Modeling the Organism: The Cell in Development

Karl Johnson , Haverford College

An online text to accompany the fourth quarter of Biology 200, Cell Structure and Function

Edition 1.2 - March 2008

Welcoming Visitors to the Wonders of the Cell

Table of Contents


Model Organism

Key Concepts





Escherichia coli

Course Introduction

Gene Expression Programs,
Origins of the Cytoskeleton

March 18

March 20

Gene Regulation in vivo:
The Lac Operon

Single-celled eukaryotes

Caulobacter crescentulus

Polarity, Differentiation, Asymmetry

March 25

Cell-Cell Recognition I:
Mating in Yeast

Saccharomyces cerevisiae

Control Networks, Genetic Switching, Plasticity of Form

March 27

Chlamydomonas reinhardtii

Microtubule Motility

April 1

Cell-Cell Recognition II: 
Mating in Chlamydomonas

Dictyostelium discoideum

Microfilament Motility,
Signaling, Cooperativity

April 3

Mid-Quarter Exam

April 3

Due by 5PM,
Monday, April 7th


Arabidopsis thaliana

Floral Morphogenesis

April 8

Playing Tag with Arabidopsis

Zea mays

The Domestication of Form

April 10


Caenorhabditis elegans

Embryogenesis, Developmental Lineages

April 15

Planarian Regeneration

Drosophila melanogaster

Patterning, Organ Identity

April 17

Sea Urchin




April 22


Xenopus laevis

April 24

Danio rerio

April 29

from Egg to Tadpole

Mammals: from Mus musculus to Homo sapiens

The Molecular and Cellular Bases of Disease, Stem Cell Biology

May 1

Final Quarter Exam

Available May 1

Due by 5PM,
Thurs, May 8th


Course Lectures: Tuesday and Thursday, 10-11:30 Sharpless Auditorium, Haverford College, Haverford PA 19041

Known issues with this site: while we have tried to make this a cross-platform, multi-browser compliant site your best experience may be on a PC using a recent version of Internet Explorer. Windows users should install QuickTime for Windows for the best image/video access (and under the Quicktime preferences select all media types). If the "notes" text seems small you can use your browser settings to increase the displayed font size to make things more readable. There are some issues with video delivery that we are still working out (this is the biggest platform/browser issue) and some videos do not play over the Internet at this time.

Sources from which images and video are cached are available in the accompanying text, and almost every image or video was downloaded from other open-access, open-source sites; my effort is largely collecting and making sense of it all. Our sincere thanks to everyone who makes their work available on the Internet for teaching purposes, and it is in reciprocity that we hope you enjoy this site. We do not claim copyright for any of this material; I have simply cached and organized freely accessible material providing a link to its source (based on the model of a web search engine). This approach was necessary to provide a stable resource in the fluid environment of the Web; if I have used an image of yours and you prefer that I substitute another, please just send me an e-mail with the specifics and I will be glad to oblige.  I hope you enjoy this resource and encourage you to check out my Cell Architecture advanced cell biology text as well!

Tips for success:
Work consistently toward your goals; pace your investment of time and effort; review material on the on-line text both before and after lecture, and discuss
your questions with others, your BQC tutors, and Karl!

Blackboard site:
We will use the course Blackboard site for testing, data sharing from lab and other course needs as they occur.

Course requirements:
There will be two exams for the quarter, a midquarter exam ( available on Thursday, April 3; to be completed by 5PM Monday, April 7th) and a final quarter exam (available on Thursday, May 1st; to be completed by 5 PM Thursday, May 8th (an extension of two days from the original due date!!!).

Late materials will be assessed a 10% penalty for each day (24 hours) they are overdue.

Mid-Quarter Exam


Final Quarter Exam


Laboratory Evauation


Quarter Grade


Biology is a subject that grows on you (in more ways than one!) and the Final Quarter Exam will be cumulative.  In addition to material covered this quarter, you are expected to know basic information covered in the prior quarters of this class as we work to integrate Cell Structure and Function as we Model the Organism.  Refer to your earlier notes and readings as you see connections to new material.

The Biology Question Center and Guided Learning Groups will continue to be available to help you master the course material.  Meeting times and locations will be posted by the student leaders on Blackboard.

Questions, comments? Please e-mail Karl Johnson

Image sources for this page are: Escherichia coli, Caulobacter crescentus, Saccharomyces cerevisiae, Chlamydomonas reinhardtii (Karl's own work); Dictyostelium discoideum, Arabidopsis thaliana, Zea mays, Caenorhabitis elegans, Drosophila melanogaster, Sea urchin, Xenopus laevis; Zebrafish; Mus musculus, Homo sapiens, all cached 070318.

This page last modified on March 13, 2008