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Lecture Notes

by: Isabella Greenspoon

Lecture Notes

Isabella Greenspoon
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Date Created: 02/11/15
Chapter 7 The Cell Cycle and Cell Division I Different Life Cycles Use Different Modes of Cell Reproduction a Cell division process by which a parent cell duplicates its genetic material and then divides into similar cells b Asexual reproduction rapid and effective means of making new individuals common in nature i Offspring are clones genetically or virtually identical to each other and the parent c Sexual reproduction fusion of 2 specialized cells called gametes result in offspring with considerable genetic variation i Meiosis cell division resulting in daughter cells with only half the genetic material of the original cell 1 Genetic material randomly separated and reorganized so that the daughter cells differ genetically from one another 2 Increases genetic diversity d Somatic cells body cells not specialized for reproduction i Contain two sets of chromosomes and the chromosomes occur in pairs called homologous pairs 1 46 chromosomes 23 from mother and 23 from father e n number of chromosomes in a gamete cell haploid i Two haploid gametes fuse to form a zygote fertilization 1 Chromosome number in zygote 2n diploid cells f Haplontic life cycle mature organism is haploid and the sygpt is the only diploid stage i Most protists fungi some green algae g Alternation of generations organism passes through haploid and diploid stages that are both multicellular i Most plants and some fungi h Diplontic life cycle organism is diploid and the gametes are the only haploid stage i Animals brown algae some fungi ll Both Binary Fission and Mitosis Produce Genetically lden calCe s a Prokaryotes divide by binary ssion i Reproductive signals initiate cell division and may originate from either inside or outside the cell ii DNA replication must occur so that each of the two new cells have a full complement of genes to complete cell functions iii Cell must distribute the replicated DNA to each of the two new cells 1 DNA segregation iv Cytoplasm must divide to form two new cells each surrounded by a cell membrane and a cell wall in organisms that have one 1 Cytokinesis v Binary ssion prokaryotes cell grow replicate its DNA separates the cytoplasm and DNA into two new cells 1 4 DNA replication begins at the origin of replication at the center of the cell 2 Chromosomal DNA replicates as the cell grows 3 The daughter DNAs separate led by the region including ori cell begins to divide Cytokinesis is complete two new cells are formed b Eukaryotic cells divide by mitosis followed by cytokinesis i Mitosis set of processes in which the chromosomes become condensed and then segregate into two new nuclei 1 3 M phase mitosis and cytokinesis DNA and proteins in each chromosomes become highly compact lnterphase cell nucleus is visible and typical cell functions occur including DNA replication in cells that are preparing to divide a 61 phase cell may spend a long time carrying out its specialized functions b S phase DNA is replicated only tiny portion of one chromosome is shown c 62 phase cell makes preparations for mitosis Prophase beginning of mitosis a Chromatids held together at the centromere until separated during anaphase b Kinetochores assemble on the centromeres one on each chromatid c Number and sizes of the condensed chromosomes constitute the karyotype d Centrosome organelle in the cytoplasm near the nucleus spindle bers form 4 Prometaphase nuclear envelope breaks down and the chromosomes attach to the spindles extending to each pole 5 Metaphase chromosomes line up at the midline 6 Anaphase chromatids separate daughter chromosomes move away from each other toward to poles 7 Telophase nuclear envelope reforms around the nucleus and the process of nuclear division is terminated 8 Cytokinesis cell separation cell membrane andor cell wall formation Ill Cell reproduction is Under Precise Control a Growth factors produced by mammals stimulate cell division and differentiation b Eukaryotic cell cycle i 61 Cells that do not divide are usually arrested interphase checkpoint triggered by DNA damage ii 5 DNA is replicated interphase checkpoint triggered by incomplete replication or DNA damage iii 62 interphase checkpoint triggered by DNA damage iv M mitosis and cytokinesis take place checkpoint triggered by a chromosome that fails to attach to the spindle c Cyclindependent kinases CDKs kinases involved in cell cycle regulation activated by the binding to the protein cyclin i Catalyze the phosphorylation of target proteins that regulate the cell cycle ii Cell cycle checkpoints speci c stages of the cell cycle signaling pathways regulate the progress of the cell cycle 1 3 during interphase 1 during mitosis iii Each CDK has its own cyclin to activate it cyclin made only at the right time IV Meiosis Halves the Nuclear Chromosome Content and Generates Diversjy a Meiosis consists of 2 nuclear divisions that reduce the number of chromosomes to the haploid number DNA only replicated once b Haploid cells produced by meiosis are genetically different from one another and from the parent cell LFunctions of meiosis iReduce the chromosome number from diploid to haploid ii Ensure that each of the haploid products has a complete set of chromosomes LGenerate genetic diversity among the products gametes dTwo unique features of meiosis I i Homologous chromosomes come together and line up along their entire lengths ii Homologous chromosome pairs separate but the individual chromosomes each consisting of two sister chromatids remain intact e Sister chromosomes separated during meiosis II which is not preceded by DNA replication i Meiosis l and II produces 4 cells not genetically identical f Crossing over results in recombinant chromatids increases genetic variation among the products of meiosis by reshuf ing genetic information between homologous chromosome pairs occurs shortly after synapsis begins i Homologous chromosomes pair by adhering along their lengths synapsis lasts from prophase l to the end of metaphase l ii Four chromatids of each pair of homologous chromosomes form a tetrad or bivalent iii Chiasmata chiasma Xshaped attachment points point where genetic material is exchanged between nonsister chromatids on homologous chromosomes 1 Does not become visible until the homologs repel each other g Independent assortment matter of chance which member of a homologous pair goes to which daughter cell at anaphasel i The greater the number of chromosomes the lower the probability of reestablishing the original parental combinations thus the greater potential for genetic diversity h Nondisjunction homologous chromosome fails to separate fails to quotdisjoinquot at anaphase l or a pair of chromatids fail to separate at anaphase ll i Failure at anaphase l two of the four daughter nuclei will each end up with both members of that homologous pair and the other two will have neither member of the pair ii Failure at anaphase ll only two of the four daughter nuclei will be affected one will have an extra chromosome and the other will have one less than the full complement of chromosomes V iii Aneuploidy condition of having an abnormal number of chromosomes common and harmful condition in humans 1 Trisomy having one extra chromosome 2 Monosomy missing one chromosome iv Polyploidy can lead to reproductive isolation and speciation 1 Most organisms are either diploid animals or haploid fungi a Triploid 3n tetraploid 4n or higher order poypoidy nuclei may form v Translocation during crossing over in meiosis I chromatids from homologous chromosome pairs break and rejoin 1 A translocation that occurs during meiosis may be carried on the gametes that result and passed on to offspring at fertilization Programmed Cell Death is a Necessary Process in Living Organisms a Necrosis cell death occurs when cells are damaged by mechanical means or toxins or are starved of oxygen or nutrients iCells swell up and burst releasing their contents into the extracellular environment bApoptosis genetically programmed series of events that result in cell death iWhy 1Cell is no longer needed by the organism 2The longer cells live the more prone they are to genetic damage that could lead to cancer iiAlso used by plant cells in hypersensitive response defense mechanism 1 Protect themselves against disease 2 Digest cell contents in the vacuole then release digested components into the vascular system LProgrammed cell death is controlled by signals which may come from inside or outside the cell 1 Internal signals may be linked to the age of the cell or the recognition of damaged DNA 2 External signals can be detected by receptors in the cell membrane in turn they activate signal transduction pathways 3Caspases class of enzymes internal and external signals lead to activation a Hydrolyze target proteins bCell dies as the caspases hydrolyze proteins of the nuclear envelope nucleosomes and cell membrane ivOncogene proteins positive regulators of the cell cycle in cancer cells 1 Derived from normal positive regulators that have become mutated to be overly active of that are present in excess and they stimulate the cancer cells to divide more often than normal cells vTumor suppressors negative regulators of the cell cycle in normal cells but in cancer cells they are inache Chapter 8 notes I Genes Are Particular and Are Inherited According to Mendel39s Laws a Blending inheritance gametes contained hereditary determinants genes that blended when the gametes fused during fertilization Particulate inheritance each determinant had a physically distinct nature when gametes fused in fertilization the determinants remained intact Pea owers have both male and female sex organs stamens and pistils which produce gametes that are contained within the pollen and ovules Character observable physical feature such as seed shape Trait particular form of a character such as round or wrinkled seeds Parental generation P plants providing and receiving the pollen males provided pollen women received pollen i First lial generation F1 the seeds and the resulting new plants ii Second lial generation F2 F1 plants selfpollinated to produce this generation Monohybrid cross crossing parental P varieties with contrasting traits for a single character subsequently planted F1 seeds and allowed the resulting plants to self pollinate to produce F2 generation i F1 offspring were not a blend of the two traits of the parents only one of the traits were present round seeds ii Some F2 offspring had wrinkled seeds the trait did not disappear 3 3 F 739739P39 Observations led to a rejection of the blending theory and supported the particulate theory Diploid state of having two copies of each gene Haploid having just one copy Homozygous two alleles that are the same Heterozygous two different alleles Phenotype physical appearance result of the genotype Genotype genetic constitution of the organism Law of segregation when any individual produces gametes the two copies of a gene separate so each gamete receives only one copy i Gametes from RR parent will all be R gametes from an rr parent will all be r Test cross used to determine whether an individual showing a dominant trait is homozygous or heterozygous i If individual being tested is homozygous dominant RR all offspring of the test cross will be Rr and show the dominant trait ii If the individual being tested is heterozygous Rr then about half of the offspring of the test cross will be heterozygous and show the dominant trait Rr and the other half will be homozygous for the recessive trait rr Dihybrid cross cross between individuals that are identical double heterozygotes i Allowed F1 parents which were all double heterozygotes to selfpollinate ii Alleles could be linked on the same chromosome 1 F1 plants would produce RY and ry gametes 2 F2 progeny would have two phenotypes in the 31 ratio Alleles could be unlinked independent 1 RY Ry rY ry gametes would be produced 2 F2 having nine different genotypes producing four phenotypes in the 9331 ratio Law of independent assortment alleles of different genes assort independently of one another during gamete formation i Segregation of the R and r alleles is independent of the segregation of the Y and y alleles ii Not as universal as the law of segregation because it does not apply to genes located near one another or on the same chromosome Probability is used to predict inheritance i 1 if an event is absolutely certain to happen ii 0 if it cannot possibly happen iii All other events are between 0 and 1 iv The probability of two independent outcomes occurring together is found by multiplying the two individual probabilities multiplication rule v The probability of an event that can occur in two or more different ways is the sum of the individual probabilities of those ways addition rule 5 Pedigrees family trees that show the occurrence of inherited phenotypes in several generations of related individuals i Do not show the clear proportions of phenotypes because humans have relatively few offspring ii Do show inheritance patterns that can provide information about the alleles controlling a particular phenotype ll Alleles and Genes Interact to Produce Phenotypes a Mutations rare stable and inherited changes in genetic material i An allele can mutate to become a different allele ii Wild type the allele that is present in most individuals in nature 1 Wildtype and mutant alleles are inherited according to Mendelian laws b Incomplete dominance intermediate phenotype alleles are neither dominant nor recessive to one another i Red and white parents produce an all pink F1 generation 1 When F1 plants selfpollinate they produce white pink and red F2 offspring in a ration of 121 c Codominance two alleles of a gene produce their phenotypes when present in a heterozygote i ABO blood group in humans ii When two different alleles IquotA and IquotB are present both alleles are expressed both enzymes are made so both types of glycoprotein on its surface gets into the bloodstream of a person d Epistasis when the phenotypic expression of one gene is affected by another gene i A dog with alleles B and E is black ii A dog with bb and E is brown iii A dog with ee is yellow regardless of it Bb alleles e Quantitative traits traits conferred by multiple genes need to be measured rather than assessed qualitatively f g III a b Genotype and environment often interact to determine the phenotype of an organism i Variables such as light temperature and nutrition can affect the phenotypic expression of a genotype Two parameters describe the effects of genes and environment on phenotype i Penetrance proportion of individuals in a group with a given genotype that actually show the expected phenotype ii Expressivity degree to which a genotype is expressed in an individual Heritability of a character is the relative contribution of genetic versus environmental factors to the variation in that character in a particular population i Provide information about whether it is more worthwhile to modify the environment or do genetic crosses to improve a phenotype Genes Are Carried on Chromosomes A gene is a sequence of DNA that resides at a particular site on a chromosome called a locus Genetic linkage of genes on a single chromosome alters their pattern of inheritance i First discovered in the fruit y Drosophia melanogaster 1 Small easily bred short generation time from fertilize egg to reproducing adult model organism Linked genes are not able to assort independently as predicted by Mendel s second law Recombinant phenotypes two homologous chromosomes can physically exchange corresponding segments during prophase l of meiosis by crossing over i Each exchange event involves 2 of the 4 chromatids in a tetrad one from each member of the homologous pair ii Can occur at any point along the length of the chromosome Recombination frequency calculated by dividing the number of recombinant progeny by the total number or progeny i Greater for loci that are farther apart on the chromosome than for loci that are closer together because crossing over is more likely to occur between genes that are far apart Autosomes chromosomes that are not sex chromosomes similar in size to one another g Sex chromosomes determine sex of organisms different in size to one another i Female two X chromosomes XX ii Male one X chromosome one Y chromosome XY iii Many genes on the X chromosome are not present on the Y 1 Males only have one copy of these genes h Hemizygous any gene that is present as a single copy in a diploid organism i Selinked inheritance inheritance of a gene that is carried on a sex chromosome i X chromosome is larger and carries more genes than the Y 1 Most examples of sexlinked inheritance involve genes that are carried on the X chromosome ii The phenotype appears much more often in males than in females because only one copy of the allele is needed for its expression in males whereas two copies must be present in females iii A male with a mutation can pass it on only to his daughters all his sons get his Y chromosome iv Daughters who receive one Xlinked mutation are heterozygous carriers 1 Phenotypically normal but they can pass the mutant allele to their sons or daughters 2 On average half their children will inherit the mutant allele since half of their X chromosomes carry the normal allele v The mutant phenotype can skip a generation if the mutation passes from a male to his daughter who will be phenotypically normal and then to her son vi The mutant allele for redgreen color blindness is expressed as an Xlinked recessive trait and therefore is always expressed in males when they carry that allele j Mitochondria and plastids including chloroplasts each contain several copies of a small chromosome that carries a small number of genes i Plastids have 5x as many genes as mitochondria ii Mitochondria and plastids are inherited only from the mother IV Prokaryotes Can Exchange Genetic Material a Prokaryotes reproduce asexually by binary ssion a process that gives rise to progeny that are virtually idenUcalgeneUcaHy b Horizontal or lateral gene transfer transfer of genes from one individual organism to another without sexual reproduction c Sex pilus initiates contact between the cells which allows gene transfer between bacteria extend from one cell the donor attaches to another the recipient and draws the two cells together i Genetic material passes through a thin cytoplasmic bridge called a conjunction tube ii No reciprocal transfer of DNA from the recipient to the donor iii Bacterial conjugation d Plasmids transfer genes between bacteria i Plasmids can move between cells during conjugation thereby transferring new genes to the recipient bacterium ii A single strand of the donor plasmid is transferred to the recipient synthesis of complementary DNA strands results in two complete copies of the plasmid one in the donor and one in the recipient Chapter 9 DNA and Its Role in Heredity I DNA Structure Re ects Its Role as the Genetic Material a DNA in the nucleus iFirst isolated in 1868 by Friedrich Miescher iiFound nuclein containing elements C H O N and P 1 Proposed that nuclein was the genetic material b DNA in the chromosomes dyes showed location and amount of DNA in cells LDNA amounts the amount of dye binding to DNA and the intensity of the color observed was directly related to the amount of DNA present iThe greater the intensity the more DNA iiVirtually all nondividing somatic cells of a particular organism have the same amount of nuclear DNA 1Amount varies from species to species LAfter meiosis gametes have half the amount of nuclear DNA as somatic cells d Many viruses including bacteriophage viruses that infect bacteria are composed of DNA and only one or a few kinds of protein i Only the viral DNA is injected into the cell during infection 1 Since the viral DNA genetically transformed the bacteria this was further evidence that DNA and not protein is the genetic material eTransgenic fertilized egg can develop into a new multicellular organism through mitosis fXray crystallography provided clues to DNA s structure iThe position of atoms in a crystallized chemical substance can be inferred by the pattern of diffraction of Xrays passed through it iiRosalind Franklin s crystallographs helped other scientists visualize the helical structure of the DNA molecule g Erwin Chargaff found that the total abundance of purines AG equaled the total abundance of pyrimidines TC iAmount of adenine equaled the amount of thymine AT and the amount of guanine equaled the amount of cytosine GC iiChargaff s rue a purine on one strand is always paired with a pyrimidine on the opposite strand 1These base pairs have the same width down the double helix h Francis Crick and James Watson used model building to solve the structure of DNA iShowed that strands run in opposite directions antiparallel 39iProposed a doublehelical structure LNucleotide bases are on the interior of the 2 strands with a sugarphosphate backbone on the outside i4 key features de ne DNA structure iDNA is a doublestranded helix of uniform diameter 1 Hydrogen bonding between the bases van der Waals forces between adjacent bases on the same strand iiThe two DNA strands are antiparallel 1 5 end of the chain is a free not connected to another nucleotide phosphate group 23 end of the chain is a free 3 hydroxyl OH group Lin DNA the outer edges of the nitrogenous bases are exposed in the major and minor grooves 1 Atoms and groups in the major groove are more accessible and tend to bind other molecules more frequently than those in the minor groove a This binding of proteins to speci c base pair sequences is the key to proteinDNA interactions which are necessary for the replication and expression of the genetic information in DNA iv The DNA double helix is righthanded j The doublehelix structure of DNA is essential to its funcUon i Storage of genetic information Base sequence of a DNA molecule can encode and store an enormous amount of information ii Precise replication during the cell division cycle Complementary base pairing iii Susceptibility to mutations Can be simple changes in the linear sequence of base pairs iv Expression of the coded information as phenotypes lnformation carried in DNA is ultimately expressed as proteins ll DNA Replicates Semiconservatively a Semiconservative replication each strand of the parental DNA acts as a template for a new strand which is added by base pairing b DNA replication takes place in two general steps iThe DNA double helix is unwound to separate the two template strands and make them available for new base pairing iiAs newly added nucleotides form complementary base pairs with template DNA they are covalently linked together by phosphodiester bonds forming a polymer whose base sequence is complementary to the bases in the template strand LDNA polymerase catalyzes the addition of nucleotides as the new DNA chain grows dOrigin of replication on to which the prereplication complex binds iOnce the prereplication complex binds to it the DNA unwinds and replication proceeds in both directions around the circle forming two replication forks 1Opening of each fork is catalyzed by DNA helicase which uses free energy from ATP hydrolysis to change shape and wedge into the DNA locally breaking hydrogen bonds between bases on the two strands and separating them e DNA replication is initiated with a primer 1 Primer short single strand of RNA or DNA in some viruses a Complementary to the DNA template and is synthesized one nucleotide at a time by the enzyme primase 2 DNA polymerase then binds and synthesizes new DNA f The two DNA strands grow differently at the replication fork g I The two DNA strands are antiparallel ii DNA polymerase replicates DNA by adding nucleotides only to the 3 end of each growing strand iii Synthesis of the leading strand is continuous iv The lagging strand is synthesized as Okazaki fragments 1 Grows in direction away from the replication fork 2 Each fragment requires its own primer to be synthesized by the primase 3 DNA polymerase adds nucleotides to the new Okazaki fragment only at the 3 end continuing until it encounters the primer on the previous fragment a A different DNA polymerase hydrolyzes the primer and replaces it with DNA b DNA ligase then catalyzes the formation of the phosphodiester linkage that nally joins the two Okazaki fragements v DNA polymerase is processive catalyzes many sequential polymerization reactions each time it binds to a DNA molecule In most cells the chromosome shortens with each replication because the nonreplicated DNA at the 3 end of the template DNA is removed i In stem cells gameteforming cells and cancer cells telomerase uses an RNA template to extend the telomere and prevent chromosome shortening Telomeres strings of repetitive sequences at the ends of their chromosomes i Prevent chromosomes from joining to other chromosomes ii Repeats bind a protein complex the shelterin complex which protects the ends from being joined together by the DNA repair system iii The average telomere length is shorter in older people After 2013 cell divisions the chromosome ends become short enough to lose their protective role and the chromosomes los their integrity i Apoptosis programmed cell death ensues cell dies ii Telomerase catalyzes the addition of any lost telomeric sequences in these cells 1 Contains an RNA sequence that acts as a template for the telomeric DNA repeat sequence 2 Cancer cells overexpress telomerase can stay alive for longer periods of time than normal cells j Errors in DNA replication can be repaired i Proofreading occurs right after DNA polymerase inserts a nucleotide 1 When a DNA polymerase recognizes a mispairing of bases it removes the improperly introduces nucleotide and tried again ii Mismatch repair occurs after DNA has been replicated 1 A portion of the DNA including the incorrect nucleotide is removed and a DNA polymerase inserts the correct sequence k Polymerase chain reaction PCR allows researcher to make multiple choices of short DNA sequences in a test tube a process referred to as DNA ampli cation i Cyclic process in which a sequence of steps is repeated over and over again ii Requires a sample of doublestranded DNA to act as the template two short arti cially synthesized primers that are complementary to the ends of the sequence to be ampli ed the four dNTPs dATP d1TP dCTP and dGTP a DNA polymerase that can tolerate high temperatures without becoming denatured salts and a buffer to maintain a near neutral pH Ill Mutations are Heritable Changes in DNA 0 Changes in the nucleotide sequence of DNA that are passed on from one cell or organism to another a Somatic mutations occur in the somatic body cells of a multicellular organism i Passed onto daughter cells during mitosis and in turn to the offspring of those cells ii Not passed on to sexually produced offspring b Germline mutations occur in the cells of the germ line specialized cells that give rise to gametes the eggs and sperm of sexual reproduction i Passes it on to a new organism at fertilization c Silent mutations do not affect gene function d Lossoffunction mutations result in either the loss of expression of a gene or in the production of a nonfunctional protein or RNA i Almost always show recessive inheritance in a diploid organism because the presence of one wildtype allele usually results in sufficient functional protein for the cell e Gainof function mutations lead to a protein with an altered function i Shows dominant inheritance because the presence of the wildtype allele does not prevent the mutant allele from functioning ii Common in cancer f Conditional mutations cause their phenotypes onu under certain restrictive conditions i Wildtype phenotype is expressed under other permissive conditions ii Temperaturesensitive show altered phenotype only at a certain temperature g Point mutation addition or subtraction of a single nucleotide base or the substitution of one base for another i Can be caused by errors in DNA replication that are not corrected during proofreading or environmental mutagens substances that cause mutations such as radiation or certain chemicals h Chromosomal mutations whole mutations can break and rejoin disrupting the sequences of genes L Fourtypes 1 Deletions result in the removal of part of the genetic material a Sever or fatal consequences 2 Duplications can be produced at the same time as deletions a Arise if homologous chromosomes broke at different positions and then reconnected to the wrong partners 3 Inversions also result from the breaking and rejoining of chromosomes a A segment of DNA may be removed and reinserted into the same location in the chromosome but ipped end over end so that it runs in the opposite direction 4 Translocations when segments of chromosomes break off and become joined to different chromosomes a May involve reciprocal exchanges of chromosome segments b Often lead to duplications and deletions i Spontaneous mutations permanent changes in the genetic material that occur without any outside in uence i DNA polymerase can make errors in replication 1 Usually repaired by the proofreading function of the replication complex but some errors escape detection and become permanent ii The four nucleotide bases of DNA have alternate structures that affect base pairing iii Bases in DNA may change because of chemical reactions iv Meiosis is nor perfect 1 Errors can result in nondisjunction and aneuploidy or chromosomal breakage and rejoining v Gene sequences can be disrupted j lnduced mutations occur when some agent from outside the cell a mutagen causes a permanent change in the DNA sequence i Some chemicals alter the nucleotide bases ii Some chemicals add groups to the bases iii Radiation damages the genetic material k Some base pairs are more vulnerable that others to mutation l Mutagens can be natural or arti cial i Radiation humanmade or natural ii Plants make thousands of small molecules that serve a range of purposes including defense against pathogens m Mutations have both bene ts and costs i Bene ts 1 Provides genetic diversity that makes natural selection possible 2 Mutations may enable species to adapt to changing conditions ii Costs 1 Harmful if they result in the loss of function of genes and their protein products or other DNA sequences that are needed for survival Chapter 10 From DNA to Protein Gene Expression I Genetics Show That Genes Code for Proteins a In PKU the enzyme that converts phenylalanine to tyrosine is nonfunctional In alkaptonuria homogentisic acid accumulates in the blood joints and urine because the enzyme that catalyzes its breakdown is de cient A mutant phenotype arises from a change in the protein s amino acid sequence Hemoglobin is easy to isolate and study i Many alterations of hemoglobin do not affect the protein s function 1 About 5 of all humans are carriers for one of these variants Exceptions to the one geneone polypeptide relationship include the alternative splicing of RNA which can produce multiple functional polypeptides from a single gene Molecular biology the study of nucleic acids and proteins focuses on gene expression Transcription information in a DNA sequence a gene is copied into a complementary RNA sequence i Messenger RNA and transcription when a particular gene is expressed the two strands of DNA unwind and separate into a coding strand and a template strand ii Template strand transcribed to produce an RNA strand by complementary base pairing iii RNA strand modi ed to produce messenger RNA mRNA 1 Eukaryotic cells mRNA processed in the nucleus and then moves to the cytoplasm where it is translated into a polypeptide Translation this RNA sequence is used to create the amino acid sequence of a polypeptide i Ribosomal RNA and translation ribosome is a protein synthesis factory with multiple proteins and several ribosomal RNAs rRNAs 1 Catalyzes peptide bond formation between amino acids to form a polypeptide Transfer RNA mediated between mRNA and protein transfer RNA tRNA can both bind a speci c amino acid and recognize a speci c sequence of nucleotides in mRNA by complementary base pairing i Recognizes which amino acid should be added next to a growing polypeptide chain DNA Expression Begins with its Transcription to RNA a Transcription formation of a speci c RNA sequence from a speci c DNA sequence requires three key components i A NDA template for complementary base pairing ii The four ribonucleoside triphosphates ATP GTP CTP and UTP to act as substrates iii An RNA polymerase enzyme b RNA polymerases from both prokaryotes and eukaryotes catalyze the synthesis of RNA from the DNA template i Processive a single enzymetemplate binding event results in the polymerization of hundreds of RNA nucleotides ii Do not require a primer c Transcription occurs in three steps i lnitiation requires a promoter a special DNA sequence to which the RNA polymerase binds very tightly 1 Promoter tells the RNA polymerase where to start transcription and which of the two DNA strands to transcribe and under what conditions 2 Transcription initiation site where transcription begins 3 Sigma factors and transcription factors help determine which genes are expressed at a particular time in a particular cell ii Elongation RNA polymerase unwinds the DNA and reads the template strand in the 3 toS direction 1 RNA polymerase adds new nucleotides to the 3 end of the growing strand beginning with the rst nucleotide at the transcription initiation site a First nucleotide in the new RNA forms its 5 end and the RNA transcript is antiparallel to the DNA template strand 2 RNA polymerase uses the ribonucleoside triphosphates ATP UTP GTP and CTP as substrates and catalyzes the formation of phosphodiester bonds between them releasing pyrophosphate in the process iii Termination particular base sequences specify termination 1 Eukaryotes multiple proteins are involved in recognizing the transcription termination site and separating the newly formed RNA strand from the DNA template and the RNA polymerase d Coding regions sequences within a DNA molecule that are eventually translated as proteins i Coding region on the DNA template strand is transcribed into a complementary mRNA molecule which has the same base sequence with Us instead of Ts as the DNA coding strand ii lntrons noncoding sequences intervening regions that interrupt the coding region iii Exons transcribed regions that are interspersed with the introns expressed regions iv Exons and introns appear in the primary mRNA transcript called the precursor RNA or premRNA but the introns are removed by the time the mature mRNA leaves the nucleus 1 PremRNA processing involves cutting introns out of the permRNA transcript and splicing together the exon transcripts e Nucleic acid hybridization method that originally revealed the existence of introns i Crucial for studying relationship between eukaryotic genes and their transcripts ii Two steps 1 The DNA to be analyzed is denatured by heat to break the hydrogen bonds between the base pairs and separate the two strands 2 A singlestranded nucleic acid from another source probe is incubated with the denatured DNA a If the probe has a base sequence complementary to the target DNA a probetarget double helix forms by hydrogen bonding between the bases i Results in doublestranded molecule called a hybrid f After premRNA is made its introns must be removed i RNA splicing removes the introns and splices the exons together g Consensus sequences short stretches of DNA that appear with little variation quotconsensusquot in many different genes i Bound by several small nuclear ribonucleoprotein particles snRNPs when premRNA is transcribed ii Other proteins bind forming a large complex called a spliceosome h While the premRNA is still in the nucleus it undergoes two processing steps one at each end of the molecule i A 5 cap G cap is added to the 5 end of the pre mRNA as it is transcribed 1 Chemically modi ed molecule of GTP 2 Facilitates the binding of mRNA to the ribosome for translation protects the mRNA from being digested by ribonucleases enzymes that break down RNAs ii A poly A tail is added to the 3 end of the premRNA at the end of transcription 1 Sequence of 100300 adenine nucleotides assist in the export of the mRNA from the nucleus and is important for mRNA stability Ill The Genetic Code in RNA is Translated into the Amino Acid Sequences of Proteins a Codons specify for a particular amino acid sequential nonoverlapping 3letter quotwordsquot i Letters are three adjacent nucleotide bases in the mRNA poynuceotide chain ii Each codon in the mRNA is complenetary to the corresponding triplet of bases in the template strand of the DNA molecule from which it was transcribed b Stop codons termination signals for translation i UAA UAG UGA ii When the translation machinery reached one of these codons translation stops and the polypeptide is released c Genetic information is encoded in 3letter units codons that are read from 5 to3 direction on the mRNA i To decode a codon nd its rst letter in the left column then read across the top to its second letter then read down the right column to its third letter d Genetic code is redundant but not ambiguous i If the code were ambiguous a single codon could specify two or more different amino acids and there would be doubt about which amino acid should be incorporated into a growing polypeptide chain ii A given amino acid may be encoded by more than one codon but each codon encodes only one amino acid e The genetic code is nearly universal i Within the mitochondria and chloroplasts the code differs slightly from that in prokaryotes and in the nuclei of eukaryotic cells ii All life came ultimately from a common ancestor f Point mutations changes in single nucleotides within a sequence con rm the genetic code i Silent mutations can occur because of the redundancy of the genetic code 1 Do not cause any change in amino acid sequence ii Missense mutations result in a change in the amino acid sequence iii Nonsense mutations result in a premature stop codon 1 Polypeptide chain would end at the amino acid translated just before the stop codon iv Frameshift mutations result from the insertion or deletion of one or more base pairs within the coding sequence 1 Can cause new triplets to be read and an altered sequence of amino acids in the resulting polypeptide IV Translation of the Genetic Code is Mediated by tRNAs and Ribosomes a Two key events must take place to ensure that the protein made is the one speci ed by the mRNA i A tRNA must chemically read each mRNA codon correctly ii The tRNA must deliver the amino acid that corresponds to the mRNA codon b tRNAs bind to particular amino acids i Covalent attachment is at the 3 end of the tRNA ii When carrying an amino acid the tRNA is said to be charged c tRNAs bind to mRNA i At the midpoint on the tRNA poynuceotide chain there is a triplet of bases called the anticodon which is complementary to the mRNA codon for the particular amino acid that the tRNA carries 1 Codon and anticodon bind together via noncovaent hydrogen bonds tRNAs interact with ribosomes by noncovaent interactions e AminoacyltRNA synthase family of enzymes that charge each tRNA with its correct amino acid i Reaction uses the energy in ATP to form a high energy bond between the amino acid and the tRNA 1 Energy in this bond is later used in the formation of peptide bonds between amino acids in a growing polypeptide chain f Translation occurs at the ribosome i Ribosomes are irregularly shaped and composed of two subunits P 1 Each subunit contains rRNA and numerous proteins ii There are 3 sites for tRNA binding E P and A 1 A amino acid site where the charged tRNA anticodon binds to the mRNA codon thus lining up the correct amino acid to be added to the growing polypeptide chain 2 P polypeptide site where the tRNA adds its amino acid to the polypeptide chain 3 E exit sire where the tRNA having given up its amino acid resides before being released from the ribosome and going back to the cytosol to pick up another amino acid and begin the process again iii Any tRNA that does not form hydrogen bonds with all three bases of the codon is ejected from the ribosome g Translation takes place in three steps i lnitiation initiation complex consists of a charged tRNA and a small ribosomal subunit both bound to the mRNA ii Elongation a charged tRNA whose anticodon is complementary to the second codon of the mRNA now enters the open A site of the large ribosomal subun 1 Large subunit then catalyzes two reactions a Breaks the bond between the methionine and its tRNA in the P site b Catalyzes the formation of a peptide bond between the methionine and the amino acid attached to the tRNA in the A site 2 Free tRNA is moved to the E site and then released as the ribosome shifts by one codon so that the growing polypeptide chain moves to the P site iii Termination elongation cycle terminates at the end of the coding sequence which is marked by a stop codon UAA UAG UGA 1 When a stop codon enter the A site it binds a protein release factor which allows hydrolysis of the bond between the polypeptide chain and the tRNA in the P site a Newly polypeptide then separate from the ribosome h Polyribosome or polysome an assemblage consisting of a strand of mRNA with its beadlike ribosomes and their growing polypeptide chains V Proteins Are Modi ed after Translation a Polypeptides are often modi ed by the addition of new chemical groups that contribute to the function of the mature protein b Protein synthesis always begins on free ribosomes oating in the cytoplasm and the default location for a protein is the cytosol c Signal sequence signal peptide a short stretch of amino acids that indicates where in the cell the polypeptide belongs i In absence of a signal sequence the protein will remain in the same cellular compartment where it was synthesized ii A signal sequence binds to a speci c receptor protein at the surface of the organelle 1 Channel forms in the organelle membrane allowing the targeted protein to move into the organelle d Many proteins are modi ed after translation i Proteolysis cutting of a polypeptide chain allowing the fragments to fold into different shapes ii Glycosylation the addition of carbohydrates to proteins to form glycoproteins 1 In the ER and the Golgi apparatus resident enzymes catalyze the addition of various oligosaccharides to certain amino acid R groups on proteins iii Phosphorylation the addition of phosphate groups to proteins and is catalyzed by protein kinase 1 Charged phosphate groups change the conformation of the protein often exposing the active site of an enzyme or the binding site for another protein 2 Phosphorylation is especially important in cell anaHng Chapter 11 Regulation of Gene Expression I Many Prokaryotic Genes Are Regulated in Operons a Promoter region of DNA containing the site where RNA polymerase binds to initiate transcription where gene expression begins b Transcription factors regulatory proteins control whether or not a gene is active repressors and activators i In negative regulation a repressor binds a speci c site in or near the promoter to prevent transcription ii In a positive regulation the binding of an activator stimulates transcription c Prokaryotes conserve energy and resources by making certain proteins only when they are needed d Lactose is Bgalactoside a disaccharide containing galactose linked to glucose i Bgalactoside permease is a carrier protein in the bacterial cell membrane that moves sugar into the cell ii Bgalactosidase is an enzyme that hydrolyzes lactose to glucose and galactose iii Bgalactoside transacetylase transfers acetyl groups from cetyl CoA to certain Bgalactosides e Inducers compounds that stimulate the transcription of speci c genes i Inducible genes genes that can be activated by inducers f Constitutive genes expressed most of the time at a constant rate g Operon cluster of genes with a single promoter i Lac operon operon that encodes the three lactose metabolizing enzymes in E coli 1 Segment of DNA that includes a promoter an operator and the three genes that code for lactosemetabolizing enzymes 2 Not transcribed at high levels unless a B galactoside such as lactose is the predominant sugar available in the cell s environment 3 Allolactose the inducer leads to synthesis of the proteins in the lactosemetabolizing pathway by binding to the repressor protein and preventing its binding to the operator ii Repressible operon switched off when its repressor is bound to its operator iii Corepressor molecule that binds to the repressor causing it to change shape and bind to the operator thereby initiation transcription h Structural gene any gene that encodes a protein that is not directly involved in gene regulation i Two regulatory systems i Inducible systems substrate of a metabolic pathway the inducer interacts with a transcription factor the repressor rendering the repressor incapable of binding to the operator and thus allowing transcription 1 Control catabolic pathways which are turned on only why the substrate is available ii Repressible systems a product of a metabolic pathway the corepressor binds to the repressor protein which is then able to bind to the operator and block transcription 1 Control anabolic pathways which are turned on until the concentration of the product becomes sufficient j Sigma factors can bind to RNA polymerase and direct the polymerase to speci c promoters in prokaryotes k Virus injects its genetic material into a host cell and in many cases it turns that cell into a virus factory i Radial change in gene expression for the host cell ii Can result in death of the cell when new viral particles are released iii Host cell begins to produce new viral particles virions which are released as the cell breaks open or lyses iv Lytic prokaryotic viral life cycle 1 Lysogenic dormant phase a Viral genome becomes incorporated into the host cell genome and is replicated along with the host genome ll Eukaryotic Genes Are Regulated by Transcription Factors a Eukaryotic promoter region of DNA near the 5 end of a gene where RNA polymerase binds and initiates transcription i TATA box rich in AT base pairs core promoter sequence b RNA polymerase II polymerase that transcribes the proteincoding genes in eukaryotes i Cannot bind to the promoter and initiate transcription by itself 1 Does so only after various general transcription factors have bound to the core promoter c During the development of a complex organism from fertilized egg to adult cells become more and more differentiated specialized d Cellular therapy providing new functional cells to patients who have diseases that involve the degeneration of certain cell types e The expression of genes can be coordinated if they share regulatory sequences that bind the same transcription factors i A single environmental signal such as a drought stress activates a transcription factor that acts on many genes f Eukaryotes are susceptible to infections by various kinds of viruses that have a variety of life cycle strategies g HIV is a retrovirus its genome is singlestranded RNA and it carries within the virion and enzyme called reverse transcriptase i Reverse transcriptase makes a DNA strand that is complementary to the RNA while at the same time degrading the RNA and making a second DNA strand that is complementary to the rst ii Resulting doublestranded DNA becomes integrated into the host s chromosome iii Integrated viral DNA is called a provirus 1 Provirus resides permanently in the host chromosome and can remain in an inactive state for years 2 During this time transcription of the viral DNA is initiated but host cell proteins called terminator factors prevent the RNA from elongating and transcription is terminated prematurely Ill Gene Expression Can Be Regulated via Epigenetic Changes to Chromatin a Eukaryotic cells are also able to regulate transcription via reversible nonsequencespecific alterations to either the DNA or the chromosomal proteins that package the DNA in the nucleus i Alterations can be passed on to daughter cells after mitosis or meiosis 1 Epigenetic changes b Chromatin remodeling alteration of chromatin structure c Nucleosome basic unit of DNA packaging a core of positively charged histone proteins around which DNA is wound i Each histone protein has a quottailquot of about 20 amino acids at its N terminus that sticks out of the compact structure and contains certain positively charged amino acids notably lysine ii Strong ionic attraction between the positively charges histone proteins and DNA which is negatively charged because of its phosphate groups d Histone acetyltransferases enzymes which add acetyl groups to these positively charged amino acids and neutralize their chargers i Majority found near gene promoters also found throughout the transcribed regions of genes ii Histone acetylation promotes transcription initiation and elongation e Histone deacetylases chromatin remodeling proteins can remove the acetyl groups from histones and repress transcription f Methylation the addition of a methyl group i Activation or repression of a gene expression depending on which lysine residue is methylated g Phosphorylation the addition of a phosphate group i Involved in chromosome condensation during mitosis and meiosis as well as affecting gene regulation h Maintenance methyltransferase catalyzes the formation of 5methylcytosine at CpG regions i Transcription repressed i Demethylase catalyzes the removal of the methyl group from cytosine j Euchromatincontains the DNA that is transcribed into mRNA k Heterochromatin any genes it contains are generally not transcribed l Epigenetic changes can be induces by the environment i Methylation patterns are stale and can be passed on from one generation to the next m Genomic imprinting offspring would inherit a maternal gene that is transcriptionally inactive methylated and a parental gene that is transcriptionally active demethylated i Males and femlaes may be the same genetically except for the X and Y chromosomes but they differ epigenetically IV Eukaryotic Gene Expression Can Be Regulated after Transcription a Alternative splicing deliberate mechanism for generating a family of different proteins with different activities and functions from a single gene i HIV genome encodes nine proteins but is transcribed as a single premRNA 1 Most of the 9 proteins are then generate by alternative splicing of this premRNA ii Fruit y sex is determine by the le gene which has four exons 1 In female embryo splicing generates two active forms of the le protein 2 In male embryo protein contains all four exons andisinac ve iii microRNA miRNA are important regulators of gene expression 1 First found in the worm Caenorhabditis elegans 2 Inhibit the translation of speci c mRNAs by causing their premature degradation iv Translation of mRNA can be regulated 1 Inhibition of translation with miRNAs 2 Modi cation of the 5 cap an mRNA that is capped with an unmodi ed GTP molecule is not translated 3 Translational repressor proteins block translation by binding to mRNAs and preventing their attachment to the ribosome a Binging of a translational repressor to mRNA blocks the mRNA from associating with the ribosome i The repressor can be removed from the mRNA via allosteric regulation v Proteins targeted for degradation are bound by ubiguitin which then directs the targeted protein to a proteasome 1 Proteasome is a complex structure where proteins are digested by several powerful proteases Chapter 13 Biotechnology I Recombinant DNA Can Be Made in the Laboratory a Recombinant DNA a single DNA molecule containing DNA sequences from two or more sources b Three key tools i Restriction enzymes for cutting DNA into pieces fragments that can be manipulated 1 Enzymes break the bonds of the DNA backbone between the 3 hydroxyl group of one nucleotide and the 5 phosphate group of the next nucleotide 2 Restriction site 4 to 6 base pairs long restriction enzymes catalyze hydrolysis of both strands of DNA 3 Sticky ends singlestranded overhangs able to form hydrogen bonds with complementary sequences on other DNA molecules 4 Blunt ends cuts directly opposite one another on the two DNA strands ii Gel electrophoresis for the analysis and puri cation of DNA fragments 1 DNA fragments move through the gel toward the positive end of the field a Small DNA molecules move faster than larger ones because spaces between the polymers of the gel are small 2 The number of fragments produced by digestion of a DNA sample with a given restriction enzyme depends on how many times that enzyme s restriction site occurs in the sample 3 DNA fragments of known size are often placed in one well of the gel to provide a standard for comparison a Tells us how large the DNA fragments are b By comparing fragment sizes obtained with two or more restriction enzymes the locations of their recognition sequences relative to one another can be worked out mapped 4 The relative intensity of a band produced by a speci c fragment can indicate the amount of that fragment iii DNA ligase for joining DNA fragments together in novel combinations forms phosphodiester bonds between fragments 1 Enzyme that joins Okazaki fragments during DNA replication 2 Sticky ends can hydrogenbond to complementary sticky ends from other DNAs and the resulting recombinant DNA can be sealed with DNA ligase ll DNA Can Genetically Transform Cells and Organis s a b Clone produce many identical copies Transformation process of inserting recombinant DNA into hostceHs i Transfection if the host cells are derived from an animal Transgenic host cell or organism that contains recombinant DNA Selectable marker genes genes that confer resistance to antibiotics Bacteria are easily grown and manipulated in the lab i Contain plasmids which are easily manipulated to carry recombinant DNA into the cell Yeast such as Saccharomyces are used as eukaryotic hosts for recombinant DNA studies i Rapid cell division ease of growth in lab relatively small genome size Plant cells are good hosts because they can be treated with hormones that make them differentiate into unspecialized stem cells i Unspecialized stem cells can be transformed with recombinant DNA and then studied in culture or grown into new plants Cultured animal cells can be used to study the expression of human or animal genes for medical purposed i While transgenic animals can also be created by inserting DNA into the nuclei of fertilized eggs A variety of methods are used to insert recombinant DNA into host cells i Electroporation a short electric shock is used to create temporary pores in the membrane through which the DNA can enter ii Cells may be chemically treated to make their outer membranes more permeable and then mixed with DNA so it can diffuse into the cells Two ways in which the newly introduced DNA can become part of a replicon within the host cell i It may be inserted into a host chromosome ii It can enter the host cell as part of a carrier DNA sequence called a vector and can either integrate into the host chromosome or have its own origin of DNA replication Plasmids as vectors i Small and easy to manipulate ii One or more restriction enzyme recognition sequences that each only occur once in the plasmid sequence 1 Easy to insert additional DNA into the plasmid before it is used to transform host cells iii Contain genes that confer resistance to antibiotics and thus can serve as selectable markers iv Bacterial origin of replication ori and can replicate independently of the host chromosome l Reporter gene any gene whose expression is easily assayed i Code for proteins that can be detected visually 1 Bgalactosidase lacZ gene codes for an enzyme that can convert the white substrate X gal into a bright blue product a Foreign DNA can be inserted into the lacZ gene inactivating it 2 Green uorescent protein GEP emits green light when exposed to ultraviolet light Ill Genes Come from Various Sources and a Genomic library a collection of DNA fragments that together comprise the genome of an organism i Can be made by breaking the DNA into small fragments incorporating the fragments into a vector and then transforming host cells within the recombinant vectors b A much smaller DNA library one that includes only genes transcribed in a particular tissue can be made from complementary DNA cDNA i lnvolves isolating mRNA from cells and making cDNA copies of that mRNA by complementary base pairing 1 Catalyzed by reverse transcriptase ii cDNA library snapshot of the transcription pattern of the cells in the sample iii Reverse transcriptase along with PCR can be used to create and amplify a speci c cDNA sequence without the need to make a library 1 RNA is isolated from cells and then reverse transcriptase is used to make cDNA from the RNA 2 PCR is used to amplify a speci c sequence directly from the cDNA a RTPCR method c Polymerase chain reaction PCR method of amplifying DNA in a test tube i Any DNA can be ampli ed as long as appropriate primers are available 1 Synthetic oligonucleotides singlestranded DNA fragments of 2040 bp are used as primers in PCR reactions 2 Ampli ed DNA can then be inserted into a plasmid to create recombinant DNA and cloned in host cells d Mutations that occur in nature have been important in demonstrating causeandeffect relationships in biology i Mutations in nature are rare events so DNA sequences can be manipulated to study the relationships ii Auxin response element short sequence of DNA that binds a speci c transcription factor 1 Found in the promoters of plant genes that are switched on in the presence of the plant hormone auxin e Homologous recombination when a pair of homologous chromosomes line up during meiosis i Chromosomes sometimes break and then rejoin in such a way that segments of the two chromosomes are exchanged f Stem cell unspecialized cell that divides and differentiates into specialized cells g RNA interference RNAi mechanisms for preventing mRNA translation h Antisense RNA bind by base pairing to the sense bases on the target mRNAs MicroRNAs and siRNAs i siRNAs target speci c mRNA molecules from speci c genes because their sequences exactly match the target sequences in the mRNAs ii miRNAs do not match their targets perfectly and therefore eac one can reduce the expression of multiple partially matching genes i DNA microarray quotgene chipquot contains a series of DNA sequences attached to a solid surface i Used to examine patterns of gene expression in different tissues and under different conditions and can be used to identify individual organisms with particular mutations IV Biotechnology Has Wide Applications a Biotechnology the use of cells or whole living organisms to make or modify materials or processes that are useful to people such as food medicines and chemicals i Bacteria and yeast cells can be transformed with almost any gene and they can be induced to express that gene at high levels and to export the protein product out of their cells b Expression vectors all characteristics of typical vectors as well as extra sequences needed for the foreign gene transgene to be expressed in the host cell i Inducible promoter responds to a speci c signal 1 Can be used so that the transgene will be expressed at high levels only when the hormone is added ii Tissuespeci c promoter expressed only in a certain tissue at a certain time 1 Used if localized expression is desired iii Signal sequences added so that the gene product is directed to an appropriate destination c Pharming the production of pharmaceuticals in farm animals or plants i Expression vector carrying a desired gene can be put into an animal egg which is implanted into a surrogate mother 1 Transgenic offspring produce the new protein in their milk a Natural quotbioreactorsquot can produce abundant supplies of the protein which can be separated easily from the other components of the milk d Human growth hormone hGH protein made in the pituitary gland and has many effects especially in growing children e Recombinant DNA has several advantages over traditional methods of breeding i The ability to identify speci c genes genetic markers ii The ability to introduce any gene from any organism into a plant or animal species iii The ability to generate new organisms quickly f Ecological management tailoring the environment to the needs of crop plants and animals i Farm field unnatural humandesigned system that must be carefully managed to maintain optimal conditions for crop growth g Public concern about biotechnology Genetic manipulation is an unnatural interference with nature Genetically altered food are unsafe to eat Genetically altered crop plants are dangerous to the environment h Bioremediation the use by humans of other organisms to remove contaminants from the environment Composting the use of bacteria and other microbes to break down large molecules including carbonrich polymers and proteins in waste products such as wood chips paper straw and kitchen scraps Wastewater treatment break down human wastes paper products and household chemicals Oil spills can be remediated by encouraging the growth of natural microorganisms that digest components of crude oil


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