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Berg • Tymoczko • Stryer Biochemistry Sixth Edition Chapter 4: DNA, RNA, and the Flow of Genetic Information Copyright © 2007 by W. H. Freeman and Company 4.1 A nucleic acid consists of four kinds of bases linked to a sugar phosphate backbone Linear polimer RNA and DNA differ in the sugar component and one of the bases Backbone of the nucleic acid Purines and pyrimidines 3’ to 5’ phosphodiester bond Greater stability of DNA than that of RNA Nucleotides are monomeric units of nucleic acids Nucleoside ( e.g. adenosine, deoxyadenosine) N-glycosidic linkage Nucleotide ( e.g. ATP, deoxyadenylate) Length of a DNA molecule 4.2 A pair of nucleic acid chains with complementary sequences can form a double-helical structure replication The double helix is stabilized by hydrogen bonds and hydrophobic interactions X-ray diffraction of DNA fiber – helical structure with two chains Regular structure with different bases Stability of the helix: hydrogen bonds, van der Waals interactions, hydrophobic interactions The double helix facilitates the accurate transmission of hereditary information Semiconservative replication Meselson and Stahl experiment: grow E. coli in 15NH4Cl first then in 14NH4Cl Density-gradient equilibrium sedimentation The double helix can be reversibly melted melting temperature, Tm hypochroism melting and annealing helicase Some DNA molecules are circular and supercoiled linear or circular superhelix relaxed or supercoiled Single-stranded nucleic acids can adopt elaborate structures stem-loop More complex structures with nonstandard pairings 4.3 DNA is replicated by polymerases that take instructions from templates DNA polymerase catalyzes phosphodiester-bond formation template, primer, dNTP template-directed enzyme high fidelity The genes of some viruses are made of RNA retrovirus reverse transcriptase 4.4 Gene expression is the transformation of DNA information into functional molecules Several kinds of RNA play key roles in gene expression tRNA, mRNA, rRNA snRNA, scRNA, miRNA, siRNA All cellular RNA is synthesized by RNA polymerases template, rNTP, a divalent metal ion (Mg2+, Mn2+) No primer, lower fidelity than DNA polymerases RNA polymerases take instructions from DNA templates coding strand, template strand Transcription begins near promoter sites and ends at terminator sites promoter and terminator Rho-independent terminator Transfer RNA is the adaptor molecule in protein synthesis an amino acid-attachment site and a template-recognition site aminoacyl-tRNA codon and anticodon 4.5 Amino acids are encoded by groups of three bases starting from a fixed point Genetic code: relation between base sequence and amino acid sequence An amino acid is encoded by a codon Nonoverlapping, no punctuation, and degenerate Major features of the genetic code Degeneracy minimizes the deleterious effects of mutations Permitting DNA base composition to vary a wide range Messenger RNA contains start and stop signals for protein synthesis Termination codons are read by release factors fMet-tRNA recognizes AUG or GUG in prokaryotes The genetic code is nearly universal Mitochondria and ciliated protozoa 4.6 Most eukaryotic genes are mosaics of introns and exons Intervening sequences or introns RNA processing generates mature RNA Colinear with the protein products splicing Many exons encode protein domains Exon shuffling Differential splicing