Return to Molecular Genetics Main Page

Prerequisite: Biology 212 (Cell Physiology); Biology 310 (Genetics) recommended

Instructor: Dr. M.J. Niles
Office: Harney 323
Office Hours: MW 11:30 am - 1:00 pm, and by appointment
Email: niles @ usfca . edu
Phone: (415) 422-2354

LECTURE - LAB schedule:  The lecture topics schedule is tentative, and lectures will be given at the beginning of the lecture/lab period, or when time permits (during long incubations, for example).
 

Date	#	Lecture Topic	Lab Text Pages
Jan 21	1	Introductory Comments Sources of DNA and RNA: organisms, cell lines and genomes Molecular Biotech’ recommended reading:   Chapters 1&2 Prep Lab, day 1: prepare individual reagents,  collect materials, prepare solutions, pour plates	1
Jan. 26	2	Molecular Genetics: a refresher course  DNA Structure Chromosomes and Chromosome Structure DNA Replication Molecular Biotech’ recommended reading:   Chapter 3 Lab 1, day 1: measurements, math and micropipettor practice	7-12
Jan. 28	3	Bacteriophage DNAs and Plasmids Molecular Biotech’ recommended reading:   Chapter 4 Lab 2, day 1: Bacterial culture techniques Streak for colony isolation  Set up liquid overnight culture	17-19 23-24
Feb. 2	4	continued Lab 2, day 2:  Results and observations / bacterial colonies  Observation of log growth, liquid culture  Plate bacteria at timed intervals	19-21 28-29
Feb. 4	5	The Manipulation of DNA Molecules: bacterial and viral enzymes used in molecular methods Lab 2, day 3: Count colonies
Feb. 9	6	continued Lab A, day 1: Genomic DNA extractions  Bacterial DNA prep Mouse DNA prep	handout
Feb. 11	7	Agarose and Polyacrylamide Gel Electrophoresis Lab A, day 2: Set up restriction digests  of genomic DNAs Lab 5, day 1: Make competent cells  (use procedure 8A)  Transform bacteria with plasmid DNA	81-84
Feb. 16	8	Movable Genes: transposable elements Lab A, day 3: Agarose gel electrophoresis of genomic DNA restriction digests Lab 5, day 2:  Observe transformed colonies  Inoculate overnight culture for plasmid miniprep	84-86
Feb. 18	9	continued Lab 6, day 1: Plasmid mini-preps	94-96
Feb. 23	10	Restriction Mapping Quiz Lab 6, day 2:  Restriction digests of plasmid  Lab B, day 1: Marker screening  of Apr, Cmr, Knr bacteria	101 handout
Feb. 25	11	continued Lab 6, day 3:  Agarose gel electrophoresis  Lab B, day 2: Pick Tcs, Tcr colonies  for overnight growth	102-108
March 2	12	Gene structure and expression; recombinant protein production Molecular Biotech’ recommended reading: Chapters 6&7 Lab B, day 3: plasmid mini-preps of pBR329 and pBR329::Tn5 (Tcs or Tcr);  set up digests
March 4	13	continued Lab B, day 4: Agarose gel electrophoresis of plasmid digests
March 9	14	The Isolation and Detection of Cloned Genes Lab B, day 5:  Restriction mapping of pBR329::Tn5
March 11	15	Midterm Exam
March 16  March 18		Spring Break
March 23	16	Gene Transfer: transfection and transgenic animals Molecular Biotech’ recommended reading:  Chapter 19 Lab 7, day 1:  Restriction digests of pKan and pAmp  (no gel electrophoresis)	115
March 25	17	continued Lab 7, day 2:  Set up ligation reactions	122
March 30	18	continued Lab 8, day 1:  Prepare competent cells  and transform ligation reactions	129-131 134-137
April 1	19	DNA Sequencing Molecular Biotech’ recommended reading:  Chapter 5 Lab 8, day 2:  Record results of ligation transformation (If proceeding to Lab 10, set up overnight culture)	137-139
April 6	20	continued Lab 9, day 1:  Replica plating of recombinant clones  or Lab 10, day 1:  plasmid preps,  set up restriction digests  Lab C, day 1:  Bacteriophage l  titration  DNA sequencing group 1, day 1	144   152-154 157-158 handout
April 8	21	The Polymerase Chain Reaction Article summary is due Lab 9, day 2:  Analysis of replica plating results  or Lab 10, day 2:  Agarose gel electrophoresis of  ligation reaction plasmid digests Lab C, day 2:  Plate bacteriophage l for DNA prep DNA sequencing group 1, day 2	145-146   158-163
April 13	22	Other Molecular Methods Lab 9, day 3:  complete lab or Lab 10, day 3:  complete lab Lab C, day 3:  Prepare phage lysate, isolate phage DNA sequencing group 2, day 1
April 15	23	Animal Cloning Lab C, day 4:  Complete phage DNA isolation, set up digests DNA sequencing group 2, day 2
April 20	24	Human Molecular Genetics Molecular Biotech’ recommended reading:  Chapter 20 Quiz Lab C, day 5:  Agarose gel electrophoresis of phage DNA digests Lab 13, day 1:  Agarose gel electrophoresis of l DNA digests Set up southern blot  DNA sequencing group 3, day 1	196-199 203-205
April 22	25	continued Lab 13, day 2:  Bake blot,  set up pre-hybe  DNA sequencing group 3, day 2	205-209
April 27	26	Laboratory - specific Lab 13, day 3:  Set up hybridization  DNA sequencing group 4, day 1	209
April 29	27	Laboratory - specific Lab 13, day 4:  Wash and develop blot  DNA sequencing group 4, day 2	213-215
May 4	28	Laboratory - specific Lab 22, day 1:  Isolate human DNA,  Set up Polymerase Chain Reactions  DNA sequencing group 5, day 1	350-351 352
May 6	29	Laboratory - specific Lab 22, day 2:  Agarose gel electrophoresis; Analysis of PCR products DNA sequencing group 5, day 2	352-357
May 11	30	Laboratory - specific Complete labs as needed

 

*Midterm exam and final:  There will be one midterm exam (100 points) and a final (200 points) as indicated in the lecture schedule.  The tests may include short essay, short answer,  fill - in, true - false and multiple choice - type questions, and will cover material presented in class (both lecture and lab topics).

*Article Summary:  There is one research article summary due on April 10th.  With assistance from the instructor, choose a primary research article in which DNA methods figure prominently.  Provide a one to two page summary (typed) of the research accomplished by that group, including the methods used.  Details of this assignment will be provided in class.

*Quizzes:  There will be two quizzes (25 points each), addressing lecture topics and lab techniques, as indicated in the schedule.

*Laboratory Notebook:  Keep a notebook, separate from your lab and lecture notes, of all the work you do in the lab.  The lab notebook format and requirements will be described in class.  Your notebook will be collected three times during the semester and graded (25 points each).

*Preparation and participation:  As far as possible, all work will be done individually and independently.  Please come to class  prepared to proceed with the experiment of the day.  Of course you may have questions; I will address questions and discuss procedural modifications before we begin.  P. and P. is worth 25 points.  There will be a loss of 5 points for each lab missed.  There are no "make up" labs.

•You may use either the bound "Computation Notebook" (gray cover) or "Laboratory Research Notebook" (brown cover).  These notebooks provide numbered, duplicate pages and are available in the Bookstore.

•Leave The first page blank so you can formulate a table of contents.

•Date each day's work.

•Most experiments will take 3 or more laboratory periods, so reserve about 5 pages for experiments in progress; we will often be completing lab experiments simultaneously, but each experiment should be documented separately.

Prior to the lab period:

1. Title each lab experiment and record a short explanatory paragraph that includes some background and the purpose of the lab.

2. List the biological materials (DNAs, bacteria, phage), reagents (include source), solutions (include recipes) and equipment required for the lab.

3. Prepare a flow chart of the procedure.  Save room in the margins for notes and alterations to be made during the lab.

During thelab period:

1. Note alterations, problems in the procedure; the resolution of problems.

2. Note details of procedure as completed; for example, exact incubation times and temperatures.

3. Note observations; for example, cloudy, clear, precipitate formed, size, color of pellet seen after centrifugation.

4. Include all data: for example, OD readings, gel photographs, plots.

5. When the experiment is complete:

6. Comment on the results, note general observations, formulate a brief conclusion.

Your notebook (duplicate pages) will be collected at random three times during the semester and graded.