304 Schedule - Biocore

Biocore 304: Cellular Biology Laboratory
-

Spring
201
1

Schedule

Your grade will be based on the assignments listed below. Note that the Subcellular Fractionation paper and Signal Transduct
ion
Poster are group grades. Check (√) assignments are scored simply adequate or inadequate; papers are graded using the criteria

d
escribed in the
Biocore Writing Manual
. Papers & assignments must be handed in on time unless you have contacted your TA
ahead
of time

to request an extension due to emergency or extenuating circumstances. Otherwise, we will deduct one grade per weekday
it is
late from the grade you would have received (
e.g.
, A
-
>AB for one day late). Note that even an F paper (one week late) counts more
than 0 (not handed in at all) when we total the final grades at the end of the semester. Late reports should be given
directly to your
TA, Janet Batzli or Michelle Harris (not put in a mailbox or submitted electronically).


Lecture topics

Week/
(date)

Lab Topic

Lab Activities/Assignments


Weight

Imaging, cell
composition

1 (Jan.
1
8
-
2
1
)

Microscopy:

Image Formation



Realign messed up microscope
–

do in lab



Cell observations/diagrams
–

do in lab





Macromolecule
structure/function,
organelles,
bioenergetics

2 (Jan.
2
4
-
2
8
)

Subcellular
Fractionation



Subcellular Fractionation pre
-
lab

due in disc.



Microscopy assignment

(produce hand drawings
with figure legends) due in lab

2
%

3%

Enzyme catalysis,
membranes &
transport, metabolic
pathways & role of
ATP

3 (
Jan
31
-

Feb
4
)

Enzyme I:
Alkaline
Phosphatase &
MM Kinetics



Enzyme pre
-
lab assignment due in disc.



Teams decide final
[
S
]

in disc



Subcell. Fract. Paper
(1/pair)

due in lab



Graphs & calculations for K
m
, V
max
–

do in lab

2
%


5
%



Glycolysis, anaerobic
energy metabolism, fat
metabolism, citric acid
cycle

4 (Feb.
7
-
1
1
)

Enzyme II:

Extended
Literature
Search/
Bioinformatics/
Statistics




Complete BLAST
&

ClustalW eTeach
es

and
Jmol
tutorial

& turn in answers to questions
at

beginning
of disc



Extended literatu
re search
(in disc)



Data Analysis pre
-
lab Part I assignment

due
beginning of lab



PL
AP physical
models
; Consurf analysis

(in lab)



Molecular structure/function:
E. coli

AP mutation
activity

(in lab)




Introduce t
-
tests, online stats materials (in lab)



Generate
enzyme
question, brief rationale,
hypothesis, tentative expt. design (1/team)



Teams sign up

for formal presentation feedback






2%














Electron transport &
ATP generation,
chloroplast &
photop
hosphoryl
-
ation, photosynthesis


5 (Feb.
1
4
-
1
8
)

Enzyme III:

Proposal
Feedback
Presentation /
Pilot Studies



Data Analysis pre
-
lab Part II:

focus on your
enzyme protocol and expected data (due in disc).



Focus on experimental design with team (in disc)



Enzyme proposal feedback presentation (1/team) in
lab



Enzyme Research Proposal
due 48h after
presentation



Enzyme question/methods/schedule (1
/team)

2%






7
%




Metabolic integration
;
DNA & chromosome
structure & replication

EXAM I
Wedne
sday
Feb.
2
3

7:15pm

6 (Feb.
2
1
-
2
5
)


Enzyme IV:

Final Experiment




Focus on Peer Review: our expectations (in disc.)
–

peer review practice exercise



Enzyme proposal returned with comments



Teams collect data (open lab)





Transcription & RNA
processing, translation
& genetic code,
mutation & DNA
repair

7 (
Feb
28
-
Mar
4
)

Molecular
Genetics I: Intro
to
C. elegans
,
heat shock
proteins, and
RNAi / GFP to

study gene
expression



Peer review

conference

Final Enzyme papers in
disc.



Start to introduce Worm unit in disc, observe
wildtype worms



Final Enzyme paper (13%)
+
peer review (2%)

+
author’s response + GEA forms

due in lab or
lecture



View Podcast on worm

morph

(Part 1)

& life
-
cycle,
RNAi, GFP

(Part 2)

before

lab





15%







In
-
class

stations:
C. elegans

gene expression
worksheet



Develop study question and tentative biorationale






Bacterial genetics,
transposable elements

8 (Mar
7
-
1
1
)

Molecular
Genetics II:
Developing
experiments on
gene expression
in
C. elegans



Worm stress
/

gene expression

+ statistics

(ANOVA, Chi
-
square)
Prelab

due in disc.



Worm proposal feedback presentations

in lab



Materials and schedule sheet
-

detailing how, when,
and who will perform each step of experiment



Mid
-
semester evaluations

3
%









Spring Recess March 14
-

18

Genetic engineering,
prokaryotic gene
regulation

9 (Mar
21
-
25)

Molecular
Genetics III:
Worm
experiments



Worm proposal mini
-
poster peer review in

discussion



Worm research proposal

poster

due in lab



Do worm experiments
-

establish treatments
, pilot
studies,

and RNAi set up, gather data




8%



Prokaryotic &
eukaryotic gene
regulation, genomics



10
(Mar.
28
-
Apr
1)

Molecular
Genetics IV:
Data
Analysis
and Poster
Development



Biocore 324 preview in lab (in disc.)




Worm data collection
and poster development




Worm data analysis
(chi
-
square)
: what do your data
indicate?



Worm proposal posters returned with comments






Protein trafficking,
cell
signaling

EXAM II
Tu
esday
Apr.
5

7:15pm

11
(Apr.
4
-
8)

Signal
Transduction I:
Intro to Yeast
System



Do genetic transformations in discussion
,
introduction to cell shape and
B
-
gal assay



Generate tentative question for Sign. Trans project
(1/team) due in
lab



C. elegans

mini
-
posters + GEA
due

in Fri. lecture






15%

G
-
linked receptors,
second messengers,
growth factors &
receptor tyrosine
kinases

12
(Apr.
11
-
15)

Signal
Transduction II:
Present
Proposals (disc
& lab);



Signal Transduct. prelab

due in disc.



Signal Transduction feedback presentation (1/team)
in lab



Intro to 2
-
way ANOVA during presentations



Materials & schedule for signal transduction project
(1/team) due in lab

3%







Ras signaling,
hormones, cytoskeletal
proteins



13
(Apr.
1
8
-
2
2
)

Signal
Transduction III:
Pilot Studies &
Your Experiment



Peer reviewers meet to discuss signal transduction
proposal papers (in disc)



Signal Transduction Proposal Paper (1
3
%) +
peer review (2%)
+ author’s response
–

due
Wed
lecture or
lab




Data collection I in lab



1
5
%

Cell movement, cell
adhesion, cell cycle

14
(Apr.
25
-
29)

Signal
Transduction IV:
Data Analysis



Genetics Concept Assessment in disc



Data collection II in lab



Cell cycle & apoptosis,
cancer

15
(May
2
-
6)

Signal
Transduction V:
Poster Presen.



Practice presentation & group poster peer review
during
discussion




Signal transduction Posters Formal
Presentations (1/team)+ GEA

forms



Final course evaluation




15%




Team work, class participation and check
assignments

3
%


Grade Breakdown

Percentage

Letter Grade

90
-
100

A

80
-
89

B

70
-
79

C

Assignments, due dates, and individual assignment weight in percent are detailed above.
Biocore 304 is a
Comm
-
B course and therefore is writing intensive. Grades on assignments
will not be curved. For those few individuals that are on the borderline at the end of the
semester, we will assign intermediate grades (AB and BC) based on our evaluation of your
part
icipation (in both lab AND discussion), teamwork and your effort.


60
-
69

D

Percentage

Letter Grade

90%

A

80%

B

70%

C

60%

D

Percentage

Letter Grade

90
-
100

A

80
-
89

B

70
-
79

C

60
-
69

D