1. LECTURE 2
1. READING ASSIGNMENT FOR NEXT WEEK: pp. 71-84, 92-94, 102-106,132-133 [Ch
1&2 REV]
PROBLEM ASSIGNMENT FOR NEXT WEEK: LG 1,2; CH 3 #2, 4, 7 PLUS:KNOW STRUCTURES OF ALL 20 AMINO
ACIDSDO ENTIRE PyMOL TUTORIAL, LG pp 302-311
FOLLOW INSTRUCTIONS EXACTLY; WE SUGGEST THAT
YOU DO THE ENTIRE TUTORIAL TWICE (!)
2. BUY THE TEXT AND LECTURE GUIDE.
7. GRADING SYSTEM FOR THIS CLASS: THANKS TO THE STUDENTS WHO CAME
WED TO FIGURE THIS OUT! (BELOW ALL ON BLACKBOARD-- NO NEED FOR
DETAILED NOTES!)A. QUIZZES WORTH 30%, MIDTERM 30%, AND FINAL EXAM 40%.
EACH EXAM IS NORMALIZED BY DIVIDING BY THE MEAN. THERE ARE
DIFFERENT VERSIONS OF EACH QUIZ, AND THERE IS A MAKE-UP FOR THE
MIDTERM AND FOR THE FINAL, BUT THE NORMALIZED SCORES CAN BE
COMPARED. NO MAKE-UP QUIZZES.
THE MEDIAN COURSE GRADE WILL BE B+. IF YOU GOT THE MEAN ON EVERY
FOR QUIZ 1 ONLY
3. REGULAR REVIEWS AND OFFICE HOURS START NEXT WEEK. ONE CHANGE:
FO HSU'S HOURS TU 8:45-10:45AM WILL BE DEDICATED TO PYMOL QUESTIONS
ONLY.
5. "INTERVIEWING AT MEDICAL/DENTAL SCHOOL" TUE 8/31 12:20PM, NORTH
ROOM IN WILLARD STRAIGHT HALL.
6. ANY INTERESTED STUDENTS: “HOW TO FIND A LAB RESEARCH POSITION.
WHAT ARE THEY LOOKING FOR?!", 2:55 - 4:00PM, TODAY IN COMSTOCK B108.
4. APPLYING TO VET MED PROGRAMS (USA AND ABROAD): MON 8/30 4:35PM,
245 WARREN HALL.

2. iii. THUS, 8 QUIZZES COUNT TOWARD YOUR GRADE. ENTERING THE LAST
WEEK OF CLASSES, IF YOU TOOK FEWER THAN 9 FOR ANY REASON, THEN
YOU WOULD BE ELIGIBLE TO TAKE THE 10th "MAKE-UP QUIZ" ON WED 12/1.
(THE SUBJECT MATTER OF THAT "MAKE-UP QUIZ" WILL BE THE LECTURES
OF THAT WEEK OF THE COURSE, NOT THE PARTICULAR QUIZ THAT YOU
MISSED). IN SUM, NO STUDENT CAN TAKE MORE THAN 9 QUIZZES, AND 8
QUIZZES COUNT TOWARD THE GRADE;
C. IF YOU MISS MORE THAN 2 QUIZZES DURING THE SEMESTER, SEE
PROF. DO NOT SEE PROF TO EXPLAIN WHY YOU MISSED 2 QUIZZES OR
ANY PARTICULAR QUIZ.
E. SEE PROF WITH ANY SPECIAL PROBLEMS. SEND E-MAIL TO GWF3,
NOT TO BIO3310 IF YOU WANT TO REACH THE PROF.
D*. IF THE FINAL EXAM GRADE IS HIGHER THAN THE AVERAGE OF (Q + MT)
THEN THE FINAL EXAM GRADE WILL BE YOUR FINAL COURSE GRADE.
ii. ONE QUIZ GRADE IS DROPPED (LOWEST SCORE OR ANOTHER MISSED
QUIZ);
B. WE WILL HAVE A TOTAL OF 10 WED MORNING QUIZZES. HERE ARE THE
DETAILS:
i. YOU CAN MISS ANY ONE OF THESE 10 QUIZZES. IN FACT, EACH
STUDENT IS ONLY ALLOWED TO TAKE 9 QUIZZES! THIS POLICY ALLOWS
STUDENTS TO MISS ONE QUIZ FOR ANY REASON (e.g. RELIGIOUS
HOLIDAY) WITH NO PENALTY;

3. WEDNESDAY’S LECTURE
THIS CLASS IS ABOUT THE CHEMICAL REACTIONS OF
LIFE:
4 MAIN CATEGORIES OF BIOMOLECULES
PROTEINS, NUCLEIC ACIDS, CARBOHYDRATES, LIPIDS
PATTERNS OF REACTIONS
--WHICH REACTIONS?
--HOW INTERCONNECTED?
--HOW TURNED OFF AND ON?
PATTERNS OF PROTEIN STRUCTURE
--WHAT PATTERNS DO WE SEE?
--WHAT IS THE ORIGIN OF THESE
PATTERNS?
--HOW DO ENZYMES CATALYZE
REACTIONS?
--HOW ARE ENZYMES UNDER CONTROL?
START AT MOST SIMPLE LEVEL: AMINO
ACIDS
CONTROL POINT
IS PROTEINS
HEXOKINASE
BRIEF
DIGRESSION TO
PyMOL

4. AMINO ACIDS
MOST SIMPLE
REPRESENTATION
CORRECTION #1
STEREOISOMERS:
1. ROTATE PLANE OF
POLARIZED
LIGHT IN OPPOSITE WAYS;
2. REACT VERY DIFFERENTLY IN
BIOLOGICAL SYSTEMS
CORRECTION #2
α
SHOWN: CORRECT
CHARGES AT pH = 7
(A ZWITTERION)
ONLY L-ISOMER AA ARE
FOUND IN PROTEINS
BECAUSE SHAPE DETAILS
ARE IMPORTANT IN
BIOLOGY!
SHAPE
CHARGE ON
IONIZABLE
GROUPS
WHY ARE CHARGES
SO IMPORTANT?!

5. ION PAIRS (PURPLE SPACEFILLING) HOLD HEMOGLOBIN
TOGETHER!
HISTIDINE
+
-
+
-
-
HIS
CAN
HAVE +
CHARG
E OR
NO
CHARG
E
ASPARTIC
ACID
HISTIDIN
E
H+
AA R
GROUP
(SIDECHAIN
)
ION PAIR
FORMS
ONLY
IF EACH
GROUP IS
CHARGED

6. DEPENDENCE OF PROTONATION OF IONIZABLE GROUP ON pH
DEFINE:
REARRANG
E
HENDERSON-HASSELBALCH EQUATION
CARBOXY
L
AMINO
NOTE! H-H EQUATION
DESCRIBES ONE IONIZATION
"EVENT"
APPLY H-H SEPARATELY TO
EACH IONIZABLE GROUP

7. WHAT TO LEARN BY USING THE H-H EQUATION
pKa = 2.4 FOR CONVENIENCE, CHOOSE pH =
2.88
pH = pKa +
LOG
[UNPROTONATE
D][PROTONATED]
2.88 = 2.4 + LOG[COO
-
]
[COOH
]
0.48 = LOG (3/1)
A SIMPLE CALC-- BUT WHAT DO WE
LEARN?!
1. FOR A SINGLE GLY AT pH = 2.88:
OUT OF EVERY 4 SEC, H+
IS "ON" FORMING COOH FOR
1 SEC H+
IS "OFF" FORMING COO-
FOR 3 SEC
TIME AVERAGE
VIEWPOINT
2. FOR A BEAKER FULL OF GLY AT pH =
2.88:
AT A GIVEN INSTANT IN TIME, 1/4 OF GLY HAVE
COOH 3/4 OF GLY HAVE
COO-
THESE ARE ALSO
PROBABILITIES FOR
GROUP BEING
PROTONATED OR UN
USE SUCH CALC TO ESTIMATE PARTIAL CHARGE ON IONIZABLE
GROUPS, AND FRACTION OF IONIZABLE GROUPS IN ION-PAIRS
SIMPLE RULES TO REMEMBER:
IF pH << pKa, THEN H+ IS PREDOMINANTLY "ON" THE
GROUP IF pH >> pKa, THEN H+ IS PREDOMINANTLY
"OFF" THE GROUP IF pH = pKa, THEN [UNPROTONATED]
CALC. FOR COOH OF
GLY,

8. FORM OF IONIZABLE GROUPS AT ANY pH
IONIZABLE GROUP
PROTONATE
D FORM
(ACID)
UNPROTONATE
D FORM (BASE) pKa RANGE FOUND IN
PROTEINS
THE IONIZABLE GROUPS IN PROTEINS ARE SHOWN BELOW
ONLY THE SIDE CHAINS SHOWN BELOW CAN IONIZE, NOT THE OTHERS!
WHY IMPORTANT TO KNOW IONIZATION STATE: 1. PROTEIN STRUCTURE;
2. PROTEIN BINDING OF OTHER MOLECULES; 3. MECHANISM OF
CATALYSIS
TABLE 3.1 & FIG. 3.5 IN TEXT MISLEADING! USE INFO FROM LECTURE AND
LECTURE GUIDE!
NOT THE FREE AA
3.0 - 4.6
7.2 - 8.2
2.3 - 4.7
(Asp) 3.3 -
5.1 (Glu)
5.6 - 7.6
4.1 - 9.5
9.1 -
11.5
9.4 -
11.6

9. AMINO ACID SIDE CHAINS
EXACTLY 20 CODED BY DNABUT: SURVEY ALL PROTEINS, FIND ~2000 DIFF AA!
THESE2000 AA ARE CHEMICALLY MODIFIED DURING/AFTER SYNTHESIS ON
RIBOSOME
NAME
3-LETTER
ABBREV.
G A V L
GLY ALA VAL LEU ILE
THE CLASS OF ALIPHATIC AA,
ARRANGED AS A PEPTIDE
GLYCINE ALANINE VALINE LEUCINE
ISOLEUCINE
THESE ARE “FREE” IN CYTOSOL (NOT
INPROTEINS); SOME HAVE BIOLOGICAL ACTIVITY, OTHERS MERELY INTERMEDIATE
ON PATHWAY OF SYNTHESIS OR DEGRADATION
100s OF “NATURALLY OCCURRING”
AA
THESE 20 ENOUGH TO CREATE EVERY POSSIBLE 3-D PATTERN NEEDED: THE
"FOLDS"
EVERY POSSIBLE 3-D PATTERN "FOLDS"

10. SOME H-BOND PROPERTIES:
-O-H O=C-
AROMATIC AMINO ACIDSAROMATIC AMINO ACIDS
PHE TYR TRP
F Y
W
PHENYLALANINE TYROSINE TRYPTOPHAN
OH
H
CHEMICAL MODIFICATION OF AMINO
ACIDS SEE WIKI
"POSTTRANSLATIONAL MODIFICATION"
SOME H-BOND
ACCEPTORS
SOME H-BOND
DONORS
DEVIATIONS FROM STRAIGHT LINE
10o
DEVIATION LOSE 6% OF
STABILITY40o
DEVIATION LOSE ALL
STABILITY
2.8 - 3.2
A
o
THE TWO
ELECTRONEGATIV
E ATOMS AND H IN
STRAIGHT LINE
1. GIVE PROTEIN NEW CATALYTIC
POWERS 2. TURN ENZYME "ON" OR
"OFF" 3. CHANGE
LOCATION, e.g. BIND MEMBRANE
CHEM
MOD

11. S-
CONTAINING
CH2S-
NUCLEOPHILEOXIDIZE TWO CYS-
SHCYS-SH SITE OF CHEM MOD.
MET SIDECHAIN:
ROLE IN
BIOSYN:
MET CONNECTED TO MUCH
METABOLISM
-OH FOUND IN ENZYME ACTIVE
SITE:
CHEM. MOD. OF SER OR THR
OH:
ALIPHATIC
-OH
DISULFIDE
BOND
e.g. ADDITION OF FATTY
ACID TO FORM THIOESTER
CYS-S-S-CYS
VERY REACTIVE!
NONPOLAR
FOR METABOLIC RXNS OF
METHYL ADDITION, MET IS MAIN
DONOR
THEREFORE:
"CONNECTED"A JARGON WORD MEANING:
[MET] IS REGULATED BY CONC. OF OTHER
MOLECULES & MET BOUND BY PROTEINS
WHERE IT TAKES PART IN BINDING
AND IN CHEM. RXN
PHOSPHATE ADDITION
(PHOSPHOESTER FORMATION) IS
MOST COMMON OF ALL CHEM. MOD!
IT CHANGES THE ENZYME!
CYS MET
C M
CYSTEINE
METHIONINE
SERINE THREONINE
SER THR
S T