Chapter 16: The Molecular Basis of Inheritance (Campbell Biology, Ninth Edition) PDF

LECTURE PRESENTATIONS For CAMPBELL BIOLOGY, NINTH EDITION Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson Chapter 16 The Molecular Basis of Inheritance...

LECTURE PRESENTATIONS For CAMPBELL BIOLOGY, NINTH EDITION Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson Chapter 16 The Molecular Basis of Inheritance Lectures by Erin Barley Kathleen Fitzpatrick © 2011 Pearson Education, Inc. 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 © 2011 Pearson Education, Inc. Figure 16.1 Concept 16.1: DNA is the genetic material Early in the 20th century, the identification of the molecules of inheritance loomed as a major challenge to biologists © 2011 Pearson Education, Inc. The Search for the Genetic Material: Scientific Inquiry 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 The key factor in determining the genetic material was choosing appropriate experimental organisms The role of DNA in heredity was first discovered by studying bacteria and the viruses that infect them © 2011 Pearson Education, Inc. 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 © 2011 Pearson Education, Inc.  When he mixed heat-killed remains of the pathogenic strain with living cells of the harmless strain, some living cells became pathogenic He called this phenomenon transformation, now defined as a change in genotype and phenotype due to assimilation of foreign DNA © 2011 Pearson Education, Inc. Figure 16.2 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  Griffith concluded that the living R bacteria had been transformed into pathogenic S bacteria by an unknown, heritable substance from the dead S cells that allowed the R cells to make capsules  In 1944, Oswald Avery, Maclyn McCarty, and Colin MacLeod announced that the transforming substance was DNA Their conclusion was based on experimental evidence that only DNA worked in transforming harmless bacteria into pathogenic bacteria Many biologists remained skeptical, mainly because little was known about DNA © 2011 Pearson Education, Inc. 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 © 2011 Pearson Education, Inc. Figure 16.3 Phage head Tail sheath Tail fiber DNA 100 nm Bacterial cell  In 1952, Alfred Hershey and Martha Chase performed experiments showing that DNA is the genetic material of a phage known as T2 To determine this, they designed an experiment showing that only one of the two components of T2 (DNA or protein) enters an E. coli cell during infection They concluded that the injected DNA of the phage provides the genetic information © 2011 Pearson Education, Inc.  Animation: Hershey-Chase Experiment © 2011 Pearson Education, Inc. Figure 16.4-1 EXPERIMENT Radioactive protein Phage Bacterial cell Batch 1: Radioactive DNA sulfur (35S) Radioactive DNA Batch 2: Radioactive phosphorus (32P) Figure 16.4-2 EXPERIMENT Radioactive Empty protein protein Phage shell Bacterial cell Batch 1: Radioactive DNA sulfur Phage (35S) DNA Radioactive DNA Batch 2: Radioactive phosphorus (32P) Figure 16.4-3 EXPERIMENT Radioactive Empty protein protein shell Radioactivity Phage (phage protein) in liquid Bacterial cell Batch 1: Radioactive DNA sulfur Phage (35S) DNA Centrifuge Radioactive Pellet (bacterial DNA cells and contents) Batch 2: Radioactive phosphorus (32P) Centrifuge Radioactivity Pellet (phage DNA) in pellet Conclusion Phage DNA entered bacterial cells, but phage proteins did not. Hershy and Chase concluded that DNA, not proteins functions as the genetic material of phage T2 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 © 2011 Pearson Education, Inc.  Animation: DNA and RNA Structure © 2011 Pearson Education, Inc.  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 © 2011 Pearson Education, Inc. Figure 16.5 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 © 2011 Pearson Education, Inc. 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 to deduce that DNA was helical The X-ray images also enabled Watson to deduce the width of the helix and the spacing of the nitrogenous bases The pattern in the photo suggested that the DNA molecule was made up of two strands, forming a double helix © 2011 Pearson Education, Inc. Figure 16.7a 5 end C G 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 DNA structure Figure 16.7b (c) Space-filling 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) © 2011 Pearson Education, Inc.  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 © 2011 Pearson Education, Inc. Figure 16.UN01 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 © 2011 Pearson Education, Inc. Figure 16.8 Sugar Sugar Adenine (A) Thymine (T) Sugar Sugar Guanine (G) Cytosine (C) Concept 16.2: 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 © 2011 Pearson Education, Inc. 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 © 2011 Pearson Education, Inc. 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  Watson and Crick’s semiconservative model of replication predicts that when a double helix replicates, each daughter molecule will have one old strand (derived or “conserved” from the parent molecule) and one newly made strand Competing models were the conservative model (the two parent strands rejoin) and the dispersive model (each strand is a mix of old and new) © 2011 Pearson Education, Inc. Figure 16.10 Parent First Second cell replication replication (a) Conservative model (b) Semiconservative model (c) Dispersive model  Experiments by Matthew Meselson and Franklin Stahl supported the semiconservative model They labeled the nucleotides of the old strands with a heavy isotope of nitrogen, while any new nucleotides were labeled with a lighter isotope © 2011 Pearson Education, Inc.  The first replication produced a band of hybrid DNA, eliminating the conservative model A second replication produced both light and hybrid DNA, eliminating the dispersive model and supporting the semiconservative model © 2011 Pearson Education, Inc. Figure 16.11a EXPERIMENT 1 Bacteria 2 Bacteria cultured in transferred to medium with medium with 15 N (heavy 14 N (lighter isotope) isotope) RESULTS 3 DNA sample 4 DNA sample Less centrifuged centrifuged dense after first after second replication replication More dense Figure 16.11b CONCLUSION Predictions: First replication Second replication Conservative model Semiconservative model Dispersive model 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 Replication © 2011 Pearson Education, Inc. Getting Started Replication begins at particular sites called origins of replication, where the two DNA strands are separated, opening up a replication “bubble” A eukaryotic chromosome may have hundreds or even thousands of origins of replication Replication proceeds in both directions from each origin, until the entire molecule is copied © 2011 Pearson Education, Inc. Figure 16.12a (a) Origin of replication in an E. coli cell Origin of replication Parental (template) strand Daughter (new) strand Double- stranded Replication fork DNA molecule Replication bubble Two daughter DNA molecules 0.5 m 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 Single-strand binding proteins bind to and stabilize single-stranded DNAhelp keep the strands seperated Topoisomerase corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands © 2011 Pearson Education, Inc. Figure 16.13 stabalizes the RNA Primase 3 Topoisomerase 5 RNA 3 primer 5 attach in the begining of the 3 nucleoti de Helicase 5 Single-strand binding proteins remember the 5 proteins used here; plus to draw the structure.  DNA polymerases cannot initiate synthesis of a polynucleotide; they can only add nucleotides to the 3 end The initial nucleotide strand is a short RNA primer © 2011 Pearson Education, Inc.  An enzyme called primase can start an RNA chain from scratch and adds RNA nucleotides one at a time using the parental DNA as a template The primer is short (5–10 nucleotides long), and the 3 end serves as the starting point for the new DNA strand © 2011 Pearson Education, Inc. Synthesizing a New DNA Strand Enzymes called DNA polymerases catalyze the elongation of new DNA at a replication fork Most DNA polymerases require a primer and a DNA template strand The rate of elongation is about 500 nucleotides per second in bacteria and 50 per second in human cells © 2011 Pearson Education, Inc.  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 As each monomer of dATP joins the DNA strand, it loses two phosphate groups as a molecule of pyrophosphate © 2011 Pearson Education, Inc. 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 T P P Pi OH P P C Pyrophosphate 3 C OH 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 © 2011 Pearson Education, Inc.  Along one template strand of DNA, the DNA polymerase synthesizes a leading strand continuously, moving toward the replication fork © 2011 Pearson Education, Inc. 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 Figure 16.15a Overview Leading strand Origin of replication Lagging strand Primer Lagging Leading strand strand Overall directions of replication Figure 16.15b Origin 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 © 2011 Pearson Education, Inc. Figure 16.16a Overview Leading Origin of replication Lagging strand strand Lagging strand 2 1 Leading strand Overall directions of replication Figure 16.16b-1 3 5 3 Template strand 5 Figure 16.16b-2 3 5 3 Template strand 5 3 RNA primer for fragment 1 5 1 3 5 Figure 16.16b-3 3 5 3 Template strand 5 3 RNA primer for fragment 1 5 1 3 5 3 Okazaki fragment 1 5 1 3 5 Figure 16.16b-4 3 5 3 Template strand 5 3 RNA primer for fragment 1 5 1 3 5 3 Okazaki fragment 1 5 1 RNA primer 3 for fragment 2 5 5 3 2 Okazaki fragment 2 1 3 5 Figure 16.16b-5 3 5 3 Template strand 5 3 RNA primer for fragment 1 5 1 3 5 3 Okazaki fragment 1 5 1 RNA primer 3 for fragment 2 5 5 3 2 Okazaki fragment 2 1 3 5 5 3 2 1 3 5 5 3 Figure 16.16b-6 3 5 3 Template strand 5 3 RNA primer for fragment 1 5 1 3 5 3 Okazaki fragment 1 5 1 RNA primer 3 for fragment 2 5 5 3 2 Okazaki fragment 2 1 3 5 5 3 2 1 3 5 5 3 2 1 3 5 Overall direction of replication Figure 16.17a Overview Leading Origin of replication Lagging strand strand Leading Lagging strand strand Overall directions of replication Leading strand 5 DNA pol III 3 Primer Primase 3 5 3 Parental DNA Figure 16.17b Overview Leading Origin of replication Lagging strand strand Leading Lagging strand strand Overall directions Leading strand of replication Primer DNA pol III Lagging strand 5 4 DNA pol I DNA ligase 35 3 3 2 1 3 5 The DNA Replication Complex The proteins that participate in DNA replication form a large complex, a “DNA replication machine” The DNA replication machine may be stationary during the replication process Recent studies support a model in which DNA polymerase molecules “reel in” parental DNA and “extrude” newly made daughter DNA molecules © 2011 Pearson Education, Inc. 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 3 Lagging strand template pol III 5 A current model of the DNA replication complex.  Proofreading and Repairing DNA legase will follow the generating of the main base and check if there is any abnormal structure then dna poly. will fix and lastly proofread 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 inserting an extra nucleotdie in the new amplification can be fixed by deleting it but a deletion of the main base cant be fixed In nucleotide excision repair, a nuclease cuts resulting in mutation. out and replaces damaged stretches of DNA tomelerase : will make a nucleotide that is complimenting the missed one less gene expression —> shorting when reach the aging stage © 2011 Pearson Education, Inc.  Figure 16.19 page1image5274432ch 16 5 the dna structure is antiprallel(3’ to 5’ and 5’ to 3’) 3 (major and minor grooves in the dna strand) backbone : phosphate 3 sugar connects with (nucleotide innerside) 5 one ring is purine and 2 rings is primidine depending on the x ray franklin made they had Nuclease experimented with the nitrogenous pairs untill they had the pairs that match with the minor and major grooves shown in the xray a-t pair has 2 bonds 5 g-c has 3 bonds (found in the centromere of 3 chromosomes) 3 pcr —> denaturation(using heat to seperate the strands of dna molecule) of dna (depending on how 5 many bonds) (dificulty varies) note: DNA exp. - high no. of g-c : more than 55% then increase polymerase temp. dna does not necesserly need to be copied inside a cell can be done in a test tube 5 3 heat resistant dna polymerase to dna replicate cuz of the high temp that may be used 3 5 PCR sequence: denaturation Annelyating DNA dna synthesis ligase semiconservative model: seperation of dna parent strands and the synthesis of matching strand for saughter strand 5 3 Replication of the dna is semiconservative Note: know the steps of dna replication ! 3 how does the bacteria exp conculuded evidence to 5 know the model of dna replication  Evolutionary Significance of Altered DNA Nucleotides Error rate after proofreading repair is low but not zero proofreading fixes 99% of occurring errors but not all Sequence changes may become permanent and can be passed on to the next generation These changes (mutations) are the source of the mechanism of evolution genetic variation upon which natural selection operates recombination (new variations): can also lead to mutation(not necessarily) , but its necessary to have different types of people dna sequence © 2011 Pearson Education, Inc. 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, so repeated rounds of replication produce shorter DNA molecules with uneven ends This is not a problem for prokaryotes, most of which have circular chromosomes © 2011 Pearson Education, Inc. Figure 16.20a 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 50 nucl. per sec where a 3 end is available 5 3 Figure 16.20b 5 3 Second round repeated with every cycle of replication 5 New leading strand 3 New lagging strand 5 3 Further rounds of replication Shorter and shorter daughter molecules  Eukaryotic chromosomal DNA molecules have special nucleotide sequences at their ends called telomeres found in the 2 ends of the dna Telomeres do not prevent the shortening of DNA molecules, but they do postpone the erosion of genes near the ends of DNA molecules It has been proposed that the shortening of telomeres is connected to aging © 2011 Pearson Education, Inc. Figure 16.21 1 m  If chromosomes of germ cells became shorter in every cell cycle, essential genes would eventually be missing from the gametes they produce shortens but not disappear An enzyme called telomerase catalyzes the lengthening of telomeres in germ cells © 2011 Pearson Education, Inc.  The shortening of telomeres might protect cells from cancerous growth by limiting the number of cell divisions There is evidence of telomerase activity in cancer cells, which may allow cancer cells to persist © 2011 Pearson Education, Inc. Concept 16.3 A chromosome consists of a DNA molecule packed together with proteins The bacterial chromosome is a double-stranded, circular DNA molecule associated with a small amount of protein once chromosomes start cell cycle —> they condense —> loss of structure/ function, the dna will denaturate or —> they loose Eukaryotic chromosomes have linear DNA stable, found in metaphase molecules associated with a large amount of protein In a bacterium, the DNA is “supercoiled” and found in a region of the cell called the nucleoid in prokaryotic which is rich in dna © 2011 Pearson Education, Inc.  Chromatin, a complex of DNA and protein, is found in the nucleus of eukaryotic cells Chromosomes fit into the nucleus through an elaborate, multilevel system of packing © 2011 Pearson Education, Inc. Figure 16.22a 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) Figure 16.22b Chromatid (700 nm) 30-nm fiber Loops Scaffold 300-nm fiber 30-nm fiber Replicated chromosome (1,400 nm) Looped domains (300-nm fiber) Metaphase chromosome  Chromatin undergoes changes in packing during the cell cycle no need size At interphase, some chromatin is organized into a 10-nm fiber, but much is compacted into a 30-nm fiber, through folding and looping Though interphase chromosomes are not highly condensed, they still occupy specific restricted regions in the nucleus © 2011 Pearson Education, Inc. Figure 16.23 karyotype —> sorting all fusion : chromosomes based on size and location of centromere, after putting them on a slide then coloring will help identify the place (sorting out) which is the density is different even though when adapting the chromosome places no. changes with time 5 m  Most chromatin is loosely packed in the nucleus during interphase and condenses prior to mitosis Loosely packed chromatin is called euchromatin During interphase a few regions of chromatin (centromeres and telomeres) are highly condensed into heterochromatin Dense packing of the heterochromatin makes it difficult for the cell to express genetic information coded in these regions in humans : hetrozygous : female xx homozygous : male xy in birds: hetrozygous : male zz homozygous : female zw © 2011 Pearson Education, Inc.  Histones can undergo chemical modifications that result in changes in chromatin organization © 2011 Pearson Education, Inc. Figure 16.UN03 amplification summary diagram DNA pol III synthesizes leading strand continuously 3 5 Parental DNA DNA pol III starts DNA synthesis at 3 end of primer, Origin of 5 continues in 5 3 direction replication 3 5 Lagging strand synthesized in short Okazaki fragments, Helicase later joined by DNA ligase Primase synthesizes 3 a short RNA primer 5 DNA pol I replaces the RNA primer with DNA nucleotides END