1. Things that may help with comprehension of bioinformatics issues in general and Rosalind problems in particular

2. Problems Counting DNA nucleotides Transcribing DNA into RNA
Complementing a strand of DNA
Rabbits and Recurrence Relations
Population growth model
GC Content

3. Problems Counting DNA nucleotides Transcribing DNA into RNA
Intro to nucleotides
What are they? Put together in genome as a string
Some cool features of genome structure
Transcribing DNA into RNA
The protein coding parts
The central Dogma
Codons and other structural elements of genes
Complementing a strand of DNA
Issues of complementarity
Rabbits and Recurrence Relations
Population growth model
GC Content
Signatures of different parts of genomes and differences among genomes

4. This course pays a bit of extra attention to data applications in the life sciences, such as DNA sequencing.

5. Bioinformatics
“the science of collecting and analyzing complex biological data such as genetic codes.”
“conceptualizing biology in terms of macromolecules (in the sense of physical-chemistry) and then applying "informatics" techniques (derived from disciplines such as applied maths, computer science, and statistics) to understand and organize the information associated with these molecules, on a large-scale.”

6. http://www. nature. com/scitable/resource

7. Characteristics of DNA relevant for bioinformatics
A linear string
Exists as double stranded helix
Each strand has directionality
Rules for pairing
Genome has different regions
Protein coding
Genetic code
RNA coding

8. >Rosalind_6404
CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCC
TCCCACTAATAATTCTGAGG
>Rosalind_5959
CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCT
ATATCCATTTGTCAGCAGACACGC
>Rosalind_0808
CCACCCTCGTGGTATGGCTAGGCATTCAGGAACCGGAGAACGCTTCAGACCAGCCCGGAC
TGGGAACCTGCGGGCAGTAGGTGGAAT

9. RNA and DNA each contain 4 Nitrogenous Bases
Figure: 10-07a
Title:
Chemical Structures of the Pyrimidines and Purines
Caption:
Chemical structures of the pyrimidines and purines that serve as the nitrogenous bases in RNA and DNA.

10. Bases, sugars, and phosphates combine to be “nucleotides”
Figure: 10-08
Title:
Nucleosides and Nucleotides
Caption:
Structures and names of the nucleosides and nucleotides of RNA and DNA.

11. RNA and DNA differ in the nature of the sugar
molecule that they contain.
Figure: 10-07b
Title:
Chemical Ring Structures of Ribose and 2-deoxyribose
Caption:
Chemical ring structures of ribose and 2-deoxyribose, which serve as the pentose sugars in RNA and DNA, respectively.
5 Carbons – (5’ and 3’)

12. The building blocks of DNA (and RNA) are
Nucleotides (=nucleoside triphosphates)
Figure: 10-09
Title:
Nucleoside Diphosphates and Triphosphates
Caption:
Basic structures of nucleoside diphosphates and triphosphates, as illustrated by thymidine diphosphate and deoxyadenosine triphosphate.

13. Nucleoside bases are linked together in chains of RNA or DNA by
phosphodiester
(phosphate-sugar)
bonds
Figure: 10-10
Title:
Phosphodiester Bonds
Caption:
(a) Linkage of two nucleotides by the formation of a C-3’-C-5’ (3’-5’) phosphodiester bond, producing a dinucleotide. (b) Shorthand notation for a polynucleotide chain.

14. RNA and DNA
differ in two ways—
1. sugar molecule
they use
2. one base-
uracil in RNA,
but thymine in
DNA.
The other
bases (adenine,
guanine, and
cytosine) occur
in both molecules.

15. Hydrogen bonds
connect A and T and
G and C.
Watson and Crick

16. Based on X-ray crystallography data from Franklin and
Wilkins, W&C proposed a double-helix model of DNA
Rosalind
Franklin

17. THE CENTRAL DOGMA

18. Transcribing a gene in more detail: Making sense of anti-sense
Sense strand: What we think of as the coding sequence for a gene. Sequence matches mRNA sequence. Also called “plus strand” or “non-template strand”.
Let’s talk more about the DNA sequence now and how genes are structures on DNA
Anti-sense strand: The strand actually read by RNA polymerase to create the mRNA in the 5’ to 3’ direction. (This strand is read in the anti-parallel direction to build RNA 5’ to 3’.) Also called “minus strand” or “template strand”.

19. Problem solving The DNA for a given gene reads as follows:
3’ TACGGTACTATC 5’
5’ ATGCCATGATAG 3’
The bottom strand shows the coding region/non-template strand.
What should the newly synthesized RNA read?
Which strand will RNA polymerase attach to, and in which direction will it read?
5’ AUGCCAUGAUAG 3’
The top strand, reading 3’ to 5’

20. THE CENTRAL DOGMA! FIGURE 12-1
Flowchart illustrating how genetic information encoded in DNA produces protein.

21. The ‘universal’ degenerate code
Theoretically a lot of other possible options (Judson & Heydon, 1999)
What does this suggest about the evolution of life on earth?
Some would work as well or better
Having a unique code might be advantageous
So why is the code universal?
Look up on web!
Darwin would say: all organisms inherited the genetic code from a common ancestor
Constraint?

22. Bioinformatics sites Translate DNA to protein
Search NCBI database to identify sequence

23. An unknown sequence for you to play around with as you wish
GGCACGAGAAAAGACTAGTTGCTCACTGGAAAAAGTCTAAAAATGAGGTTTCTCGTTGGAGCAGTATTAGTTGTTGTGTTGGTGGCTTGTGCCACGGCATTCGAAAGTGATGCCGAAACTTTTAAATCTCTTGTTGTAGAAGAAAGAAAATGCCACGGAGATGGTTCCAAGGGCTGTGCCACAAAGCCTGATGACTGGTGCTGCAAGAATACACCTTGCAAGTGCCCCGCCTGGTCCTCCACAAGTGAGTGCAGGTGCGCAATGGACTGCAGCCGAAGATGCAAAGGCAAACGAGCATTGTTGTTGCCAGTTGAGACTCACCGACTACTCTTCCCTGAACAATGGTGAAGCCATTGACATCGATATATCATCTACTGTTATGTACTGTAAAAACAAATAAAGTTACTTATGCAGTAAAAAAAAAAAAAAAAAAAAAAAAA