CHAPTER 16 THE MOLECULAR BASIS OF INHERITANCE 1

CHAPTER 16 THE MOLECULAR BASIS OF INHERITANCE 1

OVERVIEW � By the 1940’s, scientists knew that chromosomes carried hereditary material and consisted of DNA and protein. � Most thought that protein was the genetic material because: -proteins were macromolecules -little was known about nucleic acids -properties of DNA seemed too uniform to account for the multitude of inherited traits 2

Watson and Crick and their DNA Model 3

I. Concept 16. 1: DNA is the genetic material A. Evidence That DNA Can Transform Bacteria 1. In 1928 Frederick Griffith provided evidence that the genetic material was a specific molecule 2. He conducted 4 sets of experiments using two strains of pneumococcus—smooth (S) (encapsulated cells with a polysaccharide coat and caused pneumonia) and rough (R) (no coat and did not cause pneumonia) 4

� 1 st Experiment—injected live S into mouse and the mouse died (pathogenic bacteria) � 2 nd Experiment—injected live R into mouse and mouse remained healthy (nonpathogenic bacteria) � 3 rd Experiment—injected heat-killed S into mouse and mouse remained healthy (heatkilled bacteria which was pathogenic) � 4 th Experiment—injected heat-killed S and live R into mouse and mouse died of pneumonia. Examined blood and contained live S cells. 5

Griffith’s Experiment 6

3. He concluded from his experiments with Streptococcus pneumoniae that R cells had acquired from the dead S cells the ability to make the polysaccharide coats so this trait must be inheritable. 4. He could never explain the chemical nature of the “transforming agent. ” 5. This phenomenon is now called transformation (the assimilation of external genetic material by a cell) 6. In 1944, Avery, Mc. Carty, and Mac. Leod discovered that the transforming agent had to be DNA. 7. Others still believed that protein was the genetic material. 7

B. Evidence That Viral DNA Can Program Cells 1. More evidence that DNA is the genetic material came from the studies of bacteriophages (bacterial viruses) 2. In 1952, Hershey and Chase performed experiments showing that DNA was the genetic material of a phage known as T 2. �They designed an experiment to determine if protein or DNA was responsible for reprogramming a host bacterial cell. �This experiment provided evidence that nucleic acids rather than proteins were hereditary material in viruses. 8

T 2 Bacteriophage 9

Hershey and Chase Experiment 10

Hershey and Chase Experiment 11

Hershey and Chase Experiment 12

C. Additional Evidence that DNA is the Genetic Material of Cells 1. Circumstantial Evidence �A eukaryotic cell doubles its DNA content prior to mitosis �During mitosis, the doubled DNA is equally divided between two daughter cells. �An organism’s diploid cells have twice the DNA as its haploid gametes. 13

2. Experimental Evidence �Provided by Chargaff in 1950 when he analyzed the DNA composition of different organisms. He found: � DNA composition varies from species to species � In every species studied, there was a regularity in base ratios. -# of adenine = # of thymine -# of guanine = # of cytosine �A=T and G=C became known later as Chargaff’s Rule. Explanation of Chargaff’s Rule came with Watson and Crick’s structural model for DNA. 14

D. Building a Structural Model of DNA 1. By the 1950’s DNA was accepted as the genetic material, and the covalent arrangement in a nucleic acid polymer was well established. The three dimensional structure was unknown, however. 2. Among the scientist working on the problem were Linus Pauling, in California, and Maurice Wilkins and Rosalind Franklin, in London. 3. The first to come up with the correct answer were two scientists who were relatively unknown at the time— American James Watson, and Englishman Francis Crick. 15

Rosalind Franklin X ray crystallography identified that DNA was a double helix structure.

E. In April of 1953 Watson and Crick proposed the structure of DNA in a one page paper in the journal Nature. �Proposed structure: ladder-like molecule twisted into a spiral (double helix), with sugar-phosphate backbones as uprights and pairs of nitrogenous bases as the rungs. �Backbones of helix are antiparallel (run in opposite directions) �There is a specific pairing between nitrogenous bases (A with T; G with C) �Nitrogenous bases are held together by hydrogen bonds: A = T (2 hydrogen bonds) 17 G ≡ C (3 hydrogen bonds)

DNA � Covalent bonds link the units of each nucleotide. � The two strands of DNA are held together by Hydrogen bonds between the base pairs. � In Watson’s model of DNA, the sugar-phosphate backbones were antiparallel- with their subunits running in opposite directions.

�Base-pairing rule is significant because: 1. Explains Chargaff’s Rule 2. Suggest mechanism for DNA replication 3. Dictates combination of complementary base pairs, but places no restriction on the linear sequence (can be highly variable) 4. Hydrogen bonds stabilize the structure. 19

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Base Pairing 21

DNA Structure 22

DNA

II. Concept 16. 2: DNA Replication and Repair � In a second paper Watson and Crick published their hypothesis for how DNA replicates. � The model of DNA structure suggests a template mechanism for DNA replication. A. Steps to DNA Replication 1. Two DNA strands separate. 2. Each strand is a template for assembling a complementary strand. 3. Nucleotides line up singly along the template strand in accordance with the base-pairing rules (A—T; G—C) 4. Enzymes link the nucleotides together at their sugar phosphate groups. 25

DNA Replication 26

B. Watson and Crick’s Model is a Semiconservative Model for DNA Replication. � When a double helix replicates, each of the two daughter molecules will have one old or conserved strand from the parent molecule and one newly created strand. � In the late 1950’s Matthew Meselson and Franklin Stahl provided the experimental evidence to support the semiconservative model of DNA replication. 28

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C. A Closer Look at DNA Replication � The copying of DNA is remarkable in its speed and accuracy � More than a dozen enzymes and other proteins participate in DNA replication 1. Replication begins at special sites called origins of replication, where the two DNA strands are separated, opening up a replication “bubble” � These areas have a specific sequence of nucleotides. � Also creates a Replication Fork 2. A eukaryotic chromosome may have hundreds or even thousands of origins of replication 3. Replication proceeds in both directions from 30 each origin, until the entire molecule is copied

DNA Replication in Prokaryotic Cell 31

DNA Replication in a Eukaryotic Cell 32

4. At the end of each replication bubble is a replication fork, a Y-shaped region where new DNA strands are elongating 5. Helicases are enzymes that untwist the double helix at the replication forks 6. Single-strand binding protein binds to and stabilizes single-stranded DNA until it can be used as a template 7. Topoisomerase corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands 33

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8. DNA Polymerase- helps synthesize new DNA by adding nucleotides to a preexisting chain. � DNA Pol III- adds DNA nucleotide to RNA primer and continues adding nucleotides complementary to original DNA template strand. 9. DNA polymerases cannot initiate synthesis of a polynucleotide; they can only add nucleotides to the 3 end 10. The initial nucleotide strand is a short RNA primer which is formed by an enzyme called primase which uses the parental DNA as a template �The primer is short (5– 10 nucleotides long), and the 3 end serves as the starting point for 35 the new DNA strand

D. Synthesizing a New DNA Strand 1. Enzymes called DNA polymerases catalyze the elongation of new DNA at a replication fork �New nucleotides align themselves along the templates of the old DNA strands (A-T and CG). 2. Most DNA polymerases require a primer and a DNA template strand 3. The rate of elongation is about 500 nucleotides per second in bacteria and 50 per second in human cells 4. Each nucleotide that is added to a growing DNA strand is a nucleoside triphosphate 36

5. d. ATP supplies adenine to DNA and is similar to the ATP of energy metabolism 6. The difference is in their sugars: d. ATP has deoxyribose while ATP has ribose 7. As each monomer of d. ATP joins the DNA strand, it loses two phosphate groups as a molecule of pyrophosphate 37

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E. Antiparallel Elongation 1. The antiparallel structure of the double helix (two strands oriented in opposite directions) affects replication 2. DNA polymerases add nucleotides only to the free 3 end of a growing strand; therefore, a new DNA strand can elongate only in the 5 to 3 direction 3. Along one template strand of DNA, the DNA polymerase synthesizes a leading strand continuously, moving toward the replication fork 4. To elongate the other new strand, called the lagging strand, DNA polymerase must work in the direction away from the replication fork 5. The lagging strand is synthesized as a series of 39 segments called Okazaki fragments, which are joined together by DNA ligase

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DNA Replication � DNA Pol I- replaces RNA nucleotides of the primer with DNA nucleotides- moving from 5’ to 3’. � DNA Ligase- seals Okazaki fragments and newly synthesized DNA into one continuous DNA strand. (joins sugar phosphate backbone)

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F. Proofreading and Repairing DNA 1. DNA polymerases proofread newly made DNA, replacing any incorrect nucleotides 2. In mismatch repair of DNA, repair enzymes correct errors in base pairing 3. DNA can be damaged by chemicals, radioactive emissions, X-rays, UV light, and certain molecules (in cigarette smoke for example) 47

F. Proofreading and Repairing DNA 4. In nucleotide excision repair, a nuclease cuts out and replaces damaged stretches of DNA � Nucleotide Excision Repair- damaged segment of DNA is cut out, and gap is filled by DNA Pol I and DNA Ligase. � Nuclease- DNA cutting enzyme. Removes damaged DNA. 48

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G. Replicating the Ends of DNA Molecules 1. Limitations of DNA polymerase create problems for the linear DNA of eukaryotic chromosomes 2. The usual replication machinery provides no way to complete the 5 ends, so repeated rounds of replication produce shorter DNA molecules 3. Eukaryotic chromosomal DNA molecules have at their ends nucleotide sequences called telomeres 4. Telomeres do not prevent the shortening of DNA molecules, but they do postpone the erosion of genes near the ends of DNA 50 molecules

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Telomeres 52

6. If chromosomes of germ cells became shorter in every cell cycle, essential genes would eventually be missing from the gametes they produce 7. An enzyme called telomerase catalyzes the lengthening of telomeres in germ cells 8. The shortening of telomeres might protect cells from cancerous growth by limiting the number of cell divisions 9. There is evidence of telomerase activity in cancer cells, which may allow cancer cells to 53 persist

III. Concept 16. 3: A chromosome--a DNA molecule packed together with proteins 1. The bacterial chromosome is a double-stranded, circular DNA molecule associated with a small amount of protein 2. Eukaryotic chromosomes have linear DNA molecules associated with a large amount of protein 3. Chromatin is a complex of DNA and protein, and is found in the nucleus of eukaryotic cells 4. Histones are proteins that are responsible for the first level of DNA packing in chromatin 54

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5. Chromatin is organized into fibers a. 10 -nm fiber � DNA winds around histones to form nucleosome beads” � Nucleosomes are strung together like beads on a string by linker DNA b. 30 -nm fiber �Interactions between nucleosomes cause thin fiber to coil or fold into this thicker fiber c. 300 -nm fiber � The 30 -nm fiber forms looped domains that attach to proteins d. Metaphase chromosome 57� The looped domains coil further

6. Most chromatin is loosely packed in the nucleus during interphase and condenses prior to mitosis 7. Loosely packed chromatin is called euchromatin 8. During interphase a few regions of chromatin (centromeres and telomeres) are highly condensed into heterochromatin 9. Dense packing of the heterochromatin makes it difficult for the cell to express genetic information coded in these regions 10. Histones can undergo chemical modifications that result in changes in chromatin organization �For example, phosphorylation of a specific amino 58 acid on a histone tail affects chromosomal

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You should now be able to: 1. Describe the contributions of the following people: Griffith; Avery, Mc. Cary, and Mac. Leod; Hershey and Chase; Chargaff; Watson and Crick; Franklin; Meselson and Stahl 2. Describe the structure of DNA 3. Describe the process of DNA replication; include the following terms: antiparallel structure, DNA polymerase, leading strand, lagging strand, Okazaki fragments, DNA ligase, primer, primase, helicase, topoisomerase, single-strand binding proteins 4. Describe the function of telomeres 5. Compare a bacterial chromosome and a eukaryotic chromosome 60

Warm Up Exercise � What type of bonds hold the DNA together? � Which bases are purines and which are pyrimidines? � What happens in transformation?

Warm Up Exercise � Briefly state the function of the following enzymes in your own words: � Ligase � Polymerase III � Helicase � Topoisomerase � Primase