Lecture 1- overview.pdf

Test 1 : Sept 30th Lecture 1 Introduction to Bioinformatics: Genes and Genomes BIOC 3265-Principles of Bioinformatics Dr. A. T Alleyne- UWI Cave H...

Test 1 : Sept 30th Lecture 1 Introduction to Bioinformatics: Genes and Genomes BIOC 3265-Principles of Bioinformatics Dr. A. T Alleyne- UWI Cave Hill 1  LEARNING OUTCOMES At the end of this lecture, you should be able to: 1. Define the term bioinformatics 2. Describe the range of biological data used in bioinformatics 3. Memorize some basic protein letter codes 4. Recall some basic genetic codons 5. Define a contig 6. Distinguish between an open reading frame (ORF) and a UTR 7. Discuss the role of model organisms in biology 2 The Central Dogma in Molecular biology Protein RNA Translation DNA Transcription This Photo by Unknown Author is licensed under CC BY- Reverse SA transcription 4  Central Dogma violations All DNA is not transcribed into proteins or structural RNA e.g. ITS (internal untranslated) gene regions Control and regulatory regions of genes Viruses- Reverse transcription in retroviruses 5  Bioinformatics Bioinformatics is the use of computational methods for collecting, organizing, visualizing, and analyzing large amounts of biologic data. https://www.ncbi.nlm.nih.gov/pubmed/11552348 Bioinformatics (genome.gov) 6  Associated tools Computational Biology? oDesigning and validation of biological software oData science-genomics oin-silico experiments- ̶ Creating research workflows using data > - s In-vivo (living organism) 7  Nucleic acid and protein sequences Biological Data Protein and nucleic acid structures Protein structure and post- translational modifications Protein/protein interactions Protein /nucleic acid interactions Metabolic products and pathways Also mutations diseases includes , as well as interactions w/ inorganic materials 8  Databanks Comprised of: oArchival information oLogical organization of the information(structure) oTools for access to information This Photo by Unknown Author is licensed under CC BY-SA 9  Database Tools Provide answers to queries Provide mechanisms for collating results of queries May provide additional information or links to other databases Typical Bioinformatics queries: oFind a sequence similar to this one oFind a protein structure similar to this one oFind related sequences and structures with unknown structures (research queries) 10  Data analysis: genes DNA sequence analysis oPredicting genes oSequence alignments oGene annotation Genomics oSequencing of organisms Gene expression analysis oDNA microarray data analysis This Photo by Unknown Author is licensed under CC BY-SA 11 Data analysis: proteins Protein sequence analysis oSequence alignments oSecondary and tertiary structure predictions Proteomics oMass spectrometry oProtein abundance, modifications and interactions Metabolomics oMetabolic Pathway interactions 12  function of all # Learn components coding areas non-coding areas 13 14 The genetic code CODON FUNCTION UAA, UAG, Stop codons AGA AUG, AUA Start codon Methionine 15 PROTEIN LETTER CODES 16  Open reading frame (ORF) Exons are organized as operons An open reading frame or ORF is a long string of codons which codes for a gene on translation It is located by the start codon in a gene (the aa methionine) An ORF may be uninterrupted by a stop codon and can code for a fully translated protein (gene) or part of a protein ( a truncated gene) Usually begins with an initiation codon - ATG - and ends with a termination codon: TAA, TAG or TGA 17 Untranslated region- UTR 18  Genome assembly Genomes – millions of nucleotides long Assemble by breaking into small bits and then join by sequencing 19  Contig:-Overlaps in sequence assembly Here comes comes a fox. The fox a fox. The fox The fox jumps jumps over the lazy the lazy dog. Assembly: ( the contig) Here comes a fox. The fox jumps over the lazy dog. 20 Prokaryote gene structure 21 Taken from Applied Bioinformatics- PM Seltzer et al. Springer Nature 2018 22  Genome sizes Species Genome size (106 No of genes nucleotides) Drosophila melanogaster 180 13600 (fruit fly) Saccharomyces cerevisiae 12 5800 (yeast) Arabidopsis thaliana (plant) 125 25,500 v. small plant that grows in a Petri dish Caenorhabditis elegans 97 19,000 (nematode worm Homo sapiens (human) 3200 30,000-40,000 23 Genome sizes Species Genome size (106 No. of genes nucleotides) Escherichia coli K12 4.64 4400 Mycobacterium 4.41 4000 tuberculosis H37Rv Streptococcus 2.16 2300 pneumoniae 24 25 MODEL ORGANISMS Organism Genetic information viruses Protein & gene regulation, disease infection etc Yeast (Saccharomyces cerevisiae) Cell division, aging, protein secretion etc Fruit fly (Drosophila melanogaster) Nervous system formation, programmed cell death, cancer genes etc Mice brain function, cancer development, human diseases etc Bacteria DNA, protein and RNA synthesis Roundworm (Caenorhabddtis Body plan development, nervous system elegens) formation, aging etc Plant (Arabidopsis thaliana) Genetics, gene regulation, agriculture zebrafish Vertebrate body development, birth defects etc 26  REFERENCES Molecular Cell Biology 9th edition , Lodish et al Fundamental concepts of Bioinformatics, Krane, D. E. and Raymer, M. L (2003) Benjamin Cummings, CA. USA Applied Bioinformatics- P.M. Selzer et al. http://www.youtube.com/watch?v=- ygpqVr7_xs&feature=related Talking Glossary of Genetic Terms | NHGRI (genome.gov) 27