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CS515: Bioinformatic Algorithms

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1 CS515: Bioinformatic Algorithms
A Little Bit of Biology: Part II CS515: Bioinformatic Algorithms Dr. Robert Heckendorn

2 Biology up to the 1960s What is life? Let’s catalog it!
Hey wait!.... There’s a pattern… a tree of life. It is even supported by the fossil record! Evolution can explain this. But then there has to be particulate heredity. How does that work?

3 Two Kinds of Cells: Prokaryote

4 Two Kinds of Cells: Eukaryote

5 Protein: A building block of life
Structural components Enzymes act as catalysts including processing DNA Agents of process such as signaling, transduction, transportation, motor function Struct: elastin, collagen, cytoskeletal structure enzymes: DNA replication and repair, augmenting chemical reactions, (transistor of chemistry)

6 Central Dogma of Molecular Biology
DNA codes protein Central Dogma of Molecular Biology

7 Notes: DNA to Protein and other transformations
DNA transcription creates messenger RNA mRNA translation creates protein Reverse transcriptase allows the copying of RNA to DNA (retroviruses) RNA copying occurs in RNA viruses Information flows DNA to protein

8 The Structure of DNA: The Nucleotide
Sparknotes.com Note the numbering of the carbon atoms

9 The Structure of DNA: The Sugar Backbone
Read this direction Sparknotes.com

10 DNA Structure

11 The Structure of DNA: The Bases in Pairs
Sparknotes.com Pyrimidines Purines

12 The Structure of DNA: The Double Strand
Sparknotes.com

13 The Structure of DNA: The Double Strand
Sparknotes.com

14 DNA: Complementary Strings
5’ ATACGACTATTCCG 3’ 3’ TATGCTGATAAGGC 5’ The second string is written: CGGAATAGTCGTAT upstream downstream

15 The Structure of RNA Uracil for Thymine and hydroxyl group at 2’
Wikipedia on RNA Uracil for Thymine and hydroxyl group at 2’

16 Transcription Coding and noncoding strands
Rips the 5’ to 3’ DNA strand initiated by promoter Multiple copies can be made at once wikipedia RNA polymerase RNA

17 RNA folds on itself

18 The Structure of Protein: The Amino Acid
a carbon

19 The 20 Amino Acids

20 The 20 Amino Acids (cont’d)

21 Peptide Bond A residue is what is left of amino acid after water is discarded

22 Polypeptide Chain is a Protein
Alpha carbons can rotate in any angle!

23 Protein Folding

24 Protein Sequences …EADWMTVLYIWPRKKEVPQR… …CHARACTERISTICALLY…
labeled: ACDEFGHIKLMNPQRSTVWY Missing: BJOUXZ …EADWMTVLYIWPRKKEVPQR… or …CHARACTERISTICALLY…

25 Translation tRNA = transfer RNA

26 Codon to Residue Table

27 Six ways to read an RNA/DNA string
Right to left or left to right Three positions for reading frame UCAGACCUUCUA

28 Some details of DNA to protein pathway
Prokaryotes DNA is “loose” in the cell DNA is in a single gene All DNA is used for encoding (few exceptions) Eukaryotes DNA is in nucleus DNA is in multiple chromosomes RNA is edited by splicing to eliminate noncoding introns and preserve coding exons

29 Splicing of mRNA to mature mRNA

30 Splicing of mRNA to mature mRNA

31 Noncoding DNA

32 Taxonomy From Characters

33 Taxonomy From Characters
CGGGTTAGAAGTAT Taxonomy From Characters CGGAATAGTCGTAT CGGATTAGTCGTAT CGGGTTAGTCGTAT CGGGTTAGACGTAT CGGGTTAGACGTAT

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