BIOLOGY 308 GENETICS Spring, 2007
INSTRUCTORS:Dr. Alix G. Darden
Dr. Darden’s OFFICE:324 Bond Hall
Dr. Darden’s PHONE:953-7873E-MAIL: (I check regularly)
Dr. Darden’sOFFICE HOURS:M 1-2, W 4-5, F10-11, or by appointment
OBJECTIVES: Learn and understand the vocabulary and concepts of molecular and transmission genetics. Be able to apply the vocabulary and concepts of molecular and transmission genetics to problem solving. Be able to find current, reliable information in the area of genetics. Be able to perform basic genetics laboratory exercises, collect and analyze the data, report the data both orally and in writing.
CLASS POLICY
TEXTBOOK: Russell, iGenetics. My lectures are given with the expectation that you have looked over the material to be covered that day before coming to class. You are responsible for all material in the textbook, even if it has not been gone over in class, unless told otherwise. This includes knowing the information in the figures and figure legends. You are also responsible for all lecture material, even if it is not in the textbook. It is highly recommended to bring colored pencils to class. We draw a lot.
LAB MANUAL: The lab exercises are on WebCt. You need to download, print and review the lab exercise before coming to lab. You need to bring a flowchart of the day’s lab and show this to me to be allowed to START the lab. The flow chart will also be attached to the lab report. This will enable you to complete the exercise in the time allowed. The labs are designed to complement and aid in your understanding of the lecture material.
HOMEWORK: HW is assigned during the semester to be handed in and graded. Each homework is worth 10 points and the eight highest grades are counted. Homework is designed to keep students focused on critical genetic issues, keeping up with the material and to catch misunderstandings before major tests. Except for one case, HW is due on Monday’s and will be posted to WebCT by the Friday before, if not sooner.
DISCUSSION BOARD: Students are expected to check and post (a valid scientific post) a minimum of 2X per week and read all the posts weekly. You don’t need to post every time you read. I will start counting after this Friday’s lecture (1-12-07). Both lecture and lab materials are game as well as issues related to HW problems and current events.
ATTENDANCE: The attendance policy is that described in the College Handbook. PLEASE NOTE: Any student missing more than 20% of the class meetings may be given a grade of F at the instructor’s discretion according to college policy. Absence from more than two (2) laboratory periods will result in a grade of F. TESTS: There are NO make-up tests for ANY reason including being in the infirmary. Five tests are given, one is dropped.
GRADING SYSTEM:LECTURE – 75%, LAB – 25% of grade
Material handed in late losses 10% of the grade per day late, including weekends. Assignments more than a week late will receive a grade of zero.
Lecture Case Study 40 points
Lecture tests (4/5) -400 points (drop lowest test grade)
Comprehensive Final -100 points
Discussion Board 80 points
Homework (8 highest are counted)80 points (10 pts each)
Lab - Lab hand-ins/presentations 150 points (6 @ 25 pts)
2 Lab quizzes150 (75 pts each)
Lecture tests will consist of definitions of vocabulary, matching, multiple choice, short answer and problem solving. Vocabulary will be taken from the bolded words in the text and words found in titles. Late lab reports/literature searches are penalized at 10% grade reduction per day late. No reports/literature searches are accepted beyond one week after the due date. Homework will NOT be accepted late.
A = 900-1000 pointsB = 800-899C = 700-799D = 600-699F = Below 600
WebCT: Essential class information can be found on WebCT under Biology 308. 1) All grades will be posted here (“grades”), so check to make sure I don’t make mistakes. I need to see the original paper to change the grade, so save your papers. 2) All labs are on WebCT and will need to be downloaded before coming to lab found under “Lab Manual”. 3) Data generated in lab will be posted on WebCT under “Data”. 4) HW will be posted on WebCT under “Homework”. 5) The class calendar contains all due dates in an easy to read format under “Calendar”. 6)Past tests can be found as well as study guides for each test under “Past Tests” and “Study Guides”. 7) Discussion board.
Making the grade in Genetics
To succeed in genetics, you need to be working on the material all the time. I assume that for every one hour of lecture material, students will put in two hours minimum reviewing, reworking, etc the material. Studying 1-2 nights before the test will not provide you with enough time to adequately learn the material. I would suggest a minimum of five days before the exam. You need to be able to 1) understand the language, i.e. define the words, 2) apply the information through problem solving and 3) understand the concepts.
“A” or “B” student
Excellent or above average work
Understands the information – not just memorized
Utilizes facts and formulas in different applications
Works all problems
Wants to learn the information – not just receive a grade
Natural ability
Finds the material interesting
Actively and regularly participates in Discussion board
How?
Reads chapters in advance
Outlines chapters and coordinates this with class notes
Takes detailed notes in class
Alert, on-time, attentive and prepared
Contacts a classmate when absent for makeup notes
Reviews work before submission
Follows class discussion
Interactive in class
Contacts the instructor when unclear about a problem
Does all homework assignments and uses the sample exams to study
Prepares extra homework…not just those assigned
“C” student or below
Average work
Skims chapters before class
Does problems for credit only
Memorizes but doesn’t understand
Most of studying done the night before an exam
Follows in class occasionally
Takes brief notes – typically doesn’t recopy them
Learns information for the short-term (just for the exam)
When absent, doesn’t follow-up
Turns in work when completed without review or proofreading
Genetics - Biology 308 Spring 2007 Schedule
Week / LectureDates / Chap/Topic / Lab exercise / Assignments due
LR=lab report
1 / 1/10 / 1/ pp 1-12/Intro / None
1/12 / 12/pp13-38/ Mitosis/meiosis
2 / 1/17 / 12 con’t / 1)Intro to electrophoresis – reading gels
2) creating lab flowcharts
3) Cloning 1 - restriction digest, gel electrophoresis / HW#1
1/19 / 2/pp 13-38/DNA structure / Lab flow chart
3 / 1/22 / 2/ / 1) Cloning 2 – gel elution and ligation 2) Cancer case study – bibliographic database use – meet in library / HW#2
1/24 / 3/pp43-62/ DNA synthesis / Lab: 1: flow chart
2)Lab report (LR) 1 (req’d)
1/26 / 3/
4 / 1/29 / 4/67-73, 77-79 / 1) Cloning 3 – bacterial transformation
2) cloning practice problems / HW#3
1/31 / Test 1 – 12, 2, 3 / Lab: flow chart
2/2 / 4/ - The relationship between Genes and proteins
5 / 2/5 / 5/87-108 / 1) Cloning 4 – plasmid mini-prep / HW#4
2/7 / 5/DNA Expression - Transcription / Lab: 1)LR2 – cloning 1 (req)
2) Flow chart
2/9 / 5/
6 / 2/12 / 6/111-128 / 1)Cloning 5 – final gel analysis – cloning lab review / HW#5
2/14 / 6/DNA Expression - Translation / Lab: Flowchart
2/16 / Test 2 – 4 & 5
7 / 2/19 / 7/pp 133-166 / 1) Lab quiz #1 - cloning experiment and electrophoresis
2) Start discussing DNA mutation lab / HW#6
2/21 / 7/ DNA mutations, transposons, etc. / Lab: 1) LR3-cloning final (req)
2) Lab quiz
2/23 / 7/
8 / 2/26 / 8/pp 175-204 / DNA mutation lab – part 1 / HW#7
2/28 / Test 3 – 5,6,7 / Lab: Flow chart
Mid-Term grading
3/2 / 8/DNA technology
9 / 3/5 / 8/ / DNA mutation lab – part 2
Stats review in lab / HW#8
3/7 / 11/pp 271-291 Mendelian
Last day to withdraw with “W” / Lab: 1) Flow chart
2) Statistics review problems
3/9 / 11/
10 / 3/12 / 12/pp 312-330 Sex linked / DNA mutation lab presentations / HW#9
3/14 / 12/ / Lab: LR$ - DNA mutation presentations (req’d)
3/16 / 13/pp 337-354 Mendelian Extensions
11 / 3/19 / 13/ / Bioinformatics – / HW#10
3/21 / Test 4 – 8, 11, 12 / Lab: 1) Flow chart
2) LR5: DNA mutation (opt 2/3)
3/23 / 13
*********Spring Break************
12 / 4/2 / 15/412-420 / Human DNA fingerprinting –part 1 / HW#11
4/4 / 15/430-433 – Mapping Eukaryotic genes / Lab: 1) LR 6 – Bioinformatics (opt, 2/3)
2) Flow chart
4/6 / 18/pp441-454 – Bacterial genetics
13 / 4/9 / 18/ / Human DNA fingerprinting –part 2 / HW#12
4/11 / 19/pp 515-528 – Lac operon / Lab: 1) review last weeks Flow chart
4/13 / 20/pp 543-568 Eukaryotic gene regulation
14 / 4/16 / 20 / Lab quiz #2
And Lab clean-up / HW#13
4/18 / Test 5 – Chap 13,15,18 / Lab: 1)LR7: Human DNA fingerprinting(opt 2/3)2) Lab quiz
3) lab cleanup
4/20 / 20
15 / 4/23 / Wrap up / none
Sat, April 28, 8-11am - Cumulative Final Exam
Textbook Reading and Suggested Practice Problems
Reading and Suggested practice problems from the back of each chapter in Russell, iGenetics. Practice problems will not be collected and corrected. It is up to you to come to me if you are having difficulties with the problems. There is often time during lab to go over problems as a group. Problems similar to the suggested practice problems will appear on exams.
ChapterPages (# of lectures)Suggested practice problems
Chap 1 – 1-12(1)
Chap 12299-3121-12, 14,18
Chap 2 – 13-38 (2)1-18, 25-35
Chap 3 – 43-62 (2)All
Chap 4 – 67-73(top) 77-79(top)(1)1-5,7, 12,13
Chap 5 – 87-108, skim 102-106 (3)All
Chap 6 - 111-128 (2)All
Chap 7 – 133-166 (3)All
Chap 8 – 175-204 (3)1-15, 20, 25, 28, 30, 31, 35-42
Chap 11 – 271-291 (2)(All are worth solving)
Chap 12 – 312-330 (2)21-25, 35-39
Chap 13 – 337-354 (3)(All are worth solving)
Chap 15 – 412-420, 430-433 (2)1-6, 9-11, 13, 14, 18, 24
Chap 18 – 441 – 454 (2)1-10, 22
Chap 19 – 515-528 (1)1-12
Chap 20 - 543-568(3)All
Genetics Laboratory:
Preparing for Lab: Students are expected to come to lab prepared. To encourage this, you need to have a flow chart of that days lab upon entering the room. Students who come to lab without the flow chart will lose 5 points of the 25 point lab report. You will still be expected to go next door and write the flow chart before starting the lab.
Expected lab behavior: Students are expected to be quiet during lab and focused on the experiment. Your workspace should be clutter-free. Books, jackets etc. should be placed under the lab desk. Lab is not recess time. You should put your lab supplies back in the correct drawer. Make sure the numbers match. Throw out any trash test tubes, pipette tips, papers, etc. Keep your drawer neat and tidy for the next lab.
Lab reports: Six lab reports will be marked as part of your laboratory grade. Reports #1-4 are required of everyone. You may then choose which 2 of 5-7 that you hand-in.
Lab Reports
Knowledge in science is based on researchers forming hypotheses, designing and performing experiments to address these hypotheses, evaluating the results, drawing conclusions, forming new hypotheses, etc. This information is then disseminated to the scientific community in the form of publications in which the information is recorded in the basic format outlined below.
In the genetics labs the experiments are already designed. You will be expected to follow the experimental design, collect results from the experiments, analyze the results and make conclusions based on these results and your knowledge of genetics. This information will then be transmitted to me in the form of a lab report. Lab reports will be expected for most labs that are done in class. Although many labs will be done by pairs of students who will share the data, each student is expected to turn in their own, unique lab report. Reports will be presented in the following format. Lab reports not in the proper format will not get full credit.
Introduction: Background for the experiment. What previous work has laid the ground work for this experiment?
Hypothesis (15%): What hypothesis (es) is (are) you testing? The hypothesis must be a statement that can be tested experimentally.
Materials and Methods (15%): Include your flowchart of the experiment here. Briefly summarize how the experiment was done, what equipment and reagents were used. I know this information is in the lab manual, but I want you to rewrite it in your own words. Be sure to list dates and times. Give intervals for recording data (observations were made after 10 days or at 15 minute intervals, etc.)
Results (25%): This is your data. It may be expressed as numbers, graphs, photograph of a gel, description of what you saw, etc. Units of measure are very important to understanding results. Be sure you include units of measure. This is a purely factual recording of the results of an experiment. Do NOT theorize as to what the data means in this section, merely record it as you saw it. Any statistical analysis of your data, such as Chi-square analysis, should be included in this section.
Discussion (35%): Why was this experiment done? Based on your aim for the experiment and your general understanding of genetics, explain your data. Did the data prove what you set out to prove? What controls did you use? Why did you get the results that you did? If not, can you explain why not? Were the experimental conditions wrong and therefore if you repeated the experiment you would get different results? If you could “do it over”, what would you do to make it better? Does the data collected fit the original hypothesis? What is the significance of the experiment?
References (5%): List sources used to help you do the lab (i.e. the lab manual) and any other sources used to analyze the lab (i.e., the text book) EVERY LAB REPORT SHOULD HAVE REFERENCE(S)
Spelling & grammar (5%):
If you are not clear about how to write a lab report, I have examples in my office that you may look at.
Genetics Lab Flow chart
Name______Date______
Lab Flow chart – The left side needs to be done before lab and brought to class. You will not be allowed to start lab until it is done and you will loose five (5) points from your lab hand-in. The right side gets done before, during or after lab and handed in as the Materials and Methods section of your lab report.
Items needed before starting the lab, e.g, ice, water bath a particular temperature, a solution already made up, etc.
Technical Steps – Flow chart the technical steps for performing this investigation.(What am I doing?) / Conceptual Understanding – Description of what is happening scientifically at each step.
(Why am I doing this and what does it mean?)
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