3 - LECTURE 3 ANNOUNCEMENTS 1 QUIZ WEDNESDAY 9/8 AND DON'T...

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ANNOUNCEMENTS 1. QUIZ WEDNESDAY 9/8 AND DON'T BE LATE-- WE START JUST AFTER 10:10. BE SURE TO TALK TO PROF IF YOU HAVE ANY SPECIAL PROBLEMS . REALLY. 2. ON WEDNESAY 9/1: BIOLOGY OPEN HOUSE at 4:00PM. MEET PROFS AND STUDENT ADVISORS; TALK ABOUT COURSES AND RESEARCH, CLUBS, CAREERS, AND LIFE . THURS 10 - NOON WOULD BE A GOOD TIME, OR e-MAIL TO GWF3. LECTURE 3 THE FIRST PyMOL ASSIGNMENT IS THE TUTORIAL, PP. 302-311 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 i. OFFICE HOURS + REVIEWS IN SUN 9/5 3 - 5PM; ii. MALOTT HALL REVIEW SESSION rm 251 TUE 9/7 4:30 - 6PM; iii. INDIVIDUAL QUESTIONS (OFFICE HOURS) TUE 8:45 - 10:45 AM IN BIOTECH 202; 4. THREE TYPES OF PyMOL HELP: HUMAN ECOLOGY : SEPT 16 IN 280 MVR CALS : SEPT 20 IN 145 WARREN HALL ARTS : SEPT 21 IN HEC AUDITORIUM, GOLDWIN SMITH HALL ENG : SEPT 22 IN UPSON LOUNGE
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FRIDAY'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 ENVIRONMENT OF GROUP COOH COO - + H + pKa = 4 COOH COO - + H + pKa = 3
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This note was uploaded on 12/10/2011 for the course BCHEM 3350 taught by Professor Feig during the Fall '09 term at Cornell.

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3 - LECTURE 3 ANNOUNCEMENTS 1 QUIZ WEDNESDAY 9/8 AND DON'T...

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