Note: Cover -- Half Title -- Title Page -- Copyright Page -- Foreword -- Preface -- Acknowledgments -- Contents -- Special Features -- Detailed Contents -- Life Processes are Driven by Macromolecular Assemblies and Machines -- Chapter 1 The Machines and Assemblies of Life -- 1.1 EXPRESSION OF THE GENETIC BLUEPRINT -- The flow of information is not perfect and not always in one direction -- 1.2 WEAK FORCES AND MOLECULAR INTERACTIONS -- All weak forces other than hydrophobic interactions are electrostatic in origin -- Hydrophobic interactions drive the folding and assembly of macromolecules -- The energy balance in folding and assembly has both enthalpic and entropic contributions -- Size and topography matter for interaction patches -- A certain minimum strength of interaction is required for specificity -- Cooperativity enhances stability in multi-subunit complexes -- 1.3 PROTEIN FOLDING AND STABILITY -- Protein folding follows pathways populated with intermediates -- Protein structures are only marginally stable -- Protein stability correlates with size and other factors such as covalent cross-links -- Many cellular proteins denature collectively under thermal stress -- Proteins from thermophilic organisms are not very different from mesophilic homologs -- 1.4 SELF-ASSEMBLY AND SYMMETRY -- Most proteins form symmetrical oligomers with two or more subunits -- Symmetry defines a set of larger structures composed of multiple copies of identical subunits -- Line and cyclic point group symmetries generate helices and rings -- Cubic symmetry is employed in a variety of oligomeric proteins -- Assembly proceeds along pathways -- Why are there so many large macromolecular assemblies? -- 1.5 MACROMOLECULAR DYNAMICS -- Ensemble methods measure the net signal from numerous contributors -- 'Single-molecule' methods interrogate macromolecules one at a time. , Molecular dynamics models the motions of crystal structures in the presence of a force field -- 1.6 CATALYSIS -- Enzymes form highly specific but transient complexes with their substrates -- Enzyme kinetics are governed by a few equations -- A key feature of enzyme catalysis is the tight binding of the transition state -- Enzymes generate catalytic rate enhancements in multiple ways -- Enzymes can be inhibited reversibly and irreversibly -- Coupling of enzyme-catalyzed reactions allows energetically unfavorable reactions to occur -- 1.7 SIGNALING AND REGULATORY MECHANISMS -- Ligand-induced conformational change and cooperativity are widespread methods of controlling biological activity -- Allosteric proteins are regulated by a special form of cooperativity -- Allosteric enzymes do not follow Michaelis-Menten kinetics -- Allostery is mediated by protein/protein interactions and conformational changes -- Reversible covalent modification controls the activities of some proteins -- Homeostasis is an important aspect of response to environmental change -- 1.8 MACROMOLECULAR CROWDING -- Molecular crowding affects reaction rates, protein folding, assembly, and stability -- Macromolecular crowding affects diffusion rates -- Models of crowded intracellular environments can now be built -- 1.9 CELLULAR COMPARTMENTATION AND EVOLUTION -- All cells belong to one of the three Urkingdoms: Archaea, Bacteria, Eukarya -- Bacteria have an open compartment, the nucleoid, and a membrane-delimited compartment, the periplasm -- Archaea more closely resemble eukaryotes than bacteria in some key features -- Major differences exist between archaeal and bacterial cell envelopes -- Eukaryotic cell organelles probably arose by engulfing bacteria -- Higher eukaryotes have similar numbers of genes as lower eukaryotes but many more regulatory elements -- References. , Chapter 2 Chromatin -- 2.1 INTRODUCTION -- 2.2 NUCLEOSOMES AND HIGHER ORDER CHROMATIN STRUCTURES -- The core histones have a two-domain organization and structure -- Core histones assemble into H2A-H2B and H3-H4 heterodimers and form a metastable histone octamer -- A nucleosome is 147 bp of DNA wrapped around a histone octamer -- Nucleosomal DNA is a highly distorted superhelix -- Nucleosomes are assembled sequentially with the help of histone chaperones -- The structure of the nucleosome is intrinsically dynamic -- DNA sequence directs specific positioning of nucleosomes in vitro and in vivo -- Nucleosomal arrays form higher order structures that differ in their degree of condensation -- Linker histones stabilize condensed 30 nm chromatin structures -- The structure of the 30 nm fiber remains unsettled -- The 30 nm fiber has a heteromorphic structure dependent on nucleosome repeat length and packing order -- Higher order folding of nucleosomal arrays is regulated by cations and the core histone N-terminal tail domains -- Core histone isoforms have variant sequences and functions -- Core histones undergo many specific post-translational modifications with structural implications -- Chromatin architectural proteins are essential for higher order chromatin structures -- Genomic chromatin is a heterogeneous and complex macromolecular assembly -- Elucidating chromosomal architecture beyond the 30 nm fiber remains a challenge -- 2.3 REMODELING COMPLEXES -- Remodelers regulate DNA exposure in chromatin -- Remodelers can be separated into four families defined by their composition and activities -- Remodelers have specialized as well as common properties -- The disruption of histone-DNA contacts is ATP-dependent -- Remodeler regulation depends on the interplay with histone post-translational modifications. , Structural models inform how remodelers engage and remodel nucleosomes -- 2.4 EPIGENETIC MECHANISMS -- Histone post-translational modifications are carriers of epigenetic information -- Special protein domains recognize specifically modified histone residues -- The histone code hypothesis suggests that the PTM pattern of a nucleosome acts as a ' barcode' -- Methylation of CpG islands is another epigenetic marker that results in widespread gene silencing -- X-chromosome inactivation and imprinting are important epigenetic phenomena in mammalian cells -- 2.5 SUMMARY -- References -- Chapter 3 DNA Replication -- 3.1 INTRODUCTION -- 3.2 INITIATION AND ELONGATION -- A series of multiprotein complexes are recruited to the bacterial origin of DNA replication -- The active form of DnaA is an ATP-dependent oligomer -- DNA replication in eukaryotes proceeds from multiple origins -- The origin recognition complex is the homolog of the DnaA oligomer in eukaryotes -- Bacterial DnaA melts DNA at the origin to enable loading of the DnaB replicative helicase -- Eukaryotic DNA is licensed for replication when an inactive replicative helicase is loaded at the ORC in the G1 phase of the cell cycle -- Helicases use the energy of nucleotide binding and hydrolysis to unwind duplex DNA -- The MCM helicase is activated in S phase of the cell cycle -- The replicative helicases of eukaryotes and archaea track on DNA in a 3' to 5' direction -- Papillomavirus E1 helicase tracks on ssDNA in the 3' to 5' direction -- Single-stranded DNA is bound by a protective protein before it enters the DNA polymerase -- The eukaryotic ssDNA-binding protein RPA also helps organize many other proteins in the replication fork -- The RNA primers for DNA polymerases are synthesized by primase, a special polymerase. , Primases make primers of defined length but exhibit low fidelity in the copying process -- DNA is copied by DNA polymerases -- DNA polymerases contain a 3' to 5' exonuclease as well as a 5' to 3' polymerase activity -- The high fidelity of replicative polymerases arises from multiple sources -- DNA replication is continuous on one strand but not the other -- Numerous enzymes interact at a replication fork and function as a concerted giant assembly -- DNA is synthesized simultaneously on leading and lagging strands -- Three different DNA polymerases are required for DNA replication and operate differently on the leading and lagging strands -- The processivity of DNA polymerases is enhanced by a sliding clamp -- DNA Pol & -- #949 -- and Pol & -- #948 -- , together with many other proteins, associate with a sliding clamp on the DNA -- The & -- #946 -- clamp and DNA polymerase are loaded onto the RNA-primed DNA by an ATP-dependent clamp loader -- The clamp loader forms an ATP-dependent spiral structure round the primer-template junction -- The clamp loader is bound to SSB by a heterodimer of & -- #967 -- and & -- #968 -- proteins -- DNA Pol I and DNA ligase are required to fill in and close the gaps between Okazaki fragments on the lagging strand -- The replisome is held together by an array of protein/protein interactions -- A specialized set of proteins is required for RNA primer excision -- Eukaryotic DNA ligases resemble E. coli LigA but use ATP rather than NAD[sup(+)] as co-substrate -- 3.3 TERMINATION OF DNA REPLICATION -- Bacterial chromosomes contain termination sites for DNA replication -- The linear DNA in eukaryotic chromosomes is replicated by a special mechanism that also protects its ends -- Telomeric DNA is synthesized and maintained by telomerase, a specialized polymerase that utilizes RNA as a template. , Replicons and factories.