Central DogmaInformation storage in molecules
DNA
RNA
Protein
transcription
translation
replication
Proteins
Carbon-Nitrogen backboneamino 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 aa2nt => 1aa can code for (4x4)= 16 aa3nt => 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
Degenerate-- most amino acids have more than one code word
often these redundant codes share the same first two bases
The genetic code is:
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 Databasehttp://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
Genome %G+C=31%
Prochlorococcus MIT9313
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 siteSoftware/Informatics/artemis
Download Artemis V8 Save in Ocean 539D folder
Make a shortcut to the .jar file on the desktopEdit the properties of the shortcut and add
"java -mx250m -jar " to the start of the Target: field.
MED4
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Effective number of codons (Nc)
Fre
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MED4
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%G+C
#o
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