BIOL 306 - Chapter Twenty: Genomics and Proteomics

Structural Genomics

Organization and sequence of genetic information contained within a genome

Genetic Maps

Approximate locations of genes relative to location of other genes

Genetic maps are based on ________________

rates of recombination

Limitations of Genetic Maps

1. Low resolution or detail

2. Do not correspond to physical distances between genes

Physical Map

Uses direct analysis of DNA to place genes in relation to physical distances (bp, kbp, mbp)

True or False: Physical maps are higher resolution and more accurate than genetic maps

True

Structural genomics determines the DNA sequences of ________________

entire genomes

The Human Genome Project sequenced the human genome using ________________ and ________________

map-based sequencing; whole-genome shotgun sequencing

What was the first free-living organism to sequenced?

Haemophilus influenzae

Map-based sequencing relies on _______________, while whole-genome shotgun sequencing uses _______________

detailed genetic and physical maps; sequence overlaps

Steps of Map-Based Sequencing

1. DNA partially digested, resulting in overlapping fragments cloned in bacteria

2. Clones analyzed for markers or overlapping restriction sites

3. Clones assembled into contig

4. Overlapping chromosomes that efficiently cover entire chromosome selected, fractured, and cloned

5. Subclones sequenced, sequence overlaps used to assemble them in correct order

6. Sequence of large clones put together with subclones for final sequence

Steps of Whole-Genome Shotgun Sequencing

1. Genomic DNA cut into small overlapping fragments and cloned in bacteria

2. Fragments sequenced

3. Sequence overlap used to order clones

4. Computer programs assemble genomic sequence

Contig

Continuous stretch of DNA

Single-Nucleotide Polymorphism (SNP)

Site in genome where individual members of a species differ in a single base pair

Haplotype

Specific set of SNP and other genetic variants observed on a chromosome

Haplotypes are made up of a particular set of _________ at each SNP

alleles

Bioinformatics = _____________ + _____________

Molecular Biology; Computer Science

Functional Genomics

Characterizes what sequences do

Transcriptome

All RNA molecules transcribed from a genome

Proteome

All proteins encoded by a genome

Homologous Genes

Evolutionarily related genes

Orthologs vs. Paralogs

Orthologs: Homologous genes in different species

Paralogs: Homologous genes in the same species

Nucleic Acid Hybridization

Using known DNA fragment as a probe to find complementary sequence

Microarrays can be used to examine gene expression associated with ________________

disease progression

RNA sequencing is used to determine _____________ throughout the genome

the expression of genes

Steps of RNA Sequencing

1. Cellular RNA isolated from cells

2. mRNA of interest isolated

3. Reverse transcriptase used to make complimentary DNA (cDNA)

4. cDNA broken into overlapping fragments

5. Adapters with amplification and sequencing sequences added to ends of fragments

6. Fragments amplified and sequenced

7. Sequence reads assembled into RNA transcripts

Horizontal Gene Transfer

Exchange of genetic information from closely or distantly related species over evolutionary time

True or False: Horizontal gene transfer occurs more frequently in eukaryotic genomes

False: Prokaryotic genomes

The human genome is _____________ in length

3.2 billion base pairs

Only ______ of the human genome encodes proteins

1.50%

Two-Dimensional Polyacrylamide Gel Electrophoresis (2D-PAGE)

Used to separate cellular proteins

Steps of 2D-PAGE

1. Proteins separated in one dimension by charge

2. Proteins separated in second dimension by mass

3. Proteins stained

Mass Spectrometry

Used to identify proteins

Steps of Mass Spectrometry

1. Protein treated with trypsin and broken into short peptides

2. Mass spectrometer determines mass-to-charge ratio of peptides

3. Computer program analyzes profile of peaks and identifies proteins

In mass spectrometry, small molecules migrate __________ than larger molecules

more rapidly

Affinity Capture

Antibody to specific protein used to capture one protein from complex mixture of proteins

Affinity capture and protein microarrays both determine sets of ____________

interacting proteins

Protein microarrays can be used to examine interactions among __________

proteins