Genetics week 12 notes
Genetics week 12 notes Bios 206
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This 4 page Class Notes was uploaded by Becca Sehnert on Friday April 8, 2016. The Class Notes belongs to Bios 206 at University of Nebraska Lincoln taught by Dr. Christensen in Fall 2016. Since its upload, it has received 12 views. For similar materials see Genetics in Biological Sciences at University of Nebraska Lincoln.
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Date Created: 04/08/16
Genetics Week 11 Notes MONDAY Genomics: DNA sequencing is the basis for identifying and mapping all genes in a genome • Structural o Analyzing nucleotide sequences to identify genes and other sequences such as regulatory elements o Annotation –to identify genes o Sequences –thousands of genomes have been sequenced o 2 approaches § Clone by clone –takes genomes, divides into cosmids/artificial chromosomes, backs are divided then sequenced. Placed in order. Many times over. Takes forever! § Shotgun –cut into multiple overlapping fragments. Let computer find overlaps and sequence it. Old way. § Modern way –throw entire genome into generator and let it work. No cutting it up. Aligned in shotgun approach, aka contigs. § Paired end tagging –fragment genome, dilute and add DNAligase, it circularizes then combine together. Then cut somewhere and sequence through junction, can tell how far apart bases are. o Genome sequenced many times to ensure accuracy. Assem bled and compiled o Analysis of genome sequences § Identifying open reading frames (ORF) –no stop codons and may code protein § Find promoters and transcription and translation initiation sites § Finding introns and exons in euk genomes § Analyzing predicted protein sequences to predict protein function § GEN BANK –genomic database, at NCBI, online In DNA sequence, how many potential reading frames are there? a. One, the one that codes for protein b. Two, because could be in either strand of DNA c. Three, cuz ribosomes could start at any ATG in sequence d. Six, cuz could start at any position in either strand e. Larry Harshman • Functional o Attempt to identify functions of genes o Some ORF’s have known function from other organisms, others idk o BLAST compares query sequence to GenBank database o Reveals homologous genes (evolutionarily-related) in different organisms o Orthologs and Paralogs § Homologous genes from different species thought to have descended from common ancestor called orthologs. B-globin genes of human and gorilla § Homologous genes in same species called paralogs. Human a- globin and b-globin o Finding function § Gene sequence à predict polypeptide sequence § Polypeptide analyized for specific protein domains and motifs • Protein domains: ion channels, membrane-spanning regions, secretion, and export signals • Motifs: helix-turn-helix, leucine zipper, zinc finger motifs o Vibrio cholera genome –killed many people, in intestinal tract and gives you diarrhea. • Comparative • Metagenomics WEDNESDAY Human Genome Project • Less than 2% genome codes for proteins • Only 25,000 protein coding genes • Many genes code for multiple proteins • Functional categories have been assigned for human genes on basis of o Functions determined previously o Comparison to known genes and predicted protein sequences from other species o Predictions based on annotation and analysis of protein functional domains and motifs In functional genomics, gene in 2 different species thought to be descended from gene in common ancestor is an a. Ortholog b. Paralog c. Metalog d. Analog e. Lincoln log “Omics” Revolution –new era of research methods • Proteomics • Metabolomics • Metagenomics • Transcriptionmics • Et ceteromics o Stone-age genomics using small amts of ancient DNA from bone and other tissue o Data used to study evolutionary relatedness of various extinct and present-day species • J. Craig Venter –sequenced own genome. First diploid sequence, previous genome sequence composite of several individuals, aka average sequence • Single Nucleotide Polymorephisms (SNPs) o Variation between different humans = polymorphism o Single base changes SNPs o Very common! o Alleles (differs by one nucleotide o Often have no phenotype • Venter’s Sequence o > 4.1 million variants (1,288,319 novel) o 3,213,401 SNPs o 53,823 block substitutions (2-206 bp) o 292,102 heterozygous indels (1-571 bp) o 559,473 homozygous indels (1-82,711 bp) o 44% of genes are heterozygous for one or more variants o 2 chromosomes were 99.5% identical • COMPARATIVE Genomics o Prokaryotic genomes generally less than 5Mb, less than 5000 genes o Many prokaryotic geneomes are single circular DNA chromosome, but some linear and some speices have more than 1 DNA molecules o Many prokaryotes also carry 1+ plasmids o Eukaryotes –highly variable genome size! o Share 30% of human genes with yeast. 80% with mice and 98% in chimpanzees o Many mutated genes involved in human diseases are present in model organisms o Share 75% of genome with dogs. They have genetic disorders also (Epilepsy, OCD), sex chromosome aneuploids FRIDAY Comparative genomics • Identify member of multigene families including nonfunctional pseudogenes • Group of related multigene families called superfamily • A- and B- form 2 clusters, share DNA sequence identities o 3 genes in A-globin, 5 genes in B-globin Metagenomics applies genomic techniquest to envionrmental samples • Sequence genomes from entire communities • Allows identification and analysis of all organisms in sample • Bacteria in lakes, soil, ocean or bacteria and phage in gut • Sequence all DNA and put in separate genomes of every organism o Teach more about bacterial species and viruses o Great potential for identifying genes with novel functions, might advance medicine and biotechnology Transcriptome (RNA) analysis reveals profiles of expressed genes in cells and tissues • Global analysis of gene expression • Microarray analysis allows sequencing of all expressed genes simultaneously (old technology) o Look at grid and can see what is expressed and how much Transposon –McClintock Described structure of DNA –Watson and Crick “X-rays are mutagenic” –Muller Gene repression in euk –Cytosine methylation Southern blotting –Edward southern B-galactosidase expressed consitutively I- others pos Cleared of crime by DNA evidence –Buckland Proteomics identifies and analyzes proteins in cell • Kinda like exploring phenotype • Proteome –complete set of proteins encoded by genome • Genes can make different proteins • Proteins can be modified (Insulin) • Phosphorylation of proteins • 2DGE –separate by charge. Will move across pH gradient and stop when neutralized. Then separate by size (smaller goes further) o Chains –same size, same proteins with different configurations (post- transcriptional modifications) o Send to mass spectrosystem • Mass spec can be used on fossils too • Systems biology –incorporates data from areas of biology to analyze interactions (AKA Interactome) • Network map –sketch showing interacting proteins, genes, other molecules • Systems biology becoming important for drug discovery and development process • Databases being made for many human diseases
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