1. Central Dogma Information storage in molecules DNA RNA Protein transcription translation replication

2. Proteins Carbon-Nitrogen backbone amino acid side chains

3. The twenty amino acids

4. Translation: RNAProteins How do we get from bases to amino acids? 1nt => 1aa can code for 4 aa 2nt => 1aa can code for (4x4)= 16 aa 3nt => 1aa can code for (4X4x4)= 64 aa G CAC CCG CGA AG His Pro Arg The code consists of continuous Nonoverlapping triplets GCA CCC GCG AAG Ala Pro Ala Lys

5. Degenerate-- most amino acids have more than one code word often these redundant codes share the same first two bases The genetic code is:

6. The genetic code: another view Codons in the same color encode identical amino acids What are the likely effects of a mutation at the first vs. third codon position?

7. The Genetic code is universal (mostly) some exceptions- eg-Mycoplasma TGA=Trp (instead of stop) Candida cylindrica CTG= Ser (instead of Leu) mitochondrial DNA—several different exceptions depending on organism NCBI site covering alternative genetic codes: http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c The Codon Usage Database http://www.kazusa.or.jp/codon/

9. Leading vs lagging strand synthesis

10. %G+C content plotted as difference from genomic mean GC skew = (G-C)/(G+C) Theoretical range from -1 to 1 An indication of origin of replication

11. Prochlorococcus MED4 Genome %G+C=31% Prochlorococcus MIT9313 Genome %G+C=51%

12. Genetic code 61 possible codons (64-3 stop) BUT, not all are used with equal frequency

13. Measures of codon usage Measures based on a set of highly expressed genes (presumed optimal CU)  CAI (codon adaptation index)  Fop (Frequency of optimal codons)  CBI (codon bias index) Measures independent of presumed optimal codon set  Nc (effective number of codons)  RFSCU (Relative frequency of synonymous codon usage) Read more about these at  http://www.molbiol.ox.ac.uk/cu/Indices.html

14. Role of tRNA complement in translation efficiency 1 tRNA recognizes a particular codon BUT, most genomes do not have 61 tRNA genes……

15. Getting Artemis Go to Sanger center web site  Software/Informatics/artemis Download Artemis V8  Save in Ocean 539D folder Make a shortcut to the.jar file on the desktop  Edit the properties of the shortcut and add "java -mx250m -jar " to the start of the Target: field.