Biology 572 - Recombinant DNA Techniques

Working With DNA (textbook)

My new book!

  • A reference for novice or
    seasoned researchers.
  • A course reader for undergraduate or graduate students.
  • Includes problems (and solutions)
  • 414 pp


Stan Metzenberg, Ph.D.
Department of Biology, California State University Northridge

Lecture: Monday & Wednesday, 12:00-12:50 P.M., Science 2225

Laboratory Section: 1:00-3:50 A.M., Science 4109

Office Hours:
Tuesdays, Thursdays 1:00-2:00, or by appointment. Science 4100, 4103, or 4109
Best way to reach me is
by email

Reading assignments and important information

Week 1

Nucleic acids and polymerization

pdf

Bacterial plasmids and DNA transformation

pdf

 

 

Safety rules

pdf

August 29: Welcome,
safety rules.

August 31
This week and next, we're working on four problem sets:

Metric measures, DNA base pairing, Mass/mole conversions, and Solutions.




On 8/31, you will receive Cairns (1963) and a sheet on Henderson-Hasselbach for review. We will continue discussion on the four problem sets. Two of them will be due on Sept. 7th.




August 31: In laboratory - preparation of solutions and materials for the following week.

Week 2

Polymerase chain reaction

pdf

 

 

 

 

September 5 is Labor Day NO CLASS.

September 7

Assignments to complete, prior to class on Sept 7th:

  • Print out this method on preparing competent cells - bring to class Wednesday.
  • Pick up supplemental reading #1 at QuickCopies.
  • Have read the Cairns (1963) paper, for discussion in class. (distributed 8/31)
  • Complete "metric measures" and "DNA base pairing problem sets - ready to turn in on September 7th.

Sept 7: In laboratory - preparation of competent cells, for use on Sept. 12th. Discussion of Cairns (1963), and introduction to methods used.

Week 3

 

 

Site directed mutagenesis

pdf

Restriction endonucleases

pdf

September 12

September 14

Assignments to complete, prior to class:

  • Mass/mole conversions problem set is due Monday.
  • Solutions problem set is due Wednesday.
  • Possibly more - watch this site for further instructions.


In laboratory this week -

  • Methods of working with bacteria. Plasmid DNA transformation,

Week 4

Engineering DNA ends

pdf

 

 

Additional cloning methods

pdf

September 19

September 21

Additional readings -

Tindall's Preparation of Buffers




In laboratory this week -

  • Methods of working with bacteria. Plasmid DNA transformation,
  • Plasmid maintenance and curing.
  • Introduction to bacterial molecular genetics.

Week 5

DNA sequencing

pdf

 

 

September 26

September 28


Additional readings -

Pick up supplemental reading #2 at QuickCopies (after 9/22)


In laboratory this week -

  • Introduction to design principles in PCR-based gene construction.
  • Second transformation experiment - promoter silencing





September 28

EXAMINATION. 12:00 - 12:50 9/28/05

NO LABORATORY CLASS 9/28/05

Week 6

Proteins

pdf

More about proteins

pdf

October 3

October 5

In laboratory this week -

  • Restriction analysis,
  • DNA gel electrophoresis
  • Begin work on DNA Joining (at the old school) problem set

Week 7

The lac operon

pdf

Prokaryotic expression vectors

pdf

October 10

October 12

Assignments to complete, prior to class:

  • DNA Joining (at the old school) problem set is due Wednesday.

In laboratory this week -

  • Southern analysis,
  • Plan C-reactive protein cloning
  • DNA Joining (at the new school)

Week 8

Exons and coding sequences

pdf

 

 

Antibody methods

pdf

   
October 17

October 19

Assignments to complete, prior to class:

  • DNA Joining (at the new school) problem set is due Wednesday.

Week 9

Finding the gene that encodes a purified protein

pdf

   
 

 

October 24

October 26
EXAMINATION. 12:00 - 12:50 10/26/05

Week 10

Temperate bacteriophage methods

pdf

 

 

Libraries

pdf

October 31

November 2

Week 11

Virulent bacteriophage methods

pdf

High-capacity vectors

pdf

   
November 7

November 9:

Week 12

Walking in the genome

pdf

Transgenic plants

pdf

   
November 14

November 16

Week 13

Somatic cell genetics and transgenics  
DNA Detection and Hybridization  
   
November 21


November 23
Please note: A very expensive and nonrefundable plane ticket is not a valid excuse for missing class Wednesday. If you are traveling on Thanksgiving, please make arrangements accordingly.

Week 14

DNA diagnostics  
Chips and microarrays  
   
November 28

November 30
EXAMINATION. 12:00 - 12:50 11/30/05

NO LABORATORY CLASS 11/30/05

Week 15

Combinatorial genetic engineering  
Gene therapy  
   
December 5

December 7

Week 16

Final exam week
Final examination.

12:45-2:45, December 14, 2005

Employment and enjoyment
Course information

Course objectives: Students will understand key issues in recombinant DNA techniques, and be technically proficient in laboratory research, with minimal support.

Broad description of topics covered: Properties of nucleic acids and proteins. Applications of molecular biology techniques.

Course requirements and methods of evaluation: Course requirements include maintaining good class attendance, completing reading and writing assignments in a timely fashion, answering questions when called upon, and completing all quizzes, examinations, and laboratory work. The student's increase in knowledge of the subject and effort applied in the course will be the primary and secondary methods of evaluation.
On-line access to a computer with a Javascript-enabled version 4+ browser (available in library or computer labs on campus). Click here to find out what type of browser you're currently using. Prerequisites: Biology 360, or consent of instructor.

Grading criteria: Letter grades A-F, with plus/minus system. In the lecture, 50% of the grade will be determined from the examination results. 25% of the grade will be determined from attendance, and 25% of the grade will be determined from writing assignments, problem sets, and "pop quizzes", and class participation. In the laboratory, 75% of the grade will be based on writing assignments and proper maintenance of a laboratory notebook, and 25% from attendance and class participation.
Absence from class is excused for religious holidays and illness (with note from attending physician). Students are responsible for all course content, including material delivered verbally in lecture and presented in the readings. Syllabus subject to change without notice.

Biology Department Withdrawal Policy: Unrestricted withdrawals are permitted only until the end of the third week. Thereafter, requests to drop a class will be honored only when a verifiable serious and compelling reason exists and when there is no viable alternative to withdrawal. Poor performance is not an acceptable reason for withdrawal. During the last three weeks of the semester withdrawals will not be approved except when a student is withdrawing from all classes for verifiable medical reasons.

Cheating and plagiarism: All forms of cheating and plagiarism (the claiming of the work of others as your own) are expressly forbidden by University rules and will not be tolerated. Any student observed cheating or participating in any act of academic dishonesty will have his or her case referred to the Office of the Vice President of Student Affairs for possible University disciplinary action. In addition, the student may receive a failing grade in the course.

Other notices:
Safety procedures in laboratory must be followed (see handout).


Stan Metzenberg
Department of Biology
California State University Northridge
Northridge CA 91330-8303
stan.metzenberg@csun.edu

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