Introduction to Bioinformatics: Basic Concepts in Molecular Biology, Study notes of Computer Science

Download Introduction to Bioinformatics: Basic Concepts in Molecular Biology and more Study notes Computer Science in PDF only on Docsity! 1 CS 49995: Special Topic Introduction to Bioinformatics Dr. Gwenn Volkert Fall 2007 What is the course about?  Algorithmic concepts, applied to sample problems in bioinformatics  Follows the text book  “Real” bioinformatics  Follows the best journals and conferences Today’s Topic: Basic Concepts in Molecular Biology •Genetic Material •Gene Structure •Gene Expression •Gene Regulation •Genome Features •Evolution Heredity and DNA  Heredity: children resemble parents  Easy to see  Hard to explain  DNA discovered as the physical (molecular) carrier of hereditary information Life, Cells, Proteins  The study of life ⇔ the study of cells  Cells are born, do their job, duplicate, die  All these processes controlled by proteins Protein functions  “Enzymes” (catalysts)  Control chemical reactions in cell  E.g., Aspirin inhibits an enzyme that produces the “inflammation messenger”  Transfer of signals/molecules between and inside cells  E.g., sensing of environment  Regulate activity of genes 2 DNA  DNA is a molecule: deoxyribonucleic acid  Double helical structure (discovered by Watson, Crick & Franklin)  Chromosomes are densely coiled and packed DNA SOURCE: http://www.microbe.org/espanol/news/human_genome.asp Chromosome DNA The DNA Molecule G -- C A -- T T -- A G -- C C -- G G -- C T -- A G -- C T -- A T -- A A -- T A -- T C -- G T -- A ≡ Base = Nucleotide 5’ 3’ Base pairing property Protein  Proteins are sequences of amino-acids  20 possible amino acids  The amino-acid sequence “folds” into a 3-D structure called protein Protein Structure Protein DNA The DNA repair protein MutY (blue) bound to DNA (purple). PN AS cover, courtesy A m ie Boal SRC:http://www.biologycorner.com/resources/DNA-RNA.gif Cell From DNA to Protein: In picture 5 Gene structure  Exons and Introns  Introns are “spliced” out, and are not part of mRNA  Promoter (upstream) of gene Gene expression  Process of making a protein from a gene as template  Transcription, then translation  Can be regulated Gene Regulation  Chromosomal activation/deactivation  Transcriptional regulation  Splicing regulation  mRNA degradation  mRNA transport regulation  Control of translation initiation  Post-translational modification GENE ACAGTGA TRANSCRIPTION FACTOR PROTEIN Transcriptional regulation GENE ACAGTGA TRANSCRIPTION FACTOR PROTEIN Transcriptional regulation The importance of gene regulation 6 Genetic regulatory network controlling the development of the body plan of the sea urchin embryo Davidson et al., Science, 295(5560):1669-1678.  That was the “circuit” responsible for development of the sea urchin embryo  Nodes = genes  Switches = gene regulation Gene Regulation Circuits Genome  The entire sequence of DNA in a cell  All cells have the same genome  All cells came from repeated duplications starting from initial cell (zygote)  Human genome is 99.9% identical among individuals  Human genome is 3 billion base-pairs (bp) long Genome features  Genes  Regulatory sequences  The above two make up just 5% of the human genome  What’s the rest doing?  We don’t know for sure  “Annotating” the genome  Task of bioinformatics Some Genome Sizes Organism Genome size (base pairs) Virus, Phage Φ-X174; 5387 - First sequenced genome Virus, Phage λ 5×104 Bacterium, Escherichia coli 4×106 Plant, Fritillary assyrica 13×1010 Largest known genome Fungus,Saccharomyces cerevisiae 2×107 Nematode, Caenorhabditis elegans 8×107 Insect, Drosophila melanogaster 2×108 Mammal, Homo sapiens 3×109 Note: The DNA from a single human cell has a length of ~1.8 meters. Evolution  A model/theory to explain the diversity of life forms  Some aspects known, some not  An active field of research in itself  Bioinformatics deals with genomes, which are end-products of evolution. Hence bioinformatics cannot ignore the study of evolution 7 “… endless forms most beautiful and most wonderful …” - Charles Darwin Evolution  All organisms share the genetic code  Similar genes across species  Probably had a common ancestor  Genomes are a wonderful resource to trace back the history of life  Got to be careful though -- the inferences may require clever techniques Evolution  Lamarck, Darwin, Weissmann*, Mendel “Oh my dear, let us hope that what Mr. Darwin says is not true. But if it is true, let us hope that it will not become generally known!” Theory wasn’t well-received * proved Lamark wrong w/mouse tail cutting experiment Some mechanisms of evolution  New or different genes  Gene duplication : new gene  Gene mutation: different gene  New or different regulation of genes  Switches change, therefore circuit changes, even though genes are same  A difference of time scales