[3] Course materials

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Nov 15, 2013 (3 years and 8 months ago)

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Biochemistry
430
/827AG

20
10

Fall


Sep 08, 2010 to Dec 06, 2010.


-

MWF

11:30 to 12:20
-

CL 345.

Final Exam: Dec 17, 2010.


-

F

09:00 to 12:00
-

Location TBA

Dr.
Dae
-
Yeon Suh

LB317.2 Tel: 585
-
4239 suhdaey@uregina.ca


[1]

Office h
ours:
Open door policy.

Email for appointment.


[2]
Class website:

http://uregina.ca/suhdaey/index.html


Lecture handouts and reading materials are posted in advance as the lecture progresses.


[3]

Course materials


No textbook


Selected topics from cur
rent literature


Current Opinion in Chemical Biology

(reviews) (www.sciencedirect.com)


Nature, Nature Chem Biol, Science, Chemistry and Biology, C&EN, The Scientist, etc.


[4]

Mark Distribution


A
ssignments and presentations


20
%







Term paper





15%

Mid
-
term exam




20%


Final exam





45
%


[5]
Objectives


Appreciation of recent progress in chemical biology.


Ability to read and comprehend current literature.


Encourage scientific curiosity/enthusiasm.


[6]

Assignments

1. Assignments: Data analys
is & critical review of current literature.

2. Oral presentations with 5 to 7 OHP slides on current literature.


(Read the “Preparing a Scientific Presentation.”)

3. Term paper (due
Dec 6
) on any topic in the field of chemical biology with 15~20 referen
ces.

Candidate topics are listed in the class website with selected review articles that may assist you to
get started.

Candidate term paper topics (posted in the class website with links)

RNAi






















Biopolymer


















Natural p
roducts &
d
rug discovery





The RNA World







Prions


























Surface chemistry
&

Cell biology


Biosensors
















Epigenetics


















Antibiotics

















Molecular Imprinting







Bio
fuel


Artificial li
fe


Bacterial communications













Avian influenza

virus


Any other relevant topics can be chosen with prior approval.



[7]
Evaluation


Assignments & Term Paper
:


Data analysis and comprehension


Critical review and originality

Pre
sentations
:


Analysis and synthesis

Critical review and originality




Organization



Presentation skills




Final exam

is composed of closed and open sessions. In closed session, knowledge on basic
concepts and data analysis ability will be evaluated. I
n the open session, ability to analyze
data and synthesize coherent knowledge will be accessed.



Topics


Protein engineering/Directed enzyme evolution

Fluorescence proteins in cell biology

Chemical genetics (Ligandomics) & Unnatural amino acids incorpora
tion

Genomics/DNA microarrays/Functional genomics

Proteomics/Protein microarrays

Other “
-
omics”
-

Activity
-
based proteomics, Structural genomics, Pharmacogenetics, Metabonomics

Catalytic antibody

& Engineered antibody

Ribozyme/DNAzyme

Riboswitches

Combinat
orial biosynthesis & Metabolic engineering

DNA nanotechnology

&

Nucleic acid aptamers

Antibiotics resistance

Biomimetics

Chemical ecology


Antimicrobial peptides, Pheromones, other interesting natural products

Multivalent ligands


The topics may change d
epending on the progress of lecture.

Other topics that may be discussed if time permits include:

Biosensors/Molecularly imprinted polymers

Biopolymers


Biopolymers in drug delivery, Dendrimers, Hydrogels,

Membrane transporters
,

Organic receptors/Artific
ial cell signaling










BIOC
430
/827AG Chemical Biology


Chemical biology can be defined as an interdisciplinary science where chemistry is applied
to problems in biology.

The terminology itself has a very short history, having been used since 90’s.
Chemical
biology as a science discipline is expanding its scope with ever increasing rate, and it is
becoming a major field. Recent launching of journals bearing “chemical biology” in their
titles (
Nature Chemical biology

(2005),
ACS Chemical Biology

(2006
)) reflects this trend.

There is a merging of chemistry and biology, and more exciting discoveries are being made
at the interface of these two. Manifesting this trend, a total of 4 Nobel prizes in chemistry
during the past 5 years have been awarded to sc
ientists working on biological problems.

In this course, the term ‘chemical biology’ is defined as broadly as possible. Hence,
genomics/proteomics and other interesting research topics are also included in the course.


Nobel Prizes in Chemistry in the pa
st 10 years

1997


Paul D. Boyer (USA, *1918), John E. Walker (United Kingdom, *1941)


for their elucidation of the
enzymatic mechanism

underlying the synthesis of ATP

Jens C. Skou (Denmark,
*1918) for the
first discovery of an ion
-
transporting
enzyme, Na
+
, K
+
-
ATPase


1998


Walter Kohn (USA, *1923) for his development of the density
-
functional theory

John A. Pople (United Kingdom/US
A, 1925
-

2004)





for his development of computational methods in quantum chemistry (GAUSSIAN computer
programs)


1999


Ahmed H. Zewail (USA, Egypt, *1946)


for his studies of the transi
tion states of chemical reactions using femtosecond spectroscopy


2000


Alan J. Heeger (USA, *1936) , Alan G. MacDiarmid (USA, *1927), Hideki Shirakawa (Japan,
*1936)


for the discovery and d
evelopment of conductive polymers


2001

William S. Knowles (USA, *1917), Ryoji Noyori (Japan, *1938) for their work on chirally
catalysed hydrogenation reactions

K. Barry Sharpless (USA, *1
941) for his work on chirally catalysed oxidation reactions


2002


John B. Fenn (USA, *1917), Koichi Tanaka (Japan, *1959)


for their development of soft desorption ionisation met
hods for mass spectrometric
analyses of
biological macromolecules


Kurt Wüthrich (Switzerland, *1938)


for his development of
nuclear magnetic resonance spectroscopy for determining the
three
-
dimensional structure of biological macromolecules in solutio
n


2003


Peter Agre (USA, *1949)



for the discovery of water channels in cell membranes

Roderick MacKinnon (USA, *1956)





for
structural and mechanistic studies of ion channel
s in cell membranes


2004


Aaron Ciechanover (Israel, *1947) Avram Hershko (Israel, *1937) Irwin Rose (USA, *1926)


for the
discovery of ubiquitin
-
mediated protein degradation


2005

Yves Chauvin (France, *1930), Robert H. Grubbs (USA, *1942), Richard R. Schrock (USA, *1945)


for the development of the metathesis method in organic synthesis

2006
Roger D. Kornberg
(USA)


for his
studies of the molecular basis of eukaryotic transcription

2007

Gerhard Ertl

(Germany) for his studies of chemical process on solid surfaces

2008

Osamu Shimomura
,
Martin Chalfie
,
Roger Y. Tsien

for
the discovery and
development of the
gre
en fluorescent protein
, GFP

2009

Venkatraman Ramakrishnan
,
Thomas A. Steitz
,
Ada E. Yonath

for studies of the
structure and function of the
ribosome