Basic Molecular Biology Many slides by Omkar Deshpande Overview Structures of biomolecules Central Dogma of Molecular Biology Overview of this course Computer scientists vs Biologists Human Genome Program U S Department of Energy Genomics and Its Impact on Medicine and Society A 2001 Primer 2001 Watson and Crick Macromolecule Polymer Monomer DNA Deoxyribonucleotides dNTP RNA Ribonucleotides NTP Protein or Polypeptide Amino Acid Nucleic acids DNA and RNA Form the genetic material of all living organisms Found mainly in the nucleus of a cell hence nucleic Contain phosphoric acid as a component hence acid They are made up of nucleotides Nucleotides Nitrogenous Base Phosphate Group Sugar Nitrogenous Base Phosphate Group Sugar DNA A T A T G C C G G C A T C G T A G C G C The gene and the genome Genome The entire DNA sequence within the nucleus The information in the genome is used for protein synthesis A gene is a length of DNA that codes for a single protein How big are genomes Organism Genome Size Bases Estimated Genes Human Homo sapiens 3 billion 30 000 Laboratory mouse M musculus 2 6 billion 30 000 Mustard weed A thaliana 100 million 25 000 Roundworm C elegans 97 million 19 000 Fruit fly D melanogaster 137 million 13 000 Yeast S cerevisiae 12 1 million 6 000 Bacterium E coli 4 6 million 3 200 Human immunodeficiency virus HIV 9700 9 Repeats The DNA is full of repetitive elements those that occur over over over There are several type of repeats including SINEs LINEs Short Long Interspersed Elements 1 million just ALUs and low complexity elements Their function is poorly understood but they make problems more difficult Central dogma ZOOM IN tRNA transcription DNA rRNA snRNA translation mRNA POLYPEPTIDE Transcription The DNA is contained in the nucleus of the cell A stretch of it unwinds there and its message or sequence is copied onto a molecule of mRNA The mRNA then exits from the cell nucleus DNA RNA A A T A T G C G G C C G C G C G A T A C G T A U G C G T U C More complexity The RNA message is sometimes edited Exons are nucleotide segments whose codons will be expressed Introns are intervening segments genetic gibberish that are snipped out Exons are spliced together to form mRNA Splicing frgjjthissentencehjfmkcontainsjunkelm thissentencecontainsjunk Key player RNA polymerase It is the enzyme that brings about transcription by going down the line pairing mRNA nucleotides with their DNA counterparts Promoters Promoters are sequences in the DNA just upstream of transcripts that define the sites of initiation Promoter 5 3 The role of the promoter is to attract RNA polymerase to the correct start site so transcription can be initiated Promoters Promoters are sequences in the DNA just upstream of transcripts that define the sites of initiation Promoter 5 3 The role of the promoter is to attract RNA polymerase to the correct start site so transcription can be initiated Transcription key steps DNA Initiation Elongation Termination DNA RNA Transcription key steps DNA Initiation Elongation Termination Transcription key steps DNA Initiation Elongation Termination Transcription key steps DNA Initiation Elongation Termination Transcription key steps DNA Initiation Elongation Termination DNA RNA Genes can be switched on off In an adult multicellular organism there is a wide variety of cell types seen in the adult eg muscle nerve and blood cells The different cell types contain the same DNA though This differentiation arises because different cell types express different genes Promoters are one type of gene regulators Transcription recap The DNA is contained in the nucleus of the cell A stretch of it unwinds there and its message or sequence is copied onto a molecule of mRNA The mRNA then exits from the cell nucleus Its destination is a molecular workbench in the cytoplasm a structure called a ribosome Translation How do I interpret the information carried by mRNA to the Ribosome Think of the sequence as a sequence of triplets Think of AUGCCGGGAGUAUAG as AUGCCG GGA GUA UAG Each triplet codon maps to an amino acid The Genetic Code codon amino acid 1968 Nobel Prize in medicine Nirenberg and Khorana Important The genetic code is universal It is also redundant degenerate f The Genetic Code Proteins Composed of a chain of amino acids 20 possible groups R H2N C COOH H Proteins R H2N C COOH H R H2N C COOH H Dipeptide This is a peptide bond R O R II H2N C C NH C COOH H H Protein structure Linear sequence of amino acids folds to form a complex 3 D structure The structure of a protein is intimately connected to its function The 3 D shape of proteins gives them their working ability the ability to bind with other molecules Our course 2427 Part 1 DNA Assembly Evolution Alignment Part 2 Genes Prediction Regulation Part 3 Structures Interactions transcription DNA rRNA snRNA translation mRNA POLYPEPTIDE Computer Scientists vs Biologists courtesy Steven Skiena SUNY Stony Brook Computer scientists vs Biologists Biologists strive to understand the very complicated very messy natural world Computer scientists seek to build their own clean and organized virtual worlds Computer scientists vs Biologists Computer scientists get high paid jobs after graduation Biologists typically have to complete one or more post docs Computer scientists vs Biologists Nothing is ever completely true or false in Biology Everything is either true or false in computer science