DNA Chapter 16

Griffith - 1928 Streptococcus pneumoniae - bacteria that causes pneumonia in mammals R strain – harmless S strain – pathogenic mixed heat-killed S strain with live R strain bacteria and injected this into a mouse the mice died

Transformation change in genotype and phenotype due to the assimilation of a foreign substance (now known to be DNA) by a cell.

Avery and other scientists discovered that DNA is the nucleic acid that stores and transmits the genetic information from one generation of an organism to the next. Oswald Avery 1944 World knows a molecule carries the genetic information. Doesn’t know if the molecule is a: protein, lipid, carbohydrate, RNA, or DNA Avery performs Griffith’s experiment again with a twist.

What is the transforming substance? Track the infection of bacteria by viruses Viruses consist of a DNA enclosed by a protective coat of protein To replicate, a virus infects a host cell and takes over the cell’s metabolic machinery

Bacteriophages (phage) Virus that specifically attacks bacteria

Hershey and Chase T2 phage, consisting almost entirely of DNA and protein, attacks Escherichia coli label protein and DNA and then track which entered the E. coli cell during infection

How? Grew one batch of T2 phage in the presence of radioactive sulfur marking the proteins but not DNA Grew another batch in the presence of radioactive phosphorus marking the DNA but not proteins Allowed each batch to infect separate E. coli cultures

Chargaff Developed a series of rules based on a survey of DNA composition in organisms DNA is a polymer of nucleotides consists of a nitrogenous base, deoxyribose, and a phosphate group The bases = adenine (A), thymine (T), guanine (G), or cytosine (C). The four bases are found in ratios

Wilkins and Franklin X-rays are diffracted as they passed through aligned fibers of purified DNA Used to deduce the three-dimensional shape of molecules

Watson and Crick Double Helix

Purine and Pyrimidine nitrogenous bases are paired in specific combinations: adenine with thymine and guanine with cytosine

DNA Replication Because each strand is complementary to each other, each can form a template when separated

DNA Replication

semiconservative replication each of the daughter molecules will have one old strand and one newly made strand

DNA replication http://www.johnkyrk.com/DNAreplication.html

Human Cells Copy its billion base pairs and divide into daughter cells in a few hours One error per billion nucleotides

Origin of Replication Single specific sequence of nucleotides that is recognized by replication enzymes enzymes separate the strands, forming a replication “bubble” Replication proceeds in both directions until the entire molecule is copied

Anti-Parallel Each DNA strand has a 3’ end with a free hydroxyl group attached to deoxyribose and a 5’ end with a free phosphate group attached to deoxyribose.

Bubbles and Forks

DNA Polymerase

DNA polymerases can only add nucleotides to the free 3’ end of a growing DNA strand leading strand - used by polymerases as a template for a continuous complimentary strand lagging strand - copied away from the fork in short segments (Okazaki fragments)

DNA polymerase and Primers Polymerase cannot initiate synthesis of a polynucleotide can only add nucleotides to the end of an existing chain To start a new chain requires a primer a short segment of RNA

Animation: Lagging Strand Animation: Leading Strand Replication Fork Topoisomerases Helicases Single-strand binding proteins Primases (RNA primers) DNA Polymerases Ligases

Animation: DNA Replication Review DNA polymerase later replaces the primer with deoxyribonucleotides complimentary to the template

Mismatched nucleotides Reactive chemicals, radioactive emissions, X-rays, and ultraviolet light can change nucleotides in ways that can affect encoded genetic information Each cell continually monitors and repairs its genetic material over 130 repair enzymes identified in humans

In mismatch repair, special enzymes fix incorrectly paired nucleotides In nucleotide excision repair, a nuclease cuts out a segment of a damaged strand

telomeres = The ends of eukaryotic chromosomal DNA molecules – long repetitive sequences (no genes)

Telomerase uses a short molecule of RNA as a template to extend the 3’ end of the telomere

Difference between bacterial chromosomes and eukaryotic chromososes

Animation: DNA Packing Chromatin is a complex of DNA and protein, and is found in the nucleus of eukaryotic cells Histones are proteins that are responsible for the first level of DNA packing in chromatin For the Cell Biology Video Cartoon and Stick Model of a Nucleosomal Particle, go to Animation and Video Files. Animation: DNA Packing Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Nucleosomes, or “beads on a string” (10-nm fiber) Fig. 16-21a 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)

Looped domains (300-nm fiber) Metaphase chromosome Fig. 16-21b 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

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

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 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