Genomics and Functional Genomics: Mapping, Sequencing, and Proteomics Techniques

What is genomics?

The molecular analysis of the entire genome of a species.

What is a genome?

All of the genetic composition of an organism (nuclear and extranuclear).

What are the techniques for mapping chromosomes?

Cytogenetic mapping, linkage mapping, and physical mapping.

What does cytogenetic mapping determine?

The relative locations of genes and other segments of DNA along individual chromosomes.

What is the purpose of banding patterns in cytogenetic mapping?

To determine the location of specific sequences within chromosomes.

What stain is used to produce characteristic banding patterns?

Giemsa stain.

What is Fluorescent In situ Hybridization (FISH)?

A technique used in cytogenetic mapping to determine the location of specific sequences.

What does linkage mapping rely on?

The frequency of recombinant offspring.

How is map distance calculated in linkage mapping?

Map distance = (# of recombinant offspring / total # of offspring) x 100.

What is one map unit equivalent to?

1% recombinants.

What is physical mapping?

Determining the locations and distance of specific sequences within chromosomes using DNA cloning techniques.

What is a contig?

Overlapping pieces of cloned chromosomal DNA.

What are YACs?

Yeast artificial chromosomes that can accept several thousand to 2 million base pairs.

What are BACs?

Bacterial artificial chromosomes that can accept ~300,000 base pairs.

What is the goal of genome-sequencing projects?

To determine the sequence of DNA bases of the entire genome of a species.

What is shotgun sequencing?

A method used to sequence the first genome, Haemophilus influenzae.

What is next generation sequencing?

A method used for large sequencing projects, capable of sequencing thousands or millions of samples.

What is pyrosequencing?

A type of next generation sequencing that relies on the release of pyrophosphate.

What is metagenomics?

The study of a complex mixture of genetic material obtained from an environmental sample.

What are some applications of metagenomics in medicine?

Studying complex microbes in the gut and their associations with different diseases.

How can metagenomics be applied in agriculture?

By facilitating plant growth and improving yields through complex microbes.

What role do microbes play in bioremediation?

They decompose pollutants.

How do microbes contribute to global change?

They carry out half of photosynthesis and recycle nutrients.

What is one use of metagenomics in aquatic biology?

To analyze the complexity of microbial communities in water.

Which type of mapping relies on microscopy?

Cytogenetic mapping.

What was the parental generation in the fly experiment?

True-breeding flies with red eyes and long wings crossed with flies with white eyes and miniature wings.

What is the map distance of the two genes for eye color and wing length?

32.3

What is the aim of metagenomics?

Determining the sequence of DNA fragments in environmental samples.

What is functional genomics?

Determine the role of genetic sequences in a species.

What is the purpose of a DNA microarray?

Used to quantify thousands of genes simultaneously.

What is Chromatin Immunoprecipitation (ChIP)?

A method to study DNA-protein interactions as they occur in living cells.

What is RNA Sequencing (RNA-Seq)?

Sequencing of cDNA derived from RNAs using next generation DNA sequencing methods.

What is a gene knockout?

The alteration of a gene to inactivate its function.

What is proteomics?

The study of the function and interactions of proteins in a cell or organism.

What is the proteome?

The entire collection of proteins in a cell or organism.

What is alternative splicing?

The most important alteration for the size differences in proteins.

What is 2D Gel Electrophoresis?

A technique used to separate thousands of proteins.

What is mass spectrometry?

A method that measures the mass of a molecule, such as a peptide fragment.

What is a protein microarray?

Used to study protein expression and function in a cell.

What is bioinformatics?

The use of computer, mathematical tools and statistical techniques to analyze biological information.