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Remington Grenier, Mercedes Cote, Tyana Nowlan, and Rebecca Isaacs.

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1 Remington Grenier, Mercedes Cote, Tyana Nowlan, and Rebecca Isaacs

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3 Gregor Mendel found his theories of inheritance through experiments with pea plants. It was Mendel’s idea that parents pass discrete genes onto their children that preserve the parents’ identities through the generations. He found that characters, or genetically inherited characteristics that differs from person to person, were what was passed on. For each character, an organism inherits two alleles (different versions of the same gene), one from each parent. Alternative versions of genes account for variations in inherited characters. A trait is any variant of a character, such as blue or yellow color for a flower

4 Law of Segregation One of Mendel’s major hereditary laws. States that: Every organism carries a pair of alleles for each trait The members of this pair separate during gamete formation. Example: If an individual is Bb for eye color, during gamete formation, one gamete would receive a B, and the other would receive a b. Mendel determined his law of segregation while performing monohybrid crosses. Monohybrid Cross: a cross that involves a single character in which both parents are heterozygous (BbxBb).

5 Dominant vs. Recessive If two alleles at a locus differ, then one, the dominant allele (B), determines the organism's appearance. The other, the recessive allele (b), has no noticeable effect on the organism's appearance. Also known as complete dominance. Example: A purple flower that has been crossed with a white flower could either be BB or Bb because the dominant allele (B) would overpower the recessive allele (b).

6 Homozygous vs. Heterozygous Homozygous (pure): an individual is homozygous for a gene if both of the given alleles are the same. Example: BB (homozygous dominant) or bb (homozygous recessive). Heterozygous (hybrid): an individual is heterozygous for a gene if the two alleles are different. Example: Bb

7 Phenotype vs. Genotype Genotype: an organism’s genetic makeup for a given trait. Example: Considering fur color where B represents the allele for brown and b represents the allele for black, the possible genotypes include homozygous brown (BB), heterozygous brown (Bb), and homozygous recessive (bb). Phenotype: the physical expression of the trait associated with a particular genotype. Example: Phenotypes for Mendel’s peas included round or wrinkled, green or yellow, and purple or white flower.

8 Intermediate Inheritance Intermediate inheritance occurred when an individual heterozygous for a trait showered characteristics not exactly like either parent. Two major types of inheritance include incomplete dominance and codominance. Incomplete Dominance: the heterozygous genotype produces an intermediate phenotype rather than the dominant phenotype; neither allele dominates the other. Also known as “blending inheritance” Example: Crossing a snapdragon plant with red flowers with one that has white flowers yields offspring with pink flowers. Codominance: both alleles express themselves fully in a heterozygous organism. Example: Human Blood Groups

9 Other Forms of Inheritance Polygenice Inheritance: a single phenotypic character is affected by two or more genes Example: Skin Color Multiple Alleles: in the whole population, some genes have more than two alleles Example: ABO Blood Group Alleles Epistasis: one gene affects the expression of another Example: Coat Color of Mice Pleiotropy: One gene is able to affect multiple phenotypic characters Example: Sickle-Cell Disease

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11 Trait-Any detectable variant in a genetic character. Hybridization- In genetics, the mating, or crossing, of two true-breeding varieties. P Generation- The parent individuals from which offspring are serived in studies of inheritance; P stands for parental. F1 Generation- The first filial, or hybrid, offspring in a series of genetic crosses. F2 Generation- Offspring resulting from interbreeding of the hybrid F1 generation.

12 Alleles- Any of the alternative versions of a gene that produce distinguishable phenotypic effects. Dominant Allele- An allele that is fully expressed in the phenotype of a heterozygote. Recessive Allele- An allele whose phenotypic effect is not observed on a heterozygote. Homozygous- Having two identical alleles for a given gene. Heterozygous- Having two different alleles for a given gene.

13 Phenotype- The physical and physiological traits of an organism, which are determined by its genetic makeup. Genotype- The genetic makeup, or set of alleles, of an organism. Mono hybrids -An organism that is heterozygous with respect to a single gene of interest. All the offspring from a cross between parents homozygous for different alleles are monohybrids. Dihybrids- An organism that is heterozygous with respect to two genes of interest. All the offspring from a cross between parents doubly jomozygous for different alleles are dihybrids.

14 Complete Dominance- The situation in which the phenotypes od the heterozygote and dominant homozygote are indistinguishable. Incomplete Dominance- The situation in which the phenotype of heterozygotes is intermediate between the phenotypes of individuals homozygous for either allele. Co-dominance- The situation in which the phenotypes of both alleles are exhibited in the heterozygote because both alleles affect the phenotype in separate, distinguishable ways.

15 Pleiotropy- The ability of a single gene to have multiple effects. Epistasis - A type of gene interaction in which one gene alters the phenotypic effects of another gene that is independently inherited. Polygenic Inheritance- An additive effects of two or more genes on a single phenotypic character. Carriers- In genetics, an individual who is heterozygous at a given genetic locus, with one normal allele and one recessive allele. The heterozygote is phenotypically dominant for the character determined by the gene but can pass on the recessive allele to offspring.

16 Chorionic Villus Sampling (CVS)- A technique of prenatal diagnosis in which a small sample of the fetal portion of the placenta is removed and analyzed to detect certain genetic and congenital defects in the fetus.

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18 Chapter 14 Graphic In his garden Mendel bred two different colored flowers. While in the first generation the hybrids were all the same color because they were heterozygous in the F 1 generation. His breeding of the plants also shows that in the F 2 generation they follow the same guidelines that punnett squares do resulting in a 3:1 with heterozygote purple flowers and homozygous recessive white flowers.

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20 Mendelian Inheritance and Chromosome Behavior Meiosis produces haploid gametes with Meiosis 1 including the separation of homologous pairs and crossing over and Meiosis 2 including the separation of sister chromatids. The behavior of chromosomes during meiosis accounts for the law of segregation and independent assortment. This is also known as the chromosome theory of inheritance, which states that Mendelian genes have specific loci along chromosomes and these chromosomes undergo segregation and independent assortment.

21 The Chromosomal Basis of Sex The sex of a organism is an inherited phenotypic character usually determined by which sex chromosomes are present. The sex chromosomes carry genes for some traits that are unrelated to sex characteristics. Example: Recessive alleles causing color blindness are carried on the X chromosome. Fathers transmit this and other sex-linked alleles to all daughters but no sons. Any male who inherits such an allele from his mother will express the trait.

22 X-Inactivation X-inactivation: during the development of the female embryo, one of two X chromosomes in each cell remains coiled as a Barr body whose genes are not expressed. A cell expresses the alleles of the active X chromosome only. Not all cells inactivate the same X. As a result, different cells will have different active X chromosomes.

23 Linkage Linked genes are genes along the same chromosome that tend to be inherited together because the chromosome is passed a long as a unit. Linked genes lie on the same chromosome and do not follow Mendel’s law of independent assortment. Recombinant offspring exhibit new combinations of traits inherited from two parents. Due to the law of independent assortment of chromosomes, unlinked genes show a 50% frequency of recombination in the gametes. Linked genes experience crossing over between nonsister chromatids which accounts for the observed recombinants, which is always less that 50% of the total.

24 Common Disorders Simple recessive disorders in which a person must be homozygous recessive for the gene in question to have the disease include: Tay-Sachs disease: a fatal genetic storage disease that renders the body unable to break down a particular type of lipid. Cystic Fibrosis: a recessive disorder that is the most common lethal genetic disease in the United States. A defective version of a gene on chromosome 7 results in the excessive segregation of a thick mucus, which accumulates in the lungs and digestive tract.

25 Common Disorders (cntd.) Sickle Cell Anemia: a recessive disease caused by the substitution of a single amino acid in the hemoglobin protein of red blood cells, leaving hemoglobin less able to carry oxygen and also causing the hemoglobin to deform to a sickle shape when the oxygen content of the blood is low. Phenylketonuria: an autosomal recessive disease caused by a single gene defect that leaves a person unable to break down phenylalanine, which results in a by-product that can accumulate to toxic levels in the blood and cause mental retardation. Huntington disease: an autosomal dominant degenerative disease of the nervous system that shows itself when a person is in their 30s or 40s and is both irreversible and fatal.

26 Chromosomal Complications A change in the number of chromosomes in the individual structure of chromosomes, such as nondisjunction and aneuploidy, can affect the phenotype. Examples: down syndrome (aneuploidy), trisomy 21 (nondisjunction), and turner syndrome (nondisjunction). The breaking of chromosomes can result in deletions, inversions, duplications, and translocations. Examples: cri-du-chat (deletion) and chronic myelogenous leukemia (chromosomal translocation).

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28 Law of Segregation -Mendel’s first law, stating that the two alleles in a pair segregate into different gametes during gamete formation. Law of Independent Assortment - Mendel’s second law, stating the each pair of alleles segregates, or assorts, independently of each other pair during gamete formation; applies when genes for two characters are located on different pairs of homologous chromosomes.

29 Chromosome theory of inheritance- states that mendillian genes have specific loci along chromosomes and it’s the chromosomes that undergo segregation and independent assortment Wild type- the phenotype for the characteristic most commonly observed in natural populations Sex-linked gene- a gene located on either sex chromosome Duchenne muscular dystrophy- a disease characterized by a progressive weakening of the muscles and loss of coordination Hemophilia- a sex linked disorder defined by the absence of one or more of the protein required for the blood clotting factor

30 Barr body- a dense object lying along the inside of the nuclear envelope in cells of female mammals, representing a highly condensed, inactivated X chromosome Linked genes- genes located close enough together on a chromosome that they tend to be inherited together Genetic recombination- general term for the production of offspring with combinations of traits that differ from those found in either parent Parental types- an offspring with a phenotype that matches on of the parental phenotypes Recombinant types- an offspring whose phenotype differs from that of the parents

31 Crossing over-the reciprocal exchange of genetic material between nonsister chromatids during prophase I of meiosis Genetic map- an ordered list of genetic loci along a chromosome Linked map- a genetic map based on the frequencies of recombination between markers during crossing over of homologous chromosomes Map units-a unit of measurement of the distance between genes

32 Nondisjunction- an error in meiosis or mitosis in which members of a pair of homologous chromosomes or a pair of sister chromatins fail to separate properly from each other Aneuploidy- a chromosomal aberration in which in which one or more chromosomes are present in extra copies or are deficient in number Monosomic- referring to a cell that has only one copy of a particular chromosome instead of the normal two Trisomic-referring to a diploid cell that has three copies of a particular chromosome instead of the normal two

33 Polyploidy-a chromosome alteration in which the organism possesses more than two complete chromosomes sets Deletion- a mutational loss of one or more nucleotide pairs of genes Duplication-An aberration in chromosome structure due to fusion with a fragment from a homologous chromosome, such that a portion of a chromosome is duplicated.

34 Inversion-An aberration in chromosome structure resulting from reattachment of a chromosomal fragment in a reverse orientation to the chromosome from which it originated. Translocation- An aberration in chromosome structure resulting from attachment of a chromosomal fragment to a nonhomologous chromosome. Genomic imprinting-A phenomenon in which expression of an allele in offspring depends on whether the allele is inherited from the male or female parent.

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36 Chapter 15 Graphic The graphic shows Meiosis and how it demonstrates Mendel’s laws exhibited during dihybrid crossing. On one side you see the Law of Segregation which shows that the two alleles for each gene separate during gamete formation. As an example, follow the fate of the long chromosomes (carrying R and r). On the other you see the Law of Independent Assortment which shows that alleles of genes on nonhomologous chromosomes assort independently during gamete formation.

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38 DNA is the Genetic Material Experiments with bacteria and with phages provided the first strong evidence that the genetic material is DNA. Watson and Crick found that DNA is a double helix with two sugar-phosphate backbones. The “rungs” on such a ladder would represent pairs of nitrogenous bases Note that Adenine (A) always pairs with Thymine (T) and Cytosine (C) with Guanine (G).

39 DNA Replication DNA occurs in the S-phase in a semi-conservative fashion and in a 5’ to 3’ direction. Semi-Conservative: the replicated double helix consists of one old strand and one new strand.

40 Steps of DNA Replication 1. Helicase unwinds our double helix into two strands. 2. Polymerase adds nucleotides to an existing strand. Since DNA polymerase can only add DNA in the 5’ to 3’ direction, a leading strand and lagging strand are created. 3. Ligase brings together the Okazaki fragments. 4. Topoisomerase cuts and rejoins the helix. 5. RNA primase catalyzes the synthesis of RNA primers.

41 Proofreading and Repairing DNA DNA polymerases proofread new DNA, replacing incorrect nucleotides. Two repair mechanisms are mismatch repair and nucleotide excision repair. Mismatch Repair: DNA polymerases replace an incorrectly placed nucleotide with the proper nucleotide. Nucleotide Excision Repair: enzymes cut out and replace damaged stretches of DNA.

42 Replicating the Ends of DNA Molecules The ends of eukaryotic chromosomal DNA get shorter with each round of replication. Telomeres postpone the erosion of genes. Telomerase catalyzes the lengthening of telomeres in germ cells.

43 A Chromosome Consists of DNA Packed Together with Proteins Eukaryotic chromatin is composed mostly of DNA, histones, and other proteins. Histones bind to each other and to the DNA to create nucleosomes. Additional folding leads to highly condensed chromatin. In interphase cells, most chromatin is less compacted (euchromatin), but some remain highly condensed (heterochromatin).

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45 Transformation- A change in genotype and phenotype due to the assimilation of external DNA by a cell. Semiconservative Model- Type of DNA replication in which the replicated double helix consists of one old strand, derived from the old molecule, and one newly made strand. Origins of Replication-Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides.

46 Replication Fork-A Y-shaped region on a replicating DNA molecule where the parental strands are being unwound and new strands are growing. Helicases-An enzyme that untwist the double helix of DNA at the replication forks, separating the two strands and making them available as template strands. Single-strand Binding Proteins- A protein that binds to the unpaired DNA strands during DNA replication, stabilizing them and holding them apart while they serve as templates for the synthesis of complementary strands of DNA.

47 Topoisomerase- A protein that breaks, swivels, and rejoins DNA strands. During DNA replication, topoisomerase helps to relieve strain in the double helix ahead of the replication fork. Primer/Primase- An enzyme that joins RNA nucleotides to make the primer using the parental DNA strand as a template. Primer is a short stretch of RNA with a free 3’ end, bound by complementary base pairing to the template strand, that is elongated with DNA nucleotides during DNA replication.

48 DNA Polymerases- An enzyme that catalyzes the elongation of new DNA by the addition of nucleotides to the 3’ end of an existing chain. There are several different DNA polymerases; DNA polymerase III and DNA polymerase I play major roles in DNA replication in prokaryotes. Lagging Strand- A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5’-3’ direction away from the replication fork. Leading Strand-The new complementary DNA strand synthesized continuously along the template strand toward the replication fork in the mandatory 5’-3’ direction.

49 Okazaki Fragments- A short segment of DNA synthesized away from the replication fork on a template strand during DNA replication, many of which are joined together to make up the lagging strand of newly synthesized DNA. Mismatch Repair-The cellular process that uses specific enzymes to remove and replace in correctly paired nucleotides. Nuclease- An enzyme that cuts DNA or RNA either removing one or few bases or hydrolyzing the DNA or RNA completely into its component nucleotides.

50 Nucleotide Excision Repair- A repair system that removes and then correctly replaces a damaged segment of DNA using the undamaged strand as a guide. Telomeres- The tandemly repetitive DNA at the end of a eukaryotic chromosome’s DNA molecule that protects the organism’s genes from being eroded during successive rounds of replication. Telomerase- An enzyme that catalyzes the lengthening of telomeres in eukaryotic germ cells.

51 Heterochromatin-Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed. Euchromatin- The less densed form of eukaryotic chromatin that is available for transcription.

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53 Chapter 16 graphic In DNA replication at the replication fork splits you’ll see replication occurring simultaneously at two forks, one at either end of a replication bubble. Viewing each daughter strand in its entirety, you can see half of it is made continuously as the leading strand, while the other half is synthesized in fragments as the lagging strand.

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55 Evidence from the Study of Metabolic Defects DNA controls metabolism by directing cells to make specific enzymes and other proteins Beadle and Tatum did an experiment with mutant strands showed that the one gene- one enzyme hypothesis was true Genes code for polypeptide chains or for RNA molecules

56 Basic Principles of Transcription and Translation While translation is the informational transfer from nucleotide sequence in RNA to amino acid sequence in a polypeptide, transcription is the nucleotide-to- nucleotide transfer of information from DNA and RNA

57 The Genetic Code Genetic information is encoded as a sequence or codon. A codon is a three-nucleotide sequence of DNA or mRNA that spacifies a particular amino acid or termination signal; the basic unit of the genetic code. A codon must be read in the correct reading frame A reading frame is on an mRNA, the triplet grouping of ribonucleotides used by the translation machinery during polypeptide synthesis.

58 Molecular Components of Transcription RNA synthesis follows the same base-pairing rules as DNA replication, except that in RNA, uracil substitutes for thymine. It is also catalyzed by RNA polymerase. RNA polymerase is an enzyme that links ribonucleotides into a growing RNA chain during transcription.

59 Synthesis of an RNA Transcript There are three stages of transcription. Initiation Elongation Termination Initiation is when promoters signal the initiation of RNA synthesis Elongation is when the transcription factors help eukaryotic RNA polymerase recognize promoter sequences Termination is when the nucleotides signal an end to RNA synthesis

60 Important RNA Transcription Vocabulary A promoter is a specific nucleotide sequence in DNA that binds RNA polymerase, positioning it to start transcribing RNA at the appropriate place. A terminator in bacteria, a sequence of nucleotides in DNA that marks the end of agene and signals RNA polymerase to release the newly made RNA molecule and detach from the DNA. Transcription Factors are regulatory proteins that bind to DNA and affects transcription of specific genes. The transcription initiation complex is t he completed assembly of transcription factors and RNA polymerase bound to a promoter.

61 Alteration of mRNA Ends Eukaryotic mRNA molecules are processed by modification of their ends and by RNA splicing, before leaving the nucleus. The 5’ end receives a modified nucleotide cap, and the 3’ end receives a poly-A tail Poly-A tail is a sequence of 50 to 250 adenine nucleotides added onto the 3’ end of a pre-mRNA molecule. A 5’ cap is a modified form of guanine nucleotide added onto the nucleotide at the 5’ end of a pre-mRNA molecule

62 Split Genes and RNA Splicing In RNA splicing, introns are removed and exons join. RNA splicing usually is carried out by spliceosomes, but in some cases it is alone catalyzes its own splicing. Ribozymes, the catalytic ability of some RNA molecules, derives from the inherent properties of RNA. Alternative RNA splicing is allowed with the presence of introns.

63 Important RNA Splicing Vocabulary Introns are noncoding, intervening sequences within primary transcript that are removed from the transcript during RNA processing; also refers to the region of DNA from which this sequence was transcribed Exons are sequences within a primary transcript that remain in the RNA after RNA processing; also refer to the region of DNA from which this sequence was transcribed. Spliceosomes are a large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons.

64 Molecular Components of Translation Using transfer RNAs a cell translates an mRNA message into protein. After binding, tRNAs line up via their anticodons at complementary codons on mRNA. Ribosomes help facilitate this coupling tRNA is an RNA molecule that functions as an interpreter between the appropriate codons in the mRNA. Anticodons are nucleotide triplets at one end of a tRNA molecule that recognize a particular complementary codon on an mRNA molecule.

65 Building a Polypeptide Ribosomes coordinate the tree stages of peptide bonds between amino acids is catalyzed by rRNA. Ribosomes can translate a single mRNA molecule simultaneously forming a polyribosome rRNA is the most abundant type of RNA, which together with proteins makes up ribosomes.

66 Completing and Targeting the Functional Protein Modifications to protein after translation can affect their three dimensional shape. Proteins destined from the endomembrane system or for secretion are transported into the ER. These proteins have a signal peptide to which a signal-recognition particle binds, enabling the translation ribosome to bind to the ER.

67 Types of Mutations There are several different types of mutations including Point mutations-A change in a gene at a single nucleotide pair. Missense mutations- A base-pair substitution that results in a codon that codes for a different amino acid. Nonsense mutations- A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein Frame shift mutation- A mutation occurring when the number of nucleotides inserted or deleted is not a multiple of three, resulting in the improper grouping of the subsequent nucleotides into codons.

68 Important Mutation Vocabulary Insertion is a mutation involving the addition of one or more nucleotide pairs to a gene. Deletion is a mutational loss of one or more nucleotide pairs from a gene.

69 Mutagens Spontaneous mutations can occur during DNA replication, recombination, or repair. DNA damage that can alter a gene is caused by chemical and physical mutagens A mutagen is a chemical or physical agent that interacts with DNA and causes a mutation.

70 Comparing Gene Expression in Bacteria, Archaea, and Eukarya Translation can begin while transcription is still in progress because bacterial cells lack a nuclear envelope. The nuclear envelope seperates transcription from translation, and extensive RNA processing occurs in the nucleus in a eukaryotic cell. Archaeal cells show similarities to both eukaryotic and bacterial cells in their processes of gene expression

71 What Is a Gene? A gene is a region of DNA whose final functional product is either a polypeptide or an RNA molecule

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73 Gene Expression- The process by which DNA directs the synthesis of proteins or, in some cases, just RNAs. Transciption- The synthesis of RNA using a DNA template. Messenger RNA (mRNA)- A type of RNA, sythesized using adna template, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein.

74 Translation- The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of “language” from nucleotides to amino acids. Primary Transcript- an initial RNA transcript; also called pre-mRNA when transcribed from a protein-coding gene. Triplet Code- A set of three-nucleotide-long words that specify the amino acids for polypeptide chains. Template Strand- The DNA strand that provides the pattern, or template for ordering the sequence of nucleotides in an RNA transcript.

75 TATA Box- A DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex. RNA Processing- Modification of RNA transcripts, including splicing out of introns, joining together of exons, and alteration of the 5’ and 3’ ends. RNA Splicing- After synthesis of a eukaryotic primary RNA transcript, the removal of portions of the transcript that will not be included in the mRNA.

76 Ribozymes- An RNA molecule that functions as an enzyme, catalyzing reactions during RNA splicing. Alternative RNA Splicing- A type of eukaryotic gene regulation at the RNA-processing level in which different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns. Wobble- Flexibility in the base-pairing rules in which the nucleotide at the 5’ end of a tRNA anticodon can form hydrogen bonds with more than one kind of base in the third position of a codon.

77 P Site- One of a ribosome’s three binding sites for tRNA during translation. The P-site holds the tRNA carrying the growing polypeptide chain. A Site- One of a ribosome’s three binding sites for tRNA during translation. The A site holds the tRNA carrying the next amino acid to be added to the polypeptide chain. E Site- One of a ribosome’s three binding sites for tRNA during translation. The E site is the place where discharged tRNAs leave the ribosome.

78 Signal Peptide- A sequence of about 20 amino acids at or neat the leading end of a polypeptide that targets it to the endoplasmic reticulum or other organelles in a eukaryotic cell. Signal-Recognition Particle (SRP)- A protein-RNA complex that recognizes a signal peptide as it emerges from a ribosomes and helps direct the ribosome to the endoplasmic reticulum by binding to a receptor protein on the ER.

79 Base-Pair Substitution- A type of point mutation; the replacement of one nucleotide and its partner in the complementary DNA strand by another pair of nucleotides.

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81 Chapter 17 Graphic The diagram show the path from one gene to one polypeptide. In the first step of translation, RNA is copied from a DNA template. Next, in RNA processing, the pre-mRNA goes through splicing, 5-capping, and 3-polyadenylation by which it is converted into mature mRNA. This mature mRNA then proceeds to exit the nucleus and attach itself to a ribosome. In amino acid activation, amino acids are attached to their corresponding tRNA with the assistance of aminoacyl-tRNA synthetase (an enzyme) and ATP. In the last step (translation), a sequence of tRNAs give their amino acids to the polypeptide chain while mRNA moves through the ribosome. After the mRNA has completely moved through the ribosome, the polypeptide is released.

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83 Operons: The Basic Concept Cells control metabolism by regulating enzyme activity or the expression of genes coding for enzymes. Genes are often clustered into operons, with one promoter serving several adjacent genes, in bacteria. An operator site on the DNA turn the operon off and on. An operon is a unit of genetic function found in bacteria and phages, ting of a promoter, an operator, and a coordinately regulated cluster of genes whose products function in a common pathway. An operator is a sequence of nucleotides near the start of an operon to which an active repressor can attach. The binding of the repressor prevents RNA polymerase from attaching to the promoter and transcribing the genes of the operon.

84 Repressible and Inducible: Two Types of Negative Gene Regulation In a repressible operon, the repressor is active when bound to a corepressor, usually the end product of an anabolic pathway. In an inducible operon, binding of an inducer to an innately active repressor inactivates the repressor and turns on transcription. Usually functions in a catabolic pathway. Both types of operons bind to a specific repressor protein to the operator shuts off transcription

85 Negative Gene Regulation Vocabulary A repressor is a protein that inhibits gene transcription. In prokaryotes, repressors bind to the DNA in or near the promoter. In eukaryotes, repressors may bind to control elements within enhancers, to activators, or to other proteins in a way that blocks activators from binding to DNA. Corepressor is a small molecule that binds to a bacterial repressor protein and changes its shape, allowing it to switch an operon off

86 Positive Gene Regulation Some operons are subjected to positive control via stimulatory activator protein A regulatory gene is a gene that codes for a protein, such as a repressor, that controls the transcription of another gene or group of genes

87 Eukaryotic Gene Expression can be Regulated at any Stage Chromatin Modification Genes in highly compacted chromatin are generally not transcribed Histone Acetylation seems to loosen chromatin structure, enhancing transcription DNA methylation generally reduces transcription Transcription Regulation of transcription initiation; DNA control elements bind specific transcription factors Coordinate regulation

88 Eukaryotic Gene Expression can be Regulated at any Stage (cnt.) RNA processing Alternative RNA splicing mRNA degradation Each mRNA has a characteristic life span Translation Initiation of translation can be controlled via regulation of initiation factors Protein processing and degradation Protein processing and degradation by proteasomes are subject to regulation

89 Noncoding RNAs play multiple roles in controlling gene expression Chromatin modification Small RNAs can promote the formation of heterochromatin in certain regions, blocking transcription Translation miRNA or siRNA can block the translation of specific mRNAs mRNA degradation They can target specific mRNAs for destruction

90 A Genetic Program for Embryonic Development Embryonic cells undergo differentiation, becoming specialized in structure and function

91 Sequential Regulation of Gene Expression During Cellular Differentiation Differentiation is heralded by the appearance of tissue-specific proteins, which enable differentiation cells to carry out their specialized roles

92 The Multistep Model of Cancer Development Normal cells are converted to cancer cells by the accumulation of mutations affecting proto-oncogenes and tumor-suppressor genes

93 Inherited Predisposition and Other Factors Contributing to Cancer Individuals who inherit a mutant oncogene or tumor- suppressor allele have an increased risk of developing cancer. Certain viruses promote cancer by integration of viral DNA into a cells genome

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95 Inducer- A specific small molecule that binds to a bacterial repressor protein and changes the repressor’s shape so that it cannot bind to an operator, thus switching an operon in. Cyclic AMP (cAMP)- A ring-shaped molecule made from ATP that is a common intracellular signaling molecule in eukaryotic cells. Activator- A protein that binds to DNA and stimulates gene transcription. In prokaryotes, activators bind in or near the promoter; in eukaryotes, activators bind to control elements in enhancers.

96 Histone Acetylation- The attachment of acetyl groups to certain amino acids of histone proteins. Genomic Imprinting- A phenomenon in which expression of an allele in offspring depends on whether the allele is inherited from the male or female parent. Epigenetic Inheritance- Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence of a genome. Control Elements- A segment of noncoding DNA that helps regulate transcription of a gene by binding a transcription factor. Multiple control elements are present in a eukaryotic gene’s enhancer.

97 Enhancers- A segment of eukaryotic DNA containing multiple control elements, usually located far from the gene whose transcription it regulates. Proteasomes- A giant protein complex that recognizes and destroys proteins tagged for elimination by the small protein ubiquitin. MicroRNAs (miRNAs)- A small, single-stranded RNA molecule, generated from a hairpin structure on a precursor RNA transcribed from a particular gene. The miRNA associates with one or more proteins in a complex that can degrade or prevent translation of an mRNA with a complementary sequence.

98 RNA Interference (RNAi)- A technique used to silence the expression of selected genes. RNAi uses synthetic double- stranded RNA molecules that match the sequence of a particular gene to trigger the breakdown of the gene’s messenger RNA. Small Interfering RNAs (siRNAs)- A small, single- stranded RNA molecule generated by cellular machinery from a long, double-stranded RNA molecule. The siRNA associates with one or more proteins in a complex that can degrade or prevent translation of an mRNA with a complementary sequence. In some cases, siRNA can also block transcription by promoting chromatin modification.

99 Cell Differentiation- The structural and functional divergence of cells as they become specialized during a multicellular organism’s development. Cell differentiation depends on the control of gene expression. Cytoplasmic Determinants- A maternal substance, such as a protein or RNA, placed into an egg that influences the course of early development by regulating the expression of genes that affect the development fate of cells. Induction- The process in which one group of embryonic cells influences the development of another, usually by causing changes in gene expression.

100 Determination- The progressive restriction of developmental potential in which the possible fate of each cell becomes more limited as an embryo develops. Pattern Formation- The development of a multicellular organism’s spatial organization, the arrangement of organs and tissues in their characteristic places in three- dimensional space. Positional Information- Molecular cues that control pattern formation in an animal or plant embryonic structure by indicating a cell’s location relative to the organism’s body axes. These cues elicit a response by genes that regulate development

101 Homeotic Genes- Any of the master regulatory genes that control placement and spatial organization of the body parts in animals, plants, and fungi by controlling the developmental fate of groups of cells. Embryonic Lethals- A mutation with a phenotype leading to death of an embryos. Maternal Effect Gene- a gene that, when mutant in the mother, results in a mutant phenotype in the offspring, regardless of the offspring’s genotype. Egg-Polarity Genes A gene that helps control the orientation of the egg.

102 Bicoid- A maternal effect gene that codes for a protein responsible for specifying the anterior end in Drosophila. Morphogens- A substance, such as Bicoid protein in Drosophila, that provides positional information in the form of a concentration gradient along an ambryonic axis. Oncogenes- A gene found in viral or cellular genomes that is involved in triggering molecular events that can lead to cancer. Proto-Oncogenes- A normal cellular gene that has the potential to become an oncogene.

103 Tumor-Suppressor Genes- A gene whose protein product inhibits cell division, thereby preventing the uncontrolled cell growth that contributes to cancer. Ras Gene- A gene that codes for Ras ultimately resulting in stimulation of the cell cycle. P53 Gene- A tumor- suppressor gene that codes for a specific transcription factor that promotes the synthesis of cell cycle- inhibiting proteins.

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105 Chapter 18 Graphic The diagram shows a simplified overview of gene structure and expression. A protein-coding gene is defined by the extent of the primary transcript. The gene is first transcribed to yield a primary transcript, which is processed to remove the introns. The mature transcript (mRNA) is then translated into a sequence of amino acids, which defines the protein.

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107 The Discovery of Viruses Researchers discovered viruses in the late 1800s by studying a plant disease

108 Structures of Viruses A virus is a small nucleic acid genome enclosed in a protein capsid and sometimes a membranous envelope containing viral proteins that help viruses enter cells A capsid is the protein shell that encloses a viral genome. It may be rod- shaped, ployhedral, or more complex in shape

109 General Features of Viral Reproductive Cycles Viruses use enzymes, ribosomes, and small molecules of host cells to synthesize progeny viruses. Each type of virus has a characteristic host range

110 Reproductive Cycles of Phages Phages can reproduce by two alternative mechanisms Lytic cycle Virulent or temperate phage Destruction of host DNA Production of new phages Lysis of host cell causes release of progeny phages Lysogenic cycle Temperate phage only Genome integrates into bacterial chromosome as prophage, which is replicated and passed on to daughter cells and can be induced to leave the chromosome and initiate a lytic cycle

111 Reproductive Cycle of Animal Viruses Many animal viruses have an envelope. Retroviruses use the enzyme reverse transcriptase to copy their RNA. The Viral Envelope is membrane that cloaks the capsid that in turn encloses a viral genome

112 Evolution of Viruses Since viruses can reproduce only within cells, they probably evolved after the first cells appeared. Perhaps as packaged fragments of cellular nucleic acid. The origin of viruses is still being debated

113 Viral Diseases in Animals Symptoms may be caused by direct viral harm to cells or by the body’s immune response. Vaccines stimulate the immune system to defend the host against specific viruses

114 Emerging Viruses Outbreak of new viral diseases in humans is usually caused by existing viruses that expand their host territory

115 Viral Disease in Plants Viruses enter plant cells through damaged cell walls or are inherited by the parents

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117 Bacteriophages (phages)- A virus that infects bacteria; also called a phages Host range- The limited range of host cells that each type of virus can infect. Virulent phage- A phage that reproduces only by a lytic cycle Restriction enzymes- An endonuclease that recognizes and cuts DNA molecules foreign to a bacterium. The enzyme cuts at specific nucleotide sequences.

118 Temperate phages- A phage that is capable of reproducing by either a lytic or lysogenic cycle. Lysogenic cycle- A type of phage reproductive cycle in which the viral genome becomes incorporated into the bacterial host chromosome as a prophage and does not kill the host. Prophage- A phage genome that has been inserted into a specific site on a bacterial chromosome.

119 Retroviruses- An RNA virus that reproduces by certain viruses that uses RNA as a template for DNA synthesis. Reverse transcriptase- An enzyme encoded by certain viruses that uses RNA as a template for DNA synthesis. HIV- The infectious agent that causes Aids. HIV is a retrovirus. AIDS- The symptoms and signs present during the late stages of HIV infection, defined by a specified reduction in the determines which competitor gains access to a resource, such as food or mates.

120 Provirus- A viral genome that is permanently inserted into the host genome. Epidemic- A general outbreak of a disease Pandemic- A global epidemic. Viroids- Plant pathogen consisting of a molecule of naked, circular RNA a few hundred nucleotides long. Prions- An infectious agent that is a misfolded version of a normal cellular protein. Appear to increase in number by converting correctly folded versions of the protein to more prions.

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122 Chapter 19 graphic In the lytic cycle, the phage attaches to the host cell and injects its DNA. The host cell's enzymes and synthesis organelles make copies of the viral DNA and viral proteins. The viral proteins and nucleic acids then assemble themselves inside the host cell, making many copies of the original infecting virus. The host cell then bursts open, releasing hundreds of new viruses. These offspring infect new host cells and repeat the cycle. In the lysogenic cycle, a virus injects its genes into the host. The viral DNA then adds itself directly to the host cell's DNA. Each time the host cell reproduces, the viral DNA is copied along with the host's DNA. Occasionally, the viral DNA separates from the host DNA and starts a lytic cycle. New phages are then made and released.

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124 Genetics of Plants Lab This laboratory involves breeding Wisconsin Fast Plants (Brassica rapa) to apply the principles of genetics and heredity you have learned. By growing and pollinating the plants to produce offspring, you be able to determine what kind of inheritance patterns certain genes displayed. Genetic Ratios: Monohybrid Cross: 3:1 Dihybrid Cross: 9:3:3:1 Epistasis: 9:4:3 Linked Genes: 1:1 Linked Genes, with some Crossover: 4:4:1:1

125 Genetics of Plants Lab For the AP exam, you must know how to do chi-square analysis to evaluate the results of your genetic crosses. A chi-square test is used to determine if your results conform to the expected Mendelian frequencies. If your observed frequencies do not match your expected frequencies, some nonrandom mating or even crossover may be occurring. Formula for Chi-Square Test:

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127 1. What does Mendel use for his heredity experiments? A. Lavender B. Lilies C. Pea plants D. Mice E. Cats

128 2. What were the laws that Mendel created? A. Law of Gravity and Law of Segregation B. Law of Segregation and Law of Independent Assortment C. Law of Gravity and Law of Independent Assortment D. Law of Heredity and Law of Genetics

129 3.When using a punnett square, there are letters used to tell the genotype of the cross, what is the combination that shows homozygous recessive? A. PP B. pp C. pPp D. Pp E. pP

130 4. Some diseases cause multiple symptoms, what is this called? A. Genetics B. Science C. Hunger D. Pleiotrophy

131 5. What is the best thing you can do to be sure if your child has a chance of having a genetic disorder? A. Try and the find out B. Get genetic counciling C. Do not do anything D. Ask a friend

132 6. Which is not a genetic disorder? A. Cystic fibrosis B. The flu C. Sickle-cell disease D. Huntington’s disease

133 7. What does the heterozygous genotype look like? A. pp B. PP C. Pp D. None of these

134 8. What is a dihybrid? A. An individual that is heterozygous for two characters B. The phenotype C. A bird that dies

135 9. What did Morgan use in his experiments? A. Mice B. Pea plants C. Birds D. Fruit flies

136 10. What chromosome(s) is considered part of the sex-linked gene(s) A. 12 and 22 B. X and 15 C. X and Y D. 9 and 4

137 11. What is not a sex-linked gene disorder? A. Muscular dystrophy B. The common cold C. Hemophilia D. All of the above

138 12. What is it called when the members of a pair of homologous chromosomes do not move apart properly during meiosis I? A. Aneuploidy B. Trisomic C. Polyploidy D. Nondisjunction

139 13. What causes Down Syndrome? A. An extra chromosome B. Translocation C. Birth D. None of the above

140 14. Errors in meiosis or damaging agents such as radiation can cause ___________ of a chromosome? A. Creation B. Entry C. Breakage D. Nothing E. Lifting

141 15. Where are most imprinted genes located at? A. The brain B. Chromosomes C. Autosomes D. In the ear E. In the heart

142 16. _________ of the eukaryotic cell's genes are located on nuclear chromosomes. Or even in the nucleus. A. All B. None C. 3 D. 10 E. Not all

143 17. Who proposed that DNA was in the shape of a double helix A. Watson and Crick B. Mendel C. Morgan D. Franklin

144 18. Who showed that genes are located along chromosomes? A. Mendel B. Crick C. Watson D. Franklin E. Morgan

145 19. Griffith discovered what phenomenon? A. Gravity B. Mice C. Transformation D. Heredity E. Genes

146 20. How do viruses reproduce? A. They just do B. They take over a cell C. Replicate like DNA D. They don’t

147 21. What led to Watson and Crick’s discovery that DNA is a double helix? A. Viruses B. Mendel C. An x-ray D. Mice

148 22. Who created the x-ray crystallography of DNA A. Mendel B. Crick C. Watson D. Franklin E. Morgan

149 23. In DNA there are 4 nitrogenous bases, adenine (A), thymine (T), guanine (G), and cytosine ( C), what pairs up with what? A. A-C and T-G B. C-T and A-G C. A-T and C-G D. A-U and G-C

150 24. Meselson and Stahl discovered that DNA replication follows what model? A. Conservative B. Semi-conservative C. Dispersive model D. M and S model

151 25. The special sites where DNA replication begins are called_________. A. Starting sites B. Origins of replication C. Replication D. DNA site

152 26. What unwinds the parental double helix at replication forks? A. Primase B. DNA ligase C. Helicase D. Topisomerase E. Single-strand binding protein

153 27. ________ inherited by an organism leads to specific traits by dictating the synthesis of proteins and RNA molecules involved in protein synthesis. A. DNA B. RNA C. Ligase D. Genes E. Cells

154 28. Who demonstrated the relationship between genes and enzymes? A. Beadle and Tatum B. Mendel C. Garrod D. Weaver E. Watson and Crick

155 29. _________ proteins are enzymes. A. None B. Not all C. All D. None of the above

156 30. What type of RNA carries a genetic message from the DNA to protein- synthesizing machinery? A. tRNA B. rRNA C. RNA D. mRNA E. DNA

157 31. What is an example of a triplet code? A. LMN B. 123 C. KDES D. F4D E. AGT

158 32. When translating mRNA codons, what is the starting codon? A. GUG B. ACA C. AUG D. GUU E. CUG

159 33. In what direction can RNA polymerase assemble a polynucleotide? A. 3’ to 5’ B. 6’ to 2’ C. 5’ to 3’ D. Up E. Right

160 34. What are the RNA molecules that function as enzymes? A. Ribosomes B. Proteins C. DNA D. tRNA E. rRNa

161 35. What is considered the ultimate source of new genes? A. DNA B. RNA C. Proteins D. Mutations E. None of the above

162 36. Which component is NOT directly involved in translation? A. mRNA B. Ribosomes C. DNA D. GTP E. tRNA

163 37. The operon can be switched off by a protein called what? A. Enzymes B. RNA C. DNA D. Operator E. Repressor

164 38. Inducible enzymes synthesis induced by __________. A. Natural signal B. Chemical signal C. RNA D. Proteins

165 39. What hypothesis proposes that specific combinations of modifications help determine the chromatin configuration? A. Epigenetic inheritance B. Genomic imprinting C. Histone acetylation D. None of the above

166 40. To initiate transcription, eukaryotic RNA polymerase requires the assistance of what proteins? A. Histones B. Transcription factors C. Enhancers D. Inducers

167 41. To initiate transcription, eukaryotic RNA polymerase requires the assistance of what proteins? A. Chemical signals B. Viruses C. mRNA D. Histones E. Inducers

168 42. Regulation by noncoding RNAs is known to occur at what two points in the pathway of gene expression? A. mRNA translation B. Chromation configuration C. tRNA translation D. Both A and B E. Both B and C

169 43. The zygote gives rise to a large number of cells through a succession of what? A. Mitosis B. Transcription C. Morphogenesis D. Mitotic cell division

170 44. One important source of information in early development is the egg's cytoplasm because it contains both RNA and proteins encoded with the mother's ____________. A. RNA B. DNA C. Cells D. miRNA E. Ribosomes

171 45. Pattern formation in animals begins in the ________ stage. A. Fetus B. Adult C. Early embryo D. Early child E. Mid-life

172 46. ____________ contains double- stranded DNA, single-stranded DNA, double-stranded RNA, or single-stranded RNA. A. Bacteria B. Viruses C. Histones D. Prokaryotes

173 47. Bacteriophages have the most complex capsids and infec what? A. Bacteria B. Liver C. Other viruses D. DNA E. RNA

174 48. A phage reproductive cycle that culminates in death of the host cell is known as the what? A. Reproductive cycle B. Virus cycle C. Host-death cycle D. Life cycle E. Lytic cycle

175 49. What are the RNA animal viruses with the most complicated reproductive cycle? A. Bacteriophages B. Tobacco mosaic virus C. Retrovirus D. Influenza viruses

176 50. A vaccine is a __________ variant or derivative of a pathogen that stimulates the immune system to mount defenses against the harmful pathogen. A. All harmful B. All harmless C. Can be a bit harmful D. Pleasant

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178 1. C 2. B 3. B 4. D 5. B 6. B 7. C 8. A 9. D 10. C

179 11. B 12. D 13. A 14. C 15. C 16. E 17. A 18.E 19. C 20. B

180 21. C 22. D 23. C 24. B 25. B 26. C 27. A 28. A 29. B 30. D

181 31. E 32. C 33. C 34. A 35. D 36. C 37. E 38. B 39. C 40. B

182 41. A 42. D 43. D 44. B 45. C 46. B 47. A 48. E 49. C 50. B

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184 Free Response #1 1. In Order to perform DNA replication and Repair, many proteins must work together A. Explain the function of each of the following proteins in DNA replication Helicase Primase DNA Polymerase I DNA Ligase Single-strand Binding Protein B. Nuclear exccision repair is a type of DNA repair system. List and explain the steps that the cell must perform to complete this repairing system. C. When replicating the ends of DNA molecules, telomeres play a large role. Discuss the importance of telomeres in DNA replication.

185 Free Response #2 2. In humans, hemophilia is caused by an X-linked recessive gene that prevents blood from correctly clotting. Suppose a normal man reproduces with a female whose father was a hemophiliac. With this information, answer the following questions (draw punnett squares to support your answer) questions on next slide.

186 Free Response #2 (cntd.) A. What are the possible genotypes of the female’s mother B. What are the chances that the male and female’s first child will be a hemophiliac male? C. Of the girls produced, what percentage will be carriers? D. If the couple has two sons and two daughters, what are the chances that both sons will be hemophiliacs and both daughters will be carriers

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188 Free Response Answer #1 1. A.) In DNA replication there are many different and important proteins that play a role in the process. Helicase is an enzyme that untwists the double helix of DNA at the replication forks, separating them and making them available to be template strands. Primase is an enzyme that joins RNA nucleotides to make the primer using the parental DNA strand as a template. The DNA polymerase I is an enzyme that catalyzes elongation of new DNA by adding nucleotides to the 3’ end of an existing chain. DNA ligase is a linking enzyme that catalyzes the covalent bonding if the 3’ end on one DNA fragment to the 5’ end of another DNA fragment. The single-strand binding protein is a protein that binds to the unpaired DNA stands during DNA replication stabilizing them and holding them apart while they serve as templates for the synthesis of complementary strands of DNA.

189 Free Response Answer #1 (cntd.) B.) 1. A thymine dimmer distorts the DNA molecule. 2. A nuclease enzyme cuts the damaged DNA strand at two points and the damaged section is removed 3. Repair synthesis by a DNA polymerase fills in the missing nucleotides 4. DNA ligase seals the free end of the new DNA to the old DNA, making the strand complete C.) The telomere keeps an organism’s genes from being eroded while it goes through successive rounds of replication.

190 Free Response Answer #2 2. A.) The female could either have a mother who was heterozygous for the trait of hemophilia or she could have a mother who was homozygous dominant. You can determine this because a female who are homozygous recessive for the trait of hemophilia won’t survive to give birth. B.) X h Y X H X H X h X H Y X h X h X h X h Y Because the female is a carrier for the trait there’s a 1 in 4 chance of having a male hemophiliac as a first child.

191 Free Response Answer #2 (cntd.) C.) Of the two girls that could potentially be produced one would be a carrier, 25% of the total possibilities 50% of the possible females. The other female would be a hemophiliac and, therefore, wouldn’t survive past puberty. D.) Because there’s a 25% chance the couple could have a son with hemophilia and a 25% chance that they have a daughter who’s a carrier of the trait. The chances that they have two sons who are hemophiliacs and two daughters who carry the trait is 1 in 256 or.4%.


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