FINAL EXAM: Thursday March 19, 2015 8:00 a.m.

BIBC100 Structural Biochemistry – Winter 2015
BIBC 100
STRUCTURAL BIOCHEMISTRY
LECTURE:
Tuesday and Thursday 8:00 am – 9:20 am
Price Theater
INSTRUCTORS:
M. Montal
Office Hours:
Project Assistant:
LECTURE
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 (x40931)
Thursday 9:30 am – 10:20 am
2130 Pac Hall
Kathleen McPherson
Pacific Hall 3100e
(x43568)
DATE
JAN 6 8 13 15 20 22 27 29 FEB 3 5 10 12 17 19 24 26 MAR 3 5 10 12 WINTER 2015
TOPIC
Tue Thu Tue Thu Tue Thu Tue Thu Tue Thu Tue Thu Tue Thu Tue Thu Tue Thu Tue Thu STRUCTURAL PRINCIPLES Basics Motifs α domains α/β and β structures DNA structure Folding Folding and Flexibility RECOGNITION: Protein‐DNA RECOGNITION: Immune System MID‐TERM IN CLASS CATALYSIS: Proteasess TRANSDUCTION: Membranes Membrane Proteins ‐ I Membrane Proteins ‐ II Channels Receptors Receptors Protein Design X‐Ray and NMR REVIEW Branden &
Tooze
Reference
Chapter*
1 2 3 4, 5 7 6 6 8, 10 15 11 12 12 12 12 13 13 17 18 Lehninger
6th Edition
Reference
Chapter
1 & 2 3 3 & 4 3 & 4 1 & 8 4 4 28 5 6 10 & 11 10 , 11, 19 10 , 11, 19 10 & 11 12 12 4 4 FINAL EXAM: Thursday March 19, 2015 8:00 a.m. ‐ 10:59 a.m
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BIBC100 Structural Biochemistry – Winter 2015
Textbook (Required):
Edition
Lehninger Principles of Biochemistry 6th
D. Nelson & M. Cox
W.H. Freeman & Co. 2013
*Textbook (Optional)Strongly Recommended: Introduction to Protein Structure. C. Branden and
J.Tooze, 2nd Edition. Garland Publishing Co., NY 1999.
*Strongly Recommended - Kinemage Supplement to Branden and Tooze
J.S. Richardson and D.C. Richardson
Garland Publishing Co., NY
You may download the program using the following link
http://kinemage.biochem.duke.edu/
Class Websites:
Required Websites:
http://classes.biology.ucsd.edu/bibc100.WI15
http://www.rcsb.org
Course Requirements:
Midterm:
Final:
GRADE
Thursday, February 5, during class
March 19, ??-??
40%
60%
Note: Check your midterm and final exam schedules NOW. There are no
alternate exams offered for this class regardless of whether you have other
exam(s) on one day. Please plan ahead.
You are only responsible for the material covered in class, not for all the material in
each chapter. Figures from other sources will be included in the lectures. Many of these
figures will appear in the class Power Point presentations which will be available on the
class website. This class will not be podcast.
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BIBC100 Structural Biochemistry – Winter 2015
Graduate and Undergraduate Student Teaching Assistants
Graduate:
Luers, Lori Hiroko Pirahanchi, Yasaman Camelia Stoddard, Nicole Christine Van Fossan, Donald Wayne lluers@ucsd.edu ypirahan@ucsd.edu nstoddar@ucsd.edu dvanfoss@ucsd.edu Undergraduate:
Mansour, Christina Marie Ratitong, Bridget Zhao, Mitchell Jia Khasho, Nicholas Anthony Loyola, Anthony Alfaro Sinha, Joydeb Tran, Thanh Duy cmansour@ucsd.edu bratiton@ucsd.edu mjzhao@ucsd.edu nkhasho@ucsd.edu aaloyola@ucsd.edu jsinha@ucsd.edu tdt008@ucsd.edu 3
BIBC100 Structural Biochemistry – Winter 2015
BIBC 100: STRUCTURAL BIOCHEMISTRY
GRADING INFORMATION:
Plus and minus grading will not be used
MIDTERM:
Grade Revisions:
Submit request to TA no later than February 12, 2015
No grade changes after February 19, 2015
NO EXCEPTIONS
FINAL:
Grade Revisions:
Submit request to Professor or TA no later than
March 23, 2015
No grade changes after March 27, 2015
NO EXCEPTIONS
POLICY ON REGRADES:
Regrades: If a student considers that his/her exam was not properly graded, they may
turn in the unaltered, complete exam for a regrade to the TAs no later than 1 week after
the exams become available for pick-up. Students must write up on a separate sheet
attached to the exam which questions they consider require regrading and sign the
bottom of this sheet.
Students are responsible for understanding that, by requesting a regrade, the
entire exam in addition to the indicated questions will be re-evaluated, and points
may be added or taken away as a result.
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BIBC100 Structural Biochemistry – Winter 2015
BIBC 100: Structural Biochemistry
Guidelines for Class Etiquette During Examination
1. All writing instruments must contain non-erasable ink. If students choose not to write
in pen, they forfeit the opportunity for a future regrade.
2. All books and handbags should be placed at the front or back section of the
auditorium for the duration of the exam.
3. Students should sit in alternating seats whenever possible.
4. When time is called, anyone who is still writing will automatically receive a zero for
that page. THIS WILL BE STRICTLY ENFORCED. Remain in your seat and hand
your exam down the aisle.
UCSD Policy on Integrity of Scholarship and Rules of academic dishonesty will be
strictly enforced. Please see link below.
http://senate.ucsd.edu/manual/appendices/appendix2.pdf
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BIBC100 Structural Biochemistry – Winter 2015
Protein Data bank
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (PDB)
<http://www.rcsb.org/> is the single international source for 3D structure files. A four
character PDB ID is the identifier for the structure of a given Protein. Using the
identifier and the molecular viewer Jmol, or preferably Protein Workshop, you can see
and study the 3D structure of these proteins (and many, many more). Also if you have
an iPhone you can download the free Apps RCSB PDB (preferable), Molecules or
iMolview Lite.
ENJOY AND IMAGINE!
Protein
PDB ID
Hemoglobin
1A3N
GroEL/GroES complex
Chymotrypsin
Myoglobin
Myoglobin
α-hemolysin
Immunoglobulin G 2A intact
Immunoglobulin G 2A fab
fragment
Immunoglobulin G 2A fab
fragment (50.1) complex
with 16-residue peptide
Lysozyme
Bacteriorhodopsin
Aquaporin
Maltoporin
Maltoporin
Lactose permease (lactose
transporter
Aquaporin 1, AQP-1
K channel protein
Voltage-gated K channel
Voltage-gated K channel
Ras protein
Protein kinase A; R2C2
complex
Green fluorescent protein
(GFP)
Calmodulin
1AON
6GCH
1MBO
2MBW
7AHL
1IGT
1GGC
+
+
+
1GGI
1LZE
2AT9
2B6O
1AF6
1MAL
1PV7
1J4N
1BL8
1J95
2A79
5P21
1U7E
1GFL
1CLL
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BIBC100 Structural Biochemistry – Winter 2015
SHC (SH2 domain)
Bacteriorhodopsin
(rhodopsin and G protein transducin
Protein kinase (active site)
Cytochrome c oxidase
Bovine mitochondrial F1ATP Synthase
ATP synthase chain (FoF1)
Photosynthetic reaction
center
Light harvesting complex II
Bacteriorhodopsin
Photosystem II
Cytolytic α-helical toxin- cytolysin
SecA-SecYEG Protein translocation
channel
GPCR- β-adrenergic receptor
β 2 adrenergic receptor–Gs complex
1SHC
1BAC
1S9I
1OCC
1BMF
1QO1
1PRC
2BHW
1C8R
2AXT
2WCD
3DIN
2RH1
3SN6
Additional PDB codes for structures discussed in lecture appear in the Class website under
“Announcements”
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