Download Protein Similarities II

Protein Similarities II
Consider now the 84 or so amino acids in cytochrome c that vary (shown as the lighter bands above). These
are not alike in all species, yet the protein has the same function in all those species. Apparently these are
amino acids that can be replaced by other amino acids without disrupting the function of the protein.
Probably the essential ones, shown as darker regions, help to define the binding site of the protein, like so:
The "lighter" amino acids aren't necessary to the electron-carrying function; at least, they don't have to be
precisely the same for the protein to work. This isn't at all unlikely. For instance, there is an alpha helix
going up the left side of the image above. It probably has to be an alpha helix there, in order for the protein
to fold into this shape; however, lots of amino acids tend to form alpha-helix structures. Chances are you
could replace many of the amino acids in that part of the protein and it would still fold into the same shape,
and work the same way. This is true, apparently, of all 84 of the amino acids that aren't colored darkly in the
primary structure diagram above. If two organisms have the same amino acid at, say, position 50 (a light
position) in cytochrome C, is this similarity due to homology or analogy? Explain.
Please provide your answer on the separate sheet.
1
What happens to an individual if its copy of the cytochrome c gene is altered so that there is a change in one
of the 84 light amino acids? Explain.
Please provide your answer on the separate sheet.
Now
Then
Time is measured on the vertical axis. Note that, if this phylogenetic tree is correct, the time since A and B had their
last common ancestor is about twice as long as the time since C and D had their last common ancestor.
Would you expect more "light" amino acid differences, due to chance mutations, between A and B, or
between C and D? Explain.
Please provide your answer on the separate sheet.
As you've no doubt realized, the accumulation of neutral changes in molecules (neutral changes are ones that
don't affect function), as in the "light" amino acids of cytochrome C, should actually represent a sort of
"molecular clock." That is, since mutations occur by chance events, the more time two lineages
(populations, species, or larger groups) have been separate, the more opportunities there have been for them
to acquire mutations that will show up as differences in their amino acid sequence. So, we should be able to
test hypotheses about relationships. We can ask if there are any similarities at all between two organisms,
and whether those are homologies or analogies. We can also look at the amount of similarity between two
organisms and get an estimate of the time since they last had a common ancestor.
2
Consider the following hypothesis about the relatedness of some organisms: What organism does it say is
the most closely related to humans (that is, which one had a common ancestor with humans most recently)?
Please provide your answer on the separate sheet.
Now
H RM CH C HO R W F
K S Y
Wh
Then
Now try to arrange the following in order of how recently they have a common ancestor with humans,
according to the hypothesis above. For each organism below, enter a number giving its rank from most
closely related to humans (1) to most distantly related (12). If, according to the hypothesis, any of them are
not related to humans at all, enter "NR". Remember, closely related means having a recent shared ancestor;
distantly related means having a shared ancestor longer ago.
Please provide your answer on the separate sheet.
H = Humans
RM= Rhesus Monkey
CH =Chimpanzee
HO = Horse
R = Rabbit
W = Whale
F = Catfish
K = Kangaroo
S = Snake
Y = Yeast
Wh = Wheat
C = Cow
Looking at the rankings you made above, what does the hypothesis predict about the number of amino acid
differences between human's cytochrome c and the cytochrome c in each of these organisms? Explain.
Please provide your answer on the separate sheet.
3