The Molecular Basis of Inheritance: Chapter 16 PDF

The Molecular Basis of Inheritance: Chapter 16 Overview: Life’s Operating Instructions In 1953, James Watson and Francis Crick introduced an elegant double-helical model for the structure of deoxyribonucleic acid, or DNA DNA, the substance of inheritance, is the most celebrated molec...

The Molecular Basis of Inheritance: Chapter 16 Overview: Life’s Operating Instructions In 1953, James Watson and Francis Crick introduced an elegant double-helical model for the structure of deoxyribonucleic acid, or DNA DNA, the substance of inheritance, is the most celebrated molecule of our time Hereditary information is encoded in DNA and reproduced in all cells of the body This DNA program directs the development of biochemical, anatomical, physiological, and (to some extent) behavioral traits DNA is the genetic material Early in the 20th century, the identification of the molecules of inheritance loomed as a major challenge to biologists When T. H. Morgan’s group showed that genes are located on chromosomes, the two components of chromosomes—DNA and protein—became candidates for the genetic material Evidence That DNA Can Transform Bacteria The discovery of the genetic role of DNA began with research by Frederick Griffith in 1928 Griffith worked with two strains of a bacterium, one pathogenic and one harmless When he mixed heat-killed remains of the pathogenic strain with living cells of the harmless strain, some living cells became pathogenic – Transformation = change in genotype and phenotype due to assimilation of foreign DNA  Transformation Experiment EXPERIMENT Mixture of Heat-killed heat-killed Living S cells Living R cells S cells S cells and (control) (control) (control) living R cells RESULTS Mouse dies Mouse healthy Mouse healthy Mouse dies Living S cells Evidence That Viral DNA Can Program Cells More evidence for DNA as the genetic material came from studies of viruses that infect bacteria Such viruses, called bacteriophages (or phages), are widely used in molecular genetics research Additional Evidence That DNA Is the Genetic Material It was known that DNA is a polymer of nucleotides, each consisting of a nitrogenous base, a sugar, and a phosphate group In 1950, Erwin Chargaff reported that DNA composition varies from one species to the next This evidence of diversity made DNA a more credible candidate for the genetic material Additional Evidence That DNA Is the Genetic Material – Structure too! Two findings became known as Chargaff’s rules – The base composition of DNA varies between species – In any species the number of A and T bases are equal and the number of G and C bases are equal The basis for these rules was not understood until the discovery of the double helix  Sugar–phosphate Nitrogenous bases backbone 5 end Thymine (T) Adenine (A) Cytosine (C) Phosphate Guanine (G) Sugar (deoxyribose) DNA Nitrogenous base nucleotide 3 end Building a Structural Model of DNA: Scientific Inquiry After DNA was accepted as the genetic material, the challenge was to determine how its structure accounts for its role in heredity Maurice Wilkins and Rosalind Franklin were using a technique called X-ray crystallography to study molecular structure Franklin produced a picture of the DNA molecule using this technique Figure 16.6 (a) Rosalind Franklin (b) Franklin’s X-ray diffraction photograph of DNA  Franklin’s X-ray crystallographic images of DNA enabled Watson/Crick to deduce that DNA was helical The pattern in the photo suggested that the DNA molecule was made up of two strands, forming a double helix Figure 16.7 G 5 end C C G Hydrogen bond 3 end G C G C T A 3.4 nm T A G C G C C G A T 1 nm C G T A C G G C C G A T A T 3 end A T 0.34 nm T A 5 end (a) Key features of (b) Partial chemical structure (c) Space-filling DNA structure model  Watson and Crick built models of a double helix to conform to the X-rays and chemistry of DNA Franklin had concluded that there were two outer sugar-phosphate backbones, with the nitrogenous bases paired in the molecule’s interior Watson built a model in which the backbones were antiparallel (their subunits run in opposite directions)  At first, Watson and Crick thought the bases paired like with like (A with A, and so on), but such pairings did not result in a uniform width Instead, pairing a purine with a pyrimidine resulted in a uniform width consistent with the X-ray data Purine  purine: too wide Pyrimidine  pyrimidine: too narrow Purine  pyrimidine: width consistent with X-ray data  Watson and Crick reasoned that the pairing was more specific, dictated by the base structures They determined that adenine (A) paired only with thymine (T), and guanine (G) paired only with cytosine (C) The Watson-Crick model explains Chargaff’s rules: in any organism the amount of A = T, and the amount of G = C Figure 16.8 Sugar Sugar Adenine (A) Thymine (T) Sugar Sugar Guanine (G) Cytosine (C) Many proteins work together in DNA replication and repair The relationship between structure and function is manifest in the double helix Watson and Crick noted that the specific base pairing suggested a possible copying mechanism for genetic material The Basic Principle: Base Pairing to a Template Strand Since the two strands of DNA are complementary, each strand acts as a template for building a new strand in replication In DNA replication, the parent molecule unwinds, and two new daughter strands are built based on base-pairing rules Animation: DNA Replication Overview Figure 16.9-1 A T C G T A A T G C (a) Parent molecule Figure 16.9-2 A T A T C G C G T A T A A T A T G C G C (a) Parent molecule (b) Separation of strands Figure 16.9-3 A T A T A T A T C G C G C G C G T A T A T A T A A T A T A T A T G C G C G C G C (a) Parent molecule (b) Separation of (c) “Daughter” DNA molecules, strands each consisting of one parental strand and one new strand  Parent First Second cell replication replication Experiments by Matthew (a)Conservative model Meselson and Franklin Stahl supported the semiconservative model They labeled the (b)Semiconservative model nucleotides of the old strands with a heavy isotope of nitrogen, while any new nucleotides were (c) Dispersive model labeled with a lighter isotope DNA Replication: A Closer Look The copying of DNA is remarkable in its speed and accuracy More than a dozen enzymes and other proteins participate in DNA replication So What Do We Need To Know? – Structure and Function – Central Dogma – Steps of DNA Replication, Transcription, and Translation Getting Started Replication begins at particular sites called origins of replication, where the two DNA strands are separated, opening a “replication fork” Replication proceeds in both directions from each origin, until the entire molecule is copied Figure 16.12b (b) Origins of replication in a eukaryotic cell Double-stranded Origin of replication DNA molecule Parental (template) Daughter (new) strand strand Bubble Replication fork Two daughter DNA molecules 0.25 m  At the end of each replication bubble is a replication fork, a Y-shaped region where new DNA strands are elongating Helicases are enzymes that untwist the double helix at the replication forks Topoisomerase corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands Figure 16.13 Primase 3 Topoisomerase 5 RNA 3 primer 5 3 Helicase 5 Single-strand binding proteins Synthesizing a New DNA Strand Enzymes called DNA polymerases catalyze the elongation of new DNA at a replication fork – DNA polymerases add nucleotides to the 3 end Most DNA polymerases require a primer and a DNA template strand – Enzyme called primase can start an RNA chain The rate of elongation is about 500 nucleotides per second in bacteria and 50 per second in human cells  Each nucleotide that is added to a growing DNA strand is a nucleoside triphosphate dATP supplies adenine to DNA and is similar to the ATP of energy metabolism The difference is in their sugars: dATP has deoxyribose while ATP has ribose Figure 16.14 New strand Template strand 5 3 5 3 Sugar A T A T Phosphate Base C G C G G C G C DNA OH polymerase 3 A T A P Pi OH C Pyrophosphate 3 C Nucleoside 2Pi triphosphate 5 5 Antiparallel Elongation The antiparallel structure of the double helix affects replication DNA polymerases add nucleotides only to the free 3end of a growing strand; therefore, a new DNA strand can elongate only in the 5to 3direction Along one template strand of DNA, the DNA polymerase synthesizes a leading strand continuously, moving toward the replication fork Figure 16.15 Overview Leading Origin of replication Lagging strand strand Primer Lagging Leading strand strand Origin of Overall directions replication of replication 3 5 5 RNA primer 3 3 Sliding clamp DNA pol III Parental DNA 5 3 5 5 3 3 5  To elongate the other new strand, called the lagging strand, DNA polymerase must work in the direction away from the replication fork The lagging strand is synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase Figure 16.16 3 Overview 5 3 Leading Origin of replication Lagging Template strand strand strand RNA primer 5 for fragment 1 Lagging strand 3 2 1 5 Leading 1 3 strand Overall directions 5 of replication 3 Okazaki fragment 1 5 1 RNA primer 3 for fragment 2 5 5 Okazaki 3 fragment 2 2 1 3 5 5 3 2 1 3 5 5 3 2 1 3 5 Overall direction of replication Figure 16.17 Overview Leading Origin of replication Lagging strand strand Leading Lagging strand strand Overall directions Leading strand of replication 5 DNA pol III 3 Primer Primase 3 5 3 Parental DNA pol III Lagging strand DNA 5 4 DNA pol I DNA ligase 35 3 2 1 3 5 The DNA Replication Complex The proteins that participate in DNA replication form a large complex, a “DNA replication machine” Many players Do you know of primase, dna polymerase, okasaki, helicase, 3’ to 5’ directionality, etc? http://www.youtube.com/watch?v=gW3qZF9cLIA Animation: DNA Replication Review Figure 16.18 DNA pol III Parental DNA Leading strand 5 5 3 3 3 3 5 5 Connecting Helicase protein 3 5 Lagging DNA strand Lagging strand template pol III 5 3 Proofreading and Repairing DNA DNA polymerases proofread newly made DNA, replacing any incorrect nucleotides In mismatch repair of DNA, repair enzymes correct errors in base pairing DNA can be damaged by exposure to harmful chemical or physical agents such as cigarette smoke and X-rays; it can also undergo spontaneous changes In nucleotide excision repair, a nuclease cuts out and replaces damaged stretches of DNA Figure 16.19 5 3 3 5 Nuclease 5 3 3 5 DNA polymerase 5 3 3 5 DNA ligase 5 3 3 5 Evolutionary Significance of Altered DNA Nucleotides Error rate after proofreading repair is low but not zero Sequence changes may become permanent and can be passed on to the next generation These changes (mutations) are the source of the genetic variation upon which natural selection operates Replicating the Ends of DNA Molecules Limitations of DNA polymerase create problems for the linear DNA of eukaryotic chromosomes The usual replication machinery provides no way to complete the 5 ends This is not a problem for prokaryotes, most of which have circular chromosomes Eukaryotic chromosomal DNA molecules have special nucleotide sequences at their ends called telomeres Figure 16.20 5 Ends of parental Leading strand DNA strands Lagging strand 3 Last fragment Next-to-last fragment Lagging strand RNA primer 5 3 Parental strand Removal of primers and replacement with DNA where a 3 end is available 5 3 Second round of replication 5 New leading strand 3 New lagging strand 5 3 Further rounds of replication Shorter and shorter daughter molecules  If chromosomes of germ cells became shorter in every cell cycle, essential genes would eventually be missing from the gametes they produce An enzyme called telomerase catalyzes the lengthening of telomeres in germ cells Shortening of telomeres may be connected with aging and signal cell decay or death! A chromosome consists of a DNA molecule packed together with proteins Eukaryotic chromosomes have linear DNA molecules associated with a large amount of protein Chromatin, a complex of DNA and protein, is found in the nucleus of eukaryotic cells – Undergoes changes during interphase  mitosis  Nucleosome (10 nm in diameter) DNA double helix (2 nm in diameter) H1 Histone Histones tail Nucleosomes, or “beads on DNA, the double helix Histones a string” (10-nm fiber)