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Where to find me. Biochemistry part 1. Course outline. Popular books. More popular books. Very short introduction. Biological background. Ecological. SPECIES. Physiological. ORGANISM. Biological. CELL. Chemical. MOLECULE. Physical. ATOM. Molecular biology concepts.
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Biological background Ecological SPECIES Physiological ORGANISM Biological CELL Chemical MOLECULE Physical 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
Central dogma DNA RNA protein transcription translation
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 3’ OH Minor Groove 34 Å 5’ 3’ Sugar-Phosphate Backbone Major Groove 5’ 3’ Nitrogenous Base 3’ 0H C 5’ Central Axis
Inter-strand hydrogen bonding (+) (-) (-) (+) to Sugar-Phosphate Backbone Adenine Thymine to Sugar-Phosphate Backbone (-) (+) (+) (-) (+) (-) to Sugar-Phosphate Backbone to Sugar-Phosphate Backbone Guanine Cytosine Hydrogen Bond
Inter-strand hydrogen bonding Watson-Crick complement
Structure and Nomenclature of Nucleotides Nitrogenous Bases
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;
Structure of DNA T A G C C 3’ P P P OH P P 5’ Shorthand notation of a nucleic acid 5’ 3’
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%).
Central dogma DNA RNA protein transcription translation
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 b OR A B a b
DNA ligation ’ ’ ’ ’ ’ ’ Ligase joins 5' phosphate to 3' hydroxyl
Restriction endonucleases 5’ P - - OH 3’ EcoRI - P 5’ 3’ OH - HindIII AluI HaeIII
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.
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
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.,Science289 (905-920), 2000
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