BSC 219

Genomics and Proteomics

11/06/12

20.1 Structural Genomics Determines the DNA Sequences of Entire Genomes

The ultimate goal of genomic research: determining the ordered nucleotide sequences of entire genomes of organisms

Genetic maps: (linkage map) approximate locations of genes, relative to the location of other genes, based on the rates of recombination

20.1 Structural Genomics Determines the DNA Sequences of Entire Genomes

Physical map: based on the direct analysis of DNA, places genes in relation to distances measured in bp, kbp, and mbp

20.1 Structural Genomics Determines the DNA Sequences of Entire Genomes

Sequencing an entire genome:

The human genome project

Map-based sequencing: relies on detailed genetic and physical maps to align sequenced fragments

20.1 Structural Genomics Determines the DNA Sequences of Entire Genomes

Whole-genome shotgun sequencing:

Small-insert clones are prepared directly from genomic DNA and sequenced in a highly automated way.

20.1 Structural Genomics Determines the DNA Sequences of Entire Genomes

Single-nucleotide polymorphisms:

A site in the genome where individual members of a species differ in a single base pair

Haplotype: the specific set of SNPs and other genetic variants observed on a chromosome

tagSNPs

20.1 Structural Genomics Determines the DNA Sequences of Entire Genomes

Copy-number variations

The number of copies of DNA sequences varies from people to people.

Expressed-Sequence Tags (ESTs)

Markers associated with DNA sequences that are expressed as RNA

Bioinformatics:

Molecular Biology + Computer Science

20.2 Functional Genomics Determines the Functions of Genes by Using Genomic-Based Approaches

Functional genomics

characterizes what the sequences do

Transcriptome: all the RNA molecules transcribed from a genome

Proteome: all the proteins encoded by the genome

Predicting Function from Sequence

Homologous

Genes that are evolutionarily related

Orthologs

Homologous genes in different species that evolved from the same gene in a common ancestor

Paralogs

Homologous genes arising by duplication of a single gene in the same organism

Gene Expression and Microarrays

Microarrays:

Nucleic acid hybridization: using a known DNA fragment as a probe to find a complementary sequence

Gene expression and reporter sequences:

Reporter sequence: encoding an easily observed product used to track the expression of a gene of interest

20.3 Comparative Genomics Studies How Genomes Evolve

Prokaryotic Genomes

Genome size

Number of genes

Horizontal gene transfer: exchanging genetic information from closely related or distantly related species over evolutionary time

Function of genes

Eukaryotic Genomes

Genome size

Number of genes

Multigene family: a group of evolutionarily related genes that arose through repeated evolution of an ancestral gene

BSC 219

20.1 Structural Genomics Determines the DNA Sequences of Entire Genomes

The ultimate goal of genomic research: determining the ordered nucleotide sequences of entire genomes of organisms

Genetic maps: (linkage map) approximate locations of genes, relative to the location of other genes, based on the rates of recombination

20.1 Structural Genomics Determines the DNA Sequences of Entire Genomes

Physical map: based on the direct analysis of DNA, places genes in relation to distances measured in bp, kbp, and mbp

20.1 Structural Genomics Determines the DNA Sequences of Entire Genomes

Sequencing an entire genome:

The human genome project

Map-based sequencing: relies on detailed genetic and physical maps to align sequenced fragments

20.1 Structural Genomics Determines the DNA Sequences of Entire Genomes

Whole-genome shotgun sequencing:

Small-insert clones are prepared directly from genomic DNA and sequenced in a highly automated way.

20.1 Structural Genomics Determines the DNA Sequences of Entire Genomes

Single-nucleotide polymorphisms:

A site in the genome where individual members of a species differ in a single base pair

Haplotype: the specific set of SNPs and other genetic variants observed on a chromosome

tagSNPs

20.1 Structural Genomics Determines the DNA Sequences of Entire Genomes

Copy-number variations

The number of copies of DNA sequences varies from people to people.

Expressed-Sequence Tags (ESTs)

Markers associated with DNA sequences that are expressed as RNA

Bioinformatics:

Molecular Biology + Computer Science

20.2 Functional Genomics Determines the Functions of Genes by Using Genomic-Based Approaches

Functional genomics

characterizes what the sequences do

Transcriptome: all the RNA molecules transcribed from a genome

Proteome: all the proteins encoded by the genome

Predicting Function from Sequence

Homologous

Genes that are evolutionarily related

Orthologs

Homologous genes in different species that evolved from the same gene in a common ancestor

Paralogs

Homologous genes arising by duplication of a single gene in the same organism

Gene Expression and Microarrays

Microarrays:

Nucleic acid hybridization: using a known DNA fragment as a probe to find a complementary sequence

Gene expression and reporter sequences:

Reporter sequence: encoding an easily observed product used to track the expression of a gene of interest

20.3 Comparative Genomics Studies How Genomes Evolve

Prokaryotic Genomes

Genome size

Number of genes

Horizontal gene transfer: exchanging genetic information from closely related or distantly related species over evolutionary time

Function of genes

Eukaryotic Genomes

Genome size

Number of genes

Multigene family: a group of evolutionarily related genes that arose through repeated evolution of an ancestral gene

20.4 Proteomics Analyzes the Complete Set of Proteins Found in a Cell

Determination of cellular proteins

Two-dimensional polyacrylamide gel electrophoresis

Mass spectrometry

20.4 Proteomics Analyzes the Complete Set of Proteins Found in a Cell

Determination of cellular proteins

Two-dimensional polyacrylamide gel electrophoresis.

Mass spectrometry-to analyze proteins