DNA: The Carrier of Genetic Information Chapter 12

Learning Objective 1 What evidence was accumulated during the 1940s and early 1950s demonstrating that DNA is the genetic material?

The Mystery of Genes Many early geneticists thought genes were proteins Proteins are complex and variable Nucleic acids are simple molecules

Evidence for DNA DNA (deoxyribonucleic acid) Transformation experiments DNA of one strain of bacteria can transfer genetic characteristics to related bacteria

Bacteriophage Experiments Bacteriophage (virus) infects bacterium only DNA from virus enters the cell virus reproduces and forms new viral particles from DNA alone

KEY CONCEPTS Beginning in the 1920s, evidence began to accumulate that DNA is the hereditary material

Learning Objective 2 What questions did these classic experiments address? Griffith’s transformation experiment Avery’s contribution to Griffith’s work Hershey–Chase experiments

Griffith’s Transformation Experiment Can a genetic trait be transmitted from one bacterial strain to another? Answer: Yes

Griffith’s Transformation Experiment

R cells and heat-killed S cells injected Experiment 1 Experiment 2 Experiment 3 Experiment 4 R cells injected S cells injected Heat-killed S cells injected R cells and heat-killed S cells injected Figure 12.1: Griffith’s transformation experiments. Griffith was trying to develop a vaccine against pneumonia when he serendipitously discovered the phenomenon of transformation. Mouse lives Mouse dies Mouse lives Mouse dies Fig. 12-1, p. 261

Animation: Griffith’s Experiment CLICK TO PLAY

Avery’s Experiments What molecule is responsible for bacterial transformation? Answer: DNA

Hershey–Chase Experiments Is DNA or protein the genetic material in bacterial viruses (phages)? Answer: DNA

Hershey–Chase Experiments

Viruses infect bacteria 1 35S 32 P Bacterial viruses grown in 35S to label protein coat or 32P to label DNA 2 Viruses infect bacteria Figure 12.2: The Hershey–Chase experiments. Fig. 12-2, p. 262

3 4 32 P 35S 5 Agitate cells in blender Agitate cells in blender Separate by centrifugation Separate by centrifugation 32 P 35S Figure 12.2: The Hershey–Chase experiments. 5 Bacteria in pellet contain 32P-labeled DNA 35S-labeled protein in supernatant Fig. 12-2, p. 262

Viral reproduction inside bacterial cells from pellet 6 Viral reproduction inside bacterial cells from pellet 7 Cell lysis 32P 5 Figure 12.2: The Hershey–Chase experiments. 6 7 Fig. 12-2, p. 262

Learning Objective 3 How do nucleotide subunits link to form a single DNA strand?

Watson and Crick DNA Model Demonstrated how information is stored in molecule’s structure how DNA molecules are templates for their own replication

Nucleotides DNA is a polymer of nucleotides Each nucleotide subunit contains a nitrogenous base purines (adenine or guanine) pyrimidines (thymine or cytosine) a pentose sugar (deoxyribose) a phosphate group

Forming DNA Chains Backbone Phosphate group attaches to alternating sugar and phosphate groups joined by covalent phosphodiester linkages Phosphate group attaches to 5′ carbon of one deoxyribose 3′ carbon of the next deoxyribose

DNA Nucleotides

Phosphodiester linkage Thymine Adenine Nucleotide Phosphate group Cytosine Figure 12.3: The nucleotide subunits of DNA. A single strand of DNA consists of a backbone (superimposed on blue screen) made of phosphate groups alternating with the sugar deoxyribose (green). Phosphodiester linkages (pink) join sugars of adjacent nucleotides. (The nucleotide containing the base adenine is highlighted yellow.) Linked to the 1’ carbon of each sugar is one of four nitrogenous bases (top to bottom): thymine, adenine, cytosine, and guanine. Note the polarity of the polynucleotide chain, with the 5’ end at the top of the figure and the 3’ end at the bottom. Guanine Phosphodiester linkage Deoxyribose (sugar) Fig. 12-3, p. 264

Animation: Subunits of DNA CLICK TO PLAY

KEY CONCEPTS The DNA building blocks consist of four nucleotide subunits: T, C, A, and G

Learning Objective 4 How are the two strands of DNA oriented with respect to each other?

DNA Molecule 2 polynucleotide chains associated as double helix

DNA Molecule

Sugar–phosphate backbone Minor groove 3.4 nm Major groove Figure 12.5: A three-dimensional model of the DNA double helix. The measurements match those derived from X-ray diffraction images. 0.34 nm 2.0 nm = hydrogen = carbon = oxygen = atoms in base pairs = phosphorus Fig. 12-5, p. 266

Double Helix Antiparallel 5′ end 3′ end chains run in opposite directions 5′ end phosphate attached to 5′ deoxyribose carbon 3′ end hydroxyl attached to 3′ deoxyribose carbon

KEY CONCEPTS The DNA molecule consists of two strands that wrap around each other to form a double helix The order of its building blocks stores genetic information

Animation: DNA Close Up CLICK TO PLAY

Learning Objective 5 What are the base-pairing rules for DNA? How do complementary bases bind to each other?

Base Pairs Hydrogen bonding Adenine (A) with thymine (T) between specific base pairs binds two chains of helix Adenine (A) with thymine (T) forms two hydrogen bonds Guanine (G) with cytosine (C) forms three hydrogen bonds

Base Pairs and Hydrogen Bonds

Fig. 12-6a, p. 267 Figure 12.6: Base pairing and hydrogen bonding. The two strands of a DNA double helix are hydrogen-bonded between the bases. Fig. 12-6a, p. 267

Adenine Thymine Deoxyribose Deoxyribose Guanine Cytosine Deoxyribose Figure 12.6: Base pairing and hydrogen bonding. The two strands of a DNA double helix are hydrogen-bonded between the bases. Deoxyribose Deoxyribose Fig. 12-6b, p. 267

Chargaff’s Rules Complementary base pairing between A and T; G and C therefore A = T; G = C If base sequence of 1 strand is known base sequence of other strand can be predicted

KEY CONCEPTS Nucleotide subunits pair, based on precise pairing rules: T pairs with A, and C pairs with G Hydrogen bonding between base pairs holds two strands of DNA together

Learning Objective 6 What evidence from Meselson and Stahl’s experiment enabled scientists to differentiate between semiconservative replication of DNA and alternative models?

Models of DNA Replication

(a) Hypothesis 1: Semiconservative replication Parental DNA First generation Second generation Figure 12.7: Alternative models of DNA replication. The hypothesized arrangement of old (light blue) and newly synthesized (dark blue) DNA strands after one and two generations, according to (a) the semiconservative model, (b) the conservative model, and (c) the dispersive model. Fig. 12-7a, p. 268

(b) Hypothesis 2: Conservative replication Parental DNA First generation Second generation Figure 12.7: Alternative models of DNA replication. The hypothesized arrangement of old (light blue) and newly synthesized (dark blue) DNA strands after one and two generations, according to (a) the semiconservative model, (b) the conservative model, and (c) the dispersive model. Fig. 12-7b, p. 268

(c) Hypothesis 3: Dispersive replication Parental DNA First generation Second generation Figure 12.7: Alternative models of DNA replication. The hypothesized arrangement of old (light blue) and newly synthesized (dark blue) DNA strands after one and two generations, according to (a) the semiconservative model, (b) the conservative model, and (c) the dispersive model. Fig. 12-7c, p. 268

Meselson-Stahl Experiment E. coli grown in medium containing heavy nitrogen (15N) incorporated 15N into DNA Transferred from 15N to 14N medium after one or two generations, DNA density supported semiconservative replication

Meselson-Stahl Experiment

Bacteria are grown in 15N (heavy) medium. All DNA is heavy. Some cells are transferred to 14N (light) medium. Some cells continue to grow in 14N medium. Bacteria are grown in 15N (heavy) medium. All DNA is heavy. First generation Second generation High density Low density Cesium chloride (CsCl) DNA The greater concentration of CsCl at the bottom of the tube is due to sedimentation under centrifigal force. DNA is mixed with CsCl solution, placed in an ultracentrifuge, and centrifuged at very high speed for about 48 hours. Figure 12.8: The Meselson–Stahl experiment. 14N (light) DNA 14N – 15N hybrid DNA 15N (heavy) DNA DNA molecules move to positions where their density equals that of the CsCl solution. Fig. 12-8a, p. 269

One cell generation after transfer to 14N 14N (light) DNA 14N – 15N hybrid DNA 14N – 15N hybrid DNA 15N (heavy) DNA Figure 12.8: The Meselson–Stahl experiment. Before transfer to 14N One cell generation after transfer to 14N Two cell generations after transfer to 14N The location of DNA molecules within the centrifuge tube can be determined by UV optics. DNA solutions absorb strongly at 260 nm. Fig. 12-8b, p. 269

Semiconservative Replication Each daughter double helix consists of 1 original strand from parent molecule 1 new complementary strand

Learning Objective 7 How does DNA replicate? What are some unique features of the process?

DNA Replication 2 strands of double helix unwind each is template for complementary strand Replication is initiated DNA primase synthesizes RNA primer DNA strand grows DNA polymerase adds nucleotide subunits

DNA Replication

Base Nucleotide joined to growing chain by DNA polymerase Figure 12.10: A simplified view of DNA replication. DNA polymerase adds one nucleotide at a time to the 3’ end of a growing chain. Phosphates released Fig. 12-10, p. 271

Other Enzymes DNA helicases Topoisomerases open the double helix prevent tangling and knotting

KEY CONCEPTS DNA replication results in two identical double-stranded DNA molecules molecular mechanism passes genetic information from one generation to the next

Learning Objective 8 What makes DNA replication (a) bidirectional and (b) continuous in one strand and discontinuous in the other?

Bidirectional Replication Starting at origin of replication proceeding in both directions Eukaryotic chromosome may have multiple origins of replication may replicate at many points at same time

Bidirectional Replication

Origin of replication on DNA molecule DNA polymerase 3’ 3’ 5’ 5’ Figure 12.11: An overview of DNA replication. Fig. 12-11a, p. 272

Twist introduced into the helix by unwinding Single-strand binding proteins RNA primer DNA polymerase 3’ DNA helicase 3’ 3’ 5’ 3’ 5’ Direction of replication RNA primer Figure 12.11: An overview of DNA replication. Fig. 12-11b, p. 272

3’ 3’ 5’ 5’ 3’ 3’ 5’ 5’ Figure 12.11: An overview of DNA replication. Fig. 12-11c, p. 272

DNA Synthesis Always proceeds in 5′ → 3′ direction Leading strand synthesized continuously Lagging strand synthesized discontinuously forms short Okazaki fragments DNA primase synthesizes RNA primers DNA ligase links Okazaki fragments

DNA Synthesis

Direction of replication 5’ Lagging strand (first Okazaki fragment) 3’ Leading strand 5’ DNA helix RNA primer 3’ 3’ DNA polymerase 5’ 5’ Replication fork 3’ Direction of replication 5’ Lagging strand (first Okazaki fragment) Figure 12.12: Leading and lagging DNA strands. Fig. 12-12a, p. 273

3’ Leading strand 5’ 3’ RNA primers 3’ 5’ 5’ 3’ 5’ 3’ Figure 12.12: Leading and lagging DNA strands. 5’ 3’ Two Okazaki fragments 5’ Fig. 12-12b, p. 273

Third Okazaki fragment 3’ 5’ Leading strand 3’ 3’ 5’ 5’ 3’ 5’ DNA ligase Third Okazaki fragment Figure 12.12: Leading and lagging DNA strands. Lagging strand 3’ 5’ Fig. 12-12c, p. 273

Replication in Bacteria and Eukaryotes

Template DNA (light blue) New DNA (dark blue) 3’ 5’ 5’ 3’ Figure 12.13: Bidirectional DNA replication in bacteria and eukaryotes. The illustrations do not show leading strands and lagging strands. Fig. 12-13a, p. 274

Figure 12.13: Bidirectional DNA replication in bacteria and eukaryotes. The illustrations do not show leading strands and lagging strands. 340 nm Fig. 12-13b, p. 274

Single replication bubble formed from two merged bubbles 3’ 5’ Single replication bubble formed from two merged bubbles 3’ Replication “bubbles” 3’ Replication fork 5’ Figure 12.13: Bidirectional DNA replication in bacteria and eukaryotes. The illustrations do not show leading strands and lagging strands. Fig. 12-13c, p. 274

Animation: Overview of DNA replication and base pairing CLICK TO PLAY

Learning Objective 9 How do enzymes proofread and repair errors in DNA?

DNA Polymerases Proofread each new nucleotide against template nucleotide Find errors in base pairing remove incorrect nucleotide insert correct one

DNA Mutation

Mutation Figure 12.9: The perpetuation of a mutation. The process of DNA replication can stabilize a mutation (bright yellow) so that it is transmitted to future generations. Fig. 12-9, p. 270

Mutation Stepped Art Fig. 12-9, p. 270 Figure 12.9: The perpetuation of a mutation. The process of DNA replication can stabilize a mutation (bright yellow) so that it is transmitted to future generations. Stepped Art Fig. 12-9, p. 270

Mismatch Repair Enzymes recognize incorrectly paired nucleotides and remove them DNA polymerases fill in missing nucleotides

Nucleotide Excision Repair Repairs DNA lesions caused by sun or harmful chemicals 3 enzymes nuclease cuts out damaged DNA DNA polymerase adds correct nucleotides DNA ligase closes breaks in sugar–phosphate backbone

Nucleotide Excision Repair

Nuclease enzyme bound to DNA DNA lesion 5’ 3’ 3’ 5’ 5’ 3’ 3’ 5’ DNA polymerase Figure 12.14: Nucleotide excision repair of damaged DNA. DNA ligase New DNA 3’ 5’ 3’ 5’ Fig. 12-14, p. 275

Learning Objective 10 What is a telomere? What are the possible connections between telomerase and cell aging, and between telomerase and cancer?

Telomeres Eukaryotic chromosome ends noncoding, repetitive DNA sequences Shorten slightly with each cell cycle Can be extended by telomerase

Replication at Telomeres

5’ 3’ 3’ 5’ DNA replication 5’ 3’ 3’ 5’ RNA primer + RNA primer 5’ 3’ Removal of primer Figure 12.15: Replication at chromosome ends. 5’ 3’ 3’ 5’ + 5’ 3’ 3’ 5’ Fig. 12-15a, p. 276

3’ 5’ Figure 12.15: Replication at chromosome ends. Fig. 12-15b, p. 276

Cell Aging May be caused by absence of telomerase activity Cells lose ability to divide after a limited number of cell divisions

Cancer Cells Have telomerase Including human cancers to maintain telomere length and possibly resist apoptosis Including human cancers breast, lung, colon, prostate gland, pancreas