BIOLOGY 308  GENETICS              Spring, 2006

INSTRUCTORS:                 Dr. Alix G. Darden 

Dr. Darden’s OFFICE:                       324 Bond  Hall

Dr. Darden’s PHONE:                        953-7873                 E-MAIL: dardena@citadel.edu  (I check regularly)

Dr. Darden’sOFFICE HOURS:         M 2-4,  W 9-11, 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 laboratory exercises, collect and analyze the data. 

 

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.

 

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.

 

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.   All efforts to attend exams the day they are given should be made.  Students need to speak to me 24 hours before the day the exam is given if a make-up exam is to be considered. A make-up exam contract complete with date and time of make-up will be filled out and signed by student and myself.  Without this make-up contract a student will not be allowed to make-up the exam and will get a grade of “0”.  All make-ups are given before the class next meets.  Make-ups tests are not necessarily the same format as in class exams and may consist of several essay questions

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

Literature searches/society activity (2)            80 points (40 pts each)

Homework (8 highest are counted)                   80 points (10 pts each)

 

Lab -       Lab hand-ins                                                         150 points (6 @ 25 pts)

2 Lab quizzes                                                        150 (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 points             B = 800-899           C = 700-799           D = 600-699           F = 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. 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”. 


Genetics - Biology 308 Spring 2006 Schedule

 

 

Week

Lecture

Dates

Chap/Topic

Lab exercise

Assignments due

LR=lab report

1

1/11

1-Intro – pp 1-12

None

 

1/3

2-pp.13-38

 

2

1/18

2-

1)Intro to electrophoresis

2) creating lab flowcharts

3) micropipette review

HW#1

1/20

3-pp. 43-62

 

3

1/23

3-

Cancer case study – bibliographic database use – meet in library

HW#2

1/25

4 – pp. 67-73(top) 77-79(top)

 

1/27

Test 1- chap 2,3,4, lab 1

Test 1

4

1/30

5-pp. 87-108, skim 102-106

Cloning 1 - restriction digest, gel electrophoresis

HW#3

2/1

5

Case study write-up

Lab: flow chart

2/3

5

 

5

2/6

6-pp 111-128

Cloning 2 – gel elution and ligation

HW#4

2/8

6

Lab: 1)LR1 – cloning 1 (req)

2) Flow chart

2/10

7/no class

 

6

2/13

Test 2 – chap 5,6

1) Cloning 3 – bacterial transformation

2) Plant phylogeny PCR

Test 2

2/15

7-pp133-166

1)HW#5,

Lab: 1)LR2 – cloning 2 (req)

2) Flowchart

2/17

7

 

7

2/20

7

1) Cloning 4 – plasmid mini-prep

2)Plant phylogeny analysis

HW#6

2/22

8-pp175-204

Lab: 1) LR3-cloning 3 (req)

2)Flow chart

2/24

8

 

8

2/27

8

1)Cloning 5 – final gel analysis – cloning lab review

2)Statistics review

HW#7

3/1

11-pp271-291

Lab: Flow chart

Mid-Term grading

 

3/3

Test 3 – 7,8

Test 3

9

3/6

11

Lab quiz #1 - cloning experiment and electrophoresis

HW#8

3/8

12 –pp. 299-330

Last day to withdraw with “W”

Lab: 1)LR4–cloning final (req)

2) lab quiz

3/10

12

 

10

3/13

12

Human DNA fingerprinting – part 1

HW#9

3/15

13-337-354

Lit search #1

Lab: Flow chart

3/17

13

 

11

3/20

13

Human DNA fingerprinting –part 2

HW#10

3/22

15-pp 412-420, 430-433

Lab: review last weeks flow chart

3/24

Test 4 – chap 11,12,13

Test 4

*********Spring Break************

12

4/3

15

Bioinformatics – meet in computer lab – Bond 251

 

4/5

18-pp 441 – 454

Lab: 1) LR 5 – DNA fingerprinting

2) Flow chart

4/7

18

 

13

4/10

18

Genetically modified food –part 1

HW#11

4/12

19-pp. 515-528

Lab: 1)LR 6 – Bioinformatics

2) Flow chart

4/14

19

 

14

4/17

20-pp. 543-568

GM food part 2

Lab quiz #2

HW#12

4/19

20

Lit search #2 (GM food)

Lab: review last weeks flow chart

4/21

20

 

15

4/24

Test 5 – chap 15,18-20

none

Test 5

LR 7 - GM Food lab report

Sat – 4/29, 8-11    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.

 

Chapter            Pages (# of lectures)                 Suggested practice problems

 

Chap 1 –          1-12(1)                                   

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 –        299-330 (3)                             (All are worth solving)

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

                                   

 
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 understand the language, i.e. define the words, apply the information through problem solving and 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

 

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 homeworks 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 n work when completed without review or proofreading

 

 

Literature searches - Genetics – the scientific process.  These activities are designed to make you consider the science that you learn in class and in the textbook from different perspectives.  Science facts are not just generated, memorized and spit out on classroom exams.  Science is used in society by all different disciples and by all people.  This activity is meant to be fun and mind expanding.  They are open-ended activities in that you make choices about what and how you learn and you can do it in your time-frame (unless you wait until the night before at which point it will not be fun or in your time-frame).  The book reading activities will be due at the end of the semester, although you may do them whenever you have time.

¨       You are required to do three of these activities.

¨       The first two literature searches will be on assigned topics

¨       For the third activities, pick one of the following three activities

           1. Literature search on an ethical issue in genetics.  I will provide a list of possible topics

            2. Literature search on a topic of your choice dealing with something in genetics, please clear topic with instructor first.

            3. Read a book from the following list OR if you find a book that you are interested in show it to me for approval.  If you read an unapproved book without getting my prior approval, you will get no credit.  These books have to do either with the impact of genetics on society or history of genetics.  You will need to sign an honor statement that you have read the entire book and write a one page something in the book that piqued your interested, shocked you, got your attention, etc. with reference to specific incidents in the book.  I am looking for a gut level emotional response (not disgusting) that in some way makes you think differently, or think at all, about genetics and your life.  I have carefully picked these books because I have read them and found them readable, fascinating, well written by credible authors.  You can find out information about these books, reviews, etc. at amazon.com and probably other bookstores on the Web.  I personally own many of these, but would prefer that you get your own copy.  You may come look at mine to see if you would like to read a particular book.    You may need to use interlibrary loan to get some of the books.  Some are readily available at bookstores.  

 

1)***The Cobra Event, by Richard Preston

            Fictional story about biological warfare.

2)What Mad Pursuit, A personal view of Scientific Discovery, by Francis Crick (Nobel prize laureate)

163 pages. Fascinating ruminations by Francis Crick about work done on the genetic code after he won the Nobel Prize.

 

3)Mapping Fate, Alice Wexler, 1995.

            Story about Huntingtons Disease – social aspects, scientific, etc.  Written my a member of the Wexler family which has been heavily involved in fundraising and conscience raising for Huntington’s Disease. 261 pages

4)The Billion-Dollar Molecule: One Company's Quest for the Perfect Drug, by Barry Werth

            This inside account of Vertex, a start-up pharmaceutical company, conveys the exciting drama being played out in the pioneering and enormously profitable field of drug research. Vertex is dedicated to designing--atom by atom--a new life-saving immunosuppressant drug that has major implications for HIV research.

5)The Golden Helix: Inside Biotech Ventures, by Arthur Kornberg (Nobel prize laureate)

287 pages. Examination of the rise and current status of the biotechnology industry, looking at the companies and personalities who brought it to prominence.

 

6)Biohazard, by Ken Alibek. 1999

            The chilling true story of the largest covert biological weapons program in the world-told from the inside by the man who ran it.  292 pages

 

7)Rosalind Franklin, The dark lady of DNA, by Brenda Maddox. 2002

            Biography of Rosalind Franklin. 328 pages

 

8)The Triple Helix, by Richard Lewontin. 2000

            Shows that an organism is a unique consequence of both genes and environment, of both internal and external features.  129 pages.

9)Genome.  The autobiography of a species in 23 chapters. By Matt Ridley. 1999. 313 pages

 

10)Of Flies, Mice and Men, by Francois Jacob.(Nobel laureate)  1998.

     On the revolution in modern biology, by one of the scientists who helped make it. 152 pages.
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.