GTS 251 Textbook Summary genetics conceptual approach PDF

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Study Unit 1Chapter 10 : The Chemical Nature of the GeneConcepts Ch▪ The genetic material must carry large amounts of information, replicate faithfully, express its coding instructions as phenotypes, and have the capacity to vary. ▪ Details of the structure of DNA were worked out by a number of scie...

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Study Unit 1 Chapter 10: The Chemical Nature of the Gene Concepts Ch10 ▪ ▪

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The genetic material must carry large amounts of information, replicate faithfully, express its coding instructions as phenotypes, and have the capacity to vary. Details of the structure of DNA were worked out by a number of scientists. At first, DNA was interpreted as being too regular in structure to carry genetic information, but by the 1940s, DNA from different organisms was shown to vary in its base composition. The process of transformation indicates that some substance—the transforming principle —is capable of genetically altering bacteria. Avery, MacLeod, and McCarty demonstrated that the transforming principle is DNA, providing the first evidence that DNA is the genetic material. Using radioactive isotopes, Hershey and Chase traced the movement of DNA and protein during phage infection of bacteria. They demonstrated that DNA, not protein, enters the bacterial cell during phage reproduction and that only DNA is passed on to progeny phages. By collecting existing information about the chemistry of DNA and building molecular models, Watson and Crick were able to discover the three-dimensional structure of the DNA molecule. RNA serves as the genetic material in some viruses. The primary structure of DNA consists of a string of nucleotides. Each nucleotide consists of a five-carbon sugar, a phosphate group, and a nitrogenous base. There are two types of DNA bases: purines (adenine and guanine) and pyrimidines (thymine and cytosine). The nucleotides of DNA are joined into polynucleotide strands by phosphodiester bonds that connect the 3′-carbon atom of one nucleotide to the 5′-phosphate group of the next. Each polynucleotide strand has polarity, with a 5′ end and a 3′ end. DNA consists of two polynucleotide strands. The sugars and phosphate groups of each polynucleotide strand are on the outside of the molecule, and the bases are in the interior. Hydrogen bonding joins the bases of the two strands: guanine pairs with cytosine, and adenine pairs with thymine. The two polynucleotide strands of a DNA molecule are complementary and antiparallel. DNA can assume different secondary structures, depending on the conditions in which it is placed and on its base sequence. B-DNA is thought to be the most common configuration in the cell. In DNA and RNA, base pairing between nucleotides on the same strand produces special secondary structures such as hairpins. Triple-stranded DNA structures can arise when a single strand of DNA pairs with double-stranded DNA. Methyl groups may be added to certain bases in DNA. Both prokaryotic and eukaryotic DNA can be methylated. In eukaryotes, cytosine bases are most often methylated to form 5-methylcytosine, and methylation is often related to gene expression.

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Genetic material must contain complex information, be replicated accurately, code for the phenotype, and have the capacity to vary. Evidence that DNA is the source of genetic information came from the finding by Avery, MacLeod, and McCarty that transformation depends on DNA and from the demonstration by Hershey and Chase that viral DNA is passed on to progeny phages. James Watson and Francis Crick, using data provided by Rosalind Franklin and Maurice Wilkins, proposed a model for the three-dimensional structure of DNA in 1953. The results of experiments with tobacco mosaic virus showed that RNA carries genetic information in some viruses. A DNA nucleotide consists of a deoxyribose sugar, a phosphate group, and a nitrogenous base. An RNA nucleotide consists of a ribose sugar, a phosphate group, and a nitrogenous base. The bases of a DNA nucleotide are of two types: purines (adenine and guanine) and pyrimidines (cytosine and thymine). RNA contains the pyrimidine uracil instead of thymine.

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Nucleotides are joined together by phosphodiester linkages to form a polynucleotide strand. Each polynucleotide strand has a free phosphate group at its 5′ end and a free hydroxyl group at its 3′ end. DNA consists of two nucleotide strands that wind around each other to form a double helix. The sugars and phosphates lie on the outside of the helix, and the bases are stacked in the interior. The two strands are joined together by hydrogen bonding between bases in each strand. The two strands are antiparallel and complementary. DNA molecules can form a number of different secondary structures, depending on the conditions in which the DNA is placed and on its base sequence. The structure of DNA has several important genetic implications. Genetic information resides in the base sequence of DNA, which ultimately specifies the amino acid sequence of proteins. Complementarity of the bases on DNA’s two strands allows genetic information to be replicated. The central dogma of molecular biology proposes that information flows in a one-way direction, from DNA to RNA to protein. Exceptions to the central dogma are now known. Pairing between bases on the same nucleotide strand can lead to hairpins and other special secondary structures. DNA may be modified by the addition of methyl groups to the nitrogenous bases.

Study Unit 1 Chapter 11: Chromosome Structure and Organelle DNA Concepts Ch11 ▪ ▪

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Chromosomal DNA exists in the form of very long molecules that are tightly packed to fit into the small confines of a cell. Overrotation or underrotation of a DNA double helix places strain on the molecule, causing it to supercoil. Supercoiling is controlled by topoisomerase enzymes. Most cellular DNA is negatively supercoiled, which eases the separation of nucleotide strands during replication and transcription and allows the DNA to be packed into small spaces. A typical bacterial chromosome consists of a large, circular molecule of DNA that forms a series of twisted loops. Within the cell, bacterial DNA appears as a distinct clump, called the nucleoid. Chromatin, which consists of DNA complexed with proteins, is the material that makes up eukaryotic chromosomes. The most abundant of these proteins are the five types of positively charged histone proteins: H1, H2A, H2B, H3, and H4. Variant histones may at times be incorporated into chromatin in place of the normal histone types. The nucleosome consists of a core particle of eight histone proteins and the DNA that wraps around them. A single H1 histone associates with each core particle. Nucleosomes are separated by linker DNA. Nucleosomes fold to form a 30nm chromatin fiber, which appears as a series of loops that pack to create a 250-nm fiber. Helical coiling of the 250nm fiber produces a chromatid. Epigenetic changes are alterations of chromatin or DNA structure that do not include changes in the base sequence but are stable and passed on to descendant cells or organisms. Some epigenetic changes result from alterations of chromatin structure. The centromere is a region of the chromosome to which spindle microtubules attach. Centromeres display considerable variation in their DNA sequences and are distinguished by epigenetic alterations to chromatin structure, including the use of a variant H3 histone in the nucleosome. A telomere is the stabilizing end of a chromosome. At the end of each telomere are many short telomeric sequences. Eukaryotic DNA comprises three major classes: unique-sequence DNA, moderately repetitive DNA, and highly repetitive DNA. Unique-sequence DNA consists of sequences that exist in one or a few copies; moderately repetitive DNA consists of sequences that may be several hundred base pairs in length and are present in thousands to hundreds of thousands of copies. Highly repetitive DNA consists of very short sequences repeated in tandem and is present in hundreds of thousands to millions of copies. The density of genes varies greatly among and even within chromosomes. Mitochondria and chloroplasts are membrane-bounded organelles of eukaryotic cells that generally possess their own DNA. The well-supported endosymbiotic theory proposes that these organelles began as free-living bacteria that developed stable endosymbiotic relations with early eukaryotic cells.

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In most organisms, genes encoded by mtDNA and cpDNA are inherited from a single parent. A cell may contain more than one distinct type of mtDNA or cpDNA; in these cases, replicative segregation of the organelle DNA may produce phenotypic variation within a single organism, or it may produce different degrees of phenotypic expression among progeny. The mitochondrial genome consists of circular DNA with no associated histone proteins, although it is complexed with other proteins that have some histone-like properties. The sizes and structures of mtDNA differ greatly among organisms. Human mtDNA exhibits extreme economy, but mtDNAs found in yeast and flowering plants contain many noncoding nucleotides and repetitive sequences. In most flowering plants, mitochondrial DNA is large and typically has one or more large direct repeats that can recombine to generate smaller or larger molecules. All mtDNA appears to have evolved from a common bacterial ancestor, but the patterns of evolution seen in different mitochondrial genomes vary greatly. Vertebrate mtDNA exhibits rapid change in sequence but little change in gene content and organization, whereas the mtDNA of plants exhibits little change in sequence but much variation in gene content and organization. Mitochondrial DNA sequences are frequently used to study patterns of evolution. Most chloroplast genomes consist of a single circular DNA molecule not complexed with histone proteins. Although there is considerable size variation among species, the chloroplast genomes found in most plants range from 120,000 to 160,000 bp. Chloroplast DNA sequences are most similar to DNA sequences in cyanobacteria, which supports the endosymbiotic theory of chloroplast origin.

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Chromosomes contain very long DNA molecules that are tightly packed. Supercoiling results from strain produced when rotations are added to a relaxed DNA molecule or removed from it. Overrotation produces positive supercoiling; underrotation produces negative supercoiling. Supercoiling is controlled by topoisomerase enzymes. A bacterial chromosome consists of a single, circular DNA molecule that is bound to proteins and exists as a series of large loops. It usually appears in the cell as a distinct clump known as the nucleoid. Each eukaryotic chromosome contains a single, long linear DNA molecule that is bound to histone and nonhistone chromosomal proteins. Euchromatin undergoes the normal cycle of decondensation and condensation in the cell cycle. Heterochromatin remains highly condensed throughout the cell cycle. The nucleosome is a core particle of eight histone proteins and the DNA that wraps around them. Nucleosomes are folded into a 30-nm fiber that forms a series of 300-nm-long loops; these loops are anchored at their bases by proteins. The 300-nm loops are condensed to form a fiber that is itself tightly coiled to produce a chromatid. Chromosome regions that are undergoing active transcription are sensitive to digestion by DNase I, indicating that DNA is more exposed during transcription. Epigenetic changes are stable alterations of gene expression that do not require changes in DNA sequences. Epigenetic changes can take place through alterations of chromatin structure. Centromeres are chromosomal regions where spindle microtubules attach; chromosomes without centromeres are usually lost in the course of cell division. Most centromeres are defined by epigenetic changes to chromatin structure. Telomeres stabilize the ends of chromosomes. Eukaryotic DNA comprises three classes of sequences. Unique-sequence DNA exists in very few copies. Moderately repetitive DNA consists of moderately long sequences that are repeated from hundreds to thousands of times. Highly repetitive DNA consists of very short sequences that are repeated in tandem from many thousands to millions of times. Mitochondria and chloroplasts are eukaryotic organelles that possess their own DNA. The endosymbiotic theory proposes that mitochondria and chloroplasts originated as free-living bacteria that entered into a beneficial association with eukaryotic cells. Traits encoded by mtDNA and cpDNA are usually inherited from a single parent, most often the mother. Replicative segregation of organelles in cell division may produce phenotypic variation among cells within an individual organism and among the offspring of a single female.

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The mitochondrial genome usually consists of a single circular DNA molecule that lacks histone proteins. Mitochondrial DNA varies in size among different groups of organisms. Human mtDNA is highly economical, with few noncoding nucleotides. Fungal and plant mtDNAs contain much noncoding DNA between genes. Comparisons of mtDNA sequences suggest that mitochondria evolved from a bacterial ancestor. Vertebrate mtDNA exhibits rapid change in sequence but little change in gene content and organization. Plant mtDNA exhibits little change in sequence but much variation in gene content and organization. Mitochondrial DNA sequences are widely used to study evolution. Damage to mtDNA has been associated with aging in humans. Mitochondrial replacement therapy can be used to transfer nuclear DNA from a woman with a mitochondrial disorder and from a sperm into an egg cell from a healthy donor, giving rise to a baby with genetic material from three parents. This procedure has raised ethical issues and safety concerns. Chloroplast genomes consist of a single circular DNA molecule that lacks histone proteins and varies little in size. Each plant cell contains multiple copies of cpDNA. Chloroplast DNA sequences are most similar to those in cyanobacteria and tend to evolve slowly. Through evolutionary time, many mitochondrial and chloroplast genes have moved to nuclear chromosomes. In some plants, there is evidence that copies of chloroplast genes have moved to the mitochondrial genome.

Study Unit 2 Chapter 12: DNA Replication and Recombination Concepts Ch12 ▪ ▪ ▪ ▪

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Meselson and Stahl convincingly demonstrated that replication in E. coli is semiconservative: each DNA strand serves as a template for the synthesis of a new DNA molecule. Theta replication, rolling-circle replication, and linear eukaryotic replication differ with respect to the initiation and progression of replication, but all produce new DNA molecules by semiconservative replication. DNA synthesis requires a single-stranded DNA template, deoxyribonucleoside triphosphates, a growing nucleotide strand, and a group of enzymes and proteins. All DNA synthesis is 5′→3′, meaning that new nucleotides are always added to the 3′ end of the growing nucleotide strand. At each replication fork, synthesis of the leading strand proceeds continuously and that of the lagging strand proceeds discontinuously. Replication is initiated at an origin of replication, where an initiator protein binds and causes a short stretch of DNA to unwind. DNA helicase breaks hydrogen bonds at a replication fork, and single-strand-binding proteins stabilize the separated strands. DNA gyrase reduces the torsional strain that develops as the two strands of double-helical DNA unwind. Primase synthesizes a short stretch of RNA nucleotides (a primer), which provides a 3′-OH group for the attachment of DNA nucleotides to start DNA synthesis. DNA polymerases synthesize DNA in the 5′→3′ direction by adding new nucleotides to the 3′ end of a growing nucleotide strand. After primers have been removed and replaced, the break in the sugar–phosphate backbone of the new DNA strand is sealed by DNA ligase. DNA replication is extremely accurate, with less than one error per billion nucleotides. The high level of accuracy in DNA replication is produced by precise nucleotide selection, proofreading, and mismatch repair. Eukaryotic DNA contains many origins of replication. At each origin, a multiprotein origin-recognition complex binds to initiate the unwinding of the DNA. There are a large number of different DNA polymerases in eukaryotic cells.

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DNApolymerases a, d, and e carry out replication on the leading and lagging strands. Other DNA polymerases carry out DNA repair or synthesize organelle DNA. Specialized translesion polymerases are used to bypass distortions of the DNA template that normally stall the main DNA polymerases. After DNA replication, new nucleosomes quickly reassemble on the two new molecules of DNA. Nucleosomes break down in the course of replication and reassemble from a mixture of old and new histones. The reassembly of nucleosomes during replication is facilitated by histone chaperones and chromatin-assembly factors. The ends of eukaryotic chromosomes are replicated by a ribonucleoprotein called telomerase. This enzyme adds extra nucleotides to the G-rich DNA strand of the telomere. Homologous recombination requires the formation of heteroduplex DNA consisting of one nucleotide strand from each of two homologous chromosomes. In the Holliday model, homologous recombination is accomplished through a single-strand break in each DNA molecule, strand displacement, and branch migration. In the double-strand-break model, recombination is accomplished through double-strand breaks, strand displacement, and branch migration. A number of proteins have roles in recombination, including RecA, RecBCD, RuvA, RuvB, resolvase, single-strandbinding proteins, DNA ligase, DNA polymerases, and DNA gyrase.

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In theta replication, the two nucleotide strands of a circular DNA molecule unwind, creating a replication bubble. Within each replication bubble, DNA is normally synthesized on both strands and at the replication fork, producing two circular DNA molecules. Rolling-circle replication is initiated by a break in one strand of circular DNA, which produces a 3′-OH group to which new nucleotides are added while the 5′ end of the broken strand is displaced from the circle. Linear eukaryotic DNA contains many origins of replication. Unwinding and replication take place on both templates at both ends of the replication bubble until adjacent replicons meet, resulting in two linear DNA molecules. All DNA synthesis is in the 5′→3′ direction. Because the two nucleotide strands of DNA are antiparallel, replication takes place continuously on one strand (the leading strand) and discontinuously on the other (the lagging strand). Replication in bacteria begins when an initiator protein binds to an origin of replication and unwinds a short stretch of DNA, to which DNA helicase attaches. DNA helicase unwinds the DNA at the replication fork, single-strand-binding proteins bind to the single nucleotide strands to prevent secondary structures, and DNA gyrase (a topoisomerase) removes the strain ahead of the replication fork that is generated by unwinding. During replication, primase synthesizes short primers consisting of RNA nucleotides, providing a 3′-OH group to which DNA polymerase can add DNA nucleotides. DNA polymerase adds new nucleotides to the 3′ end of a growing polynucleotide strand. Bacteria have two DNA polymerases that have primary roles in replication: DNA polymerase III, which synthesizes new DNA on the leading and lagging strands, and DNA polymerase I, which removes and replaces primers. DNA ligase seals the breaks that remain in the sugar–phosphate backbone when the RNA primers are replaced by DNA nucleotides. Several mechanisms ensure the high rate of accuracy in replication, including precise nucleotide selection, proofreading, and mismatch repair. Precise replication at multiple...