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Lecture 19

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Western University
Biology 1002B
Tom Haffie

Lecture 19: Molecular Homology  Molecular evolution o Level of the gene, protein, what are the changes, nucleic acid, amino acid  Gene evolution o How do they change over time o Mutation  Indel, etc. o Duplication o Rearrangement  Rearrange parts of genes o Loss  Genes might be lost during these changes o Phenotype  Some might not affect phenotype  Some might have significant effect phenotype  Mutation to a gene, alter the shape of the protein (substrate specificity) o Phenotype is subjected to selection  Selection only acts on phenotype not the genotype (gene sequence)  Homology o Share a common ancestor o Does not mean similar o How do we know if they share a common ancestor  Tom… “look here, it’s the same gene in Volvox and in Chlamy”  Clicker question o If GlsA in Vovox and GlsA in Chlamydomonas are homologous – what do they have in common?  Identical nucleotide sequence  Identical amino acid sequence  Identical length of polypeptide  Same function  None of above is the right answer  Comparative genomics o Sequence genomes o Genome annotation o Protein prediction o Align sequences o Determine homology  Genome annotation o Sequencing is cheap, no specific mathematics o Attach biological meaning to sequence (bio informatics)  Gene prediction  Regulatory elements  Biological function through similarity searches  Automated (algorithms are created to look at specific things)  Protein-coding gene prediction o Protein coding genes  Computer algorithms  Detect: promoter elements, intron/exon boundaries, other conserved DNA motifs…  Predict how many protein coding genes are within the genome o They take out the introns and left only with exons o Predicted protein sequence o There are 6 possible reading frames  Protein prediction – find longest ORF o There are six possible reading frames  +1, +2, +3, -1, -2, -3 o Green bar goes up is start, purple going down is stop o Looking for the longest open reading frame  From the start to stop  National center for biotechnology information (NCBI) o Chlamydomonas: 15,000 predicted proteins  Now what?  Look in NCBI for similar genes  We don’t sequence proteins because it is very expensive  We just look at the predicted protein o NCBI  Genebank  Sequence database  23,500 total genomes o Looking for sequences are that are similar  Sequence alignment (DNA or protein) o Automated o Arrange sequences to show regions of similarity o Sequence similar can infer Structure and Function and evolution relatedness o BLAST – basic local alignment search tool  Local o CLUSTAL  Global o Global vs. local alignments  Global start at the beginning
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