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Biochem Brandl 12

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Western University
Biochemistry 2280A
Eric Ball

Biochem - Lecture 12 - Dec. 2nd • how do we decide if an ORF really encodes a protein? ORF’s That Encode Proteins (Usually): • contain 100 codons or greater • show a codon usage typical for the organism (codon bias) • have related sequences, encoding similar proteins in other species • ex. using a BLAST search or a multiple sequence alignment • are found expressed as mRNA • contain appropriate regulatory sequences Codon Bias: • in any organism there are preferred codons for each amino acid (codons that are used more than others) • ex. E coli uses CGC and CGU for coding arginine, over using CGA or CGG • this differs between organisms - humans use all fairly significantly, with CGG and CGC used will slightly more frequency • an ORF that displays the codon bias typical of the organism is more likely to be a protein • not all functional genes encode for proteins • also want to annotate the tRNAs, and other things, not just proteins Cancer is: • the leading cause of death in North America • strikes victims of all ages • will become even more prevalent as the population ages • 2 types of tumors • benign (adenoma) - can be removed surgically • malignant - metastasized Metastasis: • Figure 20.44 • cancer cells move to other organs • cancer cells can break through basal lamina, and break into bloodstream and lymphatic system Cancer is a Genetic Disease: • susceptibility to cancer can be inherited • retinoblastoma (a cancer of the eye) • xeroderma pigmentosa (a cancer of the skin) • some break and intestinal cancers DNA Damaging Agents
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