Biol 204 page

Biol 204: Genetics and Cellular Biology (3 credits)

Spring 2009
2:00 pm - 2:50 pm, Monday, Wednesday and Friday
Rm 104, State Museum of Art (lecture hall in the basement)
South Dakota State University, Brookings, SD

This is the second semester in a two semester series designed to introduce fundamental concepts in genetics, cellular and molecular biology. The homepage for the first semester course, Biol 202, is still available.

"Most of us spend our lives
as if we had another one in the bank."

Ben Irwin

PCR products from Biol204L
TPA with AluI = 400bp; without AluI = 100 bp

Instructor: Donald Auger (Pronounced ozh'-ay)

Office: NPB 251B (map) (office hours)
Phone: 688-6385 (please use e-mail rather than voice-mail)
E-mail: donald . auger @ sdstate . edu (no spaces)
Please do NOT use D2L to communicate with me (I don't check it often enough).

Text resources:
Cell and Molecular Biology, 4th ed., G. Karp
Essential Genetics, 4th ed., D. Hartl and E. Jones

Additional web based resources relating to the texts.
Hartl & Jones: http://www.jbpub.com/genetics/essentials4e/
Karp: http://www.wiley.com/college/karp

Course Goals: Our goal is to cover the basic issues of genetics, cell and molecular biology. Because this course is considered introductory survey, I will limit the scope to what is contained in the two textbooks. In order to allow the students to focus their studying, I will post vocabulary words for each chapter and the student will be responsible to be able to define the term and understand the concepts in the text associated with that word.
    A secondary goal is to promote careful reading skill. To that end, quizzes will contain questions that cite a specific passage in one of the textbooks. These questions will require that the student read the passage carefully since the required answer is not simply a correct answer but the one that is specified in the passage.

Grading: There will be four exams during the semester (Feb. 1, Feb. 29, Apr. 4 and Apr. 25) and one during final exams week (May 7). The first exam covers only two chapters is 50 points; the next three will be worth 100 points; the final is 300 points. In addition there will be on-line quizzes, posted on the web most Fridays. Answers will be due prior to the first class the following week. The quizzes will contribute up to 150 points (18.75% of the total grade) based upon the total percent of correct answers.
    Exams must be taken at the appointed time, except for SDSU excused absences or unexpected emergencies, which must also be excused. In those cases make-up exams will be scheduled after the regular exam date. No exams will be given in advance. The format of the make-up exam may be different from the rest of the class, e.g., I could choose to use essay questions. Contesting grades of quizzes, exams and labs are to be initiated within one week of answers being posted. They can be initiated either in person or by e-mail.

A = 720 points (90%) or upper 20% of class
B = 640 points (80%) or upper 30% of class
C = 480 points (60%) or upper 50% of class
D = 400 points (50%) or upper 60% of class
F < 400 points and lower 40% of class

I am rather rigid on following the grading structure. For example: 89% is a B. Also, there is no extra credit; grades are based upon quizzes and exams only.
    Except for examinations, class attendance is not required, but students are responsible for class material. Students are entitled to reasonable accommodations under the provisions of the Americans with Disabilities Act. Those in need of such accommodation should notify the instructor and make appropriate arrangements with the SDSU Office of Disability Services, 110 West Hall, 688-4505 or 688-4032. Refer to your student handbook for policies on academic integrity. Cheating on exams can result in failure of the exam.
    The BOR policy manual states: Freedom in learning. Students are responsible for learning the content of any course of study in which they are enrolled. Under Board of Regents and University policy, student academic performance shall be evaluated solely on an academic basis and students should be free to take reasoned exception to the data or views offered in any course of study. Students who believe that an academic evaluation is unrelated to academic standards but is related instead to judgment of their personal opinion or conduct should first contact the instructor of the course. If the student remains unsatisfied, the student may contact the department head and/or dean of the college which offers the class to initiate a review of the evaluation.

Syllabus:

Date	Topic	Readings
Jan. 16	DNA (quiz 1)	H&J ch. 6
Jan. 19	Holiday
Jan. 21	DNA (YouTube: Replication; PCR)	DNA rep. model
Jan. 23	Prokaryote genetics (quiz 2)	H&J ch. 7
Jan. 26	Prokaryote genetics (YouTube phage)
Jan. 28	Review session (old questions)	Vocabulary
Jan. 30	EXAM 1 (keys a, b, c)	(H&J 6 & 7)
Feb. 2	Gene expression (YouTube: 1, 2, 3 )	H&J ch. 8
Feb. 4	Gene expression (YouTube: 4, 5, 6 )
Feb. 6	Gene regulation (quiz 3) (missing slides)	H&J ch. 9
Feb. 9	Gene regulation (epigenetics )	YouTube: lac, trp
Feb. 11	Gene reg. & Genomics & biotech.	H&J ch. 10
Feb. 13	Genomics & biotech. (quiz 4)	YouTube: cloning
Feb. 16	Holiday
Feb. 18	Genomics & biotech. (Microarray)
Feb. 20	Development (quiz 5)	H&J ch. 11
Feb. 23	Development & Mutations	H&J ch. 12
Feb. 25	Review session (old questions)	Vocabulary
Feb. 27	EXAM 2 (keys a, b, c)	(HJ 8 - 11)
Mar. 2	Mutation and DNA repair
Mar. 4	Mut. and Repair; Pop. genetics	H&J ch. 14
Mar. 6	Population genetics (quiz 6)
Mar. 9 - 13	Spring Break
Mar. 16	Population genetics	Buzzard watch
Mar. 18	Complex inheritance	H&J ch. 15
Mar. 20	Comp. inher. & the nucleus (quiz 7)	Karp ch. 12 (nucl. pore)
Mar. 23	Cellular reproduction	Karp ch. 14
Mar. 25	Cellular reproduction (missing slides)
Mar. 27	Cell repro. & Cell signaling (quiz 8)	Karp ch. 15
Mar. 30	Cell signaling
Apr. 1	Review session (old questions)	(vocab.)
Apr. 3	EXAM 3 (keys a, b, c)	HJ12, 14, 15 & Kp12, 14
Apr. 6	Cell signaling (YouTube: GPCR1, 2)	Dog size, apoptosis
Apr. 8	Cancer (YT: Steroid, Ras ) (quiz 9)	H&J Ch. 13
Apr. 10 - 13	Easter Recess
Apr. 15	Cancer	Karp Ch. 16
Apr. 17	The immune response (quiz 10)	Karp Ch. 17
Apr. 20	The immune reponse (YT: immune)
Apr. 22	Review (old questions)	Vocabulary
Apr. 24	EXAM 4 (keys: a, b, c)	H&J 13, K15-17
Apr. 27	Review 1	HJ 6 - 10
Apr. 29	Review 2	HJ 11 - 15 Kp 12
May 1	Review 3	Kp 14-17 HJ 13
May 7	FINAL EXAM	2 pm at Art Museum

Laboratory (Biol 204L) SAG 305 (1 credit)

Section	Time	Instructor
Biol 204L-S01	Wednesday 10:00 am - 12:50 pm	Don Auger / Xin Fang
Biol 204L-S02	Wednesday 3:00 pm - 5:50 pm	Xin Fang
Biol 204L-S03	Wednesday 6:00 pm - 8:50 pm	Xin Fang
Biol 204L-S04	Thursday 8:00 am - 10:50 am	Sibongile Mafu
Biol 204L-S05	Thursday 11:00 am - 1:50 pm	Sibongile Mafu
Biol 204L-S06	Thursday 2:00 pm - 4:50 pm	Sibongile Mafu
Biol 204L-S07	Thursday 6:00 pm - 8:50 pm	Yusheng Wu
Biol 204L-S08	Friday 11:00 am - 1:50 pm	Yusheng Wu

Grading

The grade for the laboratory is separate from the lecture class (1 credit).

25% Preparation (see procedures in Lab 1)
    Have procedures filled out before lab starts (10%)
    Procedures correctly laid out and easy to follow (15%)
25% Attendance/participation
25% Quality of lab report (established in Lab 1)
    Each week of lab you will receive a grade of up to 75 points on your lab report that reflects the above criteria.
25% Lab performance quizzes.

Attendance is required. An unexcused absence will result in loss of credit for that week's laboratory. An excused absence will allow for a report to be filled out from lab mate's data, but will still result in loss of credit for attendance (i. e., 25% for that lab). Full preparation credit can still be achieved by submitting a sheet showing correctly laid out procedures prior to the lab being missed (either by giving to Dr. Auger or sending it along with a lab mate).

Attendance is not enough; you must participate to the degree possible. The main purpose of these laboratories is to give you hands-on experience. Mistakes will be tolerated (within reason). This portion of the grade is subjectively decided by the laboratory instructor.

The format and expectations for the lab reports is given in the first lesson and also will be covered in class.

Grades will be assigned as follows;
    90% or above = A
    80% or above = B
    70% or above = C
    60% or above = D
    Below 60% = Bad


Syllabus/lab protocols

Date	Laboratory
Jan. 21 - 23	No lab
Jan 28 - 30	1) Reintroduction to lab & PCR TPA PCR
Feb. 4 - 6	2) PCR (part2)
Feb. 11 - 13	3) RNA I
Feb. 18 - 20	4) RNA II
Feb 25 - 27	5) Bacterial transformation (plasmids)
Mar. 4 - 6	6) Genomics and bioinformatics & quiz
Mar. 11 - 13	Spring break
Mar. 18 - 20	7) Phylogenetic analysis
Mar. 25 - 27	8) Population and selection & Problem session slides
Apr. 1 - 3	9) Complex traits
Apr. 8 - 10	Easter break
Apr. 15 - 17	10) DNA extraction for sequencing
Apr. 22 - 24	11) DNA preparation for sequencing (at Biostress lab)
Apr. 29-May 1	12) DNA sequencing & quiz