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)

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