Reading Schedule
Non-journal readings come from Life 8th Ed., by Purves et al.

1) Learning Molecular Tools

Week #1 (Jan 11 - 15)

Week #2 (Jan 18 - 22)

Week #3 (Jan 25 - 29)

Week #4 (Feb 1- Feb 5)

2) Virtual Reprints

A. Structure - Function: How do Calcium Pumps of the SR/ER work?

B. What is a Green Fluorescent Protein (GFP) and why is it so popular?

C. How do proteins "know" when to stay in the ER?

D. Methods that have produced a big impact.

E. How does a mammalian fetus know if it is supposed to be male or female?

F. How do cells in an embryo know which type of cell they should be?

Starting at Square One - learning the tools

Molecular Biology Lecture Schedule for First 3 Weeks and First Exam

Readings come from Life8th Ed., by Purves et al.

Week #1 (Jan 11 - 15) (return to the begining)


 entrance exam, introdution, syllabus


pg 57-60 * Section 3.5
figures 3.23-24

* figure 11.9

* ATP v. dATP v. ddATP

* ATP v. cAMP


pg 239-241* Four key features...

pg 262-264 * Transcription occurs....stop @ The Genetic Code...

pg 187-188 * Eukaryotic... stop @ Overview: Mitosis...

* Jmol image of double stranded DNA

* Jmol image of DNA polymerase in action

* Different form of DNA polymerase
Dimeric DNA Polymerase III (b subunit) from E. coli (sliding DNA clamp structure)


pg 241-249 * Section 11.3

* DNA replication (front view)
* DNA replication (back left view)
* DNA replication (back right view)
* DNA replication (view from above)

* AFM Image of DNA - produced by John Cowan ('97)


* Jmol image of T7 RNA pol

pg 313 - 322 Sections 14.2-14.4 * The structure...stop @ Gene experession can be...

pg 324 - 326 * Section 14.5...

pg 261-262 * Section 12.3...stop@ The information for protein...

* Animation of transcription

* Jmol image of Cro dimer binding to DNA

* Jmol image of TATA-binding protein


pg 264 -272 * The Genetic Code... stop@ Section 12.5

pg 272-274 * Section 12.5

* Jmol image of aspartyl-tRNA synthase

* Compare two t-RNAs

* Animation of translation

Week #2 (Jan 18 - 22) (return to the beginning)

Martin Luther King, Jr. Day - Classes Cancelled



 pg 359 * First two paragraphs in Section 16.3

pg 562 * Table 26.1 (compare with Section 4.2)


pg 293 - 295 * Plasmids are... stop@Transposable elements...

pg 358-359 * Section 16.2

* Image of a real plasmid

* cartoon of plasmid used for expression

* Blue/White Selection with lacZ disruption (scroll down some)

* polylinker in BioBricks

* figures 16.7, 16.8, 16.9, 16.10


pg 360 * Viruses as vectors

pg 283 - 287 * Section 13.1... stop @ Animal viruses...

* Table 13.1


 pg 354-355 * Gel electrophoresis... stop@ Single nucleotide...

* gel simulator to illustrate how % matrix impacts resolution


* Calculating MW on a gel

* Example of a protein Gel


* figure 16.2

* Southern blot

* Image of a Real Southern Blot

* Northern blot

 cDNA pg 363 * cDNA libraries....

* figure 13.6 and 16.12

* making cDNA


pg 250 -251 * The Polymerase Chain Reaction...

* figure 11.23

* Home Movie showing PCR

Animation of PCR

 sequencing &


pg 251-253 * The Nucleotide sequence...

* figure 11.24

* dideoxyribonucleotides (Jmol image)

* Sanger Method online (student page)

* cycle sequencing

* automated sequencer (non-gel based, capillary electrophoresis)

* non-radioactive sequencing (compare non-rad & radioactive processes)


pg 314* Research Method: Nucleic Acid Hybridization

pg 355 * Research Method: Southern Blotting

Week #3 (Jan 25 - 29) (return to the beginning)


pg 353-354 * Restriction enzymes....

pg 358 - 359 * Section 16.2

* figures 16.1, 16.2, 16.7. 16.9, 16.10, 16.11

* movie of a restriction enzyme in action

* BioBricks and compatible sticky ends

* Cloning BioBrick parts


pg 381 - 382* Genetic markers...stop @ Disease-causing...

figures 16.4; figure 17.8, 17.12

* Southern blot

* Image of a Real Southern Blot

* Northern blot


pg 362 - 363 * Section 16.4...stop @ DNA mutations can....

*Cloning DNA (animation)


Web Pages


Your web pages are ready to go

You need to practice these

 amino acids/
side groups

pg 42-49 * Section 3.2

* Table 3.2 (you must memorize 1 letter code)

* How big are proteins?

* How big are cells?

* Table of amino acid abbreviations
(you must memorize one letter code)


* Protein Structures in Jmol

* Tertiary Structure (IDH)

* phospholamban homopentamer

pg 272 -274 * Section 12.5

pg 99 - 101 * Membrane Proteins... stop @ Membrane Carbohydrates

* Figures 5.1, 5.2, 5.3, 5.4, 5.5, 5.6 (focus on the proteins)


pg 362 - 364 * Section 16.4

Lambda Libraries

 reporter genes

pg 361 * Reporter genes...


* LacZ


pg 367 - 369* Expression vectors...stop @ DNA manipulation...

Epitope tags

 antisense pg 365 * Antisense RNA... stop @ DNA chips....

Week #4 (Feb 1 - Feb 5) (return to the beginning)


pg 407 - 408 * Section 18.3...stop @ Two types...

* figures 18.6, 18.9, 18.11, + Table 18.3

* Jmol image of an Antibody

* movie of antibody binding to epitope

* mAb's - How to make them written by Rahul Karnik ('00)

* Multiple antibodies used at the same time

Antibody labeling ER in muscles (SER)

 Use an antibody to clone a cDNA
 protein gels *  SDS-PAGE
 western blots

Western blot method


Distributed Monday Feb 1due Wednesday Feb. 3 at class time

Wed. Feb 3

HTML Helpful Hints

Virtual Reprints for Molecular Biology - Spring 2005
(Preliminary Readings come from Life, by Purves et al., 8th edition)

(return to the beginning)


Fri. Feb 5 and Mon. Feb. 8

Section I (How do Calcium Pumps of the SR/ER work?)

Preliminary Reading

a) Homology

b) Inhibitors

c) Calcium pump role in cell physiology

One panel from a poster describing how immunofluorescence labeling is done.
See immunofluorescence labeling of calcium pump in skeletal muscle.


Wed. Feb. 10

Preliminary Reading

a) See immunofluorescence labeling of calcium pump in non-muscle cell grown in culture.
Where is SERCA2 located in non-muscle cells?

b) Use Streptolysin-O (SLO) to selectively permiabilize the plasma membrane.
What is SLO? What does it do? How does it work?

c) Jmol images of SERCA1a prior to and after the phosphate binding.

d) Hydropathy plots online


Fri. Feb. 12 - Mon. Feb. 15

Preliminary Reading
See a cartoon showing sodium pump subunit assemply.
How do the two sodium subunits fit together?

b) Immunopecipitation Method - Animation

c) liposome method


(return to the beginning)

Section II (Green Fluorescent Protein (GFP))

Mon. Feb. 15


Wed. Feb. 17

First Web Page Due at Class Time
optional help session on Orthologs

Fri. Feb. 19

Preliminary Reading
What is FRAP?

Nobel Prize for GFP

Student Web Page on GFP

Mon. Feb. 22

Optional Reading

Required Reading

Optional Reading

Required Reading

Additional Sources of Information

(return to the beginning)

Section III (How do cells know to keep some proteins in the ER?)

Wed. Feb. 24 - Fri. Feb. 27

Preliminary Reading


Saturday February 27 - (spring break) - Sunday March 7

Second Web Page Due March 10
Mon. March 8 - Fri. March 12

Preliminary Reading


Mon. March 15 - Wed. March 17

Fri. March 19
Second Exam distributed by email

Amino Acid Structures for in-classs discussion

Second Exam due Monday March 22 at class time

(return to the beginning)

Section IV (Methods that Push the Envelope)

Wed. March 24

1) New Cloning Strategies

Preliminary Reading

A. Enhancer Traps

Fri. March 26

B. Yeast Two-hybrids

Monday March 29

2) Building a Better Mouse

cell-specific knockouts

Optional Reading: single-copy insertions

Wed. March 31

3) Faster Knockouts or Knockdowns

Preliminary Reading


Friday April 2


(return to the beginning)


Mon. April 5 Easter Break!


Section V (Sex determination in Mammals)

Wed. April 7

Preliminary Reading
in situ
a) cartoon of in situ hybridization method
b) FISH Read 3 links under FISH in left frame (near bottom)
c) RT-PCR - requires Flash Plug-in


Fri. April 9

Third Web Page Due
(no class)

Mon. April 12

Optional Reading

Wed. April 14

Preliminary Reading
(Read points 1, 2, and 3 under the heading of "Differences in electrophoretic mobilities of wildtype and mutant nucleic acids") - written by John A. Wagner at School of Medical Sciences, Cornell University.

JMol tutorial of SRY binding to DNA (Note the shape of the DNA.)

Karyotyping and G-banding (click on the word "G-banding" and read the text above)


Read Abstract Only

(return to the beginning)

Fri. April 16

Conversation with Jef Boeke, JHU


Image courtesy of Stephen W. Paddock, Eric J. Hazen, and Peter J. DeVries (Univ. Wisconsin - Madison)

Section VI (Homeobox Genes and Their Functions)

Mon. April 19

Preliminary Reading

a) development of axis

Fly Parts

b) heat shock

c) CAT assay



Wed. April 21

Optional Reading


Fri. April 23

Preliminary Reading
Antennapedia and body parts

Read For Highlights Only


Mon. April 26

Preliminary Reading

Read For Highlights Only


Wed. April 28

Preliminary Reading
Bone formation


Final Web Page Due Friday April 30

no class meeting

Mon. May 3

Preliminary Reading


Wed. May 5

Final Exam Distributed and Fellowship Slide Show

Course Evaluations

(return to the beginning)

Final Exam Due May 10, 9am

Graduation, May 16

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