DNA Structure

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DNA Structure and Functions : 

DNA Structure and Functions BIOLOGY

Discoveries: The Chemical Nature of DNA : 

Discoveries: The Chemical Nature of DNA 1869—Fredrich Miescher named the chemical nuclei contained nuclein. Other chemists discovered it was acidic and named it nucleic acid. It was soon realized that there were two types of nucleic acids: DNA and RNA. Early in the 20th century, 4 types of nucleotides were discovered.

The Search for Genetic Material Leads to DNA : 

Once Morgan showed that genes are located on chromosomes, proteins and DNA were the candidates for the genetic material. Until the 1940s, the specificity of function of proteins seemed to indicate that they were the genetic material. However, this was not consistent with experiments with microorganisms, like bacteria and viruses. The Search for Genetic Material Leads to DNA Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

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Frederick Griffith (1928) studied Streptococcus pneumoniae, a bacterium that causes pneumonia in mammals. The R strain was harmless. The S strain was pathogenic. Griffith mixed heat-killed S strain with live R strain bacteria and injected this into a mouse. The mouse died and he recovered the pathogenic strain from the mouse’s blood. Griffith called this transformation, a change in genotype and phenotype due to the assimilation of a foreign substance by a cell. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

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Oswald Avery, Maclyn McCarty and Colin MacLeod (1944) announced that they found that only DNA transformed the cells. To replicate, a virus infects a host cell and takes over the cell’s metabolic machinery. Viruses that specifically attack bacteria are called bacteriophages or just phages. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

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The fact that cells double the amount of DNA in a cell prior to mitosis and then distribute the DNA equally to each daughter cell provided some circumstantial evidence that DNA was the genetic material in eukaryotes. Similar circumstantial evidence came from the observation that diploid sets of chromosomes have twice as much DNA as the haploid sets in gametes of the same organism. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Watson and Crick Discovered the Structure of DNA by Building Models of X-ray Data : 

Watson and Crick Discovered the Structure of DNA by Building Models of X-ray Data Maurice Wilkins and Rosalind Franklin used X-ray crystallography to study the structure of DNA. X-rays are diffracted as they passed through purified, crystallized DNA. The diffraction pattern can be used to deduce the three-dimensional shape of molecules. James Watson learned from their research that DNA was helical in shape.

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Watson and his colleague Francis Crick began to work on a model of DNA with two strands, the double helix. The key breakthrough came when Watson put the sugar-phosphate chain on the outside and the nitrogen bases on the inside of the double helix. The sugar-phosphate chains of each strand are like the side ropes of a rope ladder. Pairs of nitrogen bases, one from each strand, form rungs. The ladder forms a twist every ten bases. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

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Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 16.5

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The nitrogenous bases are paired in specific combinations: adenine with thymine and guanine with cytosine. Only a pyrimidine-purine pairing would produce the2-nm diameter indicated by the X-ray data. Watson and Crick determined that chemical side groups off the nitrogen bases would form hydrogen bonds, connecting the two strands. In April 1953, Watson and Crick published a succinct, one-page paper in Nature reporting their double helix model of DNA.

Base Pairing Enables Existing DNA Strands to Serve as Templates for New Strands : 

Base Pairing Enables Existing DNA Strands to Serve as Templates for New Strands When a cell copies a DNA molecule, each strand serves as a template for ordering nucleotides into a new complimentary strand. Nucleotides line up along the template strand according to the base-pairing rules. Nucleotides are linked to form new strands.

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Watson and Crick’s model, semiconservative replication, predicts that when a double helix replicates each of the daughter molecules will have one old strand and one newly made strand. Fig. 16.8

A Large Team of Enzymes and Other Proteins Carries Out DNA Replication : 

It takes E. coli less than an hour to copy each of the 5 million base pairs in its single chromosome and divide to form two identical daughter cells. A human cell can copy its 6 billion base pairs and divide into daughter cells in only a few hours. This process is remarkably accurate, with only one error per billion nucleotides. More than a dozen enzymes and other proteins participate in DNA replication. A Large Team of Enzymes and Other Proteins Carries Out DNA Replication Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

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The replication of a DNA molecule begins at special sites, origins of replication. In bacteria, this is a single specific sequence of nucleotides. In eukaryotes, there may be thousands of origin sites per chromosome. The DNA strands separate forming a replication “bubble” with replication forks at each end. The replication bubbles elongate as the DNA is replicated and eventually fuse. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

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DNA polymerases catalyze the elongation of new DNA. As nucleotides align with complementary bases along the template strand, they are added to the growing strand by the polymerase. The strands in the double helix are antiparallel. 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. The 5’ --> 3’ direction of one strand runs counter to the 3’ --> 5’ direction of the other strand.

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DNA polymerases can only add nucleotides to the free 3’ end of a growing DNA strand. A new DNA strand can only elongate in the 5’-->3’ direction. This creates a problem at the replication fork because one parental strand is oriented 3’->5’ into the fork, while the other antiparallel parental strand is oriented 5’->3’ into the fork. At the replication fork, one parental strand (3’-> 5’ into the fork), the leading strand, can be used by polymerases as a template for a continuous complimentary strand. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

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The other parental strand (5’->3’ into the fork), the lagging strand, is copied away from the fork in short segments (Okazaki fragments). Okazaki fragments, each about 100-200 nucleotides, are joined by DNA ligase to form the sugar-phosphate backbone of a single DNA strand. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 16.13

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DNA polymerases cannot initiate synthesis of a polynucleotide. Starting a new chain requires a primer, a short segment of RNA about 10 nucleotides long. Primase, an RNA polymerase, links ribonucleotides that are complementary to the DNA template into the primer. DNA polymerase can then add new nucleotides away from the fork until it runs into the previous Okazaki fragment. The primers are converted to DNA before DNA ligase joins the fragments together. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

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Fig. 16.16 To summarize, at the replication fork, the leading stand is copied continuously into the fork from a single primer. The lagging strand is copied away from the fork in short segments, each requiring a new primer.

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In addition to primase, DNA polymerases, and DNA ligases, several other proteins have prominent roles in DNA synthesis. A helicase untwists and separates the template DNA strands at the replication fork. Single-strand binding proteins keep the unpaired template strands apart during replication. Fig. 16.15

Enzymes Proofread DNA During Its Replication and Repair Damage in Existing DNA : 

DNA polymerase proofreads each new nucleotide as soon as it is added. Mistakes during the initial pairing of template nucleotides and complementary nucleotides occurs at a rate of one error per 10,000 base pairs. If there is an incorrect pairing, the enzyme removes the wrong nucleotide and then resumes synthesis. The final error rate is only one per billion nucleotides. Enzymes Proofread DNA During Its Replication and Repair Damage in Existing DNA

Slide 23: 

In mismatch repair, special enzymes fix incorrectly paired nucleotides. In nucleotide excision repair, a nuclease cuts out a segment of a damaged strand. The gap is filled in by DNA polymerase and ligase. Fig. 16.17

The Ends of DNA Molecules are Replicated By a Special Mechanism : 

Limitations of DNA polymerase create problems. The usual replication provides no way to complete the 5’ ends of daughter DNA strands. Repeated rounds of replication produce shorter and shorter DNA molecules. The Ends of DNA Molecules are Replicated By a Special Mechanism Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

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The ends of eukaryotic chromosomal DNA molecules, the telomeres, have special nucleotide sequences. In human telomeres, this sequence is typically TTAGGG, repeated between 100 and 1,000 times. Telomeres protect genes from being eroded through multiple rounds of DNA replication. Fig. 16.19a

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Eukaryotic cells have evolved a mechanism to restore shortened telomeres. Telomerase uses a short molecule of RNA as a template to extend the 3’ end of the telomere. There is now room for primase and DNA polymerase to extend the 5’ end. It does not repair the 3’-end “overhang,”but it does lengthenthe telomere. Fig. 16.19b

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Telomerase is not present in most cells of multicellular organisms so the DNA of dividing somatic cells and does tend to become shorter. Telomere length may be a limiting factor in the life span of certain tissues and the organism. Telomerase is present in germ-line cells, ensuring that zygotes have long telomeres. Active telomerase is also found in cancerous somatic cells. This overcomes the progressive shortening that would eventually lead to self-destruction of the cancer. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings