TEACHER PAGE:
Relating Molecular Sequences to Evolutionary Relationships
Part One: DNA Sequence – Conservation of Genes (Requires the Computer Lab)
Use the following DNA sequence in the BLAT data base to determine similarities and differences in
genetic code.
1. Type the following sequence into the BLAT database. Go to http://genome.ucsc.edu/cgibin/hgBlat . In the box provided, type in the following sequence without spaces.
GTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTA
CCATAAATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTACAAGC
AAGTACAGCAATCAACCCTCAACTATCACACATCAACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATA
CCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCA
AATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAAT
ATCCCGCACAAGAGTGCTACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATC
CGACATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACG
ATGGATCACAGGTCTATCACCCTATTAACC
*Remind students to be very careful when typing into BLAT. Simple mistakes can change results. Suggest
that students write marks on their paper to keep track of their place. If students have odd results make sure
they check their set up of the search, it should look like this…
Genome:
Human
Assembly:
Mar. 2006
Query type:
BLAT's guess
Sort output:
query,score
Output type:
hyperlink
2. Once you type in the sequence for this short section of DNA, press submit. Your results will look
something like this…
ACTIONS
QUERY
SCORE START END QSIZE IDENTITY CHRO STRAND START
END
SPAN
-------------------------------------------------------------------------------------------------browser details YourSeq
499
1
510
537 99.1%
M
+
16061
16571
511
browser details YourSeq
216
45
537
537 87.0%
17
+
21944385 21944880
496
3.Click on browser for your first query result, it has 99.1% identity and is most like your gene! *If
students click details they will get different types of results. While this will show how the DNA is similar or different
at each location, it will not match the rest of this sheet. However, it can be used by the student if you wish to
extend the level for advanced students.
4. Notice all the blue peaks… these are areas of conservation. The gray and black lines
underneath the blue peaks show the amount of similarity between the human portion and the
animal sequences. Each darkened space represents a base that is the same in those sequences.
5. Look at Mouse, Dog, Platypus, Chicken and Stickleback to answer the following questions.
Questions:
1.
Using the scale at the top of the chart, which section of the gene is most similar
among mammals?
16400-16550
2.
List the animals in order of MOST like the human sequence to the one least like the
human sequence.
Mouse, Platypus, Dog, Stickleback, Chicken
3. Notice there is no results for the Rhesus Monkey or the Lizard. Why might this data be
missing?
Answers will vary – data not available, different families then the human, might not
have the gene
4.
Why could there be different reasons for these two species to not have data in this
location? (HINT: How are these animals similar or different to humans?)
Should discuss that while monkeys should have similar DNA but the Lizards may very
well NOT have that section of DNA at all.
Part Two: Amino Acid Sequence – Conservation of Proteins
Use the attached sheet to compare the amino acid sequence for the protein of each of the
animals. The three letter codes are abbreviations for the amino acids.
1. Compare the amino acid sequence of Cytochrome c for each species to the sequence of
the human. Determine the number of differences between each species.
Species
Horse
Chicken
Tuna
Frog
Shark
Turtle
Monkey
Rabbit
# Differences from the Human Cytochrome c
6
7
9
8
13
8
2
4
1. According to your analysis of the amino acid sequences, which species listed is most
closely related to humans? Monkey
2. Which species is least closely related to humans? Shark
Compare the amino acid sequence of hemoglobin for each species to the sequence of the
human. Determine the number of differences between each species.
Species
Chimp
Gorilla
Monkey
Horse
# Differences from Human Hemoglobin
0
1
2
4
1. List the four vertebrate sequences in descending order according to how similar they
are to human hemoglobin. (most to least) Chimp, Gorilla, Monkey, Horse
2. According to your analysis of the amino acid sequences, which species listed is most
closely related to humans? Chimp
3. Which species is least closely related to humans? Horse
4. What is the difference between gorilla and human hemoglobin?One amino acid
different
5. What might have been responsible for this change (from question 4)?Mutation
Part Three: Analysis Questions
Use information you have gathered from both of these activities to answer the following
questions.
1. How is this method (using sequence) different from other methods used to
determine evolutionary relationships?
This looks at the code of the organism where other forms look at physical structure and
expression of the code in the organism.
2. If the amino acid sequences are similar between two species, why would you expect
their DNA to be similar?
DNA sequence determines Amino Acid sequence through transcription and translation.
3. Proteins are sometimes called “biological clocks”. Why might we be able to use
protein (think sequences) to determine relative age of organisms?
Organisms more closely related have diverged more recently from each other. This
means the organisms that are further apart have an older divergence. This helps us
determine a timeline of when organisms diverged, or a “clock”.
4. How do molecular biologists help evolutionary biologist determine relationships
among animals?
They allow the evolutionary biologist to see the framework sequence and not just the
outer phenotype. This can help solidify relationships or break down faulty ones.
5. If you have a section of DNA that shows exact bands of DNA but the organisms do not
show the same traits, what can you say is happening? (HINT: Is the sequence
changing or is something else happening to the organism?)
Answers will vary BUT it should discuss expression of DNA as proteins.
Cytochrome c Amino Acid Sequences
Horse
Gln
Ala
Pro
Phe
Thr
Thr
Asp
Lys
Asn
Lys
Gly
Ile
Thr
Lys
Glu
Glu
Thr
Leu
Met
Glu
Lys
Ala
Thr
Asn
Glu
Chicken
Gln
Ala
Glu
Phe
Ser
Thr
Asp
Lys
Asn
Lys
Gly
Ile
Thr
Gly
Glu
Asp
Thr
Leu
Met
Glu
Asp
Ala
Thr
Ser
Lys
Tuna
Gln
Ala
Glu
Tyr
Ser
Thr
Asp
Lys
Ser
Lys
Gly
Ile
Val
Asn
Asn
Asp
Thr
Leu
Met
Glu
Ser
Ala
Thr
Ser
Frog
Gln
Ala
Ala
Phe
Ser
Thr
Asp
Lys
Asn
Lys
Gly
Ile
Thr
Gly
Glu
Asp
Thr
Leu
Met
Glu
Ser
Ala
Gly
Ser
Lys
Human
Gln
Ala
Pro
Tyr
Ser
Thr
Ala
Lys
Asn
Lys
Gly
Ile
Ile
Gly
Glu
Asp
Thr
Leu
Met
Glu
Lys
Ala
Thr
Asn
Glu
Shark
Gln
Ala
Gln
Phe
Ser
Thr
Asp
Lys
Ser
Lys
Gly
Ile
Thr
Gln
Gln
Glu
Thr
Leu
Arg
Ile
Lys
Thr
Ala
Ala
Ser
Turtle
Gln
Ala
Glu
Phe
Ser
Thr
Asp
Lys
Asn
Lys
Gly
Ile
Thr
Gly
Glu
Glu
Thr
Leu
Met
Glu
Asp
Ala
Thr
Ser
Lys
Monkey
Gln
Ala
Pro
Tyr
Ser
Thr
Asp
Lys
Asn
Lys
Gly
Ile
Ile
Gly
Glu
Asp
Thr
Leu
Met
Glu
Lys
Ala
Ala
Asn
Glu
Rabbit
Gln
Ala
Tyr
Pro
Ser
Thr
Asp
Lys
Asn
Lys
Gly
Ile
Thr
Gly
Glu
Asp
Thr
Leu
Met
Glu
Lys
Ala
Thr
Asn
Glu
Hemoglobin Amino Acid Sequence
Human
Thr
Leu
Ser
Glu
Leu
His
Cys
Asp
Lys
Leu
His
Val
Asp
Pro
Glu
Asn
Phe
Arg
Leu
Leu
Gly
Asn
Val
Leu
Val
Csy
Val
Leu
Ala
Chimpanzee
Thr
Leu
Ser
Glu
Leu
His
Cys
Asp
Lys
Leu
His
Val
Asp
Pro
Glu
Asn
Phe
Arg
Leu
Leu
Gly
Asn
Val
Leu
Val
Csy
Val
Leu
Ala
Gorilla
Thr
Leu
Ser
Glu
Leu
His
Cys
Asp
Lys
Leu
His
Val
Asp
Pro
Glu
Asn
Phe
Lys
Leu
Leu
Gly
Asn
Val
Leu
Val
Csy
Val
Leu
Ala
Monkey
Gln
Leu
Ser
Glu
Leu
His
Cys
Asp
Lys
Leu
His
Val
Asp
Pro
Glu
Asn
Phe
Lys
Leu
Leu
Gly
Asn
Val
Leu
Val
Csy
Val
Leu
Ala
Horse
Thr
Leu
Ser
Glu
Leu
His
Cys
Asp
Lys
Leu
His
Val
Asp
Pro
Glu
Asn
Phe
Arg
Leu
Leu
Gly
Asn
Val
Leu
Ala
Leu
Val
Val
Ala
His
His
His
His
Arg