BIOCHEMISTRY - L. Stryer - 1984

VOLUME 3

Part IV INFORMATION

CHAPTER 24 DNA: THE GENETIC ROLE, STRUCTURE, AND REPLICATION

Summary

DNA is the molecule of heredity in all prokaryotic and eukaryotic organisms. In Viruses, the genetic material is either DNA or RNa. Cellular DNA generally consists of two very long helical polynucleotide chains wound around a common axis. The two strands of The Double Helix are oriented in opposite directions (antiparallel). The sugar-phosphate backbone of each strand lies on the outside of the double helix, while the purine and pyrimidine bases are on the inside. The two strands are held together by Hydrogen Bonds between Base Pairs. Adenine (A) always pairs with thymine (T), and guanine (G) with cytosine (C). Thus, the strands of the double helix are mutually complementary. The Genetic information is encoded in The sequence of bases along the chain. Most DNA molecules are circular. The axis of the double helix in circular DNA can itself twist to form a superhelix. Supercoiled DNA has a more compact conformation than relaxed DNA.

During METABOLISM/36.html">DNA Replication, the two strands of the double helix unwind and separate as new strands are synthesized. Each parental strand serves as a template for The formation of a new complementary strand. Thus, DNA replication is semi-conservative—each daughter molecule receives one strand from the parental DNA molecule. DNA replication is a complex process involving numerous Proteins, including Three types of DNA polymerases and DNA ligase. The activated precursors for DNA Synthesis are four deoxyribonucleoside 5'-triphosphates. The new strand is synthesized in the 5' → 3' direction. This synthesis proceeds via a nucleophilic attack of the internal phosphorus atom of the incoming deoxynucleoside triphosphate by the 3'-hydroxyl terminus of the primer strand. Crucially, DNA polymerase catalyzes the formation of a phosphodiester bond only if the Base of the incoming nucleotide is complementary to the base on the template strand. In other words, DNA polymerases are template-directed Enzymes. DNA polymerases I, II, and III also possess 3' → 5' exonuclease activity, which enhances replication fidelity by removing mismatched residues. Furthermore, DNA polymerases I and III exhibit 5' → 3' nuclease activity, which plays a vital role in DNA Replication and Repair mechanisms.

DNA replication in E. coli Cells begins at a precisely defined site (THE ORIGIN OF replication) and proceeds bidirectionally. At the Replication fork (where two DNA strands become four), both parental DNA strands serve as templates for the synthesis of new DNA. The rep protein unwinds the parental DNA utilizing the energy of ATP Hydrolysis. Unwinding is also facilitated by DNA gyrase, which acts as a molecular swivel and introduces negative supercoils into the parental DNA. One DNA strand (the leading strand) is synthesized continuously, whereas the other (the lagging strand) is synthesized in fragments approximately 1kb in length. Because the lagging strand is assembled from discrete fragments, polymerization in the 5' → 3' direction results in overall chain growth in the 3' → 5' direction. The synthesis of new DNA is preceded by the synthesis of An RNA primer. Subsequently, the RNA component within the newly formed RNA-DNA hybrid is hydrolyzed and replaced by DNA. DNA ligase then joins the newly synthesized DNA fragments that are paired with the same template strand. This reaction utilizes NAD⁺ as an energy source.

DNA Damage caused by ionizing radiation, ultraviolet light, and various chemical agents is continuously repaired. For example, pyrimidine dimers induced by ultraviolet light are excised by a specific endonuclease. Uracil, which arises from the Spontaneous deamination of cytosine in DNA, is removed by a glycosylase that distinguishes between uracil and thymine.

Restriction enzymes recognize specific sequences exhibiting twofold rotational Symmetry and hydrolyze a single phosphodiester bond in each DNA strand within that region. These endonucleases can be used to cleave DNA molecules into specific fragments suitable for further study. The Development of Methods that enable the rapid determination of nucleotide sequences in DNA through specific Cleavage and electrophoretic Separation of products has revolutionized The Study of Introduction/20.html">DNA Structure.