-field of genetics that attempts to understand the content, organization, function, and evolution of genetic information contained in whole genomes
-shares and acquires databases in Europe and Japan
-Each sequence deposited in GenBank receives an accession number: is a unique identifier given to a DNA or protein sequence record to allow for tracking of different versions of that sequence record
-BLAST( Basic Local Alignment Search Tool) : software application used to compare a segment of DNA to sequences throughout the major databases
-BLAST searches calculates a similarity score—also called the identity value—determined by the sum of identical matches between aligned sequences divided by the total number of bases .
-can confirm or refute computational predictions about genome functions, and it also considers how how genes are expressed and the regulation of gene expression
-begins with ATG
-Ends with TAA, TAG, or TGA
-sequence analysis: BLAST search for homologous sequence of newly sequenced DNA
– Motifs: helix-turn-helix, leucine zipper, or zinc finger motifs
-The project began in 1990 under the direction of Dr. James Watson. – Dr. Francis Collins led the project under the coordination of the DOE and the National Center of Human Genome Research (NIH).
> 2% codes for proteins ( abt 20,000 protein-coding genes).
-research and practical applications
-study of gene and genome evolution and relationship between organisms and their environment
—Compares similarities and differences in gene content, function, and organization among genomes of different organisms
Set up to safeguard personal genome information from being used in discrimination.
– generation of different protein molecules from the same pre-mRNA by incorporation of a different set and order of exons into the mRNA product
-many associated with disease conditions (example: sickle-cell anemia and cystic fibrosis)
– • Extensive maps have been developed for genes implicated in human disease conditions (ALS, Alzheimer’s, cataracts, deafness, several cancers, etc.
. – taxicogenomics.
– metagenomics. – pharmacogenomics.
– Nutrigenomics (new field focusing on interactions between diet and genes.
– Single-nucleotide polymorphisms (SNPS) & copy number variations (CNVs)
-used to study the evolutionary relatedness of various extinct and present-day species
– Egyptian mummy
-PGP sequences diploid genomes.
– Has already revealed over 3.3 million gut microbe genes
– Will provide insight into genome evolution and speciation
– Incorporates the study of gene and genomic evolution
– Explores the relationship between organisms and the environment
– Studies differences and similarities between organisms and how differences contribute to phenotype, life cycles, etc
-Bacteria have a single, circular chromosome w/ substantial variation
-Gene density is very high in prokaryotes
-Bacterial DNA contains operons
– (gene density) varies from chromosome to chromosome
-introns: variation in genomes and in genes
-repetitive sequences : about half of the human genome is repetitive DNA
-many genetic orders with humans
– over 400 single-gene disorders
-speciation event that separated humans and chimps occurred less than 6.3 million years ago
-studies indicate that genome evolution, speciation, and gene expression are interconnected
-central in our understanding of cardiovascular disease, aging, diabetes, cancer, depression, osteoporosis and many other aspects of human health
– their genome is suited for comparison to humans
-Sequence alignment and homology searches demonstrate that the sea urchin contains many genes with important functions in humans.
– Have 23,500 genes, including representative genes for all major gene families
– Have genes involved in immunity
– Have nearly 1000 light-sensing genes
A comparative genomic analysis will help identify areas in the genome where humans have undergone rapid evolution since diverging from Neanderthals.
– 99 percent identical
– 78 new protein-coding sequences since divergence
-The genome of non-African H. sapiens contains approximately 1-4 percent of sequences inherited from Neanderthals
– Globin family gene
– group of related multigene families
-one of the best-studied examples of gene family
– Myoglobin (oxygen-carrying protein) is found in muscle. – Hemoglobin is made up of α- and β-globin (Figure 18-10).
– Arose due to gene duplication, nucleotide substitution, and chromosomal translocation
– This method has a great potential for identifying genes with novel functions, some of which may have valuable applications in medicine and biotechnology.
– both qualitatively, by identifying which genes are expressed and which are not,
– and quantitatively, by measuring the varying levels of expression of different genes.
– how gene expression dictates and controls the physiology of differentiated cells.
– mechanisms of disease development that result from or cause gene-expression changes in cells
– Microarrays, also known as gene chips, consist of glass microscope slides onto which single-stranded DNA molecules are attached using a high-speed robotic arm called an arrayer
— A single microarray can have over 20,000 different spots of DNA
-encoded by the genome of a cell, tissue, or organism
– Can be used to reconcile differences between the number of genes in a genome and the number of different proteins produced
– Allows comparison of proteins in normal and diseased tissue
-Proteins with potential therapeutic properties are top priority.
– Matrix-assisted laser desorption ionization (MALDI) is used for proteomic analysis of tissue samples treated under different conditions
-MALDI produces a peptide “fingerprint” that is characteristic of the protein being analyze
– Used to examine protein-protein interactions, detect protein markers for disease diagnosis, and study biosensors to detect pathogenic microbes
– Results suggest that T. rex proteins samples contained collagen, a major matrix component of bone, ligaments, tendons, and skin.
– Interactome describes the interacting components of a cell.
– Helps modeling of intricate potential interactions of molecules involved in normal and disease processes
– a network map illustrating the complexity of interactions between genes involved in 22 different human diseases