20 1 structural genomics determines the dna sequences of entire genomes
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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

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20 1 structural genomics determines the dna sequences of entire genomes
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 genomes1
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 genomes2
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


Concept check 1
Concept Check 1 Entire Genomes

A contig is:

  • a set of molecular markers used in genetic mapping

  • a set of overlapping fragments that form a continuous stretch of DNA

  • a set of fragments generated by a restriction enzyme

  • a small DNA fragment used in sequencing


Concept check 11
Concept Check 1 Entire Genomes

A contig is:

  • a set of molecular markers used in genetic mapping

  • a set of overlapping fragments that form a continuous stretch of DNA

  • a set of fragments generated by a restriction enzyme

  • a small DNA fragment used in sequencing


20 1 structural genomics determines the dna sequences of entire genomes3
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 genomes4
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 genomes5
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
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
Predicting Function from Sequence by Using Genomic-Based Approaches

  • 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


Concept check 3
Concept Check 3 by Using Genomic-Based Approaches

What is the difference between orthologs and paralogs?

  • Orthologs are homologous sequences; paralogs are analogous sequences.

  • Orthologs are more similar than paralogs.

  • Orthologs are in the same organism; paralogs are in different organisms.

  • Orthologs are in different organisms; paralogs are in the same organism.


Concept check 31
Concept Check 3 by Using Genomic-Based Approaches

What is the difference between orthologs and paralogs?

  • Orthologs are homologous sequences; paralogs are analogous sequences.

  • Orthologs are more similar than paralogs.

  • Orthologs are in the same organism; paralogs are in different organisms.

  • Orthologs are in different organisms; paralogs are in the same organism.


Gene expression and microarrays
Gene Expression and Microarrays by Using Genomic-Based Approaches

  • 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
20.3 Comparative Genomics Studies How Genomes Evolve by Using Genomic-Based Approaches


Prokaryotic genomes
Prokaryotic Genomes by Using Genomic-Based Approaches

  • 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
Eukaryotic Genomes by Using Genomic-Based Approaches

  • 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
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 cell1
20.4 Proteomics Analyzes the Complete Set of Proteins Found in a Cell

  • Determination of cellular proteins

    • Two-dimensional polyacrylamide gel electrophoresis.

    • Mass spectrometry