The writing of this book is based on: 1. earlier experience writing textbooks for biology students with a university-level background in biology and biochemistry with many (> 200) ?gures in these books (in Hungarian), 2. and on the necessity to present university lectures as power point presentations to catch the interest of s- dents. The author realizes that young readers who were grown up in an information society are relactant to read too much unless they have to take exams. Even then they prefer books which contain illustrations for a better understanding. In collaboration with colleagues, referees and members of the publishing staff an extensive set of photographs and illustrations were collected to provide a graphic follow-up to the text. Further aids for the student, instructor and the curious reader are provided by summaries, extensive sets of readings and references for each chapter, a glossary of the terms, list of abbreviations and a DVD with a red-blue eyeglass to visualize three dimensional chromatin structures. The reader could ask: Why another book on apoptosis? The answer to the question is related to the de?nition of the process. The term apoptosis has been introduced to describe typical morphological changes leading to controlled se- destruction of cells. The ?rst demonstrated biochemical feature of this type of cell death was internucleosomal fragmentation, which was occasionally preceded by the generation of large DNA fragments.
I. DNA EMPIRE Summary Historical events leading to the recognition of core processes of genetic information RNA World Pre-RNA World Additional arguments supporting the RNA World hypothesis Basic principles of the transfer of genetic information Core information processes belonging to the DNA Empire When did DNA evolve? Molecular oxygen serving the transition from RNA World to DNA Empire Saturation of seawater with oxygen and development of oxygen atmosphere Advantage of oxygen production Oxygen the Janus faced molecule Protection of anaerobes from oxygen toxicity Free radical formation during the synthesis of deoxyribonucleotides Cellular responses to DNA damage Conceptual changes in gene stability Primary information on cytotoxicity obtained at DNA level Detection of genotoxic changes at the structural level of DNA Enzymatic detection of cellular lesions: too late Early detection of cytotoxicity: at DNA level Conclusions References II. STRUCTURAL ORGANIZATION OF DNA Summary Building blocks of nucleic acids Structure of nucleotides Nucleic acid bases Types Aromatic character, planar structure of nucleic acid bases Free nucleic acid bases Light absorption Apolar interactions Hypochrome, hyperchrome effect Major, minor and rare bases Base analogues Antimetabolites Sugar component of nucleotides Why ribose was selected as the sugar component of nucleic acids Criteria for sugar selection Phosphate as nucleotide component Bond types in nucleotides Nomenclature of bases, nucleosides and nucleotides Metabolism of nucleotides De novo biosynthesis Basic conception of biosynthesis Ribonucleotide biosynthesis Deoxyribonucleotide biosynthesis dNDP--dNTP conversion dUMP formation Thymidilate formation (dUMP--dTMP) Regulation of nucleotide biosynthesis Degradation of nucleotides Biosynthesis of coenzymes Tissue specific purine synthesis Function of nucleotides DNA structure Structural levels of DNA Primary structure of DNA Secondary DNA structures H-bonds B-DNA A-DNA Z-DNA Cruciform DNA Bent DNA structures Transition from right-handed to left-handed DNA Tetraplex (quadruplex) DNA Differences in the structure of DNA and RNA Tertiary structure of DNA (topology) Thermodinamic aspects of supercoiling Topoisomerases Models of gyrase action Sign inversion and torsional model of supercoiling Rotating model of negative supercoiling Topology of eukaryotic DNA Nucleosome, the supercoil analogue in eukaryotes Supranucleosomal (chromosomal) organization of DNA Early chromatin models Solenoid versus zig-zag model Possible fibril arrangements Hairpin model Plectonemic model of chromatin condensation Chromosomes of animal cells Eukaryotic genome size and DNA compaction Chromosome number Metaphase chromosomes Centromere and teleomere regions of chromosomes Variation in DNA content, C-value paradox Variation in chromosome number Karyotype, chromosome size Genetic linkage Physical mapping Sex chromosomes Chromosomal aberrations Genetic diversity Eukaryotic cell cycle Cytogenetics Genes Temporal and spatial order of gene replication DNA is replicated and repaired in several subphases References III. CHROMATIN CONDENSATION Summary Importance of chromatin condensation Active and inactive chromatin Euchromatin and heterochromatin Histone code hypothesis Chromosome arrangement in the nucleus Models of chromosome condensation Chromatin folding in the interphase nucleus is poorly understood Chromatin models Review of methodologies Methods to visualize chromosome condensation during the cell cycle Centrifugal elutriation Permeable cellsTe