Media
Theater M110 - Tuesday and
Thursday, 2:00 - 3:45 PM
Lindsay Hinck
351 Sinsheimer, Office, 459-5253
324 Sinsheimer, Lab, 459-2546
Email address: hinck@biology.ucsc.edu I
answer class emails on Friday morning
Course Web Site – http://bio.classes.ucsc.edu/bio110/
Podcasts of lectures available
at: https://media4.ucsc.edu/webcast/
Text: Alberts et al. –
Molecular Biology of the Cell, 5th Edition, 2008
QuickTime conversions for animations
for those of you who have the new version of Quicktime
http://www.garlandscience.com/textbooks/0815341059.asp?type=resources
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Topic |
Chapters |
Exam # |
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Sep 24 |
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1 |
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Sep 29 |
Ch. 8 not sections
on NMR, Mass Spec, FRET and genetics (553-566) Ch. 9 all |
1 |
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Oct 1 |
L3: Plasma
Membrane Structure and Function I |
Ch. 3 125-142; 153-159; Ch. 10 |
1 |
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Oct 6 |
L4: Plasma
Membrane Function II |
Ch. 11 |
1 |
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Oct 8 |
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Munro.pdf, Cell V48,
p899-907 |
1 |
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Oct 13 |
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Ch. 12 p695-704 & 723-745 Ch. 6, p388-399 Munro et al., Cell V48, p899-907 |
1 |
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Oct 15 |
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Ch. 13 |
1 |
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Exam 1 |
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Oct 22 |
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Ch. 15 |
2 |
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Oct 27 |
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Ch. 15 |
2 |
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Oct 29 |
Ch. 15/16 |
2 |
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L11: The Cytoskeleton – Microtubules |
Ch. 16 |
2 |
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Nov 5 |
L12: The Cytoskeleton – Microfilaments |
Ch. 16 |
2 |
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Nov 10 |
Exam 2
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Nov 12 |
Cell Division and Cycle Regulation |
Ch 17 |
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Cell Cycle Regulation and Cell Death |
Ch. 17, 18 |
3 |
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Nov 19 |
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Ch. 4 |
3 |
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Nov 24 |
L16: Cell-Cell Interactions/Extracellular Matrix |
Ch. 19 |
3 |
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Nov 26 |
HOLIDAY |
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Dec 1 |
L17: Cell Biology of Development and Cancer |
Ch. 20, 22, 23 Selected reading to be determined |
3 |
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Dec 3 |
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3 |
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Dec 8 |
Exam 3 12:00
– 3:00 PM |
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There is no requirement to
attend section and you may attend any section and as many sections as you
like. In general, the TAs will
answer questions and go over problem sets and practice exams. Exams are distributed in section.
Beginning Week of 9/28/09
|
Sec |
Day |
Time |
Building |
Room |
TA |
|
A |
Mon |
2:00PM-3:10PM |
Phys Sciences |
136 |
Gary Longo |
|
B |
Mon |
3:30PM-4:40PM |
Phys Sciences |
136 |
Gary Longo |
|
C |
Thur |
8:30AM-9:40AM |
PhysSciences |
130 |
Mikhail Binnewies |
|
D |
Fri |
9:30AM-10:40AM |
PhysSciences |
130 |
Duylinh Nguyen |
|
E |
Fri |
11:00AM-12:10PM |
PhysSciences |
130 |
Duylinh Nguyen |
|
G |
Thur |
10:00AM-11:10AM |
Earth & Marine |
B214 |
Mikhail Binnewies |
|
H |
Thur |
12:00PM-1:10PM |
Earth & Marine |
B214 |
David Ludwig |
|
I |
Fri |
2:00PM-3:10PM |
Eight Acad |
252 |
Assistance with Disabilities
Students with disabilities
who need special assistance with this course should provide the course
coordinator with documentation from the Disabilities Resource Center at the
first two meetings of the class. You can make an appointment 9-2089 or email
drc@ucsc.edu
Thimann 347,
Monday 1-2pm and Tuesdays 12:00-1:00 pm
Duylinh Nguyen: dlnguyen87@gmail.com
Thimann
347, Monday and Tuesdays at 9-10am
4) apoptosis
http://stke.sciencemag.org/content/vol2007/issue380/images/data/tr1/DC1/Apoptosis_WEHI.mov
http://www.jove.com/index/details.stp?ID=662
6) rap cell
biology
7) cilia and flagella
http://www.northland.cc.mn.us/biology/biology1111/animations/flagellum.html
http://learn.genetics.utah.edu/content/begin/cells/scale/
There will be three exams. The
first two will each cover the material from one third of the course and each
will be worth 100 points. The third and final exam will be comprehensive,
covering both the material covered in the final third of the course as well as
key material covered in the earlier part of the quarter; it will be worth 150
points. The exam dates and the classes covered on each exam are indicated in
the syllabus. The exam format will be multiple choice. You will need to bring
the pink, whole page scantron sheets to exams. These are available at the
bookstore.
Cheating on exams will not be
tolerated. Evidence of cheating
will result in a zero score for that exam and will be reported to the relevant
College Provost.
Make-up exams will only be allowed
if there is a legitimate reason such as illness, serious family emergency, or a
University sponsored event. The make-up will be an oral exam given by me. You
are responsible for contacting me BEFORE the exam to notify me of your illness
or other excuse. YOU are also responsible for contacting me AFTER the exam to
schedule your make-up. The make-up must be scheduled within 48H of the exam.
Exams
are graded by computer. If you have a question about an exam grade, you must
talk with me within a week after the exams are handed back.
Biochemistry Review Guide
Chapters 2,3 and 4 of your
textbook covers many of these concepts.
You should be familiar with
the following-
Covalent
bonds
Ionic
bonds
Hydrogen
bonds
van
der Waals forces
Sugars
and Polysaccharides
simple
monosaccharides (CH2O)n
glucose,
fructose, ribose
glycogen,
starch
Fatty
acids and lipids
Basic
fatty acid structure
CH3(CH2)nCOOH
Basic
structure of a triglyceride = glycerol + 3 fatty acid chains
Basic
structure of phospholipid
Nucleotides and Nucleic Acids
Bases
- A, C, G, T, U
Base
+ (ribose or deoxyribose) = nucleoside
Nucleoside
+ phosphates = nucleotide
purines
vs. pyrimidines - be able to draw basic ring structure for each
ribo-
vs. deoxyribonucleic acid (be able to draw the sugar/phosphate backbone for
each)
Amino Acids and Proteins
Know
the basic structure of an amino acid
Know
the names of the 20 amino acids (knowing their 1 letter abbreviation
is also helpful)
For
each amino acid you should know which of the folllowing four categories
it belongs in:
non-polar
polar
charged
basic
charged
acidic
Draw
a peptide bond
Draw
a disulfide bridge between cysteines
Protein
structure
primary
structure - amino acid sequence
secondary
structure - alpha helices and beta sheets
tertiary
structure - longer range interactions leading to domains and
final folded form of single polypeptide
quaternary
structure - interactions between different polypeptides
to form a multiprotein complex
Understand
the importance of hydrophobic interactions in protein folding
Know
how alpha helices and parallel or antiparallel beta sheets work to mask
the polar peptide bonds in a folded protein - be able to draw
these structures
Understand
the idea of a domain in a folded protein
Understand
the Gibbs free energy equation and know what each term means
DG = DH - TDS
Reactions
with a negative DG value will
proceed spontaneously, but they must overcome
an activation energy barrier
Enzymes
act as biological catalysts to lower the activation energy for a reaction.
Enzymes
do not alter the DG of a reaction.
Reactions
with a positive DG will not proceed
spontaneously, however they can be coupled
to reactions with a larger negative DG value.
Many
reactions are coupled to hydrolysis of ATP.
ATP
--> ADP + Pi DG = -7.3 kcal/mol
The
energy from ATP hydrolysis can be coupled to a reaction with a positive DG to allow it to proceed.