3 - LECTURE 3 ANNOUNCEMENTS 1. QUIZ NEXT WEDNESDAY 9/9....

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ANNOUNCEMENTS 1. QUIZ NEXT WEDNESDAY 9/9. DON'T BE LATE-- WE START JUST AFTER 10:10. BE SURE TO TALK TO PROF F. IF YOU HAVE ANY SPECIAL PROBLEMS. REALLY. 2. PROF. F. WOULD LIKE TO MEET WITH ANY INTERESTED STUDENTS ON FRIDAY 9/4. TOPIC: “HOW TO FIND A LAB FOR UNDERGRAD RESEARCH AT CORNELL. WHAT ARE THEY LOOKING FOR?! WHAT DO I DO WHEN I GET THERE?!” COMSTOCK B108, 3:25 - 4:15PM . THURS 10 - NOON WOULD BE A GOOD TIME, OR e-MAIL TO GWF3. LECTURE 3 c. THE FIRST PyMOL ASSIGNMENT IS THE TUTORIAL, PP. 300-309 OF THE LG. ALL INSTRUCTIONS ARE THERE. USE THE CD-ROM THAT CAME WITH THE LG, AND GO THROUGH IT SYSTEMATICALLY . CARPENTER RED COMPUTER LAB b. OFFICE HOURS + REVIEWS IN SUN 9/6 3 - 5PM; FIRST PROF'S REVIEW SESSION WILL BE IN MALOTT HALL rm 253 TUE 9/8 4:30 - 6PM 3. PyMOL: a. IF YOU CANNOT RUN PyMOL BECAUSE YOU HAVE A NEW 64-BIT WINDOWS COMPUTER: WE ARE WORKING ON A FIX. WE HAVE UPLOADED THE NEWEST VERSIONS OF PyMOL ONTO THE BLACKBOARD SITE. TRY ONE OF THESE, AND LET BERTHELEAU KNOW AT BMN27.
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MONDAY'S LECTURE IONIZABLE GROUPS; HOW TO USE THE HENDERSON-HASSELBALCH EQ. NOTES ON H-H EQ: HIGHER pKa MEANS HIGHER AFFINITY FOR H + IF pH >> pKa THEN H + IS PREDOMINANTLY OFF IF pH << pKa THEN H + IS PREDOMINANTLY ON pH = pKa + log[UN]/[PROT] WHEN [UN]/[PROT] = 1, pH = pKa EASY TO CONVERT FROM CALC RATIO TO FRACTION : e.g. LET RATIO [UN]/[PROT] = 3, WHAT IS THE FRACTION OF IONIZABLE GROUPS THAT ARE PROTONATED? [UN]/[PROT] = 3 = 3/1; TOTAL CONC IS (3 + 1), AND FRACTION PROTONATED IS 1/4 IMPORTANCE OF UNDERSTANDING IONIZATION BEHAVIOR: 1. pKa CAN BE CHANGED! pKa DEPENDS ON LOCAL
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3 - LECTURE 3 ANNOUNCEMENTS 1. QUIZ NEXT WEDNESDAY 9/9....

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