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MOLECULAR GENETICS DNA.

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1 MOLECULAR GENETICS DNA

2 What is the significance of DNA? Why is it so important?
Because it is universal. It is the genetic material for all forms of life. It points to a common evolutionary origin of all living things. Why is it relevant in your life today? The knowledge of DNA have changed our lives drastically. From forensics to the biotechnology industry, in agriculture and in medicine to name just a few areas.

3 Where is DNA and what does it do?
DNA is packed in the chromosomes and the chromosomes are in the nucleus of all eukaryotic cells. What is DNA’s function? DNA’s function is to store and transfer genetic information from one generation to the next. To do this we need mitosis and meiosis so we can copy our own DNA and pass it on.

4 What kind of information is encoded in DNA?
Instructions of how to make proteins.

5 What does DNA look like? DNA is a nucleic acid.
Nucleic acids are made up of nucleotides. ( remember that a nucleotide consists of three parts: a 5 carbon sugar, a phosphate group and a nitrogen base) DNA looks like a twisted staircase. The handrails or sides are also called its backbone and are made up of sugars and phosphate groups connected to each other. The paired bases made up the rungs of the ladder connecting the two strands.

6 The structure of DNA Consists of two nucleotide strands wrapped around each other in a double helix Twist Figure 10.3C

7 DNA and RNA are polymers of nucleotides
DNA is a nucleic acid Made of long chains of nucleotide monomers DNA polynucleotide A C T G Sugar-phosphate backbone Phosphate group Nitrogenous base Sugar O O– P CH2 H3C N H Nitrogenous base (A, G, C, or T) Thymine (T) Sugar (deoxyribose) DNA nucleotide Figure 10.2A

8 The base-pairing rules dictate the combinations of nitrogenous bases that form the “rungs” of DNA.
However, this does not restrict the sequence of nucleotides along each DNA strand. The linear sequence of the four bases can be varied in countless ways. Each gene has a unique order of nitrogen bases. In April 1953, Watson and Crick published a succinct, one-page paper in Nature reporting their double helix model of DNA Fig. 16.5 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

9 DNA has four kinds of nitrogenous bases
A, T, C, and G A pairs with T and G pairs with C C O N H H3C Thymine (T) Cytosine (C) Adenine (A) Guanine (G) Purines Pyrimidines Figure 10.2B

10 Nitrogenous base (A, G, C, or U)
RNA is also a nucleic acid But has a slightly different sugar And has U instead of T Nitrogenous base (A, G, C, or U) Phosphate group O O– P CH2 H C N OH Uracil (U) Sugar (ribose) Key Hydrogen atom Carbon atom Nitrogen atom Oxygen atom Phosphorus atom Figure 10.2C, D

11 A little history… In April 1953, James Watson and Francis Crick
published a model for the structure of deoxyribonucleic acid or DNA. won the Nobel prize for it Your genetic material is the DNA you inherited from your parents. Nucleic acids are unique direct their own replication. The resemblance of offspring to their parents depends on the precise replication of DNA transmission from one generation to the next. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

12 The Search for Genetic Material
Once Thomas Morgan’s group showed that genes are located on chromosomes, the two constituents of chromosomes - proteins and DNA - were the candidates for the genetic material. Until the 1940s, abundance and variety of proteins seemed to indicate that proteins were the genetic material. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

13 Still nobody knew what was the genetic material
Early 1900”s everyone “knew” that the genetic material was protein. In Fred Griffith trying to produce a vaccine against pneumonia made scientist doubt . Griffith said that protein was not the genetic material because heat denatures proteins and in his experiments heat did not denatured the genetic material Still nobody knew what was the genetic material

14 Griffith called this phenomenon transformation, a change in genotype and phenotype due to the assimilation of a foreign substance (now known to be DNA) by a cell. Fig. 16.1 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

15 1944, Oswald Avery, McCarty and MacLeod announced that the transforming substance was DNA.
Still, many biologists were skeptical. this reflected a belief that the genes of bacteria could not be similar in composition and function to those humans. Avery confirmed Griffith discovery and that the genetic material was a nucleotide and not a protein

16 THE STRUCTURE OF THE GENETIC MATERIAL
Experiments showed that DNA is the genetic material The Hershey-Chase experiment showed that certain viruses reprogram host cells To produce more viruses by injecting their DNA Head Tail Tail fiber DNA 300,000 Figure 10.1A

17 What did Hershey and Chase do?
They showed that the genetic material of a virus is DNA. They separated the protein coat and the DNA of the virus (a phage known as T2) and tagged it with a radioactive isotope and then traced it. The protein coat remained outside and only the DNA when inside the bacteria.

18 In 1952, Alfred Hershey and Martha Chase showed that DNA was the genetic material of the phage T2.( a phage is a virus that attacks bacteria) The T2 phage (the virus), consisting almost entirely of DNA and protein, attacks Escherichia coli (E. coli), a common intestinal bacteria of mammals. This phage can quickly turn an E. coli cell into a T2-producing factory that releases phages when the cell ruptures. Fig. 16.2a Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

19 The Hershey-Chase experiment
Phage Bacterium Radioactive protein DNA Empty protein shell Radioactivity in liquid Pellet Centrifuge Batch 1 Radioactive protein Batch 2 Radioactive DNA Radioactivity in pellet Figure 10.1B Mix radioactively labeled phages with bacteria. The phages infect the bacterial cells. 1 Agitate in a blender to separate phages outside the bacteria from the cells and their contents. 2 Centrifuge the mixture so bacteria form a pellet at the bottom of the test tube. 3 Measure the radioactivity in the pellet and the liquid. 4

20 Chargaff’s Rules By 1947, Erwin Chargaff already knew that DNA was a polymer of nucleotides consisting of a nitrogenous base, deoxyribose ( a sugar), and a phosphate group. By 1947 Chargaff had developed rules saying that The bases could be adenine (A), thymine (T), guanine (G), or cytosine (C). Chargaff rule: A always pairs with T and C always pairs with G In any one species, the four bases are found in characteristic, but not necessarily equal, ratios. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

21 He found a regular ratio of nucleotide bases which are known as Chargaff’s rules.
The number of adenines was approximately equal to the number of thymines (%T = %A). The number of guanines was approximately equal to the number of cytosines (%G = %C). Human DNA is 30.9% adenine, 29.4% thymine, 19.9% guanine and 19.8% cytosine. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

22 By 1950 DNA was accepted by scientists as the genetic material but nobody knew its structure
Many scientists wanted to be the first to discover it

23 Race for the Prize By the beginnings of the 1950’s, the race was on to move from the structure of a single DNA strand to the three-dimensional structure of DNA. Among the scientists working on the problem were Linus Pauling, in California, and Maurice Wilkins and Rosalind Franklin, in London. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

24 The story of DNA :The social nature of science
In 1951 James Watson went to Europe (after completing his PhD) and met Crick. Francis Crick was a graduate student working in hemoglobin in Cambridge, England. They talked about DNA Crick and Watson teamed up to work on the structure of DNA. Watson went to London to hear a lecture by Rosalind Franklin on DNA. She and Maurice Wilkins were authorities on X-ray diffraction and had been working on the DNA structure on the same lab. R.Franklin made observations about her X ray diffraction of DNA. Watson didn’t understand about X-ray crystallography so he didn’t get much out of Franklin’s lecture. Rosalind Franklin was a well know physical chemist because of her previous work on carbon fiber technology. She was invited to King’s College in London to set up an X-ray diffraction lab. She was not told of Wilkins interest in her DNA work. Wilkins did not know about Franklin. He treated her as a lab technician or a secretary, attacked her behind her back. Watson and Crick made a model of DNA that was all wrong because they did not have Franklin’s information. Watson believed that the sugar-phosphate backbone was on the inside and the bases sticking out. Franklin knew it was on the inside.

25 The story continues…. In December 1952 Watson and Crick learned that Linus Pauling was working on DNA structure. They asked Pauling for a copy of his paper and Pauling sent one to Watson. They also got the information from Chargaff about the bases A-t ans C-G. Wilkins allowed Crick to get Franklin’s information from her lab’s annual report without asking Franklin. He gave Franklin’s X ray pictures to Crick. They learned all the positions and measurements from Franklin’s picture and build a model in which everything fit except the bases. Examining Chargaff rules they build an accurate model of DNA in March 1953. When Watson and Crick wrote their results in a scientific journal Franklin was given no credit Franklin died in 1958 (breast cancer) without ever knowing her data was used to figure the structure of DNA. Franklin’s failure was due to her social isolation because Watson and Crick had many contacts in her lab, lots of friends and people supporting and consulting with them.

26 DNA is a double-stranded helix
James Watson and Francis Crick Worked out the three-dimensional structure of DNA, based on work by Rosalind Franklin Figure 10.3A, B

27 Maurice Wilkins and Rosalind Franklin used X-ray crystallography to study the structure of DNA.
In this technique, X-rays are diffracted as they passed through aligned fibers of purified DNA. The diffraction pattern can be used to deduce the three-dimensional shape of molecules. James Watson learned from their research that DNA was helical in shape and he deduced the width of the helix and the spacing of bases. Fig. 16.4

28 Watson and Crick James Watson and his colleague Francis Crick began to work on a model of DNA with two strands, the double helix. They decided on a helix shape after seeing Franklin’s X ray. They build their model to scale to conform to the X ray data. Using molecular models made of wire, they first tried to place the sugar-phosphate chains on the inside.. However, this did not fit the X-ray measurements and other information on the chemistry of DNA. In 1953 Watson and Crick won the Nobel prize for discovering the structure of DNA

29 The Molecule Comes Together
The key breakthrough came when Watson put the sugar-phosphate chain on the outside and the nitrogen bases on the inside of the double helix. The sugar-phosphate chains of each strand are like the side ropes of a rope ladder. Pairs of nitrogen bases, one from each strand, form rungs. The ladder forms a twist every ten bases. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

30 The nitrogenous bases are paired in specific combinations: adenine with thymine and guanine with cytosine. Pairing like nucleotides did not fit the uniform diameter indicated by the X-ray data. A purine-purine pair would be too wide and a pyrimidine-pyrimidine pairing would be too short. Only a pyrimidine- purine pairing would produce the 2-nm diameter indicated by the X-ray data. The key breakthrough came when Watson put the sugar-phosphate chain on the outside and the nitrogen bases on the inside of the double helix. The sugar-phosphate chains of each strand are like the side ropes of a rope ladder. Pairs of nitrogen bases, one from each strand, form rungs. The ladder forms a twist every ten bases. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

31 In addition, Watson and Crick determined that chemical side groups off the nitrogen bases would form hydrogen bonds, connecting the two strands. Based on details of their structure, adenine would form two hydrogen bonds only with thymine and guanine would form three hydrogen bonds only with cytosine. This finding explained Chargaff’s rules. Fig. 16.6 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

32 The structure of DNA Consists of two nucleotide strands wrapped around each other in a double helix Twist Figure 10.3C

33 The base-pairing rules dictate the combinations of nitrogenous bases that form the “rungs” of DNA.
However, this does not restrict the sequence of nucleotides along each DNA strand. The linear sequence of the four bases can be varied in countless ways. Each gene has a unique order of nitrogen bases. In April 1953, Watson and Crick published a succinct, one-page paper in Nature reporting their double helix model of DNA Fig. 16.5 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

34 Protein synthesis DNA RNA protein

35 What type of chemical bonds hold the DNA molecule together?
The sugar-phosphates are joined by covalent bonds which are strong The base pairs that form the rungs of the ladder are hydrogen bonds. Hydrogen bonds are easily broken which is good when the DNA molecule is going to replicate.

36 Replication When? Replication occurs during the “S” phase of the cell cycle It requires lots of enzymes Ex: enzymes unwinds the double helix breaks the hydrogen bonds between the paired bases and other enzymes separate the two strands and add new nucleotides. The main team of enzymes are the DNA polymerases

37 Form Predicts Function
The specific pairing of nitrogenous bases in DNA was the flash of inspiration that led Watson and Crick to the correct double helix. The possible mechanism for the next step, the accurate replication of DNA, was clear to Watson and Crick from their double helix model. In a second paper Watson and Crick published their hypothesis for how DNA replicates. Essentially, because each strand is complementary to each other, each can form a template when separated. The order of bases on one strand can be used to add in complementary bases and therefore duplicate the pairs of bases exactly. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

38 DNA replication is a complex process
Due in part to the fact that some of the helical DNA molecule must untwist G C A T Figure 10.4B

39 Replication is Relatively Fast and Very Accurate
It takes E. coli less than an hour to copy 5 million base pairs in its chromosome and divide to form two identical daughter cells. A human cell can copy its 6 billion base pairs and divide into daughter cells in only a few hours. This process is remarkably accurate, with only one error per billion nucleotides. More than a dozen enzymes and other proteins participate in DNA replication.

40 Enzymes: Helicase, DNA polymerase and ligase
Helicase: Is the enzyme that untwists the double helix at the replication forks DNA polymerase: is the enzyme that adds nucleotides to the existing chain. It catalizes the elongation of the new DNA strand. It also does proof-reading to remove mistakes. Ligase: a linking enzyme. It bonds fragments, like glue

41 DNA REPLICATION DNA replication depends on base pairing
DNA replication starts with the separation of DNA strands (done by an enzyme) Then enzymes use each strand as a template to assemble new nucleotides into complementary strands.( DNA polymerase and ligase) A with T C with G A T C G Parental molecule of DNA Both parental strands serve as templates Two identical daughter molecules of DNA Nucleotides Figure 10.4A

42 When a cell copies a DNA molecule, each strand serves as a template for ordering nucleotides into a new complimentary strand. One at a time, nucleotides line up along the template strand according to the base-pairing rules. The nucleotides are linked to form new strands.

43 Each strand serves as a template (blueprint) for the synthesis of a new strand
DNA polymerase can only work in one direction so each new molecule is made up of an old and a new strand. Since DNA is a very long molecule replication occurs simultaneously at many sites called replication forks the enzyme ligase joins them

44 Errors Errors are made frequently during replication. DNA polymerase may skip a nucleotide or add an extra one or put one in the wrong place. Very few errors remain because a system of enzymes ( repair nuclease) that detect and repair the errors. Those errors that remain are called MUTATIONS

45 Watson and Crick’s model, semiconservative replication, predicts that when a double helix replicates each of the daughter molecules will have one old strand and one newly made strand. Other competing models, the conservative model and the dispersive model, were also proposed. Fig. 16.8 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

46 The first replication in the 14N medium produced a band of hybrid (15N-14N) DNA, eliminating the conservative model. A second replication produced both light and hybrid DNA, eliminating the dispersive model and supporting the semiconservative model. Experiments in the late 1950s by Matthew Meselson and Franklin Stahl supported the semiconservative model, proposed by Watson and Crick, over the other two models. In their experiments, they labeled the nucleotides of the old strands with a heavy isotope of nitrogen (15N) while any new nucleotides would be indicated by a lighter isotope (14N). Replicated strands could be separated by density in a centrifuge. Each model: the semi-conservative model, the conservative model, and the dispersive model, made specific predictions on the density of replicated DNA strands. Fig. 16.9 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

47 Each strand of the double helix
Is oriented in the opposite direction P HO OH A C G T 2 1 3 4 5 5 end 3 end Figure 10.5B

48 Using the enzyme DNA polymerase
The cell synthesizes one daughter strand as a continuous piece The other strand is synthesized as a series of short pieces Which are then connected by the enzyme DNA ligase 3 5 Daughter strand synthesized continuously Daughter strand synthesized in pieces Parental DNA DNA ligase DNA polymerase molecule Overall direction of replication Figure 10.5C

49 Protein synthesis DNA RNA protein

50 THE FLOW OF GENETIC INFORMATION FROM DNA TO RNA TO PROTEIN
The DNA genotype is expressed as proteins, which provide the molecular basis for phenotypic traits The information constituting an organism’s genotype Is carried in its sequence of its DNA bases A particular gene, a linear sequence of many nucleotides Specifies a polypeptide

51 Genetic information written in codons is translated into amino acid sequences
The “words” of the DNA “language” Are triplets of bases called codons The codons in a gene Specify the amino acid sequence of a polypeptide

52 DNA molecule Gene 1 Gene 2 Gene 3 DNA strand Transcription RNA Codon
Translation Polypeptide RNA Amino acid Codon A C G U Gene 1 Gene 2 Gene 3 DNA molecule Figure 10.7

53 The genetic code is the Rosetta stone of life
Nearly all organisms Use exactly the same genetic code Figure 10.8A UUC UGU UGC UGA Stop Met or start Phe Leu Ile Val Ala Thr Pro Ser Asn Lys His Gln Asp Glu Arg Gly Cys Tyr G A C U Third base Second base First base UUA UUU CUC CUU CUG CUA AUC AUU AUG AUA GUC GUU GUG GUA UCC UCU UCG UCA CCC CCU CCG CCA ACC ACU ACA GCC GCU GCG GCA UAC UAU UAG Stop UAA Stop CAC CAU CAG CAA AAC AAU AAG AAA GAC GAU GAG GAA UGG Trp CGC CGU CGG CGA AGC AGU AGG AGA GGC GGU GGG GGA UUG

54 An exercise in translating the genetic code
Figure 10.8B T A C G U Transcription Translation RNA DNA Met Lys Phe Polypeptide Start condon Stop condon Strand to be transcribed

55 Transcription produces genetic messages in the form of RNA
A close-up view of transcription RNA polymerase RNA nucleotides Direction of transcription Template Strand of DNA Newly made RNA T C A G U Figure 10.9A

56 In the nucleus, the DNA helix unzips
And RNA nucleotides line up along one strand of the DNA, following the base pairing rules As the single-stranded messenger RNA (mRNA) peels away from the gene The DNA strands rejoin

57 Transcription of a gene
RNA polymerase DNA of gene Promoter DNA Terminator Area shown In Figure 10.9A Growing RNA Completed RNA polymerase Figure 10.9B 1 Initiation 2 Elongation 3 Termination

58 Eukaryotic RNA is processed before leaving the nucleus
Noncoding segments called introns are spliced out And a cap and a tail are added to the ends Exon Intron Exon Intron Exon DNA Cap Transcription Addition of cap and tail RNA transcript with cap and tail Introns removed Tail Exons spliced together mRNA Coding sequence Nucleus Cytoplasm Figure 10.10

59 Transfer RNA molecules serve as interpreters during translation
Takes place in the cytoplasm

60 A ribosome attaches to the mRNA
And translates its message into a specific polypeptide aided by transfer RNAs (tRNAs) Amino acid attachment site Hydrogen bond RNA polynucleotide chain Anticodon Figure 10.11A

61 Ribosomes build polypeptides
A ribosome consists of two subunits Each made up of proteins and a kind of RNA called ribosomal RNA tRNA molecules mRNA Small subunit Growing polypeptide Large subunit Figure 10.12A

62 The subunits of a ribosome
Hold the tRNA and mRNA close together during translation tRNA-binding sites Large subunit Next amino acid to be added to polypeptide Growing polypeptide tRNA mRNA- binding site mRNA Small subunit Codons Figure 10.12B, C

63 An initiation codon marks the start of an mRNA message
Start of genetic message End Figure 10.13A

64 mRNA, a specific tRNA, and the ribosome subunits
Assemble during initiation Met Initiator tRNA 1 2 mRNA Small ribosomal subunit Start codon Large ribosomal subunit A site U A C A U G P site Figure 10.13B

65 Elongation adds amino acids to the polypeptide chain until a stop codon terminates translation
Once initiation is complete Amino acids are added one by one to the first amino acid

66 Each addition of an amino acid
Occurs in a three-step elongation process Amino acid Polypeptide P site A site Anticodon mRNA Codons 1 Codon recognition mRNA movement Stop codon 2 Peptide bond formation New Peptide bond Figure 10.14 3 Translocation

67 The mRNA moves a codon at a time
And a tRNA with a complementary anticodon pairs with each codon, adding its amino acid to the peptide chain

68 Elongation continues Until a stop codon reaches the ribosome’s A site, terminating translation

69 Review: The flow of genetic information in the cell is DNARNAprotein
The sequence of codons in DNA, via the sequence of codons Spells out the primary structure of a polypeptide

70 Summary of transcription and translation
DNA Transcription     mRNA is transcribed from a DNA template. 1 mRNA RNA polymerase Amino acid Translation      Each amino acid attaches to its proper tRNA with the help of a specific enzyme and ATP. 2 Enzyme ATP tRNA Anticodon       Initiation of polypeptide synthesis The mRNA, the first tRNA, and the ribosomal subunits come together. 3 Initiator tRNA Large ribosomal subunit Start Codon Small ribosomal subunit mRNA New peptide bond forming Growing polypeptide Elongation 4 A succession of tRNAs add their amino acids to the polypeptide chain as the mRNA is moved through the ribosome, one codon at a time. Codons mRNA Polypeptide 5 The ribosome recognizes a stop codon. The poly-peptide is terminated and released. Termination Figure 10.15 Stop codon

71 Mutations can change the meaning of genes
Mutations are changes in the DNA base sequence caused by errors in DNA replication or recombination, or by mutagens C T A Normal hemoglobin Mutant hemoglobin DNA G U Sickle-cell hemoglobin Normal hemoglobin DNA Glu Val mRNA Figure 10.16A

72 Substituting, inserting, or deleting nucleotides alters a gene
With varying effects on the organism Normal gene mRNA Base substitution Base deletion Missing Met Lys Phe Gly Ala Ser Leu His A U G C Protein Figure 10.16B

73 Viral DNA may become part of the host chromosome
MICROBIAL GENETICS Viral DNA may become part of the host chromosome Viruses Can be regarded as genes packaged in protein

74 When phage DNA enters a lytic cycle inside a bacterium
It is replicated, transcribed, and translated The new viral DNA and protein molecules Then assemble into new phages, which burst from the host cell

75 In the lysogenic cycle Much later
Phage DNA inserts into the host chromosome and is passed on to generations of daughter cells Much later It may initiate phage production

76 The AIDS virus makes DNA on an RNA template
HIV, the AIDS virus Is a retrovirus Envelope Glycoprotein Protein coat RNA (two identical strands) Reverse transcriptase Figure 10.21A

77 Inside a cell, HIV uses its RNA as a template for making DNA
To insert into a host chromosome Viral RNA RNA strand Double- stranded DNA Viral RNA and proteins CYTOPLASM NUCLEUS Chromosomal DNA Provirus DNA RNA Figure 10.21B 1 2 3 4 5 6

78 10.22 Bacteria can transfer DNA in three ways
Bacteria can transfer genes from cell to cell by one of three processes Transformation, transduction, or conjugation DNA enters cell Fragment of DNA from another bacterial cell Bacterial chromosome (DNA) Phage Fragment of DNA from another bacterial cell (former phage host) Sex pili Mating bridge Donor cell (“male”) Recipient cell (“female”) Figure 10.22A–C

79 Once new DNA gets into a bacterial cell
Part of it may then integrate into the recipient’s chromosome Recipient cell’s chromosome Recombinant chromosome Donated DNA Crossovers Degraded DNA Figure 10.22D

80 Bacterial plasmids can serve as carriers for gene transfer
Are small circular DNA molecules separate from the bacterial chromosome

81 Plasmids can serve as carriers
For the transfer of genes Plasmids Colorized TEM 2,000 Cell now male Plasmid completes transfer and circularizes F factor starts replication and transfer Male (donor) cell Bacterial chromosome F factor (plasmid) Recombination can occur Only part of the chromosome transfers F factor starts replication and transfer of chromosome Origin of F replication Bacterial chromosome F factor (integrated) Recipient cell Figure 10.23A–C


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