Evolutionary Genetics
September 30, 2011
Actin Experiment – Take Home Assessment:
Please complete the following assignment using your laptop and what you
have learned thus far about bioinformatics to complete the following
assignment. Answer the questions within this document using a different
font to differentiate the questions from your answers. You may also use
your course packet and notes from class to complete this assignment.
However, you may not work with your classmates on this assignment. It is
pledged work, and thus, it must be completed independently. Please write
out and sign the honor code once you have completed this assignment.
Assignment is due on Friday, October 7, 2011 at the start of class.
If you need some help from me, please set up tutorial as early in the
week as possible, as I am away with volleyball at the area tournament
on both Tuesday and Thursday afternoon this week!
Below is sequence from two PCR products of a segment of an actin gene using
a different set of primers (so you should not expect for this to look like the
one we did in class). One sequence is from genomic DNA and the other
sequence is from cDNA. After running PCR on both, the PCR products were
sent off to be sequenced and the sequence is shown below.
>Actin genomic PCR product 2
agatcaccctgtgctgctgaccgaggcccctctcaaccccaaggccaacagagagaaaat
gacgcagattatgtttgaaaccttcgaatgcccagcaatgtatgttgctatcgaggctgt
tctttcgttgtacgctagtgggcgaacaactggtaagatggctgtcgcctcagatatata
tagtgatatgcactacaaagatcatacatacatacggcaatcctgacacggtctctttgt
caaatatctctgtgtgcaggtattgtgatggattcaggtgatggtgtgagccacacggtt
ccaatttatgaaggatacacacttcctcatgctattctccgtttggatcttgcggggcgt
gacctcaccgaccacctaatgaagatcctcacagagagagggtactccctcactacgagc
gctgagcgggagattgtcagggacataaaggagaagcttgcctacgttgcccttgattat
gaacaggagctggagactgccaagagcagctcctctgtcgagaagagctacgagatgcct
gatggtcaggtcatcaccattgggtcagaaaggttcaggtgccccgaggtgttgttccaa
ccatcccttgttggcatggaatcgcctagcgtccatgaggccacgtacaactccatcatg
aagtgtgatgttgatatcaggaaggatttgtatggtaacgttgtcctcagtgggggtttt
accatgtttcctgggattgccgatcgtatgagcaaggagatcacgtccctagttcctagc
agcatgaaggttaaagtagttgcgccacctagaaggaagtacagtgtctggatcggtggc
tctattttggcttctctcagcacttttcagcaggtcttctctttcttactttattctttc
ataagcagtaggcttttatcattcaactcctcttcatcgagaacctacagcagccttgac
catgttgggtgtgtgtgctttttttgtagttaaagtgcgaaataacccattatataccaa
ctcaatttggttaaactggcttgtgatgcactcttttttacctaaaaacgcaattggaat
acaaatatattcttgcttcagtcagtcactccagttttctagtatcaacttctctcaggg
cccatttggaacgaaggaaatatgaaggatttttgaaggattttcgaaggattcatttcc
tacatagaagttttctatgtgaccctttggaacacaggatttaattctatcaatttcttt
gaaatttctatggattgctttccttcatacaagttttggaggaaaataacgagctcatct
cttggaaaatttcctatgactcttatctctctattcaaattcatgtatagcacccaaagg
ctaggtgagaaattttgctacgttctcaatttctgtaggattgcaattcataggcaatta
tagtcatgtgttttctctattcctgtgttttcgtattcttctgttcaaaagggggctagt
aggcactgcacagtgctccacctccgcgtgtgttaacatacgtgttaatcattacagaca
tagacccaaacccgatagtaacatctttttgaggcaaatgaaaagagcccaaggcctttt
tcttcgacgatagatataagcgggatgtggaaatggaattactagtgtgatagcaccgaa
tatttttcttgcattgccattacttgcactcattattttaatttgcatttctttgacaat
gggcaactgtgttggcagatgtggatctccaagggagagtatgacgaaactggtccgggc
attgtccacatgaagtgcttctaa
>Actin cDNA PCR product 2
agatcaccctgtgctgctgaccgaggcccctctcaaccccaaggccaacagagagaaaat
gacgcagattatgtttgaaaccttcgaatgcccagcaatgtatgttgctatcgaggctgt
tctttcgttgtacgtattgtgatggattcaggtgatggtgtgagccacacggttccaatt
tatgaaggatacacacttcctcatgctattctccgtttggatcttgcggggcgtgacctc
accgaccacctaatgaagatcctcacagagagagggtactccctcactacgagcgctgag
cgggagattgtcagggacataaaggagaagcttgcctacgttgcccttgattatgaacag
gagctggagactgccaagagcagctcctctgtcgagaagagctacgagatgcctgatggt
caggtcatcaccattgggtcagaaaggttcaggtgccccgaggtgttgttccaaccatcc
cttgttggcatggaatcgcctagcgtccatgaggccacgtacaactccatcatgaagtgt
gatgttgatatcaggaaggatttgtatggtaacgttgtcctcagtgggggttttaccatg
tttcctgggattgccgatcgtatgagcaaggagatcacgtccctagttcctagcagcatg
aaggttaaagtagttgcgccacctagaaggaagtacagtgtctggatcggtggctctatt
ttggcttctctcagcacttttcagcaggacaatgggcaactgtgttggcagatgtggatc
tccaagggagagtatgacgaaactggtccgggcattgtccacatgaagtgcttcta
Answer the following questions about PCR, genomic DNA and cDNA. Then,
use sequence analysis software, as completed in class, to determine the
following (5 points each):
1) What are the components of a PCR (ie – what reagents do you mix up to
successfully complete PCR), and two, what are the steps of PCR, and the
temperatures associated with each step?
2) What is the difference between the genomic DNA and cDNA?
3) Why is it important to determine the exon/intron structure of a gene?
4) How many introns are in the genomic DNA in the above example?
5) What are the start and stop positions of the intron (or introns)?
6) Draw a diagram (this is a picture of the exon/intron structure which
should include numbers where the exons/introns start and stop) of the
genomic and cDNA products showing the exon/intron structure of the gene
before and after splicing.
7) How much smaller is the cDNA PCR product? Why? (this number should
be as close as you can get it, but if it is off by a couple, it will be OK)! 
From Carroll’s Book:
1.
As the closing statement in the preface of Carroll’s book, The Making
of the Fittest, he states, “The body of new evidence that I will
describe in this book clinches the case for biological evolution as the
basis for life’s diversity, beyond any reasonable doubt.” Using the
three main components of evolution, as set forth by Darvin (and which
you should now know from your reading), Carroll has begun the process
of unveiling the biological processes that explain life’s complexity
today. Show how each of these three components contributes to life’s
diversity by using examples Carroll has already used to illustrate
evolution in the first couple of chapters in his book. (15 points)