (optional) |
Chapter 15, Box 28.1 pg 576 Beadle and Tatum animation- click on test tubes (optional) |
Sep.
30 W
|
Ch. 4 (sec. 4.3); Ch 16 pp. 338-341
|
Ch. 4 (sec. 4.3); Ch 16 (through section 16.1) | |
Oct. 2 F |
Eukaryotic
transcription and splicing |
Ch. 16 (section 16.2); pg. 438-439 (gene # and alternate splicing) Nobel Prize for split genes (optional) |
Ch. 16 (section 16.2); pg. 426-427 (Why do humans have so few
genes?) Nobel Prize for split genes (optional) |
Oct. 5 | Translation Quiz 4 due |
Ch. 16 (sections 16.3, .4, .5) Essay on antibiotics pg.358-9 | Ch. 16 (sections 16.3, .4, .5) |
Oct. 7
|
DNA mutation
and repair
|
Ch. 14 (sec. 14.5, 14.6); Ch. 16 (sec. 16.6); essay pg. 535
|
Ch. 14 (sec. 14.5); Ch. 16 (sec. 16.6) If needed review Ch. 3 sec. 3.4 on protein structure. |
Oct. 9 |
DNA sequencing |
Ch. 19 (intro, sec. 19.1, .2, .3) Plasmid (downloaded with Flowers) Techniques page if you're interested (for PCR animation click on techniques, amplifying, PCR). |
Ch. 19 (intro, sec. 19.1, .2, .3) Plasmid (downloaded with Flowers) Techniques page if you're interested (for PCR animation click on techniques, amplifying, PCR). |
Oct. 12
|
No class- reading
day
|
|
. |
Oct. 14 W |
Approaches II: DNA
sequencing PCR |
Ch. 20 (Pg. 427, recent
technological advances, fig. 20.1) |
Summary Table, pg. 406-407. |
Oct. 16 |
Darwin and evidence for evolution | Chapter 1, sec. 1.2 Chapter 23, pg. 494-503 |
Chapter 1, sec. 1.2 Ch. 24 pg. 481-489 |
Oct.
19 M
|
natural selection | Chapter 23, pg. 503-end | Ch. 24 pg. 490-end |
Oct.
21
W |
EXAM
2 Bring code with notes on back. |
Bring code with notes on back. Also calculator and 8.5 x 11 with notes. | Bring code with notes on back. Also calculator and 8.5 x 11 with notes. |
Oct.
23 F
|
natural selection | Chapter 23, pg. 503-end | Ch. 24 pg. 490-end |
Oct.
26 M |
Evolutionary Processes | Ch. 24(sections 24.1 and 24.3) Bring a calculator to class. |
Ch. 25 (sections 25.1 and 25.3) Bring a calculator to class. |
Oct.
28 W |
Evolutionary Processes
Quiz 6 in class |
Ch. 24(sections 24.2 to end) Quiz 6 in class |
Ch. 25 (sections 25.2, 25.4, 25.5) Quiz 6 in class |
Oct.
30 F |
Evolutionary Processes | Ch. 24(sections 24.3 to end) | Ch. 25 (sections 25.5, 25.6) |
Nov.
2
M |
Speciation | Ch. 25 | Chapter 1 (sec. 1.3) Ch. 26 (start through 26.2) |
Nov.
4 W |
Speciation Quiz 7 handed out |
Ch. 25 | Ch. 26 (26.3 through end) |
Nov.
6 F |
Ch. 17 (Intro, sections .1, .2 and .3) |
Ch. 17 (Intro, sections .1, .2 and .3) | |
Nov.
9
M |
Ch. 17 (section 17.4) operon
practice
|
Ch. 17 (section 17.4) operon practice | |
Nov. 11 |
DNA binding proteins |
Ch. 17 (section 17.5) footprinting animation |
Ch. 17 (section 17.5) footprinting animation |
Nov. 13 | EXAM 3 | ||
Nov. 16 |
Ch. 18 (pp. 382-383, 18.3, 18.4) |
Ch. 18 (pp.
370-371, 18.3, 18.4) |
|
Nov.
18
|
Ch. 18 (18.5)
|
Ch. 18 (18.5)
|
|
Nov. 20 | Approaches: Measuring Gene Expression: Northern blots, RT-PCR, cDNA microarrays; Western blots |
Box
19.2 pp. 412-413; Ch. 20 pp. 440 DNA microarrays DNA Chip (optional) Quiz 8 in class |
Box
19.1 pp. 398-399; Ch. 20 (section 20.4) DNA Chip (optional) Quiz 8 in class |
Nov 23-27 | Thanksgiving break | ||
Nov. 30 | Approaches continued Measuring Gene Expression: Northern blots, RT-PCR, cDNA microarrays; Western blots |
Box
19.2 pp. 412-413; Ch. 20 pp. 440 DNA microarrays DNA Chip (optional) |
Box
19.1 pp. 398-399; Ch. 20 (section 20.4) NOTE THAT WE ARE AHEAD OF SCHEDULE AND WILL START MATERIAL A DAY EARLIER THAN POSTED. |
Nov. 30/ Dec. 2 |
Special topic: RNAi animation and RNAi Nobel |
RNAi and riboswitches: Gibbs (2003) Scientific American article (local access only) p-body articles on moodle site |
RNAi and riboswitches: Gibbs (2003) Scientific
American article (local access only) pp. 381-382 p-body articles on moodle site |
Dec. 2 and 4 |
gene
therapy changing the information |
Chap 19 (sec. 19.4) zinc
finger nuclease article on moodle knock out mice (optional) |
Chap 19 (sec. 19.5) zinc
finger nuclease article on moodle knock out mice (optional) |
Dec. 7 | Phylogenies | Chapter
1, sec. 1.3 Chapter 26 |
Chapter
1, sec. 1.3 Bioskills 2, Chapter 27 |
Dec. 9 | Phylogenies/evo-devo |
Chapter 26 | Chapter
27 class evaluations |
Dec. 11 | evo-devo | readings
on Moodle Ch. 22 (sec. 22.1); pg. 714 |
readings
on Moodle |
Dec. 14 | factors influencing phenotype | Quiz 10 due | Quiz
10 due readings on Moodle |
|
Exam 4 | December 18th 1:30 p.m. | December 18th 1:30 p.m. |