UNT BIOL 3451 - Genomics, Bioinformatics, and Proteomics (4 pages)

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Genomics, Bioinformatics, and Proteomics



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Genomics, Bioinformatics, and Proteomics

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Finished up sequencing techniques and began discussing genomics, bioinformatics, and proteomics.


Lecture number:
27
Pages:
4
Type:
Lecture Note
School:
University of North Texas
Course:
Biol 3451 - Genetics
Edition:
1
Documents in this Packet
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BIOL 3451 1st Edition Lecture 27 Outline of Last Lecture I 20 2 DNA Libraries Are Collections of Cloned Sequences II 20 3 The Polymerase Chain Reaction Is a Powerful Technique for Copying DNA III 20 4 Molecular Techniques for Analyzing DNA IV 20 5 DNA Sequencing Is the Ultimate Way to Characterize DNA Structure at the Molecular Level Outline of Current Lecture I 20 5 DNA Sequencing Is the Ultimate Way to Characterize DNA Structure at the Molecular Level II 21 1 Whole Genome Shotgun Sequencing Is a Widely Used Method for Sequencing and Assembling Entire Genomes III 21 2 DNA Sequence Analysis Relies on Bioinformatics Applications and Genomic Databases IV 21 3 Functional Genomics Attempts to Identify Potential Functions of Genes and Other Elements in a Genome V 21 4 The Human Genome Project Reveals Many Important Aspects of Genome Organization in Humans Current Lecture I 20 5 DNA Sequencing Is the Ultimate Way to Characterize DNA Structure at the Molecular Level o dideoxynucleotide chain termination sequencing Sanger sequencing used to be the most common DNA sequencing that was developed by Sanger Fig 20 15 and 20 16 Involves addition of a small amount of one modified deoxyribonucleotide called dideoxynucleotide which causes DNA synthesis to terminate This caused Gilbert s technique to fall to the way side Now Sanger s not used much anymore o Computer automated high throughput DNA sequencing Since early 1990s DNA sequencing has largely been done through computer automated Sanger reactionbased technology Generates large amounts of sequence DNA Enabled the rapid progress of the Human Genome Project These notes represent a detailed interpretation of the professor s lecture GradeBuddy is best used as a supplement to your own notes not as a substitute II Large scale genome sequencing is automated and uses fluorescent dyelabeled dideoxynucleotides Fig 20 16 and 20 17 o Next generation sequencing NGS technologies allows faster and cheaper genomic sequencing to take place Now it s a fraction of a cent per nucleotide Just sequence any organism for the heck of it that s how good the technology is now Sequencing technologies have cut sequencing costs in half about every two years 21 1 Whole Genome Shotgun Sequencing Is a Widely Used Method for Sequencing and Assembling Entire Genomes o Genome complete set of DNA in a single cell of an organism o Genomics study of genomes allows sequencing of entire genomes This includes Structural genomics Functional genomics Comparative genomics Metagenomics o Structural genomics focuses on sequencing genomes and analyzing nucleotide sequences to identify genes and other important sequences such as generegulatory elements Both of these are approaches used in sequencing genomes Clone by clone method Whole genome shotgun method favored because it is easier to do was used to generate first genome sequence Fig 21 1 Fragment entire chromosome using restriction enzymes then you sequence them then they are adjoined called continuous fragments or contigs Fig 21 2 Algorithm based computer programs developed to create DNAsequence alignment where similar bases are lined up for comparison a Done by identifying overlapping sequences to reconstruct chromosome o Computer automated DNA sequencing instruments utilized dideoxynucleotides labeled with fluorescent dyes A single reaction tube is used Sequencing reaction mixtures are separated on an ultra thin diameter polyacrylamide tube gel called a capillary gel DNA fragments moving through the gel are scanned with a laser beam different wavelengths emitted by dye on fragments III IV detector amplifies these lights and then feeds this info to a computer Processed and converted into the DNA sequence Clone by clone approach generates contigs aligned by fingerprinting the clones and a minimal number of overlapping clones are then sequenced Fig 21 3 Organizes sequencing of contigs from a restriction map instead of random sequencing and assembly o Compiling designate a sequence as final when error cutoff is determined Genome is then analyzed to identify gene sequences regulatory elements and other features that reveal important information 21 2 DNA Sequence Analysis Relies on Bioinformatics and Genomic Databases o Bioinformatics uses computer based approaches to analyze data Gene structure Gene sequence and expression Protein structure and function o GenBank one of the most important genomic databases Maintained by National Center for Biotechnology Information NCBI Each sequence receives an accession number o Annotation process by identifying Genes Regulatory sequences of genes Functions of genes o BLAST software that compares segments of genomic DNA to sequences throughout major database to identify similarly aligning sequences Fig 21 4 Identification of open reading frames requires translation of all six reading frames Fig 21 4 21 5 21 6 Note the sequences found in 21 6 protein coding gene promoter sequence initiation sequence three exons o Open reading frames ORFs stretches of nucleotides that when translated to protein by computer analysis generate a series of amino acids prior to a stop codon and are suggestive of a protein encoding gene Fig 21 7 21 3 Functional Genomics Attempts to Identify Potential Functions of Genes and Other Elements in a Genome o Functional Genomics study of gene functions based on resulting RNAs or possible proteins they encode as well as regulatory elements Fig 21 8 Arabidopsis thaliana great plant used as a genetic model most plants have really big genomes but this one doesn t BLAST used to screen databases to compare sequence to known sequence to find it V Homologous genes genes that are identified that are evolutionary related in other organisms Orthologs homologous genes from different species thought to have descended from a common ancestor Paralogs homologous genes in the same species Fig 21 9 compares portions of human leptin gene LEP with its homolog in mice ob Lep When sequences missing there is usually three lets us know that genes are in sets of three o Gene sequences used to predict polypeptide sequence Polypeptide can be analyzed for specific protein domains and motifs Protein domains ion channels membrane spanning regions secretion export signals Motifs helix turn helix leucine zipper zinc finger motifs o Different genomic techniques that are mapping protein DNA interactions and useful in identifying gene regulated by DNA binding transcription factors Chromatin immunoprecipitation ChIP


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