BIOCHEMISTRY LABORATORY II BCHS 4311 Spring 2014

Lab Coordinator: Dr. Donna Pattison Office: Room 108C, Science Teaching Laboratory Building Phone Number: 713-743-2642 e-mail: dpattison@uh.edu Office Hours: Monday and Wednesday 10-11 am or by appointment Teaching Assistant:________________________________ TA e-mail:_______________________________________ Text: Laboratory DNA Science; Bloom, Freyer, and Micklos (1996) [ISBN: 0-80533040-2] A calculator may be helpful. Lab Coats and Goggles are REQUIRED. You will also need a tear-out lab notebook with duplicate pages. Goggles, lab coats and notebooks are available for purchase at Research Stores in Fleming Room 70 in the basement. Course Overview and Objectives: Students will gain first-hand experience using some of the most common and useful tools employed by biochemists and molecular biologists today. By the end of the course students will understand and be able to set up a polymerase chain reaction, clone a gene into a vector, transform a cloning vector into a cell line, and purify expressed protein. Students will be able to explain when and why scientists would use these particular methods in the laboratory. Students will be able to follow the scientific method from start to finish. Students will develop their own problem to explore in the context of the biomaterials project. They will establish a hypothesis, design experimental methods, conduct the experiement, analyze the data, and communicate their findings to their peers in both oral and written form. Students will learn the basics of professional writing for the sciences and demonstrate mastery of the skill in two written manuscript papers during the course.

Week January 13-14

Lab Lab Orientation and Safety Micropipetting, Sterile Techniques and Bacterial Culture Techniques (Labs 1 and 2) Research Databases and Referencing Tools: Labs will meet in the Training Room 10F in the library basement

January 15-16

January 20-21 January 22-January 23 January 27-28 January 29-30

No labs. Martin Luther King Day Use of Bioinformatics to Investigate -Lactamase Lac Operon (separate handout) Effects of DNA Methylation on Restriction (Lab 4); Quiz 1 Southern Hybridization of DNA (Lab 13A); Southern Hybridization of DNA (Lab 13B and C) Southern Hybridization of DNA (Lab 13D) Construction of a Genomic Library of DNA (Lab 14A/B) Quiz 2 Construction of a Genomic Library of DNA (Lab 15B) Construction of a Genomic Library of DNA (Lab 16A) Construction of a Genomic Library of DNA (Lab 16B); Editing Workshop for Southern Hybridization Paper (Complete Southern Blot paper drafts due) Construction of a Genomic Library of DNA (Lab 16C); Southern Blot Paper Due Human DNA Fingerprinting (Lab 23); Quiz 3 Cloning by PCR (Lab 18A) SPRING BREAK Cloning by PCR (continued; Lab 18B and C) Cloning by PCR (continued; Lab 19A and B) Cloning by PCR (continued; Lab 20B); Quiz 4 Purify Ubx protein

February 3-4 February 5-6 February 10-11 February 12-13

February 17-18 February 19-20 February 24-25

February 26-27

March 3-4

March 5-6 March 10-13 March 17-18 March 19-20 March 24-25 March 26-27

March 31-April 1 April 2-3

Purify Ubx protein; CV and Cover Letter due Student Designed Materials Experiments: Creating ropes and sheets Student Designed Materials Experiments: Creating ropes and sheets Student Designed Materials Experiments: continued Student Designed Materials Experiments: continued Ubx Paper editing workshop; Complete Ubx DRAFT due Work on seminar presentations; Complete Ubx paper due Cumulative Final Ubx Saturday Research Seminar

April 7-8

April 9-10 April 14-15 April 16-17 April 21-22 April 24-25 April 26th

Please note the above schedule is TENTATIVE. The schedule is subject to change based on the availability of materials from our suppliers and the need to allow some flexibility in the time needed to complete the lab exercises. Attendance and Grading Attendance is MANDATORY in both lab and lecture. Guesting: If you miss a lab for an excused reason, inform your TA as soon as possible. Make arrangements another TA (see schedule posted on classroom door) to guest in their lab. You may guest up to two times in a semester. Please contact your regular TA and the TA with whom you will be guesting for permission. No more than 4 students will be permitted to guest in a single section. You do NOT need to ask Dr. Pattison for permission. You are also required to fill out the guesting form (located on the TA bench at the front of the room) when you arrive for the section in which you are guesting. There are no labs on Fridays. You will take the quiz for the lab section you are visiting. Absences: As the main point of a laboratory course is to gain hands-on experience in lab techniques, if you fail to attend more than two labs, you will automatically fail the course unless you provide evidence of extenuating circumstances that are excused under university policies. It is YOUR responsibility to deal with attendance issues PROMPTLY. If there are extenuating circumstances and you have already guested twice, you must speak with both your TA AND Dr. Pattison.

Late work: Failure to hand in 2 or more lab reports will result in an F even if you attended the lab. Lab reports are due at the start of class. Reports will be subjected to a ten percent loss in points for failure to turn the report in at the start of class and for each day beyond the due date. Lab reports that are more than 7 days late will receive a zero. Arriving Late: You are expected to arrive in class on time. You will not receive additional time to complete a quiz if you are late. Points will be deducted from your participation grade for tardiness. If you are more than 15 minutes late, you are considered absent and will not be allowed to participate in the lab. You will need to guest in another lab to obtain credit for that lab. Academic Dishonesty: Academic dishonesty will not be tolerated. This includes, but is not limited to, plagiarism. Penalties will be matched to the degree of the transgression. Potential penalties include a zero on the assignment to an F in the entire course. Do your own work. Your degree is meaningless and undeserved otherwise. Incomplete Grade Policy: A temporary grade of I can be assigned by the instructor when a student is currently (A) passing a course or (b) still has a reasonable chance of passing in the judgment of the instructor, but for non-academic reasons beyond their control have not completed a relatively small part of all course requirements. After the student and the instructor agree that the student shall receive an I grade, an Incomplete Grade Agreement form must be completed and filed with the Office of Undergraduate Affairs (124F, Science Building). Further information on I grades can be found at http://www.uh.edu/academics/catalog/general/acade2.html#grades. Students with Special Needs: The Americans with Disabilities Act of 1990 requires that universities make reasonable accommodations to persons with disabilities as defined in the act. Students who feel they need assistance as defined by the guidelines set forth in the act should contact the lab coordinator, Dr. Pattison, to discuss appropriate arrangements. Laboratory Attire: Lab coats are required. You will not be allowed to attend the lab without a lab coat. Safety goggles will be required for certain labs. Gloves will be provided as needed. Please inform your instructor if you are allergic to latex. Grades Library Training 10 points Lab reports (Tear-out) 290 points (see below) Southern Blotting Paper 100 points Ubx Project 240 points Curriculum vitae/cover letter 20 points Lab Participation 20 points Clicker Questions/Attendance 50 points Quizzes 200 points (4 quizzes /50 points each) Cumulative Final 100 points 1030 points total

Ubx Project Initial experiment idea (10 points) Experimental Protocol (30 points) Oral presentation (50 points) Final paper (on student designed experiment) (150 points)

Tear-Out Lab Reports: Micropipetting, Sterile Techniques and Bacterial Culture Techniques (20 points) Lac Operon (50 points) Bioinformatics (20 points) Effects of DNA Methylation on Restriction (50 points) Genomic Library (50 points) Cloning by PCR (50 points) DNA Fingerprinting (50 points) Grade Assignments 92.0 100% A 90.0 - 91.9% A88.0 - 89.9% B+ 82.0 87.9% B 80.0 81.9% B78.0 79.9% C+ 72.0 77.9% C 70.0 71.9% C68.0 69.9% 62.0 67.9% 60.0 61.9% 59.9%

D+ D DF

Important Dates: January 29: Last day to drop class without a grade March 26: Last day to drop class with a W