Lesson 4
Introduction: In different organisms the amino acid sequences of proteins with the same function are similar, but
not identical. These differences can be used to indicate how closely organisms are related. This activity uses the
amino acid sequences from certain globin proteins.
Goal: The students will determine the number of differences in fragments of several globin molecules and will
construct a phylogeny showing which polypeptides are most similar and which are most different. The students
will be able to see the chronological order in which the proteins diverged from each other.
Directions:
1. Count the number of differences in amino acids between protein fragment #1 and protein fragment #2 (a
blank will be scored as a difference). The box below shows you how to score the differences.
The circled letters indicate differences in each protein fragment; thus, there are 3 differences between the
amino acid sequences in polypeptides #1 and #2.
These are different globin molecule fragments. The letters are symbols for the amino acids in the
sequence of the molecule. (See Table 1.)
#1 VNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR-#2 VNFKLLSHCLLVTLACHHPTEFTPAVHASLDKFFLAAVTVLTSKYR-#3 ENFRLLGNVLVCVLAHHFGKFFTPPVQAAYQKVVAGVANALAHKYH-#4 ENFKLLGNVLVCVLAHHFGKFFTPOVQAAYQKVGVAGVANALAKYH-#5 KYLEFISECIIQVLQSKHPGDFGADAQGAMNKALELFRKDMASNYKELGFQG
Table 1. Amino Acid Symbols
A = alanine
G = glycine M = methionine S = serine
C = cysteine
H = histidine N = asparagine T = threonine
D = aspartic acid I = isoleucine P = proline
V = valine
E = glutamic acid K = lysine
Q = glutamine W = tryptophan
F = phenylalanine L = leucine R = arginine
Y = tyrosine
2. In the same way as step one, count the number of differences in the fragments making comparisons
between each pair (1<-->2, 3, 4, 5; 2<-->3, 4, 5; 3<-->4, 5; 4<-->5) and write the number of differences in
the following chart.
We can assume that these five proteins diverged from a common ancestor-protein sometime in the past;
they diverged�changed but did not replace�this ancestor-protein over time. It is most likely that the
genes which held the recipes for these proteins have been duplicated several times to allow for these
changes. Using this concept, place the protein fragments in the "tree" on the next page.
1. Describe the reason you put each fragment in its particular location on the "tree."
2. Species X and Y have 25 amino acid differences. Species X and B have 10 amino acid differences in the
same protein. Species Y and B have 27 amino acid differences.
a) Which organism (X, Y, or B) diverged from the common ancestor first? ____________ Explain your
reasoning.
b) Which pair of organisms--X & Y, X & B, or Y & B--are likely to share more characteristics than the
other two pairs. ______________ Again, explain your reasoning.
key