Molecular Sequences & Primate Evolution: An Amino Acid Example

Overview & Concepts

In this activity students will used macromolecular data to construct a cladogram of 7 primate species and 1 non-primate species.  This will convey to students the idea that monophyleticism in both the recent and the more distant past can be inferred from macromolecular data. Students will compare and analyze amino acid sequences using NCBI’s BLAST tool.

This activity has been adapted from a paper-based activity: MOLECULAR SEQUENCES & PRIMATE EVOLUTION: AN AMINO ACID EXAMPLE by Martin Nickels, Craig Nelson, Doug Karpa-Wilson, Steve Freedberg and Nathan Murphy.  It is intended to introduce introductory level biology students to the idea of bioinformatics. 

Grade Level: 

Concepts Covered: 

Biological/evolutionary relationship, descent by modification, common ancestor, protein, amino acid, bioinformatics, cladistics

Prior Knowledge Required: 

Protein structure and function, proteins as a translated gene product, biological organization.

Activity Notes

Days to Teach: 

Two 50 minute class periods plus potential homework components.


Student procedure, student worksheets A and B, student data sheet, teacher keys: procedure and data sheet, computers with internet access, NCBI's BLAST tool.

Teaching Tips / Activity Overview: 

1. Pre-lab discussion. Discuss hemoglobin structure & function. Discuss use of BLAST: 15 minutes in class.

2. Complete activity, students will analyze data on BLAST, fill in worksheets A and B, answer questions in lab protocol, and write a final summarizing paragraph: 70 minutes.

  • Students should not begin the activity with all of the student materials.  Distribute as follows:
    • Begin with ‘Procedure’ and ‘Worksheet A’
    • Distribute ‘Worksheet B’ to students only when they request it.  They will be prompted to ask for it in section E of the procedure.
  • As such, copy the procedure as one packet and worksheets A and B each as separate worksheets.
  • If possible, the data sheet should be made available to students electronically.  This will assist in their loading the amino acid sequences into BLAST. 
  • Emphasize that students will have to make a significant number of comparisons using BLAST, each species must be compared with every other species.  If working in groups, students may wish to divide up this task.
  • Likewise, it may be helpful to demonstrate the use of BLAST, especially if a smart board and/or LCD projector is available to project the BLAST tool for full class viewing.

3. Final summarizing paragraph: Homework, depending upon time requirements.

4. Wrap-up discussion, discuss results, interpretation of data, and use of bioinformatics tools: 15 minutes.

  • It is also helpful to conduct a final review of the activity, generally after students have submitted their work or after it has been evaluated and returned.  In this review emphasize the results and how these suggest the idea of relationship by common ancestry.


Student responses to open-ended questions, worksheets A and B items, and the final summary paragraph will be evaluated for accuracy and quality of response.


  • Have students use NCBI search tools to find all or some of the amino acid sequences themselves and then align the sequences themselves using BLAST according to lab protocol.
  • Have students research and select another amino acid sequence to use in constructing an additional cladogram with as many of these organisms as possible.  Discuss the reality of multiple sources of information being used to construct cladograms.
  • Have students compare all eight amino acid sequences in one alignment in order to discuss protein structure, conserved regions, and redundancy in the genetic code.


  • Evolution and the Nature of Science Institutes, based at Indiana University.  Included similar activities, including the original version of the activity from which this has been adapted.
  • Understanding Evolution from the University of California Museum of Paleontology, a good resource for tutorials on many facets of evolutionary theory, including common ancestry.
  • The National Center for Biotechnology Information, the National Library of Medicine’s collection of bioinformatic and genetic search and comparison tools, including BLAST.


These teacher notes and resources were produced by Ray Mount based upon the following resources:Craig Nelson & Martin Nickels, Edited by Larry Flammer. MOLECULAR SEQUENCES & PRIMATE EVOLUTION: Amino Acid Differences in Beta Hemoglobins in Primates.  The current activity is an adapted version of the Nelson & Nickels activity, which is a paper-based activity.  The original Nelson & Nickels activity can be found here:

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