Presentation on theme: "Basic Molecular Biology"— Presentation transcript:
1 Basic Molecular Biology (Borrowed from “An Introduction to Bioinformatics Algorithms” by Neil C. Jones and Pavel A. Pevzner and further modified by Prof. Natalio Krasnogor)Basic Molecular Biology
2 All living things are made of Cells Cell Signaling Outline For Section 1:All living things are made of CellsProkaryote, EukaryoteCell SignalingWhat is Inside the cell: From DNA, to RNA, to Proteins
3 CellsHard Fact! No pre-medieval fairy tales like ID, Adam&Eve, etcFor more information:“The Major Transitions in Evolution” by M. Smith and E. SzathmaryFundamental working units of every living system.Every organism is composed of one of tworadically different types of cells:prokaryotic cells oreukaryotic cells.Prokaryotes and Eukaryotes are descended from the same primitive cell.All extant prokaryotic and eukaryotic cells are the result of a total of 3.5 billion years of evolution by natural selection.Crowded slideOrganism of life….Cells
4 Cells 70% water 7% small molecules 23% macromolecules Chemical composition-by weight70% water7% small moleculessaltsLipidsamino acidsnucleotides23% macromoleculesProteinsPolysaccharideslipids
5 Life begins with CellA cell is the smallest structural unit of an organism that is capable of sustained independent functioningAll cells have some common featuresWhat is Life? Can we create it in the lab? Read:The imitation game—a computational chemical approach to recognizing life. Nature Biotechnology, 24: , 2006
7 All Cells have common Cycles Born, eat, replicate, and die
8 Prokaryotes and Eukaryotes According to the most recent evidence, there are three main branches to the tree of life.Prokaryotes include Archaea (“ancient ones”) and bacteria.Eukaryotes are kingdom Eukarya and includes plants, animals, fungi and certain algae.
9 Prokaryotes and Eukaryotes, continued Single cellSingle or multi cellNo nucleusNucleusNo organellesOrganellesOne piece of circular DNA (plasmid)ChromosomesNo mRNA post transcriptional modificationExons/Introns splicing
10 Prokaryotes v.s. Eukaryotes Structural differences Eubacterial (blue green algae)and archaebacteriaonly one type of membrane--plasma membrane formsthe boundary of the cell properThe smallest cells known are bacteriaEcoli cell3x106 protein moleculespolypeptide species.Eukaryotesplants, animals, Protista, and fungicomplex systems of internal membranes formsorganelle and compartmentsThe volume of the cell is several hundred times largerHela cell5x109 protein molecules,000 polypeptide speciesStructural differencesTwo columns labelled prokaryotes and eukaryotes
11 Signaling Pathways: Control Gene Activity Instead of having brains, cells make decisions through complex networks of chemical reactions, called pathwaysSynthesize new materialsBreak other materials down for spare partsSignal to eat, die, reproduce, sporulate, etcEven Bacteria are smart entities. Read:Bacteria Harnessing Complexity by E. Ben-Jacob and colleagues
13 Cells Information and Machinery Cells store all information to replicate itselfHuman genome is around 3 billions base pairs longAlmost every cell in human body contains same set of genesBut not all genes are used or expressed by those cellsMachinery:Collect and manufacture componentsCarry out replicationKick-start its new offspring(A cell is like a car factory but FAR more complex and efficient)
14 Overview of organizations of life Nucleus = libraryChromosomes = bookshelvesGenes = booksAlmost every cell in an organism contains the same libraries and the same sets of books.Books represent all the information (DNA) that every cell in the body needs so it can grow and carry out its various functions.Moreover, more recent discoveries suggest that the books, bookshelves and libraries are not passive waiting to be read but are, sometimes, rewriting and rewiring themselves!
15 Terminology a bacteria contains about 600,000 DNA base pairs The genome is an organism’s complete set of DNA.a bacteria contains about 600,000 DNA base pairshuman and mouse genomes have some 3 billion.human genome has 23 distinct chromosomes.Each chromosome contains many genes.Genebasic physical and functional units of heredity.specific sequences of DNA bases that encode instructions on how and when to make proteins.ProteinsMake up the cellular structurelarge, complex molecules made up of smaller subunits called amino acids.
16 All Life depends on 3 critical molecules DNAsHold information on how cell worksRNAsAct to transfer short pieces of information to different parts of cellProvide templates to synthesize into proteinProteinsForm enzymes that send signals to other cells and regulate gene activityForm body’s major components (e.g. hair, skin, etc.)Are life’s laborers!Computationally, all three can be represented as sequences of a certain 4-letter (DNA/RNA) or 20-letter (Proteins) alphabet
17 DNA, RNA, and the Flow of Information ReplicationTranscriptionTranslationWeismann Barrier / CentralDogma ofMolecular Biology
18 Overview of DNA to RNA to Protein A gene is expressed in two stepsTranscription: RNA synthesisTranslation: Protein synthesis
19 DNA: The Basis of Life Deoxyribonucleic Acid (DNA) DNA is a polymer Double stranded with complementary strands A-T, C-GDNA is a polymerSugar-Phosphate-BaseBases held together by H bonding to the opposite strand
20 RNARNA is similar to DNA chemically. It is usually only a single strand. T(hyamine) is replaced by U(racil)Some forms of RNA can form secondary structures by“pairing up” with itself. This can have impact on its properties dramatically.DNA and RNAcan pair witheach other.tRNA linear and 3D view:
21 RNA, continued Several types exist, classified by function: hnRNA (heterogeneous nuclear RNA): Eukaryotic mRNA primary transcipts with introns that have not yet been excised (pre-mRNA).mRNA: this is what is usually being referred to when a Bioinformatician says “RNA”. This is used to carry a gene’s message out of the nucleus.tRNA: transfers genetic information from mRNA to an amino acid sequence as to build a proteinrRNA: ribosomal RNA. Part of the ribosome which is involved in translation.
22 TranscriptionTranscription is highly regulated. Most DNA is in a dense form where it cannot be transcribed.To start, transcription requires a promoter, a small specific sequence of DNA to which polymerase can bind (~40 base pairs “upstream” of gene)Finding these promoter regions is only a partially solved problem that is related to motif finding.There can also be repressors and inhibitors acting in various ways to stop transcription. This makes regulation of gene transcription complex to understand.
23 Definition of a GeneRegulatory regions: up to 50 kb upstream of +1 siteExons: protein coding and untranslated regions (UTR)1 to 178 exons per gene (mean 8.8)8 bp to 17 kb per exon (mean 145 bp)Introns: splice acceptor and donor sites, junk DNAaverage 1 kb – 50 kb per intronGene size: Largest – 2.4 Mb (Dystrophin). Mean – 27 kb.
25 Splicing and other RNA processing In Eukaryotic cells, RNA is processed between transcription and translation.This complicates the relationship between a DNA gene and the protein it codes for.Sometimes alternate RNA processing can lead to an alternate protein (splice variants) as a result. This is true in the immune system.
26 Proteins: Crucial molecules for the functioning of life Structural Proteins: the organism's basic building blocks, eg. collagen, nails, hair, etc.Enzymes: biological engines which mediate multitude of biochemical reactions. Usually enzymes are very specific and catalyze only a single type of reaction, but they can play a role in more than one pathway.Transmembrane proteins: they are the cell’s housekeepers, eg. By regulating cell volume, extraction and concentration of small molecules from the extracellular environment and generation of ionic gradients essential for muscle and nerve cell function (sodium/potasium pump is an example)Proteins are polypeptide chains, constructed by joining a certain kind of peptides, amino acids, in a linear wayThe chain of amino acids, however folds to create very complex 3D structures
27 Translation The process of going from RNA to polypeptide. Three base pairs of RNA (called a codon) correspond to one amino acid based on a fixed table.Always starts with Methionine and ends with a stop codon
29 Protein Structure: Introduction Different amino acids have different propertiesThese properties will affect the protein structure and functionHydrophobicity, for instance, is the main driving force (but not the only one) of the folding process
30 Protein Structure: Hierarchical nature of protein structure Primary Structure = Sequence of amino acidsMKYNNHDKIRDFIIIEAYMFRFKKKVKPEVDMTIKEFILLTYLFHQQENTLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKIAERVTLFDQIIKQFNLADQSESQMIPKDSKEFLNLMMYTMYFKNIIKKHLTLSFVEFTILAIITSQNKNIVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHAEQLLAQVNQLLADKDHLHLVFESecondary StructureTertiaryLocal InteractionsGlobal Interactions
31 Protein Structure: Why is structure important? The function of a protein depends greatly on its structureThe structure that a protein adopts is vital to it’s chemistryIts structure determines which of its amino acids are exposed to carry out the protein’s functionIts structure also determines what substrates it can react with
32 Protein Structure: Mostly lacking information Therefore, it is clear that knowing the structure of a protein is crucial for many tasksHowever, we only know the structure for a very small fraction of all the proteins that we are aware ofThe UniProtKB/TrEMBL archive contains ( ) sequencesThe PDB archive of protein structure contains only 84223(76669) structuresIn the native state, proteins fold on its own as soon as they are generated, amino-acid by amino-acid (with few exceptions e.g. chaperones) can we predict this process as to close the gap between protein sequences and their 3D structures?
33 Central Dogma of Biology: A Bioinformatics Perspective The information for making proteins is stored in DNA. There is a process (transcription and translation) by which DNA is converted to protein. By understanding this process and how it is regulated we can make predictions and models of cells.AssemblyProtein Sequence/Structure AnalysisSequence analysisGene FindingComputational Problems