DNA and Chromosome Structure PDF

Chapters 10-11 – DNA and chromosome structure BIOL2301: Genetics Teaching team: Sara Good October 7th, 2024 Agenda today 1. Characteristics of genetic material 2. DNA and RNA structure Copyright © 2024 Summations Knowledge Inc. All Rights Reserved Characteristic of...

Chapters 10-11 – DNA and chromosome structure BIOL2301: Genetics Teaching team: Sara Good October 7th, 2024 Agenda today 1. Characteristics of genetic material 2. DNA and RNA structure Copyright © 2024 Summations Knowledge Inc. All Rights Reserved Characteristic of genetic material Characteristic of genetic material All living organisms share the same genetic language of nucleic acids. Acceptance of nucleic acids as genetic material came after 1950. Lack of understanding of DNA structure hindered acceptance. Four essential characteristics of genetic material were recognized: 1. Complex information storage. 2. Faithful replication during cell division. 3. Encoding of phenotype, expressed as traits. 4. Capacity to vary, reflecting genetic diversity among species and individuals. Copyright © 2024 Summations Knowledge Inc. All Rights Reserved DNA and RNA structure Early studies of DNA by chemists 1868 1887 Late Early 1940s- 1800s 20th 1950s century Johann Friedrich Several Albrecht Phoebus Miescher researchers kossel Aaron Levene Erwin Chargaff Johann Friedrich Discovery that the Albrecht Kossel Phoebus Aaron Levene Erwin Chargaff and Miescher isolates nuclei physical basis of identifies four discovers DNA's colleagues disprove the from pus, discovers heredity lies in the nitrogenous bases in structure as linked tetranucleotide nuclein. nucleus. DNA. repeating units called hypothesis, introduce nucleotides, proposes Chargaff's rules. the tetranucleotide hypothesis. Copyright © 2024 Summations Knowledge Inc. All Rights Reserved Early studies of DNA by biologists Biologists sought to identify the carrier of genetic information alongside chemists unraveling DNA's structure. Gregor Mendel laid the groundwork for understanding heredity in 1866, yet the physical nature of hereditary information remained a mystery. By the early 1900s, biologists inferred genes were located on chromosomes, composed of DNA and protein. Crucial experiments on bacteria and viruses in the early 20th century provided compelling evidence supporting DNA as the genetic material over protein. Copyright © 2024 Summations Knowledge Inc. All Rights Reserved Discovery of transforming principle In 1928, Fred Griffith observed a phenomenon called transformation while studying Streptococcus pneumoniae. Transformation: the process where nonvirulent bacteria acquire the genetic virulence of dead virulent bacteria, leading to a permanent genetic change. Griffith isolated different strains of S. pneumoniae, including virulent (smooth, S) and nonvirulent (rough, R) forms. Copyright © 2024 Summations Knowledge Inc. All Rights Reserved Discovery of transforming principle Possibility 1 Incomplete sterilization, but this was improbable due to the control experiment's negative outcome. Possibility 2 Spontaneous mutation of nonvirulent bacteria to the virulent form, which didn't align with observed bacterial characteristics. Conclusion Nonvirulent bacteria were transformed, acquiring genetic virulence from dead virulent bacteria. Despite uncertainty about the mechanism, Griffith proposed the existence of a "transforming principle" within the dead bacteria. Copyright © 2024 Summations Knowledge Inc. All Rights Reserved Identification of transforming principle Oswald Avery, initially skeptical of Griffith's findings, embarked on research to understand the transforming substance. After successfully repeating Griffith's experiments, Avery, Colin MacLeod, and Maclyn McCarty isolated and partially purified the transforming substance. Copyright © 2024 Summations Knowledge Inc. All Rights Reserved Identification of transforming principle Their research revealed that the transforming substance had a chemical composition resembling DNA, not proteins. Enzymatic tests demonstrated that proteins were not responsible for the transforming activity, whereas DNA-degrading enzymes abolished it. The transforming substance precipitated similarly to purified DNA and absorbed ultraviolet light like DNA, supporting its DNA nature. Copyright © 2024 Summations Knowledge Inc. All Rights Reserved The Hershey-Chase experiment Alfred Hershey and Martha Chase conducted a study on the T2 bacteriophage to determine whether protein or DNA was transmitted during phage reproduction. T2 bacteriophage: a virus that is composed of approximately 50% protein and 50% DNA, and it infects Escherichia coli bacteria by injecting its genetic material. Copyright © 2024 Summations Knowledge Inc. All Rights Reserved The Hershey-Chase experiment Bacteriophages reproduce by attaching to the outer wall of a bacterial cell and injecting their DNA into the cell. Once inside the bacterial cell, the phage DNA replicates and directs the synthesis of phage proteins. The newly synthesized phage DNA becomes encapsulated within the phage proteins, forming progeny phages. Eventually, the progeny phages lyse or break open the bacterial cell, releasing them to infect other cells. Copyright © 2024 Summations Knowledge Inc. All Rights Reserved The Hershey-Chase experiment Hershey and Chase used radioactive isotopes of phosphorus (32P) and sulfur (35S) as tracers to follow the fate of DNA and protein, respectively. They grew E. coli in media containing either 32P or 35S to label the phage DNA and protein, respectively, in separate experiments. They demonstrated that DNA, not protein, is the genetic material of phages. Copyright © 2024 Summations Knowledge Inc. All Rights Reserved Meanwhile Edwin Chargaff’s had made the following observation: Chargaff’s rules Adenine is always equal to thymine (A = T), Guanine is always equal to cytosine (G = C). TABLE 10.1 Base composition (percent*) of DNA from different sources and ratios of bases Ratio (A + G)/ Source of DNA A T G C A/T G/C (T + C) E. coli 26.0 23.9 24.9 25.2 1.09 0.99 1.04 Yeast 31.3 32.9 18.7 17.1 0.95 1.09 1.00 Sea urchin 32.8 32.1 17.7 18.4 1.02 0.96 1.00 Rat 28.6 28.4 21.4 21.5 1.01 1.00 1.00 Human 30.3 30.3 19.5 19.9 1.00 0.98 0.99 *Percentage in moles of nitrogenous constituents per 100 g; atoms of phosphate in hydrolysate corrected for 100% recovery. Source: E. Chargaff and J. Davidson (eds.), The Nucleic Acids, Vol 1 (New York: Academic Press, 1955). © Macmillan Learning  Watson and Crick’s Discovery of the Three-Dimensional Structure of DNA Early investigations by Miescher, Kossel, Levene, Chargaff, and others laid the groundwork by establishing DNA's chemical composition and the role of nucleotides. In 1947, William Astbury initiated the study of DNA's three-dimensional structure using X-ray diffraction, though the resolution was insufficient for a clear picture. Copyright © 2024 Summations Knowledge Inc. All Rights Reserved Watson and Crick’s Discovery of the Three-Dimensional Structure of DNA Rosalind Franklin's X-ray diffraction images, obtained at King's College in London, provided crucial insights into DNA's structure. James Watson and Francis Crick didn't collect new data but used available information to construct models, incorporating Franklin's high-quality X-ray images. Watson and Crick’s Discovery of the Three-Dimensional Structure of DNA Watson's recognition of adenine bonding with thymine and guanine with cytosine allowed them to develop a model consistent with Chargaff's base ratio findings. Watson and Crick's model revealed DNA as a double helix, with nucleotides forming complementary base pairs and sugars-phosphates on the outside. RNA as genetic material While most organisms utilize DNA for genetic information, some viruses, like the tobacco mosaic virus (TMV), rely on RNA. Ribonucleic acid (RNA): a molecule essential for various biological processes, including protein synthesis and genetic regulation. RNA as genetic material Fraenkel-Conrat and Singer produced hybrid viruses by mixing RNA and protein from different TMV strains, observing that the new viral progeny resembled the strain of the isolated RNA, affirming RNA's role as the carrier of genetic information. In the same year, Alfred Gierer and Gerhard Schramm further confirmed TMV's RNA as the genetic material, showing that isolated TMV RNA alone could infect tobacco plants and direct new TMV particle production. Primary structure of DNA - Nucleotides Nucleotides: building blocks of nucleic acids, consisting of a sugar molecule, a phosphate group, and a nitrogenous base. DNA's sugars are pentose sugars: ribose in RNA and deoxyribose in DNA. Nitrogenous bases in DNA are purines (adenine and guanine) and pyrimidines (cytosine, thymine in DNA, and uracil in RNA). The nitrogenous base forms a covalent bond with the 1- carbon atom of the sugar, creating a nucleoside. The phosphate group, bonded to the 5-carbon atom of the sugar, makes DNA acidic and forms nucleotides. DNA nucleotides are deoxyribonucleotides, and RNA nucleotides are ribonucleotides. Primary structure of DNA - Nucleotides 10.3 DNA Consists of Two Complementary and Antiparallel Nucleotide Strands That Form a Double Helix (2 of 11) 10.3 DNA Consists of Two Complementary and Antiparallel Nucleotide Strands That Form a Double Helix (3 of 11) Primary structure of DNA - Polynucleotide strands Polynucleotide strands: chains of nucleotides linked by phosphodiester bonds, forming the backbone of DNA and RNA molecules. The backbone of the strand comprises alternating sugars and phosphate groups, with the bases projecting away from the axis. Polynucleotide strands exhibit directionality, with the 5' end having a free phosphate group and the 3' end having a free hydroxyl group. RNA also forms polynucleotide strands through phosphodiester linkages, similar to DNA. Primary structure of DNA - Polynucleotide strands Copyright © 2024 Summations Knowledge Inc. All Rights Reserved Secondary structure of DNA - The double helix The double helix: the twisted structure formed by two polynucleotide strands of DNA wound around each other. The sugar-phosphate linkages are on the outside, while the bases are stacked in the interior. The two strands run in opposite directions, known as antiparallel, with the 5' end of one strand opposite the 3' end of the other. Hydrogen bonds between bases on opposite strands hold the two strands together. Adenine pairs with thymine through two hydrogen bonds, and cytosine pairs with guanine through three hydrogen bonds. The complementary nature of DNA strands ensures efficient and accurate replication. Stacking interactions stabilize the DNA molecule, allowing for variation in the base sequence and the storage of genetic information. Secondary structure of DNA - The double helix Copyright © 2024 Summations Knowledge Inc. All Rights Reserved Different secondary structures The double helix: the twisted structure formed by two polynucleotide strands of DNA wound around each other. The sugar-phosphate linkages are on the outside, while the bases are stacked in the interior. The two strands run in opposite directions, known as antiparallel, with the 5' end of one strand opposite the 3' end of the other. The two strands are held together by two types of molecular forces: 1. Hydrogen bonds between bases on opposite strands hold the two strands together. 2. Stacking interactions stabilize the DNA molecule, allowing for variation in the base sequence and the storage of genetic information. The complementary nature of DNA strands ensures efficient and accurate replication. Different secondary structures The B-DNA structure: described by Watson and Crick, is the most stable configuration under physiological conditions. B-DNA is a right-handed helix with approximately 10 base pairs per 360-degree rotation, exhibiting a slim and elongated structure. B-DNA structure features major and minor grooves, important for protein binding involved in genetic regulation. Different secondary structures Different secondary structures The A-DNA structure: another secondary structure of DNA, is shorter, wider, and also a right-handed helix, observed under conditions with less water. Different secondary structures The Z-DNA structure: a radically different secondary structure, forms a left-handed helix, characterized by a zigzagging sugar-phosphate backbone, and may play a role in gene expression.  10.4 Special DNA-structures: hair pin loops © Macmillan Learning 10.4 Special DNA Structure: triple helix H-DNA: three- stranded (triplex); formed when DNA unwinds and one strand pairs with double-stranded DNA from another part of the molecule Often occurs in long sequences of only purines or only pyrimidines Common in mammalian genomes © Macmillan Learning  10.4 Special DNA Structures: methylated DNA DNA methylation Methyl groups added to nucleotide bases Related to gene expression in eukaryotes Affects the three- dimensional structure of DNA © Macmillan Learning  DNA must be tightly packed to fit in small spaces (Fig. 11.1) – DNA in E. coli about 1000 times as long as the cell itself Supercoiling – Positive supercoiling, Figure 11.2(b) – Negative supercoiling, Figure 11.2(c) – Topoisomerase: enzyme responsible for adding and removing turns in the coil © Macmillan Learning Bacterial DNA is highly folded into a series of twisted loops. © Macmillan Learning  11.1 Large Amounts of DNA Are Packed in eukaryotic cells Eukaryotic chromosomes Chromatin structure (Table 11.1) – Euchromatin – Heterochromatin – Histone proteins  TABLE 11.1 Characteristics of euchromatin and heterochromatin Characteristic Euchromatin Heterochromatin Chromatin condensation Less condensed More condensed Location On chromosome At centromeres, arms telomeres, and other specific places Type of sequences Unique sequences Repeated sequences* Presence of genes Many genes Few genes* When replicated Throughout S phase Late S phase Transcription Often Infrequent Crossing over Common Uncommon © Macmillan Learning *Applies only to constitutive heterochromatin.  11.1 Large Amounts of DNA Are Packed into a Cell (4 of 4) Chromatin structure – Nucleosome – Linker DNA – High-order chromatin structure ▪ 30-nm fiber ▪ 300-nm loops ▪ 250-nm-wide fiber  11.1 Large Amounts of DNA Are Packed in eukaryotic cells The nucleosome is the fundamental repeating unit of chromatin. © Macmillan Learning 11.1 Large Amounts of DNA Are Packed in eukaryotic cells © Macmillan Learning  Chromosomal puffs are regions of relaxed chromatin where active transcription takes place © Macmillan Learning  DNase I sensitivity is correlated with the transcription of globin genes in chick embryos. © Macmillan Learning  Variation in DNA methylation at the agouti locus produces different coat colors in mice. © Macmillan Learning DNA at the ends of eukaryotic chromosomes consists of telomeric sequences. © Macmillan Learning  TABLE 11.2 DNA sequences typically found in telomeres of various organisms Organism Sequence Tetrahymena (protozoan) 5'–TTGGGG–3' 3'–AACCCC–5' Saccharomyces (yeast) 5'–T1−6GTG2–3–3' 3'–A1−6CAC2–3–5’ Caenorhabditis (nematode) 5'–TTAGGC–3' 3'–AATCCG–5' Vertebrate 5'–TTAGGG–3' 3'–AATCCC–5 Arabidopsis (plant) 5'–TTTAGGG–3' 3'–AAATCCC–5' © Macmillan Source: V. A. Zakian, Science 270:1602, 1995. Learning  The Mitochondrial Genome Mitochondrial genomes are small and vary greatly (Table 11.4) Human mtDNA: circular, 16,569 base pairs; encodes two rRNAs, 22 tRNAs, and 13 proteins (Fig. 11.16) Yeast mtDNA: five times as large as human; encodes 2 rRNAs, 25 tRNAs, and 16 polypeptides (Fig. 11.17) Flowering-plant mtDNA: extensive size variation (Fig. 11.18)  The human mitochondrial genome, consisting of 16,569 bp, is highly economical in its organization, with few sequences that do not code for RNA or protein. © Macmillan Learning