Essentials of Genetics Chapter 18

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genome
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the complete set of DNA in a single cell of an organism
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genomics
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the study of genomes’ -field of genetics that attempts to understand the content, organization, function, and evolution of genetic information contained in whole genomes
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structural genomics
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focuses on sequencing genomes and analyzing nucleotide sequences to identify genes and other important sequences such as gene-regulatory regions
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whole genome-shotgun sequencing
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restriction enzymes digest genomic DNA into contigs, which are then sequenced and aligned using bioinformatics to identify overlapping fragments based on sequence identity
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1st computer-automated DNA sequencing instruments can process millions of base pairs per day. What type of sequencing was this designed for ?
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High-throughout sequencing
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Bioinformatics uses computer-based approaches to organize and analyze data. What are some of the most important applications of Bioinformatics?
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whole genome shotgun sequencing enables
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scientists to assemble sequence maps of entire genomes and is the most widely used strategy for sequencing
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GenBank
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the largest and most important -available database of DNA sequences and maintained by the National Center for Biotechnology Information (NCBI -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
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What is Annotation and BLAST ?
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-annotation is the process of identifying (genes regulatory sequences and functions) -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 .
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Hallmark Characteristics of Genes (Prok or EuK) can be searched on bioinformatics software. Give an of such characteristics example.
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Regulatory sequences found upstream are marked by identifiable sequences such as promoters, enhancers, and silencers.
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functional genomics
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the study of gene functions, based on the resulting RNAs or proteins they encode, and considers the functions of other components of the genome, such as gene-regulatory elements -can confirm or refute computational predictions about genome functions, and it also considers how how genes are expressed and the regulation of gene expression
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Open reading frames (ORFs)
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found in protein-coding genes, are sequences that are translated into the amino acid sequence of a protein -begins with ATG -Ends with TAA, TAG, or TGA
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How can you study or predict gene/ protein function ?
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-resulting RNA or possible proteins as well as regulatory elements -sequence analysis: BLAST search for homologous sequence of newly sequenced DNA
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Orthologs vs. Paralogs
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Homologous genes from different species thought to have descended from a common ancestor are called orthologs. Homologous genes in the same species are called paralogs.
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Gene sequence can be used to predict a polypeptide sequence then analyzed for protein domains and motifs to determine function. What are examples of protein domains and motifs?
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-Protein domains: ion channels, membrane-spanning regions, binding, secretion, and export signals – Motifs: helix-turn-helix, leucine zipper, or zinc finger motifs
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Human Genome Project
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-was a coordinated international effort to sequence and identify all the genes of the human genome -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).
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comparative genomics
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answers questions about genetics and other aspects of biology through the analysis of genomes from different organisms -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
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Celera Genomics
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a privately funded human genome project, was to use whole-genome shotgun sequencing and computer-automated high-throughput DNA sequencers. Set up to safeguard personal genome information from being used in discrimination.
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Alternative splicing
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-many genes are able to code for multiple proteins – generation of different protein molecules from the same pre-mRNA by incorporation of a different set and order of exons into the mRNA product
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single-nucleotide polymorphisms (SNPs)
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-a variation in a single nucleotide pair in DNA usually detected during genomic analysis. Present in at least 1 percent of a population a SNP is useful as a genetic marker -many associated with disease conditions (example: sickle-cell anemia and cystic fibrosis)
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copy number variations (CNVs)
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DNA segments larger than 1 kb that are repeated a variable number of times in the genome
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What is the Human Genome Project’s most valuable contribution ?
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-the identification of disease genes and the development of new treatment strategies. – • Extensive maps have been developed for genes implicated in human disease conditions (ALS, Alzheimer’s, cataracts, deafness, several cancers, etc.
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Areas of biological research having an “omics” connection are _______
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> continually developing – proteomics. – metabolomics. – glycomics . – taxicogenomics. – metagenomics. – pharmacogenomics. – transcriptomics. – Nutrigenomics (new field focusing on interactions between diet and genes.
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Percentage of genes that the same regardless of racial or ethnic origins? where are the most genetic differences resulting from?
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-99.9% – Single-nucleotide polymorphisms (SNPS) & copy number variations (CNVs)
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Stone-age genomics ? examples?
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-uses small amounts of ancient DNA from bone and other tissue -used to study the evolutionary relatedness of various extinct and present-day species – Egyptian mummy – Mosses – Platypus – Mammoths
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Encyclopedia of DNA Elements (ENCODE)
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was created with the aim of using both experimental approaches and bioinformatics to identify and analyze functional elements that regulate expression of human genes
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Personal Genome Project (PGP)
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-As of 2010 many personal genomes have been done. -PGP sequences diploid genomes.
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Human Microbiome Project
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A $115 million, 5-year project to complete the genomes of 600-1000 microorganisms, bacteria, viruses, and yeast that live on and inside humans – Has already revealed over 3.3 million gut microbe genes
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Genome 10K
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-Genome scientists and museum curators have proposed sequencing 10,000 vertebrate genome the Genome 10k plan – Will provide insight into genome evolution and speciation
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Comparative genomics
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compares the genomes of different organisms in order to answer questions about genetics and other aspects of biology – 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
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Prokaryotes and Eukaryotes
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-Many prokaryotes genomes are already sequenced -Bacteria have a single, circular chromosome w/ substantial variation -Gene density is very high in prokaryotes -Bacterial DNA contains operons
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Eukaryotes
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-eukaryotic genomes are similar different species, highly variable – (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
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complete sequences of various organism show the number of genes humans share with other species is very high ranging from about _____ percent of the genes in yeast to _____ percent in mice and ______percent in chimpanzees
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30, 80, 98
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transcriptome
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all the RNA molecules transcribed from a genome
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Dog genome
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-completed in 2005 and share 75 percent of our genes -many genetic orders with humans – over 400 single-gene disorders -sex-chromosome aneuploides -multifactorial diseases -behavioral conditions
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Chimpanzee Genome
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-human & chimpanzee sequences differ by less than 2% -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
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Rhesus Monkey Genome
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-is one of the most important model organisms in biomedical research -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
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Sea Urchin Genome
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Sea urchins are shallow-water marine invertebrates -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
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Neanderthal Genome
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-A rough draft of the Neanderthal (Homo neanderthalensis) genome shows two-thirds of the genome. 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
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What is the estimated years that genomic studies suggest interbreeding took place between Neanderthals and modern humans?
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-45,000 to 80,000 years ago -The genome of non-African H. sapiens contains approximately 1-4 percent of sequences inherited from Neanderthals
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-Multigene families -Superfamily – Globin family gene
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– share similar but not identical DNA sequences – group of related multigene families -one of the best-studied examples of gene family
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Globin family gene
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An ancestral gene encoding an oxygen transport protein was duplicated (800 mya), producing two sister genes. One of the genes evolved into the modern-day myoglobin gene and the other into globin genes encoding hemoglobin (Figure 18-9). – 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
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Metagenomics (environmental genomics )
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is the use of whole-genome shotgun approaches to sequence genomes from entire communities of microbes in environmental samples of water, air, and soil.
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The general method for metagenomics is to sequence genomes for all microbes in a given environment
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-This will teach us more about millions of species of bacteria as well as viruses, particularly bacteriophages. – This method has a great potential for identifying genes with novel functions, some of which may have valuable applications in medicine and biotechnology.
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Transcriptome analysis vs. global analysis
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Transcriptome analysis or global analysis of gene expression studies the expression of genes by a genome – both qualitatively, by identifying which genes are expressed and which are not, – and quantitatively, by measuring the varying levels of expression of different genes.
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Transcriptome analysis provides insights into
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-normal patterns of gene expression to understand how a cell or tissue type differentiates during development. – 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
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Dna Microarray analysis , gene chips
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-enables researchers to analyze all of a sample’s expressed genes simultaneously – 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
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Proteomics , proteome
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-is the identification, characterization, and quantitative analysis of all proteins -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
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Protein Structure Initiative (PSI)
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-is a 10-year project designed to analyze the three-dimensional structures of more than 4000 protein families. -Proteins with potential therapeutic properties are top priority.
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Mass spectrometry, Matrix-assisted laser desorption ionization
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Mass spectrometry (MS) techniques -analyze ionized samples in gaseous form and measure the mass-to-charge (m/z) ratio of different ions in a sample. – 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
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Protein microarrays
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are designed around the same basic concept as microarrays (gene chips) and are often constructed with antibodies that recognize and bind to different proteins. – Used to examine protein-protein interactions, detect protein markers for disease diagnosis, and study biosensors to detect pathogenic microbes
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Identification of Collagen in T. rex
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Mass spectrometry analysis of bone -tissue from a T. rex skeleton estimated at over 68 million years old demonstrated that fossilization does not fully destroy all protein in well-preserved fossils. – Results suggest that T. rex proteins samples contained collagen, a major matrix component of bone, ligaments, tendons, and skin.
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Systems biology, interactome
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Systems biology incorporates data from genomics, transcriptomics, proteomics, and other areas of biology as well as engineering applications to further elucidate components of interacting pathways and the interrelationships of molecules. – Interactome describes the interacting components of a cell.
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network map
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-is a sketch showing the interacting proteins, genes, and other molecules. – 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

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