Transcript Lecture
Central Dogma Information storage in molecules replication DNA transcription RNA translation Protein Proteins Carbon-Nitrogen backbone amino acid side chains The twenty amino acids Translation: RNA Proteins 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 The code consists of continuous Nonoverlapping triplets GCA CCC GCG AAG Ala Pro Ala Lys G CAC CCG CGA AG His Pro Arg The genetic code is: Degenerate-most amino acids have more than one code word often these redundant codes share the same first two bases 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? 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/ Leading vs lagging strand synthesis %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 Prochlorococcus MED4 Prochlorococcus MIT9313 Genome %G+C=31% Genome %G+C=51% Genetic code 61 possible codons (64-3 stop) BUT, not all are used with equal frequency 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 Role of tRNA complement in translation efficiency 1 tRNA recognizes a particular codon BUT, most genomes do not have 61 tRNA genes…… 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. 0 0. 36 0. 33 0. 29 0. 26 0. 22 0. 19 0. 16 0. 50 100 63 200 0. 46 300 59 400 0. 43 500 55 MED4 0. 39 %G+C 51 47 43 39 35 31 25 Frequency #of genes MED4 200 150 100 50 0 Effective number of codons (Nc)