Lecture03_NA_Genes_51-73_2ppg

Lecture03_NA_Genes_51-73_2ppg - Macromolecules of Life...

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Unformatted text preview: 1/1/12 Macromolecules of Life Proteins Nucleic acids Carbohydrates Lipids 51 ComposiGon of Nucleic Acids Nucleotide Nitrogenous bases Phosphate group is bonded to 5ʹ′ carbon of sugar Phosphate group 5-­‐carbon sugar Nitrogenous base Nitrogenous base is bonded to 1ʹ′ carbon of sugar Cytosine (C) Uracil (U) in RNA Thymine (T) in DNA Pyrimidines Purines are larger than pyrimidines Sugars Guanine (G) Ribose in RNA Deoxyribose in DNA Adenine (A) Purines 52 1 1/1/12 Nucleic Acid Polymer Precursors •  Nucleoside Triphosphates are the building blocks of nucleic acid polymers Is this a DNA or RNA precursor? RNA DNA •  The addiGon of phosphate groups H! –  Results in an “acGvated” monomer –  Raises the potenGal energy of the monomer –  Allows the otherwise endergonic process of polymerizaGon to proceed, with the assistance of enzymes 53 DissecGon of the building block Nitrogenous BASE Nucleoside Triphosphate (NTP) Nucleotide Nomenclature (naming system): NTP: ATP, UTP, CTP, GTP Nucleoside dNTP: dATP, dTTP/TTP, dCTP, dGTP Deoxynucleoside triphosphate: Deoxyadenosine triphosphate, thymidine triphosphate, deoxycyGdine triphosphate, deoxyguanosine triphosphate NDP: Nucleoside diphosphate NMP: Nucleoside monophosphate (nucleo;de) 54 2 1/1/12 PolymerizaGon & Polarity Sugar-­‐phosphate backbone of RNA 5ʹ′ end of nucleic acid Condensa;on reac;on Phosphodiester linkage 3ʹ′ end of nucleic acid: new nucleoGdes are added to the unlinked 3ʹ′ carbon 55 How do nucleosides differ from nucleoGdes? 1  NucleoGdes have a base and a sugar, whereas nucleosides also have a phosphate group 2  Nucleosides have a base and a sugar, whereas nucleoGdes also have a phosphate group 3  Both have bases and sugars 4  Only nucleoGdes have a 2’ OH group 56 3 1/1/12 Rosalind Franklin’s X-ray diffraction pattern of DNA 1.  2.  3.  The cross pa[ern suggested a helical pitch angle about 45° Axial reflecGons gave repeaGng units of 3.4 and 34 Å Radial reflecGons gave a fiber width of 20 Å 57 Watson & Crick, 1953 Maurice Wilkens gave them Rosalind Franklin’s X-ray diffraction data Double helix •  DNA has a sugar-phosphate backbone •  Nitrogenous bases extend from backbone •  DNA strands have 5’ to 3’ polarity •  Amounts of A & T in DNA were equal •  Amounts of C & G were also equal Base pairing •  Line up the strands in opposite (antiparallel) directions •  They realized that antiparallel strands formed a spiral, or helix, because certain bases fit together within the helix to form hydrogen bonds •  The existing strands of DNA could serve as a template for production of new strands 58 4 1/1/12 Francis Crick James Watson 59 Hydrogen bonds form between A:T pairs and between G:C pairs The two strands are of opposite polarity: G:C A:T anti-parallel They each form a α-helix (right or lefthanded coil, like a spring) All cellular DNA is double strand (dsDNA) and relatively rigid InteracGve models: h[p://www.umass.edu/molvis/tutorials/dna/dnapairs.htm 60 5 1/1/12 Structure of the DNA Double Helix •  Narrow (minor) and wide (major) grooves are formed because when the strands wind around each other the complementary bases are not Length of one directly opposite to one complete turn of helix (10 rungs per another turn) 3.4 nm •  The major groove has bases more accessible to the environment Major groove Minor groove Distance between bases 0.34 nm –  As a result, proteins are able to recognize these structures and bind in a sequence-­‐specific fashion Width of the helix 2.0 nm 61 Summary 62 6 1/1/12 How do the strands of DNA interact when forming new strands? •  •  •  Semiconservative replication: Each old DNA strand is copied to generate a new strand. Each new double helix is composed of one strand of old DNA and one strand of newly synthesized DNA Conservative replication: The original double helix is copied but remains unchanged. One copy is composed of old strands and the other of new strands Dispersive replication: The replication process generates two new double helices, with new and old sections of DNA mixed together randomly sic las ment C ri pe Ex 63 Meselson-­‐Stahl Experiment, 1958 X This data is inconsistent with the conservaGve replicaGon hypothesis 64 7 1/1/12 DNA forms a template for its own synthesis 65 DNA Synthesis 3ʹ′ end of strand 3ʹ′ end of strand 3ʹ′ 3ʹ′ 5ʹ′ end of strand 5ʹ′ end of strand 5ʹ′ 5ʹ′ 3ʹ′ 5ʹ′ Phosphodiester bond 5ʹ′ 3ʹ′ end 5ʹ′ end of strand 5ʹ′ 5ʹ′ end of strand 3ʹ′ Synthesis reaction 3ʹ′ The energy for this reac;on derives from cleavage of pyrophosphate from the dNTP (As a result, the reac;on in cells is exergonic) 3ʹ′ end of strand Pyrophosphate DNA Polymerase PPi DNA Polymerase adds deoxynucleotides to only the 3’ end of a growing DNA chain. Hence, DNA synthesis always proceeds in a 5’ to 3’ direction 66 8 1/1/12 DNA replica;on: How chromosomes (gene-­‐carrying structures) replicate Bacterial chromosomes have a single point of origin Electron micrograph of a chromosome being replicated Old DNA 3ʹ′ Origin of replication 5ʹ′ New DNA 3ʹ′ 5ʹ′ Replication proceeds in both directions DNA synthesis is bidirec;onal EukaryoGc chromosomes have mulGple points of origin 3ʹ′ 5ʹ′ 5ʹ′ 3ʹ′ 5ʹ′ 5ʹ′ 3ʹ′ 5ʹ′ 3ʹ′ 3ʹ′ Old DNA New DNA Replication is bidirectional How fast? 50nt/sec in eukaryotes, 1000 nt/sec in bacteria Replication bubble 3ʹ′ 5ʹ′ Replication fork 67 RNA Can Form Varied Structures Loop Hairpin Single-­‐stranded region forms a loop Stem Double-­‐stranded region forms a double helix •  RNA is more flexible than DNA because: –  The subsGtuGon of Uracil for Thymine –  OH versus H at 2’ posiGon of ribose Nitrogenous bases 68 9 1/1/12 RNA as the First Life Form? •  Like DNA, RNA is: –  An informaGon containing molecule (heritable) –  Can serve as a template to copy itself •  ConformaGonally, RNA is: –  Extremely versaGle, though not nearly as much as proteins –  Can stabilize some transiGon states and thus catalyze some reacGons –  Ribozymes can catalyze hydrolysis and condensaGon of phosphodiester linkages 69 Which of the following properGes do proteins, DNA and RNA have in common? They all have: 1.  EnzymaGc acGvity 2.  Variable secondary structures 3.  Invariable backbone structures 4.  N-­‐ and C-­‐terminal orientaGon 10 1/1/12 Problem: What are genes made of? Era: The early 20th Century Contenders: Protein and DNA •  Bettor’s odds favored proteins: –  The field of protein chemistry was more advanced than that of nucleic acid chemistry •  There is great variability in the types of proteins present in a cell, and proteins were known to be specific in their function or role –  The information content of proteins (20 AA “letters”) is far greater than DNA (4 base “letters”) •  DNA was believed to be too simple a molecules to carry genetic material of cell –  Protein function is subject to change over time 71 Hershey & Chase ONLY VIRAL GENES ENTER A CELL THAT IS BEING INFECTED. Virus protein coat T2 Phage are: obligate intracellular phage parasites – they require host cells Virus genes and host cell metabolic machinery to Host cell reproduce 1. Start of infection. 2. Virus genes direct T2 consists almost entirely of protein & DNA Virus genes enter host cell. Protein coat does not. the production of new virus particles. 3. End of infection. New generation of virus particles bursts from host cell. The virus’ protein coat stays outside the host cell Proteins contain sulfur and DNA contains phosphorus Virus protein coat New virus particles They grew virus in radioactive sulfur (S35) or phosphorus (P32) Which one was injected into the cell? 72 11 1/1/12 ic ass nt Cl rime pe Ex Hershey-­‐Chase Experiment, 1952 The claim that a seemingly simple molecule, DNA, contained all of the information for life’s complexity was finally accepted 73 12 ...
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This note was uploaded on 03/08/2012 for the course BIOL 180 taught by Professor Freeman during the Fall '07 term at University of Washington.

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