Chapter 16 188 The Molecular Basis of Inheritance DNA is the molecule of inheritance. In 1868, Friedrich Miescher, a Swiss biochemist, discovered the cell nucleus contained protein and deoxyribonucleic acid, which he called nuclein. In 1914, Robert Feulgen, a German chemist, devised a method of staining nucleic acid. The solution was later called Feulgen stain.

Fig. 16-1 Figure 16.1 How was the structure of DNA determined?

188 In 1928, Fred Griffith, an English pathologist, discovered the process of transformation between S-type (S: smooth; virulent) and R-type (R: rough; avirulent) pneumococci (Streptococcus pneumoniae). In 1944, O.T. Avery, Colin MacLeod, and Maclyn McCarty of the Rockefeller Institute, discovered the so-called transforming factor was DNA.

Fig. 16-2 EXPERIMENT RESULTS Mixture of heat-killed S cells and living R cells EXPERIMENT Living S cells (control) Living R cells (control) Heat-killed S cells (control) RESULTS Figure 16.2 Can a genetic trait be transferred between different bacterial strains? Mouse dies Mouse healthy Mouse healthy Mouse dies Living S cells

188 DNA as the genetic material was confirmed by Alfred D. Hershey and Martha Chase of the Carnegie Laboratory of Genetics.

Fig. 16-3 Phage head Tail sheath Tail fiber DNA 100 nm Bacterial cell Figure 16.3 Viruses infecting a bacterial cell DNA 100 nm Bacterial cell

Fig. 16-4-1 EXPERIMENT Radioactive protein Phage Bacterial cell DNA Batch 1: radioactive sulfur (35S) DNA Radioactive DNA Figure 16.4 Is protein or DNA the genetic material of phage T2? Batch 2: radioactive phosphorus (32P)

Fig. 16-4-2 EXPERIMENT Empty protein shell Radioactive protein Phage Bacterial cell Batch 1: radioactive sulfur (35S) DNA Phage DNA Radioactive DNA Figure 16.4 Is protein or DNA the genetic material of phage T2? Batch 2: radioactive phosphorus (32P)

Fig. 16-4-3 EXPERIMENT Empty protein shell Radioactivity (phage protein) in liquid Radioactive protein Phage Bacterial cell Batch 1: radioactive sulfur (35S) DNA Phage DNA Centrifuge Radioactive DNA Pellet (bacterial cells and contents) Figure 16.4 Is protein or DNA the genetic material of phage T2? Batch 2: radioactive phosphorus (32P) Centrifuge Radioactivity (phage DNA) in pellet Pellet

188-189 Additional evidence that DNA is the genetic material is based on the discovery of the doubling of DNA in eukaryotes prior to mitosis, and that gametes of the same organism have half the amount of DNA as the diploid cells. Chargaff’s rules: the amount of adenine approximately equaled the amount of thymines, and the amount of guanines approximately equaled the amount of cytosines.

189 In 1953, James Watson and Francis Crick proposed the double helix molecular model for DNA. Nucleotide: Phosphate-Sugar-Nitrogenous base Nitrogenous bases: Adenine (A) Purines Guanine (G) Cytosine (C) Pyrimidines Thymine (T) RNA contains uracil (U) instead of thymine.

Fig. 16-8 Adenine (A) Thymine (T) Guanine (G) Cytosine (C) Figure 16.8 Base pairing in DNA Guanine (G) Cytosine (C)

Sugar–phosphate backbone 5 end Sugar (deoxyribose) 3 end Fig. 16-5 Sugar–phosphate backbone 5 end Nitrogenous bases Thymine (T) Adenine (A) Figure 16.5 The structure of a DNA strand Cytosine (C) Phosphate DNA nucleotide Sugar (deoxyribose) 3 end Guanine (G)

Fig. 16-7a 5 end Hydrogen bond 3 end 1 nm 3.4 nm 3 end 0.34 nm Figure 16.7 The double helix 3 end 0.34 nm 5 end (a) Key features of DNA structure (b) Partial chemical structure

Table 16-1

190 DNA Replication On 3’ to 5’ strand: 1. DNA helicase untwists and breaks the hydrogen bonds. 2. Primase synthesizes RNA primer (about 10 bases long). 4. DNA polymerase III 5. DNA polymerase I erases RNA primer and replaces it with DNA nucleotides. This new strand of DNA that runs from 5’ to 3’ direction is called a leading strand.

Nucleoside triphosphate Fig. 16-14 New strand 5 end Template strand 3 end 5 end 3 end Sugar A T A T Base Phosphate C G C G G C G C DNA polymerase 3 end A T A Figure 16.14 Incorporation of a nucleotide into a DNA strand T 3 end C Pyrophosphate C Nucleoside triphosphate 5 end 5 end

190 On 5’ to 3’ strand: 1. DNA helicase 2. RNA primer synthesized by primase 3. DNA polymerase III 4. DNA polymerase I (eraser enzyme) erases RNA primer and replaces it with DNA nucleotides to make Okazaki fragment (about 1,000 to 2,000 bases long) 5. DNA ligase joins the Okazaki fragments to form a lagging strand

Fig. 16-UN3 DNA pol III synthesizes leading strand continuously 3 5 Parental DNA DNA pol III starts DNA synthesis at 3 end of primer, continues in 5  3 direction 5 3 5 Lagging strand synthesized in short Okazaki fragments, later joined by DNA ligase Primase synthesizes a short RNA primer 3 5

Fig. 16-9-3 A T A T A T A T C G C G C G C G T A T A T A T A A T A T A (a) Parent molecule (b) Separation of strands (c) “Daughter” DNA molecules, each consisting of one parental strand and one new strand Figure 16.9 A model for DNA replication: the basic concept

Fig. 16-10 (a) Conservative model (b) Semiconserva- tive model First replication Second replication Parent cell (a) Conservative model (b) Semiconserva- tive model Figure 16.10 Three alternative models of DNA replication (c) Dispersive model

Bacteria cultured in medium containing 15N 2 Fig. 16-11a EXPERIMENT 1 Bacteria cultured in medium containing 15N 2 Bacteria transferred to medium containing 14N RESULTS 3 DNA sample centrifuged after 20 min (after first application) 4 DNA sample centrifuged after 20 min (after second replication) Less dense Figure 16.11 Does DNA replication follow the conservative, semiconservative, or dispersive model? More dense

Semiconservative model Fig. 16-11b CONCLUSION First replication Second replication Conservative model Semiconservative model Figure 16.11 Does DNA replication follow the conservative, semiconservative, or dispersive model? Dispersive model

193 Differences in DNA synthesis: Prokaryotes Eukaryotes Rate of synthesis: 500 base pairs 50 base pairs per second per second Initial sites: one many

194 Telomeres are the special nucleotide sequences at the ends of DNA. They do not contain genes. They consist of repeated sequence of typically TTAGGG in humans, which repeats from 100 to 1,000 times. Telomere protects the organism’s genes from being eroded through successive DNA replications. The telomere and its associated proteins prevent the ends from activating the cells system for monitoring DNA damage.

Fig. 16-20 Figure 16.20 Telomeres 1 µm

191 Eukaryotes produce telomerase, a special enzyme that contains a molecule of RNA along its protein, to lengthen the telomeres. The RNA of the telomerase has a sequence which serves as the template for new telomere segments. Telomerase is present in germ line cells that give rise to gametes. The enzyme produces long telomeres in germ cells and in the newborn. The enzyme is also found in cancerous cells. It contributes to the immortality of the cells.

Chromatin is organized into fibers 10-nm fiber 195 Chromatin is organized into fibers 10-nm fiber DNA winds around histones to form nucleosome “beads” Nucleosomes are strung together like beads on a string by linker DNA 30-nm fiber Interactions between nucleosomes cause the thin fiber to coil or fold into this thicker fiber Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Fig. 16-21a DNA, the double helix Histones Nucleosome (10 nm in diameter) DNA double helix (2 nm in diameter) H1 Histone tail Histones Figure 16.21a Chromatin packing in a eukaryotic chromosome DNA, the double helix Histones Nucleosomes, or “beads on a string” (10-nm fiber)

Fig. 16-21b 30-nm fiber Looped domains (300-nm fiber) Chromatid (700 nm) 30-nm fiber Loops Scaffold 300-nm fiber Figure 16.21b Chromatin packing in a eukaryotic chromosome Replicated chromosome (1,400 nm) 30-nm fiber Looped domains (300-nm fiber) Metaphase chromosome

195 300-nm fiber Metaphase chromosome The 30-nm fiber forms looped domains that attach to proteins Metaphase chromosome The looped domains coil further The width of a chromatid is 700 nm Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Loosely packed chromatin is called euchromatin 195 Most chromatin is loosely packed in the nucleus during interphase and condenses prior to mitosis Loosely packed chromatin is called euchromatin During interphase a few regions of chromatin (centromeres and telomeres) are highly condensed into heterochromatin Dense packing of the heterochromatin makes it difficult for the cell to express genetic information coded in these regions Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Histones can undergo chemical modifications that result in changes in chromatin organization For example, phosphorylation of a specific amino acid on a histone tail affects chromosomal behavior during meiosis Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

195 Alternative Forms of DNA: Right-handed DNA: A-DNA has 11 base pairs per turn. B-DNA (the classic DNA proposed by Watson and Crick) has 10 base pairs per turn. C-DNA has 9 base pairs per turn. Left-handed DNA: Z-DNA has 12 base pairs per turn. The biological significance of these different forms of DNA is not fully understood.