Transcript PPT1
Where to find me name danny van noort Office Room 410 building #139 (ICT) tel: 880 9131 email [email protected] web http://bi.snu.ac.kr/ Biochemistry part 1 Course outline 1 Introduction 2 Theoretical background Biochemistry/molecular biology 3 Theoretical background computer science 4 History of the field 5 Splicing systems 6 P systems 7 Hairpins 8 Micro technology introductions Microreactors / Chips 9 Microchips and fluidics 10 Self assembly 11 Regulatory networks 12 Molecular motors 13 DNA nanowires 14 Protein computers 15 DNA computing - summery Popular books More popular books Very short introduction Biological background Ecological Physiological Biological Chemical Physical SPECIES ORGANISM CELL MOLECULE ATOM Molecular biology concepts Role of molecules in cells Perform various chemical reactions necessary for life => diverse 3D structures necessary Pass on the instructions for making an organism =>simple 1D medium sufficient Types of molecules in cells Proteins: 3D structures DNA: 1D medium RNA: intermediary between DNA and proteins Cells Humans 60 trillion cells 320 cell types Organisms Classified into two types: Eukaryotes contain a membrane-bound nucleus and organelles (plants, animals, fungi,…) Prokaryotes lack a true membrane-bound nucleus and organelles (single-celled, includes bacteria) Not all single celled organisms are prokaryotes! Chromosomes • In eukaryotes, nucleus contains one or several double stranded DNA molecules organized as chromosomes • Humans: – 22 Pairs of autosomes – 1 pair sex chromosomes Chromosomes Central dogma DNA transcription RNA translation protein deoxyribonucleic acid DNA (deoxyribonucleic acid) The sequence of the human genome has 2.91 billion base pairs (bp) and approximately 35,000 genes. (last count 2003) DNA (deoxyribonucleic acid) Watson & Crick (1953): Nature 25: 737-738 Molecular Structure of Nucleic Acids: a structure for deoxyribose nucleic acid. Nobel Prize, 1962. DNA (deoxyribonucleic acid) Nucleotide: purine or pyrimidine base deoxyribose sugar phosphate group Purine bases A(denine), G(uanine) Pyrimidine bases C(ytosine), T(hymine) Structure of DNA 5’ C 20 Å 34 Å 3’ OH Minor Groove 5’ 3’ 3’ 5’ Sugar-Phosphate Backbone Major Groove Nitrogen ous Base 3’ 0H Central Axis C 5’ Inter-strand hydrogen bonding (+) (-) (-) (+) to Sugar-Phosphate Backbone Adenine Thymine to Sugar-Phosphate Backbone (-) (+) (+) (-) (+) (-) to Sugar-Phosphate Backbone Guanine Hydrogen Bond Cytosine to Sugar-Phosphate Backbone Inter-strand hydrogen bonding Watson-Crick complement 20 Structure and Nomenclature of Nucleotides Nitrogenous Bases O NH2 N N N H N Adenine (6-amino purine) NH2 N N H 2 N H purine Cytosine (2-oxy-4-amino pyrimidine) N H O Thymine (2-oxy-4-oxy 5-methyl pyrimidine) 4 NH NH O 8 O O 7 N N 4 N9 H 3 Guanine (2-amino-6-oxy purine) N 5 1N N HN H2N 6 N H O Uracil (2-oxy-4-oxy pyrimidine) 3 N 2 5 N 1 6 pyrimidine Structure of DNA Nucleic acids are polynucleotides; Nucleotides are linked by phosphodiester bridges from 3’ to 5’; Polymers of ribonucleotides are ribonucleic acids, or RNA; Polymers of deoxyribonucleotides are deoxyribonucleic acids, or DNA; Sugar backbone Structure of DNA NH2 N N N 5’ O N O H O O H H O H OH P N N O- O O H O Shorthand notation of a nucleic acid H H O H OH P -O 3’ O- T NH N NH2 P A P 5’ G P C P C P 3’ OH Single stranded polynucleotide 5’ GTAAAGTCCCGTTAGC 3’ Double stranded polynucleotide 5’ GTAAAGTCCCGTTAGC 3’ | | | | | | | | | | | | | | | | 3’ CATTTCAGGGCAATCG 5’ Structure of DNA The B-form is the common natural form, prevailing under physiological conditions of low ionic strength and high degree of hydration. The Z-form (Zigzag chain) is observed in DNA G-C rich local region. The A-form is sometimes found in some parts of natural DNA in presence of high concentration of cations or at a lower degree of hydration (<65%). 27 Central dogma Central dogma DNA transcription RNA translation protein Replication of DNA Replication of DNA Replication of DNA During replication, the DNA helix is unraveled and its two strands are separated. An area known as the replication bubble forms and progresses along the molecule in both direction. Then each DNA strand serves as a template for the synthesis of a new complementary strand. Each daughter DNA molecule is an exact copy of its parent molecule, consisting of one old and one new DNA strand. Thus the replication is semi-conservative Strand hybridisation A B a b 100° C HEAT A B a b COOL A B a OR b A B a b DNA ligation ’ ’ ’ ’ ’ Ligase joins 5' phosphate to 3' hydroxyl ’ Restriction endonucleases EcoRI HindIII AluI HaeIII DNA polymerase ribonucleic acid RNA (ribonucleic acid) Similar to DNA Thymine (T) is replaced by uracil (U) Forms secondary or tertiary structures RNA can be: Single stranded Double stranded Hybridized with DNA RNA (ribonucleic acid) Types of RNAs: Transfer RNA (adaptor molecule) Messenger RNA (template for protein synthesis) Ribosomal RNA (protein synthesis) Small nuclear RNA (splicesomal RNA) Small nucleolar RNA (ribosomal RNA processing) Interference RNA (gene silencing) microRNA (translation regulation) Virus RNA (code virus genome) In comparison with DNA structures, much less is known about RNA structures. Most RNA are associated with proteins which facilitate their structural folding. RNA secondary structure mRNA Messenger RNA Linear molecule encoding genetic information copied from DNA molecules Transcription: process in which DNA is copied into an RNA molecule mRNA processing Eukaryotic genes can be pieced together Exons: coding regions Introns: non-coding regions mRNA processing removes introns, splices exons together Processed mRNA can be translated into a protein sequence mRNA processing Parts List: mRNA is template tRNA ribosomes amino acids aminoacyl tRNA transferases mRNA processing Transcription Scientists first 3-D pictures of the "heart" of the transcription machine. Ribosomal RNA Secondary Structure Of large ribosomal RNA Tertiary Structure Of large ribosome subunit Ban et al., Science 289 (905-920), 2000 Translation Translation tRNA Transfer RNA Well-defined three-dimensional structure Critical for creation of proteins tRNA Amino acid attached to each tRNA Determined by 3 base anticodon sequence (complementary to mRNA) Translation: process in which the nucleotide sequence of the processed mRNA is used in order to join amino acids together into a protein with the help of ribosomes and tRNA tRNA structure tRNA structure Secondary Structure Of large ribosomal RNA Tertiary Structure Of large ribosome subunit TyC Loop Anticodon Stem Variable loop D Loop Anticodon Loop Translation codons Translation initiation Translation elongation Translation termination Translation codons