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Pseudogene Lesson C:
Exploring Primate Pseudogenes
With Biology Workshop

Author Anonymous





Not Ready for Use Yet


Students use Biology Workbench to explore DNA sequence data for the GULOP gene in humans, chimpanzees, orangutans, and crab-eating macaques and the beta globin gene and its pseduogene in humans, gorillas, and chimpanzees.


Many features of modern organisms reflect the structure of their ancestors in ways that are not adaptive.


1. DNA sequences from different species can be compared by aligning them.
2. Software has been created to facilitate sequence comparisons.
3. Some sequence differences involve similar amino acids.
4. Existence of pseudogenes provides a record of evolutionary history, with relative timing and degrees of relationships.


   Students will....

1. Use CLUSTALW to align two or more sequences.
2. Use BOXSHADE to color-code an alignment.

(Click here to get PDF files for downloading)
computers with an Internet connection [may require Windows/PC systems].
Student Handout: :Lesson C: "Exploring Primate Pseudogenes with Biology Workbench" (Background, Procedures and Report Form).


45 minutes
STUDENT HANDOUTS See Materials (above)



Excellent Teacher Background on Pseudogenes and Intergenic Analyses can be found online at:
1. This lesson assumes a basic understanding of enzyme structure/function and of gene expression (protein synthesis). It is intended to follow lessons A and B in this suite: "Why Do We Need Vitamin C In Our Diet?" and "What Can Pseudogenes Tell Us About Common Ancestry?"

2. This lesson would fit nicely near the end of an introductory unit on DNA structure and function., or, in concert with the other two lessons in this suite, it would be appropriate in a unit on evolution, or classification and biological relationships.

3. Prepare enough copies of the Student Handout for every student or pair of students. Have extra Report Forms.

4. You should DO the exercise online, following the instructions on the Student Handout BEFORE doing this lesson in class. You might want to place the two URLs needed in the "Favorites" or "Bookmarks" list on each student computer, for their convenience.

5. Click here for an animated PowerPoint presentation that nicely introduces the concepts in this lesson, including the One-Gene-One-Enzyme idea, how the GULO gene and pseudogenes compare, and how the inability for primates to make vitamin C points to common ancestry. This link will take you to the script for the PPP and how to request the PPP itself.




1. Have students work in pairs (even if there are enough computers for them to work alone.)
2. Briefly introduce the background information.
3. Pass out the Stuudent Handout and Report Forms.
4. Have students work through the exercise being careful to follow the steps as written.
5. Students are to hand in their Report Forms completed for you to look over.

Lead a discussion in which teams share their observations and conclusions.


1. Check student Report Forms for clarity, logic, etc.
2. Assign a particular comparison for which a plot is to be turned in.



1. This lesson was meant to follow the lessons A and B: "Why Do We Need Vitamin C in Our Diet?" and "What Can Pseudogenes Tell Us About Common Ancestry?", but could be used alone if students were given some of the background information from these lessons.
2. The procedures learned in this lesson could be used to explore other data sets available in the DataSets account on Biology Workbench. (See Preparation for how to access these.)
3. Students may notice that Workbench can be used to draw rooted and unrooted trees from alignments. The unrooted trees are easier to interpret, so if you decide to have them draw trees, we recommend their using DRAWTREE rather than DRAWGRAM. Even so, the tree produced is technically a "gene tree" (based on a single gene) and may conflict with accepted phylogenies. This is the reason we chose not to include tree drawing in this lesson.


Chang, L.Y.; Slightom, J.:
Isolation and nucleotide sequence analysis of the beta-type globin pseudogene from human, gorilla, and chimpanzee.
J Mol Biol 180:767-84, 1984. PubMed ID: 6098690

Ohta, Y; Nishikimi, M.:
Random nucleotide substitutions in primate nonfunctional gene for L-gulono-gamma-lactone oxidase, the missing enzyme in L-ascorbic acid biosynthesis.
Biochim Biophys Acta 1472:408-11, 1999. PubMed ID: 10572964

Saitou, N; Nei, M.:
The number of nucleotides required to determine the branching order of three species, with special reference to the human-chimpanzee-gorilla divergence.
J Mol Evol 24:189-204, 1986. PubMed ID: 3104615

Excellent Teacher Background on Pseudogenes and Intergenic Analyses can be found online at:

Feature article in the online newsletter The Scientist for 1/27/03
Provides lucid description of the many ways genes are duplicated in nature, a primary mechanism of evolution, leading to gene families and pseudogenes.
Patterns seem to suggest major duplications initiated vertebrate origins at the onset of the Cambrian, with subsequent pulses of duplication leading to major jumps in vertebrate evolution.


Some of the ideas in this lesson may have been adapted from earlier, unacknowledged sources without our knowledge. If the reader believes this to be the case, please let us know, and appropriate corrections will be made. Thanks.

1. Original author requests anonymity.

2. Edited / Revised for website by L. Flammer 2/2002; again 7/17/03

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