DNA

1. An Information Flow in Biology Primer replication (mutation!) genes DNA Nucleic acids ~ “software” (nucleotides) transcription messages RNA (nucleotides) translation Protein (amino acids) ~ “hardware”

2. Examples of DNA and Protein Structure • DNA: • http://www.clunet.edu/BioDev/omm/dna.htm • Protein: • amino acids (http://www.clunet.edu/BioDev/omm/aa/aa.htm) • antibody (http://www.clunet.edu/BioDev/omm/ig/molmast.htm) • HIV reverse transcriptase (http://www.clunet.edu/BioDev/omm/hivrt/hivrt.htm)

3. An Evolution by Natural Selection Primer • Mutations (hence new varieties) do not arise because they are needed -- they arise by chance • Mutations merely furnish random raw material for evolution, and rarely, if ever determine the course of the process • Natural selection is the differential reproduction of genotypes (genes) • Evolution is the change in the genetic composition of a population over time – “Natural Selection is not Evolution” – Ronald Fisher, The Genetical Theory of Natural Selection • [see the Weasel applet for a demonstration of the power of selection]

4. time species gene frequency

5. Chapter VI …Organs of extreme perfection and complication. -- To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree. Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real. … Chapter VI …Organs of extreme perfection and complication. -- To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, abserd in the highest possible degree. Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperible by our imagination, can hardly be considered real. … Chapter VI …Organs of extreme perfection and complication. -- To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, abserd in the highest possible degree. Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possesser, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperible by our imagination, can hardly be considered real. … Chapter VI …Organs of extreme perfection and complication. -- To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, abserd in the highest possible degree. Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real. … Chapter VI …Organs of extreme perfection and complication. -- To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, abserd in the highest possible degree. Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperible by our imagination, can hardly be considered real. … Chapter VI Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possesser, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperible by our imagination, can hardly be considered real. … …Organs of extreme perfection and complication. -- To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, abserd in the highest possible degree.

6. A phylogeny of Chapter VI’s Chapter VI Chapter VI Chapter VI Chapter VI Chapter VI Chapter VI

7. Determining Similarity* To determine how similar your sequence is to other sequences in the database, you rely on scores determined by the program you are using. The scores are generated in different ways for each of the different programs, but, in general scores are determined by substitution matricies. To understand how these matricies work, let's look at he simplest case: aligning two nucleotide sequences. Generally, when two nucleotide sequences are aligned, the scores are as follows: +2 = identity -1 = mismatch * This slide modified fromAndreas Matern’s presentation (http://www.people.cornell.edu/pages/alm13/blast/lecture4.html) Example Score GAAGCC 2+2-1-1+2+2=6 GATACA GATCCCACA 2+2+2-1-1-1+2+2+2=9 gap GAT - - - ACA GATAC - 2+2+2+2+2-1=9 gap GATACA Example Score GATACA 2+2+2+2+2+2=12 GATACA GATACC 2+2+2+2+2-1=9 GATACA GAAACA 2+2-1+2+2+2=9 GATACA Situation for protein is more complex!

8. This slide taken from Andreas Matern’s presentation (http://www.people.cornell.edu/pages/alm13/blast/lecture6.html) BLAST - Basic Local Alignment Search Tool J. Mol. Biol. (1990) 215: 403-410. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ BLAST sifts through the huge amounts of data in a database, scanning a nucleotide database at 2 x 106 bases per second, and a protein database at 500,000 residues a second! How does it do it so fast? Well, this is a little hairy -- and probably more statistics than anyone really needs to know. I'll try to add some of the statistical stuff at a later date, but for now remember that, as previously mentioned, BLAST does not go through each an every sequence, it uses a LOCAL alignment heuristic. Without belaboring the statistics, BLAST divides your sequence into words - smaller segments with a given length (w). Nucleotides are normally broken up into words of length w = 12. Then, BLAST goes through the database (which has also been broken up into words) to find pairs with a score above a predetermined threshold. However, using a statistical heuristic which Karlin and Altschul developed, BLAST can eliminate some of these attempted word pairings by estimating a score at which a match is no better than chance. By ignoring all searches at and below this score, BLAST can effectively disregard a great deal of the database. BLAST finds only those pairs that contain a score of at least T - a threshold value. Once it finds a hit, it then tries to extend that hit until a cutoff score (S) is reached. Extending means that it adds letters to the ends of the word pair and then assesses the new score. To reiterate: 1.Cut up the sequences into smaller pieces called words 2.Ignore all pairs below the threshold score 3.Try to extend all remaining hits until you get to a cutoff score In the original BLAST paper, Altschul et al go through a series of tests to generate (via random simulation and through real data) values of w, T, and S which are the most biologically relevant and yet computationally useful. Generally speaking, the lower the threshold (T) value is, the greater the chance of finding a "hit" of at least S. However, small values of T increase the number of hits, and therfore the amount of time it takes for BLAST to sort through the database.

9. Let’s do a Blast search

11. Protein Tyrosine Kinases (PTK’s) Protein Tyrosine Phosphatases (PTP’s)

12. DPez: 1252 aa, ~ 140kD WIP PTP FERM 27% identical, 47% similar to human WIP 34% identical, 46% similar to human Pez 37% identical, 53% similar to human Pez

13. FERM PTP