Chapter 21: Genomic, Bioinformatics, and Proteomics Summary (Page1)- Genome: complete set of DNA in a single cell of an organism- Structural Genomics: focuses on sequencing genomes and analyzing nucleotide sequences to identify genes and other important sequences such as a gene-regulatory regionso Whole-genome shotgun sequencing: most widely used strategy for sequencing and assembling an entire genome (aka shotgun cloning)o Restriction enzymes: DNA-digested enzymes that cut the phosphdiester backbone of the DNA at specific sequences Can partially digest by cutting at different sites- DNA is incubated only for a short timeo Contiguous fragments: overlapping fragments that are adjoining segments that collectivelyform one continuous DNA molecule within a chromosomeo In Computer-automated DNA sequencing instruments, a reaction tube is used with dideoxynucleotides and a capillary gel A computer then scans the tube with a laser beamo High-throughput sequencing: early computer-automated sequencers could process millions of base pairs in a dayo Clone-by-Clone approach (map based cloning): individual fragments from restriction digests of chromosomes are aligned to create the restriction maps of a chromosome Initial progress in human genome project^o Bioinformatics: the use of computer hardware and software and mathematics applications to organize, share, and analyze data related to the gene structure, gene sequence and expression, and protein structure and functiono Annotation: a process that relies heavily on bioinformatics and a wealth of different software tools are available to carry it out After a genome has been sequence and compiled, scientists are faced with the task of identifying gene-regulatory sequences and other sequences of interest in the genome so that the gene maps can be developed BLAST: software application that we can use to compare a segment of genomic DNA to sequences in the data base- Similarity score (identity value): determined by the sum of identical matches between aligned sequences divided by the total number of bases alignedo A translation program predicts six possible polypeptide sequences- Functional Genomics: the study of gene functions, based on the resulting RNAs or possible proteins they encode, and the functions of other components of the genomeo Homologous genes: genes that are evolutionarily related Orthologs: mouse and human alpha-globin, homologous in different species with a common gene from a common ancestor Paralogs: homologous genes in same species- Human genome project: coordinated international effort to determine the sequence of the human genome and to identify all the genes it contains, finished in ‘03o Protein-coding sequences= 2%o Human genomes are 99.5% similaro 20,000 protein-coding geneso Genes produce more than one proteino Alternative splicing generates multiple mRNA molecules, and thus multiple proteins from asingle gene through different combinations of intron-exon arrangementso Single-nucleotide polymorphisms (SNPs) associated with disease conditionsChapter 21: Genomic, Bioinformatics, and Proteomics Summary (Page2)o Copy number variations (CNVs) duplications or deletions of several hundred or several thousand base pairso 41.7% of genome- molecular function is unknowno NCBI database map viewer: program that maps geneso Proteomics: the analysis of all the proteins in a cell or tissueo Transciptomics: the analysis of all expressed genes in a cell or tissue- Stone Age Genomics: analysis of “ancient” DNA from bones and other tissues from animals that are tens of thousands of years old- Personal Genome Project: George Church has recruited volunteers to provide DNA for individual genome sequencing - Human Microbiome project: complete the genomes of 600-1000 microorganisms, bacteria, viruses,and yeast the live INSIDE humans- Genome 10K: sequence 10,000 vertebrate genomes- Comparative genomics: compares the genomes of different organisms to answer questions about genetics and other aspects of biologyo Some bacteria can have larger genomes than eukaryoteso Gene density: prokaryotes denser than eukaryoteso Introns: size is eukaryotes is generally crenelated with genome size, few exceptions- Share 75% genes with dogs, 98% with chimpanzees- Beta- Globin gene cluster contains 5 geneso Demethylation can turn off sickle
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