11 DNA and Its Role in Heredity

11 The Structure of DNA DNA is a polymer of nucleotides. The four nucleotides that make up DNA differ only in their nitrogenous bases. There are two purines (adenine and guanine) and two pyrimidines (cytosine and thymine).

11 The Structure of DNA English physicist Francis Crick and American geneticist James D. Watson established the general structure of DNA. The results of X-ray crystallography convinced them that the DNA molecule was helical. DNA has two polynucleotide chains running antiparallel to each other.

Figure 11.6 (b) DNA Is a Double Helix

11 The Structure of DNA Four features summarize the molecular architecture of DNA:  The DNA molecule is a double-stranded helix.  The diameter of the DNA molecule is uniform.  The twist in DNA is right-handed.  The two strands run in different directions (they are antiparallel).

11 The Structure of DNA The sugar–phosphate backbones of each strand coil around the outside of the helix. The nitrogenous bases point toward the center of the helix. Hydrogen bonds between complementary bases hold the two strands together. A always pairs with T (two hydrogen bonds). G always pairs with C (three hydrogen bonds).

11 The Structure of DNA The phosphate groups link the 3 carbon of one deoxyribose molecule to the 5 carbon of the next. Thus a single strand of DNA has a 5  phosphate group at one end (the 5 end) and a free 3 hydroxyl group at the other end (the 3 end). In a double helix, the 5 end of one polypeptide is hydrogen-bonded to the 3 end of the other, and vice versa.

Figure 11.7 Base Pairing in DNA Is Complementary

11 The Structure of DNA The genetic material performs four important functions:  It stores all of an organism’s genetic information.  It is susceptible to mutation.  It must be precisely replicated in the cell division cycle.  It is expressed as the phenotype.

11 Determining the DNA Replication Mechanism Theoretically, DNA could serve as its own template in one of three different ways:  Semiconservative replication would use each parent strand as a template for a new strand (this is the correct one).  Conservative replication would build an entirely new double helix based on the template of the old double helix.  Dispersive replication would use fragments of the original DNA molecule as templates for assembling two molecules.

Figure 11.8 Three Models for DNA Replication ►

11 The Molecular Mechanisms of DNA Replication DNA replication takes place in two steps:  The hydrogen bonds between the two strands are broken, making each strand available for base pairing.  The new nucleotides are covalently bonded to each growing strand.

11 The Molecular Mechanisms of DNA Replication In DNA replication, nucleotides are added to the 3 end of the growing strand. The three phosphate groups of the deoxyribonucleoside triphosphate are attached to the 5 position of the sugar. Energy for synthesis of nucleotides to the growing chain comes from breaking the bonds between these three phosphates.

Figure Each New DNA Strand Grows from its 5 End to its 3 End

11 The Molecular Mechanisms of DNA Replication A huge protein complex catalyzes DNA replication. This replication complex recognizes an origin of replication on a chromosome. DNA replicates in both directions from the origin, forming two replication forks. In DNA replication, both strands of DNA act as templates.

11 The Molecular Mechanisms of DNA Replication Small chromosomes, such as those found in bacteria, have a single origin of replication. Large chromosomes can have hundreds of origins of replication. Replication occurs at many different sites simultaneously.

11 The Molecular Mechanisms of DNA Replication DNA polymerases cannot build a strand without having an existing strand, called a primer, to start from. In DNA replication, the primer strand is a short strand of RNA complementary to the DNA template strand. An enzyme makes the primer strand.

Figure No DNA Forms without a Primer

11 The Molecular Mechanisms of DNA Replication Recall that new bases are always added to the 3 end of a growing DNA strand. The strands in the template DNA are antiparallel, however. As a result, as the strands pass through the replication complex, one strand (the leading strand) will be in the correct orientation for addition of new nucleotides. The other strand (the lagging strand) will be in the reverse orientation.

Figure The Two New Strands Form in Different Ways

11 The Molecular Mechanisms of DNA Replication Because of its backward orientation, the lagging strand must grow in relatively small, discontinuous pieces, called Okazaki fragments. Each Okazaki fragment requires an RNA primer strand. DNA polymerase synthesizes complementary DNA starting from the 3 end of the new primer and working toward the previous Okazaki fragment.

Figure Many Proteins Collaborate at the Replication Fork

11 The Molecular Mechanisms of DNA Replication When DNA polymerase reaches the previous Okazaki fragment, it is released. The RNA primer of the previous Okazaki fragment is then replaced with DNA.

Figure The Lagging Strand Story (Part 1)

Figure The Lagging Strand Story (Part 2)

11 DNA Proofreading and Repair The vast majority of DNA errors are neutral at best and fatal at worst. To minimize the number of errors, our cells have three DNA repair mechanisms:  Proofreading  Mismatch repair  Excision repair

11 DNA Proofreading and Repair As they add new bases to a growing strand, DNA polymerases make a proofreading check. When a DNA polymerase recognizes an error, it removes the wrong nucleotide and puts in correct one. This proofreading function reduces the overall error rate to about one base in a billion.

11 DNA Proofreading and Repair The mismatch repair mechanism scans new DNA for mismatched base pairs. This mechanism can distinguish between the template strand and the new strand. Thus, this mechanism can determine which base is correct (the base on the template strand) and which base needs to be replaced.

11 DNA Proofreading and Repair Excision repair proteins operate over the life of a cell. DNA is subject to damage by chemicals, radiation, and random spontaneous chemical reactions. Excision repair enzymes “inspect” the cell’s DNA for damage, then cut the damaged strand and remove it.

Figure DNA Repair Mechanisms

11 Practical Applications of DNA Replication The polymerase chain reaction (PCR) technique is a simple method for making multiple copies of a DNA sequence. PCR cycles through three steps:  Double-stranded fragments of DNA are heated to denature them into single strands.  A short primer is added, along with the four dNTPs.  DNA polymerase catalyzes the production of new DNA strands.

Figure The Polymerase Chain Reaction

11 Practical Applications of DNA Replication PCR did not become practical until the discovery of a DNA polymerase that could survive the heat required to denature the DNA. Such a DNA polymerase was found in bacteria that live in hot springs at Yellowstone National Park. PCR has had an enormous impact on genetic research.