Molecular biology: structure and dynamics of genomes and proteomes
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| Format: | Buch |
| Sprache: | English |
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Boca Raton ; London ; New York
CRC Press, Taylor & Francis Group
2023
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| Ausgabe: | Second edition |
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| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | xxi, 709 Seiten Illustrationen, Diagramme 28 cm |
| ISBN: | 9780367678098 0367678098 9780367674083 0367674084 |
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| 245 | 1 | 0 | |a Molecular biology |b structure and dynamics of genomes and proteomes |c Jordanka Zlatanova, Kensal E. van Holde |
| 250 | |a Second edition | ||
| 264 | 1 | |a Boca Raton ; London ; New York |b CRC Press, Taylor & Francis Group |c 2023 | |
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| 650 | 4 | |a Molecular biology | |
| 650 | 4 | |a Genomes | |
| 650 | 4 | |a Proteomics | |
| 650 | 4 | |a Molecular Biology / methods | |
| 650 | 4 | |a Genome / physiology | |
| 650 | 4 | |a Proteome / physiology | |
| 650 | 4 | |a Transcription, Genetic / genetics | |
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Datensatz im Suchindex
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| adam_text | vii Contents Preface xvii Acknowledgments xix About the Authors xxi Chapter l:To the Cell and Beyond: The Realm of Molecular Biology 1 1.1 2 INTRODUCTION 1.2 THE VITAL ROLE OF MICROSCOPY IN BIOLOGY 2 The light microscope led to the first revolution in biology Biochemistry led to the discovery of the importance of macromolecules in life’s structure and processes The electron microscope provided another order of resolution 2 6 6 1.3 FINE STRUCTURE OF CELLS AND VIRUSES AS REVEALED BY MICROSCOPY 8 1.4 ULTRAHIGH RESOLUTION: BIOLOGY AT THE MOLECULAR LEVEL Fluorescence techniques allow for one approach to ultra resolution Confocal fluorescence microscopy allows observation of the fluorescence emitted by a particular substance in a cell FIONA provides ultimate optical resolution by use of fluorescence FRET allows distance measurements at the molecular level Single-molecule cryo-electron microscopy is a powerful new technique The atomic force microscope feels molecular structure X-ray diffraction and nuclear magnetic resonance provide resolution to the atomic level Chemical imaging, the new powerful combination of imaging techniques 10 10 10 11 12 13 14 15 Chapter 2: From Classical Genetics to Molecular Genetics 2.1 INTRODUCTION 2.2 CLASSICAL GENETICS AND THE RULES OF TRAIT INHERITANCE 20 25 26 27 2.3 THE GREAT BREAKTHROUGH TO MOLECU LAR GENETICS 27 Bacteria and bacteriophage exhibit genetic behavior and serve as model systems Transformation and transduction allow transfer of genetic information The Watson-Crick model of DNA structure provided the final key to molecular genetics
27 29 30 2.4 MODEL ORGANISMS 31 2.5 WHOLE GENOMES AND EVOLUTION 33 Evolutionary theory: From Darwin to the present day Human-driven evolution: The story of Vavilov The tree of life based on sequencing of thousands of spe cies: Back to the two-domain tree of life Key concepts Further reading Videos on the Internet 33 36 36 36 37 37 Chapter 3: Proteins 3.1 12 39 INTRODUCTION 39 Proteins are macromolecules with enormous variety in size, structure, and function Proteins are essential for the structure and functioning of all organisms 39 41 41 3.2 PROTEIN STRUCTURE 1.5 MOLECULAR GENETICS: ANOTHER FACE OF MOLECULAR BIOLOGY 15 Key concepts Further reading Videos on the Internet Gregor Mendel developed the formal rules of genetics Mendel s laws have extensions and exceptions Genes are arranged linearly on chromosomes and can be mapped The nature of genes and how they determine phenotypes was long a mystery 15 16 17 19 19 20 Proteins are homogeneous polypeptides and amino acids are their building blocks Fred Sanger and the sequence of insulin In proteins, amino acids are covalently connected to form polypeptides 3.3 LEVELS OF STRUCTURE IN THE POLYPEP TIDE CHAIN 42 42 44 46 The primary structure of a protein is a unique sequence of amino acids A protein’s secondary structure involves regions of regular folding stabilized by hydrogen bonds 46 50
viii Contents Each protein has a unique three-dimensional tertiary structure The tertiary structure of most proteins is divided into distinguishable folded domains Algorithms are now used to identify and classify domains in proteins of known sequence Some domains or proteins are intrinsically disordered Quaternary structure involves associations between pro tein molecules to form aggregated structures 53 55 58 62 64 Genes coding for selectable markers are inserted into vectors during their construction Bacterial plasmids were the first cloning vectors Recombinant bacteriophages can serve as bacterial vectors Cosmids and phagemids expand the repertoire of cloning vectors 5.5 EXPRESSION OF RECOMBINANT GENES Expression vectors allow regulated and efficient expres sion of cloned genes Shuttle vectors can replicate in more than one organism 126 3.5 HOW ARE PROTEINS DESTROYED? The proteasome is the general protein destruction system 70 71 3.6 THE PROTEOME AND PROTEIN INTERAC TION NETWORKS 73 New technologies allow a census of an organism s pro teins and their interactions Key concepts Further reading Videos on the Internet 73 76 76 77 5.6 INTRODUCING RECOMBINANT DNA INTO HOST CELLS Numerous host-specific techniques are used to introduce recombinant DNA molecules into living cells Chapter 4: Nucleic Acids 79 5.7 POLYMERASE CHAIN REACTION AND SITEDIRECTED MUTAGENESIS 4.1 INTRODUCTION Protein sequences are dictated by nucleic acids 80 80 4.2 CHEMICAL STRUCTURE OF NUCLEIC ACIDS DNA and RNA have similar but different chemical structures Nucleic acids (polynucleotides) are polymers
of nucleotides 80 80 82 4.3 PHYSICAL STRUCTURES OF DNA Discovery of the B-DNA structure was a breakthrough in molecular biology A number of alternative DNA structures exist Although the double helix is quite rigid, it can be bent by bound proteins DNA can also form folded tertiary structures Closed DNA circles can be twisted into supercoils 83 4.4 PHYSICAL STRUCTURES OF RNA RNA can adopt a variety of complex structures but not the В-form helix 95 4.5 ONE-WAY FLOW OF GENETIC INFORMATION 99 4.6 METHODS USED TO STUDY NUCLEIC ACIDS Key concepts Further reading Videos on the Internet 100 108 108 109 95 Chapter 5: Recombinant DNA: Principles and Applications 111 5.1 INTRODUCTION Cloning of DNA involves several fundamental steps 112 112 5.2 CONSTRUCTION OF RECOMBINANT DNA MOLECULES Restriction endonucleases and ligases are essential tools in cloning 5.3 VECTORS FOR CLONING 125 125 65 65 66 91 91 92 121 122 5.4 ARTIFICIAL CHROMOSOMES AS VECTORS Bacterial artificial chromosomes meet the need for cloning very large DNA fragments in bacteria Eukaryotic artificial chromosomes provide proper maintenance and expression of very large DNA fragments in eukaryotic cells 3.4 HOW DO PROTEINS FOLD? Folding can be a problem Chaperones help or allow proteins to fold 83 89 118 5.8 SEQUENCING OF ENTIRE GENOMES Genomic libraries contain the entire genome of an organ ism as a collection of recombinant DNA molecules There are two approaches for sequencing large genomes 5.9 MANIPULATING THE GENETIC CONTENT OF EUKARYOTIC ORGANISMS Making a transgenic mouse involves numerous steps To inactivate,
replace, or otherwise modify a particular gene, the vector must be targeted for homologous recombination at that particular site 5.10 PRACTICAL APPLICATIONS OF RECOMBI NANT DNA TECHNOLOGIES Hundreds of pharmaceutical compounds are produced in recombinant bacteria Plant genetic engineering is a huge but controversial industry Gene therapy is a complex multistep process aiming to correct defective genes or gene functions that are responsible for disease Delivering a gene into sufficient cells within a specific tis sue and ensuring its subsequent long-term expression is a challenge CRISPR, the new technology to change genomic DNA sequence at a predefined position Jurassic Park or de-extinction Cloning of whole animals by nuclear transfer Key concepts 125 125 126 128 128 128 129 131 131 132 133 133 134 135 135 137 141 142 143 145 146 Further reading Videos on the Internet 147 148 149 113 Chapter 6: Protein-Nucleic Acid Interactions 151 113 6.1 118 6.2 DNA-PROTEIN INTERACTIONS DNA-protein binding occurs by many modes and mechanisms INTRODUCTION 151 152 152
Contents Site-specific binding is the most widely used mode 154 Most recognition sites fall into a limited number of classes 155 Most specific binding requires the insertion of protein into a DNA groove 156 Some proteins cause DNA looping 157 There are a few major protein motifs of DNA-binding domains 158 Helix-turn-helix motif interacts with the major groove 158 Zinc fingers also probe the major groove 158 Leucine zippers are especially suited for dimeric sites 159 6.3 RNA-PROTEIN INTERACTIONS 6.4 STUDYING PROTEIN-NUCLEIC ACID INTERACTIONS 159 168 168 169 Chapter 7:The Genetic Code, Genes, and Genomes 171 GENES AS NUCLEIC ACID REPOSITORIES OF GENETIC INFORMATION 171 Our understanding of the nature of genes is constantly evolving 171 The central dogma states that information flows from DNA to protein 172 It was necessary to separate cellular RNAs to seek the adaptors 174 Messenger RNA, tRNA, and ribosomes constitute the protein factories of the cell 174 7.2 RELATING PROTEIN SEQUENCE TO DNA SEQUENCE IN THE GENETIC CODE 175 The first task was to define the nature of the code 175 7.3 SURPRISES FROM THE EUKARYOTIC CELL: INTRONS AND SPLICING Eukaryotic genes usually contain interspersed noncoding sequences 7.4 GENES FROM A NEW AND BROADER PER SPECTIVE Protein-coding genes are complex Genome sequencing has revolutionized the gene concept Mutations, pseudogenes, and alternative splicing all con tribute togene diversity 7.5 COMPARING WHOLE GENOMES AND NEW PERSPECTIVES ON EVOLUTION Genome sequencing reveals puzzling features of genomes How are DNA sequence types and functions
distributed in eukaryotes? Key concepts Further reading Videos on the Internet Chapter 8: Physical Structure ofthe Genomic Material 179 179 180 180 180 181 HIGHER-ORDER CHROMATIN STRUCTURE Nucleosomes along the DNA form a chromatin fiber The chromatin fiber is folded, but its structure remains controversial The organization of chromosomes in the interphase nucleus is still obscure 191 8.2 CHROMOSOMES OF VIRUSES AND BACTERIA 192 192 200 213 214 216 217 217 218 219 221 225 225 226 Chapter 9: Transcription in Bacteria 227 9.1 228 INTRODUCTION 9.2 OVERVIEW OF TRANSCRIPTION 228 There are aspects of transcription common to all organisms Transcription requires the participation of many proteins Transcription is rapid but is often interrupted by pauses Transcription can be visualized by electron microscopy 228 229 232 233 RNA POLYMERASES AND TRANSCRIPTION CATALYSIS 235 9.3 RNA polymerases are a large family of enzymes that pro duce RNA transcripts of polynucleotide templates Initiation requires a multisubunit polymerase complex, termed the holoenzyme The initiation phase of bacterial transcription is frequent ly aborted Elongation in bacteria must overcome topological problems There are several mechanisms for transcription termina tion in bacteria Antisense transcription in bacteria is widespread and might have numerous functions Understanding transcription in bacteria is useful in clini cal practice Key concepts Further reading Videos on the Internet INTRODUCTION 213 Chromosomes condense and separate in mitosis A number of proteins are needed to form and maintain mitotic
chromosomes Centromeres and telomeres are chromosome regions with special functions There are a number of models of mitotic chromosome structure Key concepts Further reading Videos on the Internet 182 191 201 8.5 MITOTIC CHROMOSOMES 182 184 188 189 189 201 Eukaryotic chromosomes are highly condensed DNA-protein complexes segregated into a nucleus 201 The nucleosome is the basic repeating unit of eukaryotic chromatin 203 Histone nonallelic variants and postsynthetic modifica tions create a heterogeneous population of nucleosomes 206 The nucleosome family is dynamic 211 Nucleosome assembly in vivo uses histone chaperones 212 9.4 MECHANICS OF TRANSCRIPTION IN BACTERIA 8.1 Generally, viruses are packages for minimal genomes Bacterial chromosomes are organized structures in the cytoplasm 8.3 EUKARYOTIC CHROMATIN 8.4 162 Key concepts Further reading Videos on the Internet 7.1 DNA-bending proteins and DNA-bridging proteins help to pack bacterial DNA 235 237 237 241 242 244 246 247 249 250 250 ix
x Contents Chapter 10: Transcription in Eukaryotes 251 10.1 INTRODUCTION Transcription in eukaryotes is a complex, highly regulated process Eukaryotic cells contain multiple RNA polymerases, each specific for distinct functional subsets of genes 10.2 TRANSCRIPTION BY RNA POLYMERASE II The yeast Pol II structure provides insights into transcrip tional mechanisms The structure of Pol II is more evolutionarily conserved than its sequence Nucleotide addition during transcription elongation is cyclic Transcription initiation depends on multisubunit protein complexes that assemble at core promoters An additional protein complex is needed to connect Pol II to regulatory proteins Termination of eukaryotic transcription is coupled to polyadenylation of the RNA transcript 10.3 TRANSCRIPTION BY RNA POLYMERASE I 10.4 TRANSCRIPTION BY RNA POLYMERASE III RNA polymerase III specializes in transcription of small genes 10.5 TRANSCRIPTION IN EUKARYOTES: PERVA SIVE AND SPATIALLY ORGANIZED Control of the trp operon involves both repression and attenuation 291 շ5շ The same protein can serve as an activator or a repressor: the ara operon 294 252 11.5 OTHER MODES OF GENE REGULATION IN BACTERIA 295 DNA supercoiling is involved in both global and local regulation of transcription 299 DNA methylation can provide specific regulation 29θ 11.6 COORDINATION OF GENE EXPRESSION IN BACTERIA 297 252 շ53 255 257 262 Networks of transcription factors form the basis of coordi nated gene expression 2Э8 Key concepts Further reading Videos on the Internet 2θ2 Chapter 12: Regulation ofTranscription in
Eukaryotes 301 263 12.1 INTRODUCTION 302 257 264 264 Most of the eukaryotic genome is transcribed Transcription in eukaryotes is not uniform within the nucleus Active and inactive genes are spatially separated in the nucleus 285 288 269 270 10.6 METHODS FOR STUDYING EUKARYOTIC TRANSCRIPTION 2γ1 12.2 REGULATION OF TRANSCRIPTION INITIATION: REGULATORY REGIONS AND TRANSCRIPTION FACTORS Core and proximal promoters are needed for basal and regulated transcription Enhancers, silencers, insulators, and locus control regions are all distal regulatory elements Some eukaryotic transcription factors are activators, others are repressors, and still others can be either, depending on context Regulation can use alternative components of the basal transcriptional machinery Mutations in gene regulatory regions and in transcriptional machinery components lead to human diseases 299 299 300 302 302 303 306 A battery of methods is available for the study of transcription Key concepts Further reading Videos on the Internet 271 277 277 շ78 Chapter 11: Regulation ofTranscription in Bacteria 279 11.1 INTRODUCTION 230 11.2 GENERAL MODELS FOR REGULATION OF TRANSCRIPTION 2θθ The polymerase may stall close to the promoter Transcription elongation rate can be regulated by elongation factors 280 12.4 TRANSCRIPTION REGULATION AND CHROMATIN STRUCTURE 309 What happens to nucleosomes during transcription? 309 Regulation can occur via differences in promoter strength or use of alternative σ factors Regulation through ligand binding to RNA polymerase is called stringent control 11.3 SPECIFIC REGULATION
OFTRANSCRIPTION Regulation of specific genes occurs through cis-trans interactions with transcription factors Transcription factors are activators and repressors whose own activity is regulated in a number of ways Several transcription factors can act synergistically or in opposition to activate or repress transcription 11.4 TRANSCRIPTIONAL REGULATION OF OPERONS IS IMPORTANT TO BACTERIAL PHYSIOLOGY The lac operon is controlled by a dissociable repressor and an activator 281 282 282 284 285 2g5 285 12.3 REGULATION OF TRANSCRIPTIONAL ELONGATION 307 308 308 308 309 12.5 REGULATION OF TRANSCRIPTION BY HISTONE MODIFICATIONS AND VARIANTS Modification of histones provides epigenetic control of transcription Gene expression is often regulated by histone post-translational modifications Readout of histone post-translational modification marks involves specialized protein molecules Post-translational histone marks distinguish transcrip tionally active and inactive chromatin regions Some genes are specifically silenced by post-translational modification in some cell lines Polycomb protein complexes silence genes through H3K27 trimethylation and H2AK119 ubiquitylation 311 311 312 313 314 315 316
Contents Heterochromatin formation at telomeres in yeast silences genes through H4K16 deacetylation 318 HPl-mediated gene repression in the majority of eukary otic organisms involves H3K9 methylation 318 Poly(ADP)ribosylation of proteins is involved in tran scriptional regulation 319 Histone variants H2A.Z, H3.3, and H2A.Bbd are present in active chromatin 319 MacroH2A is a histone variant prevalent in inactive chromatin 321 Problems caused by chromatin structure can be fixed by remodeling 321 Endogenous metabolites can exert rheostat control of transcription 323 12.6 DNA METHYLATION DNA methylation patterns in genomic DNA may partici pate in regulation of transcription Carcinogenesis alters the pattern of CpG methylation DNA methylation changes during embryonic development DNA methylation is governed by complex enzymatic machinery There are proteins that read the DNA methylation mark 12.7 LONG NONCODING RNAS IN TRANSCRIP TIONAL REGULATION Noncoding RNAs play surprising roles in regulating tran scription The sizes and genomic locations of noncoding transcripts are remarkably diverse 324 325 327 327 328 328 329 329 330 12.8 METHODS FOR MEASURING THE ACTIVITY OF TRANSCRIPTIONAL REGULATORY ELE MENTS 333 Key concepts Further reading Vidoes on the Internet 334 335 336 Chapter 13: Transcription Regulation in the Human Genome 339 13.1 INTRODUCTION 340 Rapid full-genome sequencing allows deep analysis 340 13.2 BASIC CONCEPTS OF ENCODE 340 ENCODE depends on high-throughput, massively proces sive sequencing and sophisticated computer algo rithms for analysis The ENCODE
project integrates diverse data relevant to transcription in the human genome 13.3 REGULATORY DNA SEQUENCE ELEMENTS Seven classes of regulatory DNA sequence elements make up the transcriptional landscape 13.4 SPECIFIC FINDINGS CONCERNING CHRO MATIN STRUCTURE FROM ENCODE Millions of DNase I-hypersensitive sites mark regions of accessible chromatin DNase I signatures at promoters are asymmetric and stereotypic Nucleosome positioning at promoters and around TFbinding sites is highly heterogeneous 340 342 342 342 343 343 344 345 The chromatin environment at regulatory elements and in gene bodies is also heterogeneous and asymmetric 13.5 ENCODE INSIGHTS INTO GENE REGULATION Distal control elements are connected to promoters in a complex network Transcription factor binding defines the structure and function of regulatory regions Transcription factors interact in a huge network TF-binding sites and TF structure co-evolve DNA methylation patterns show a complex relationship with transcription 13.6 ENCODE OVERVIEW 346 346 346 348 349 351 352 353 What have we learned from ENCODE, and where is it leading? 353 Certain methods are essential to ENCODE project studies 354 13.7 BEYOND THE ENCODE PROJECT 356 Key concepts Further reading Videos on the Internet 357 357 358 Chapter 14: RNA Processing 359 14.1 INTRODUCTION 360 Most RNA molecules undergo post-transcriptional processing 360 There are four general categories of processing 360 Eukaryotic RNAs exhibit much more processing than bacterial RNAs 360 14.2 PROCESSING OF TRNAS AND RRNAS 361 tRNA processing is similar in all organisms All
three mature ribosomal RNA molecules are cleaved from a single long precursor RNA 361 361 14.3 PROCESSING OF EUKARYOTIC MRNA: END MODIFICATIONS 364 Eukaryotic mRNA capping is co-transcriptional Polyadenylation at the З -end serves a number of functions Chemical modifications of eukaryotic RNAs and their roles 364 364 366 14.4 PROCESSING OF EUKARYOTIC MRNA: SPLICING 368 The splicing process is complex and requires great precision 368 Splicing is carried out by spliceosomes 368 Splicing can produce alternative mRNAs 369 Tandem chimerism links exons from separate genes 371 Trans-splicing combines exons residing in the two complementary DNA strands 376 14.5 REGULATION OF SPLICING AND ALTERNA TIVE SPLICING 376 Splice sites differ in strength Exon-intron architecture affects splice-site usage Cis-trans interactions may stimulate or inhibit splicing RNA secondary structure can regulate alternative splicing Sometimes alternative splicing regulation needs no auxiliary regulators The rate of transcription and chromatin structure may help regulate splicing 376 376 377 379 379 379 14.6 SELF-SPLICING: INTRONS AND RIBOZYMES 381 A fraction of introns is excised by self-splicing RNA There are two classes of self-splicing introns 381 381
χϋ Contents 14.7 OVERVIEW: THE HISTORY OF AN MRNA MOLECULE 382 Proceeding from the primary transcript to a functioning mRNA requires a number of steps mRNA is exported from the nucleus to the cytoplasm through nuclear pore complexes RNA sequence can be edited by enzymatic modification even after transcription 382 383 383 14.8 RNA QUALITY CONTROL AND DEGRADATION Bacteria, archaea, and eukaryotes all have mechanisms for RNA quality control Archaea and eukaryotes utilize specific pathways to deal with different RNA defects 14.9 BIOGENESIS AND FUNCTIONS OF SMALL SILENCING RNAS 385 385 386 386 386 390 393 394 Chapter 15: Translation: The Players 395 15.1 INTRODUCTION 396 15.2 A BRIEF OVERVIEW OF TRANSLATION 396 Three participants are needed for translation to occur 396 15.3 TRANSFER RNA 398 tRNA molecules fold into four-arm cloverleaf structures tRNAs are aminoacylated by a set of specific enzymes, aminoacyl-tRNA synthetases Aminoacylation of tRNA is a two-step process Quality control or proofreading occurs during the amino acylation reaction Insertion of noncanonical amino acids into polypeptide chains is guided by stop codons 398 400 400 401 402 407 The Shine-Dalgarno sequence in bacterial mRNAs aligns the message on the ribosome 407 Eukaryotic mRNAs do not have Shine-Dalgarno sequenc es but more complex 5 - and З -untranslated regions 408 Overall translation efficiency depends on a number of factors 410 15.5 RIBOSOMES 410 The ribosome is a two-subunit structure comprising rRNAs and numerous ribosomal proteins 411 Functional ribosomes require both subunits, with specific
complements of RNA and protein molecules 411 The small subunit can accept mRNA but must join with the large subunit for peptide synthesis to occur 413 Ribosome assembly has been studied both in vivo and in vitro 414 The expanding riboverse 417 Key concepts 419 Further reading 420 Videos on the Internet 420 Chapter 16: Translation: The Process 421 16.1 INTRODUCTION 422 16.2 AN OVERVIEW OF TRANSLATION: HOW FAST AND HOW ACCURATE? 422 424 Cryo-EM allows visualization of discrete kinetic states of ribosomes X-ray crystallography provides the highest resolution Single-pair fluorescence resonance energy transfer allows dynamic studies at the single-particle level 424 425 427 16.4 INITIATION OF TRANSLATION 427 Initiation of translation begins on a free small ribosomal subunit Cryo-EM provides details of initiation complexes Start site selection in eukaryotes is complex 427 428 429 16.5 TRANSLATIONAL ELONGATION All ssRNAs are produced by processing from larger precursors Key concepts Further reading Videos on the Internet 15.4 MESSENGER RNA 16.3 ADVANCED METHODOLOGY FOR THE ANALYSIS OF TRANSLATION 430 Decoding means matching the codon to the anticodon carrying aminoacyl-tRNA Accommodation denotes a relaxation of distorted tRNA to allow peptide bond formation Peptide bond formation is accelerated by the ribosome The formation of hybrid states is an essential part of trans location Structural information on bacterial elongation factors provides insights into mechanisms There is an exit tunnel for the peptide chain in the ribosome Translation elongation in eukaryotes involves even
more factors Ribosome stalling during translation elongation 430 432 432 434 436 438 439 439 16.6 TERMINATION OF TRANSLATION 440 RF3 aids in removing RF1 andRF2 Ribosomes are recycled after termination Our views of translation continue to evolve Key concepts Further reading Videos on the Internet 441 442 443 443 444 445 Chapter 17: Regulation ofTranslation 447 17.1 INTRODUCTION 448 17.2 REGULATION OF TRANSLATION BY CON TROLLING RIBOSOME NUMBER 448 Ribosome numbers in bacteria are responsive to the environment 448 Ribosome numbers in eukaryotes: Control and conse quences of dysrégulation 449 Synthesis of ribosomal components in bacteria is coordinated 450 Regulation of the synthesis of ribosomal components in eukaryotes involves chromatin structure 451 17.3 REGULATION OF TRANSLATION INITIATION Regulation of translation initiation is ubiquitous and remarkably varied Regulation may depend on protein factors binding to the 5 - огЗ -ends ofmRNA Cap-dependent regulation is the major pathway for con trolling initiation Initiation may utilize internal ribosome entry sites 5 -3 -UTR interactions provide a novel mechanism that regulates initiation in eukaryotes 454 454 454 455 455 457
xiii Contents Riboswitches are RNA sequence elements that regulate initiation in response to stimuli 457 Repeat-associated non-AUG translation 459 MicroRNAs can bind to mRNA, thereby regulating translation 460 17.4 REGULATION OF THE ELONGATION PROCESS 17.5 mRNA STABILITY AND DECAY IN EUKARYOTES 461 463 The two major pathways of decay for nonfaulty mRNA molecules start with mRNA deadenylation 464 The 5 - 3 pathway is initiated by the activities of the decapping enzyme Dcp2 465 The 3 - 5 pathway uses the exosome, followed by a dif ferent decapping enzyme, DcpS 466 There are additional pathways for mRNA degradation 468 Unused mRNA is sequestered in P bodies and stress granules 468 Cells have several mechanisms that destroy faulty mRNA molecules 471 mRNA molecules that contain premature stop codons are degraded through nonsense-mediated decay or NMD 472 No-go decay (NGD) functions when the ribosome stalls during elongation 473 Non-stop decay or NSD functions when mRNA does not contain a stop codon 473 493 Acetylation mainly modifies interactions Several classes of glycosylated proteins contain added sugar moieties Mechanisms of glycosylation depend on the type of modi fication Ubiquitylation adds single or multiple ubiquitin mol ecules to proteins through an enzymatic cascade Specificity of ubiquitin targeting is determined by a spe cial class of enzymes The structure of protein-ubiquitin conjugates determines the biological role of the modification Polyubiquitin marks proteins for degradation by the proteasome Sumoylation adds single or multiple SUMO molecules to
proteins 494 500 502 504 509 509 510 18.6 PROTEIN CO-TRANSLATIONAL FOLDING 512 18.7 THE GENOMIC ORIGIN OF PROTEINS 513 Key concepts Further reading Videos on the Internet 513 514 515 Chapter 19: DNA Replication in Bacteria 517 518 17.6 SUMMARY OF TRANSLATION REGULATION 474 19.1 INTRODUCTION Key concepts Further reading Videos on the Internet 474 474 476 19.2 FEATURES OF DNA REPLICATION SHARED BYALL ORGANISMS 518 Chapter 18: Protein Processing and Modification 477 18.1 INTRODUCTION 478 18.2 STRUCTURE OF BIOLOGICAL MEMBRANES 478 Biological membranes are protein-rich lipid bilayers Numerous proteins are associated with biomembranes 478 479 18.3 PROTEIN TRANSLOCATION THROUGH BIO LOGICAL MEMBRANES Protein translocation can occur during or after translation Membrane translocation in bacteria and archaea primar ily functions for secretion Membrane translocation in eukaryotes serves a multitude of functions Integral membrane proteins have special mechanisms for membrane insertion Vesicles transport proteins between compartments in eukaryotic cells 18.4 PROTEOLYTIC PROTEIN PROCESSING: CUT TING, SPLICING, AND DEGRADATION Proteolytic cleavage is sometimes used to produce mature proteins from precursors Some proteases can catalyze protein splicing Controlled proteolysis is also used to destroy proteins no longer needed 18.5 POST-TRANSLATIONAL CHEMICAL MODIFI CATIONS OF SIDE CHAINS Modification of side chains can affect protein structure and function Phosphorylation plays a major role in signaling 479 480 480 481 482 484 485 485 486 488 489 489 491 Replication on both strands
creates a replication fork Mechanistically, synthesis of new DNA chains requires a template, a polymerase, and a primer DNA replication requires the simultaneous action of two DNA polymerases Other protein factors are obligatory at the replication fork 518 520 520 521 19.3 DNA REPLICATION IN BACTERIA Bacterial chromosome replication is bidirectional, from a single origin of replication DNA polymerase III catalyzes replication in bacteria Sliding clamp ß, or processivity factor, is essential for processivity The clamp loader organizes the replisome The full complement of proteins in the replisome is orga nized in a complex and dynamic way DNA polymerase I is necessary for maturation of Okazaki fragments 523 523 523 523 523 524 528 19.4 THE PROCESS OF BACTERIAL REPLICATION 530 The replisome is a dynamic structure during elongation 530 19.5 INITIATION AND TERMINATION OF BACTE RIAL REPLICATION 532 Initiation involves both specific DNA sequence elements and numerous proteins Termination of replication also employs specific DNA sequences and protein factors that bind to them 532 534 19.6 DNA REPLICATION AND BACTERIAL CELL CYCLE 536 19.7 BACTERIOPHAGE AND PLASMID REPLICATION 540 Rolling-circle replication is an alternative mechanism Phage replication can involve both bidirectional and rolling-circle mechanisms 542 543
xiv Contents Key concepts Further reading Videos on the Internet 543 546 547 Chapter 20: DNA Replication in Eukaryotes 549 20.1 INTRODUCTION 550 20.2 REPLICATION INITIATION IN EUKARYOTES 550 Replication initiation in eukaryotes proceeds from mul tiple origins 550 Eukaryotic origins of replication have diverse DNA and chromatin structure depending on the biological species 553 There is a defined scenario for formation of initiation complexes 559 Re-replication must be prevented 561 Histone methylation regulates onset of replication licensing 561 20.3 REPLICATION ELONGATION IN EUKARYOTES 561 Eukaryotic replisomes both resemble and significantly differ from those of bacteria 561 Other components of the bacterial replisome have func tional counterparts in eukaryotes Eukaryotic elongation has some special dynamic features 564 565 20.4 REPLICATION OF CHROMATIN 565 Chromatin structure is dynamic during replication Histone chaperones may play multiple roles in replication Both old and newly synthesized histones are required in replication 565 566 567 Epigenetic information in chromatin must also be replicated 568 20.5 THE DNA END-REPLICATION PROBLEM AND ITS RESOLUTION Telomerase solves the end-replication problem Alternative lengthening of telomeres pathway is active in telomerase-deficient cells Holliday junctions are the essential intermediary struc tures in HR 21.4 HOMOLOGOUS RECOMBINATION IN EUKARYOTES Proteins involved in eukaryotic recombination resemble their bacterial counterparts HR malfunction is connected with many human diseases Meiotic recombination allows exchange
of genetic infor mation between homologous chromosomes in meiosis 21.5 NONHOMOLOGOUS RECOMBINATION Transposable elements or transposons are mobile DNA sequences that change positions in the genome Many transposons are transcribed but only a few have known functions There are several types of transposons DNA class II transposons can use either of two mecha nisms to transpose themselves Retrotransposons, or class I transposons, require an RNA intermediate 21.6 SITE-SPECIFIC RECOMBINATION Bacteriophage λ integrates into the bacterial genome by site-specific recombination Immunoglobulin gene rearrangements also occur through site-specific recombination Key concepts Further reading Videos on the Internet 590 590 591 593 596 596 596 598 601 602 602 603 603 616 616 617 570 Chapter 22: DNA Repair 619 570 22.1 INTRODUCTION 620 22.2 TYPES OF LESIONS IN DNA 622 572 20.6 MITOCHONDRIAL DNA REPLICATION 573 Natural agents, from both within and outside a cell, can change the information content of DNA Are circular mitochondrial genomes myth or reality? Models of mitochondrial genome replication are contentious 574 574 22.3 PATHWAYS AND MECHANISMS OF DNA REPAIR 20.7 REPLICATION IN VIRUSES THAT INFECT EUKARYOTES 575 Retroviruses use reverse transcriptase to copy RNA into DNA Key concepts Further reading Videos on the Internet 575 578 579 580 Chapter 21: DNA Recombination 581 21.1 INTRODUCTION 582 21.2 HOMOLOGOUS RECOMBINATION 582 Homologous recombination plays a number of roles in bacteria 583 Homologous recombination has multiple roles in mitotic cells 584 Meiotic exchange is essential to
eukaryotic evolution 584 21.3 HOMOLOGOUS RECOMBINATION IN BACTERIA 584 End resection requires the RecBCD complex 585 586 Strand invasion and strand exchange both depend on RecA Much concerning homologous recombination is still not understood 589 587 622 624 DNA lesions are countered by a number of mechanisms of repair 624 Thymine dimers are directly repaired by DNA photolyase 626 The enzyme Oe-alkylguanine alkyltransferase is involved in the repair of alkylated bases 628 Nucleotide excision repair is active on helix-distorting lesions 628 The role of TFIIH in NER 629 Base excision repair corrects damaged bases 630 Mismatch repair corrects errors in base pairing 630 Methyl-directed mismatch repair in bacteria uses meth ylation on adenines as a guide 631 Mismatch repair pathways in eukaryotes may be directed by strand breaks during DNA replication 632 Repair of double-strand breaks can be error-free or error-prone 633 Homologous recombination repairs double-strand breaks faithfully 633 Nonhomologous end-joining restores the continuity of the DNA double helix in an error-prone process 634 22.4 TRANSLESION SYNTHESIS 635 Many repair pathways utilize RecQ helicases 637
Contents 22.5 CHROMATIN AS AN ACTIVE PLAYER IN DNA REPAIR 637 Key concepts Further reading Videos on the Internet 652 653 654 Histone variants and their post-translational modifications are specifically involved in DNA repair 638 22.6 SUMMARY OF DNA REPAIR 644 Glossary 655 22.7 OVERVIEW: THE ROLE OF DNA REPAIR IN LIFE 645 Index 695 XV
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vii Contents Preface xvii Acknowledgments xix About the Authors xxi Chapter l:To the Cell and Beyond: The Realm of Molecular Biology 1 1.1 2 INTRODUCTION 1.2 THE VITAL ROLE OF MICROSCOPY IN BIOLOGY 2 The light microscope led to the first revolution in biology Biochemistry led to the discovery of the importance of macromolecules in life’s structure and processes The electron microscope provided another order of resolution 2 6 6 1.3 FINE STRUCTURE OF CELLS AND VIRUSES AS REVEALED BY MICROSCOPY 8 1.4 ULTRAHIGH RESOLUTION: BIOLOGY AT THE MOLECULAR LEVEL Fluorescence techniques allow for one approach to ultra resolution Confocal fluorescence microscopy allows observation of the fluorescence emitted by a particular substance in a cell FIONA provides ultimate optical resolution by use of fluorescence FRET allows distance measurements at the molecular level Single-molecule cryo-electron microscopy is a powerful new technique The atomic force microscope feels molecular structure X-ray diffraction and nuclear magnetic resonance provide resolution to the atomic level Chemical imaging, the new powerful combination of imaging techniques 10 10 10 11 12 13 14 15 Chapter 2: From Classical Genetics to Molecular Genetics 2.1 INTRODUCTION 2.2 CLASSICAL GENETICS AND THE RULES OF TRAIT INHERITANCE 20 25 26 27 2.3 THE GREAT BREAKTHROUGH TO MOLECU LAR GENETICS 27 Bacteria and bacteriophage exhibit genetic behavior and serve as model systems Transformation and transduction allow transfer of genetic information The Watson-Crick model of DNA structure provided the final key to molecular genetics
27 29 30 2.4 MODEL ORGANISMS 31 2.5 WHOLE GENOMES AND EVOLUTION 33 Evolutionary theory: From Darwin to the present day Human-driven evolution: The story of Vavilov The tree of life based on sequencing of thousands of spe cies: Back to the two-domain tree of life Key concepts Further reading Videos on the Internet 33 36 36 36 37 37 Chapter 3: Proteins 3.1 12 39 INTRODUCTION 39 Proteins are macromolecules with enormous variety in size, structure, and function Proteins are essential for the structure and functioning of all organisms 39 41 41 3.2 PROTEIN STRUCTURE 1.5 MOLECULAR GENETICS: ANOTHER FACE OF MOLECULAR BIOLOGY 15 Key concepts Further reading Videos on the Internet Gregor Mendel developed the formal rules of genetics Mendel's laws have extensions and exceptions Genes are arranged linearly on chromosomes and can be mapped The nature of genes and how they determine phenotypes was long a mystery 15 16 17 19 19 20 Proteins are homogeneous polypeptides and amino acids are their building blocks Fred Sanger and the sequence of insulin In proteins, amino acids are covalently connected to form polypeptides 3.3 LEVELS OF STRUCTURE IN THE POLYPEP TIDE CHAIN 42 42 44 46 The primary structure of a protein is a unique sequence of amino acids A protein’s secondary structure involves regions of regular folding stabilized by hydrogen bonds 46 50
viii Contents Each protein has a unique three-dimensional tertiary structure The tertiary structure of most proteins is divided into distinguishable folded domains Algorithms are now used to identify and classify domains in proteins of known sequence Some domains or proteins are intrinsically disordered Quaternary structure involves associations between pro tein molecules to form aggregated structures 53 55 58 62 64 Genes coding for selectable markers are inserted into vectors during their construction Bacterial plasmids were the first cloning vectors Recombinant bacteriophages can serve as bacterial vectors Cosmids and phagemids expand the repertoire of cloning vectors 5.5 EXPRESSION OF RECOMBINANT GENES Expression vectors allow regulated and efficient expres sion of cloned genes Shuttle vectors can replicate in more than one organism 126 3.5 HOW ARE PROTEINS DESTROYED? The proteasome is the general protein destruction system 70 71 3.6 THE PROTEOME AND PROTEIN INTERAC TION NETWORKS 73 New technologies allow a census of an organism's pro teins and their interactions Key concepts Further reading Videos on the Internet 73 76 76 77 5.6 INTRODUCING RECOMBINANT DNA INTO HOST CELLS Numerous host-specific techniques are used to introduce recombinant DNA molecules into living cells Chapter 4: Nucleic Acids 79 5.7 POLYMERASE CHAIN REACTION AND SITEDIRECTED MUTAGENESIS 4.1 INTRODUCTION Protein sequences are dictated by nucleic acids 80 80 4.2 CHEMICAL STRUCTURE OF NUCLEIC ACIDS DNA and RNA have similar but different chemical structures Nucleic acids (polynucleotides) are polymers
of nucleotides 80 80 82 4.3 PHYSICAL STRUCTURES OF DNA Discovery of the B-DNA structure was a breakthrough in molecular biology A number of alternative DNA structures exist Although the double helix is quite rigid, it can be bent by bound proteins DNA can also form folded tertiary structures Closed DNA circles can be twisted into supercoils 83 4.4 PHYSICAL STRUCTURES OF RNA RNA can adopt a variety of complex structures but not the В-form helix 95 4.5 ONE-WAY FLOW OF GENETIC INFORMATION 99 4.6 METHODS USED TO STUDY NUCLEIC ACIDS Key concepts Further reading Videos on the Internet 100 108 108 109 95 Chapter 5: Recombinant DNA: Principles and Applications 111 5.1 INTRODUCTION Cloning of DNA involves several fundamental steps 112 112 5.2 CONSTRUCTION OF RECOMBINANT DNA MOLECULES Restriction endonucleases and ligases are essential tools in cloning 5.3 VECTORS FOR CLONING 125 125 65 65 66 91 91 92 121 122 5.4 ARTIFICIAL CHROMOSOMES AS VECTORS Bacterial artificial chromosomes meet the need for cloning very large DNA fragments in bacteria Eukaryotic artificial chromosomes provide proper maintenance and expression of very large DNA fragments in eukaryotic cells 3.4 HOW DO PROTEINS FOLD? Folding can be a problem Chaperones help or allow proteins to fold 83 89 118 5.8 SEQUENCING OF ENTIRE GENOMES Genomic libraries contain the entire genome of an organ ism as a collection of recombinant DNA molecules There are two approaches for sequencing large genomes 5.9 MANIPULATING THE GENETIC CONTENT OF EUKARYOTIC ORGANISMS Making a transgenic mouse involves numerous steps To inactivate,
replace, or otherwise modify a particular gene, the vector must be targeted for homologous recombination at that particular site 5.10 PRACTICAL APPLICATIONS OF RECOMBI NANT DNA TECHNOLOGIES Hundreds of pharmaceutical compounds are produced in recombinant bacteria Plant genetic engineering is a huge but controversial industry Gene therapy is a complex multistep process aiming to correct defective genes or gene functions that are responsible for disease Delivering a gene into sufficient cells within a specific tis sue and ensuring its subsequent long-term expression is a challenge CRISPR, the new technology to change genomic DNA sequence at a predefined position Jurassic Park or de-extinction Cloning of whole animals by nuclear transfer Key concepts 125 125 126 128 128 128 129 131 131 132 133 133 134 135 135 137 141 142 143 145 146 Further reading Videos on the Internet 147 148 149 113 Chapter 6: Protein-Nucleic Acid Interactions 151 113 6.1 118 6.2 DNA-PROTEIN INTERACTIONS DNA-protein binding occurs by many modes and mechanisms INTRODUCTION 151 152 152
Contents Site-specific binding is the most widely used mode 154 Most recognition sites fall into a limited number of classes 155 Most specific binding requires the insertion of protein into a DNA groove 156 Some proteins cause DNA looping 157 There are a few major protein motifs of DNA-binding domains 158 Helix-turn-helix motif interacts with the major groove 158 Zinc fingers also probe the major groove 158 Leucine zippers are especially suited for dimeric sites 159 6.3 RNA-PROTEIN INTERACTIONS 6.4 STUDYING PROTEIN-NUCLEIC ACID INTERACTIONS 159 168 168 169 Chapter 7:The Genetic Code, Genes, and Genomes 171 GENES AS NUCLEIC ACID REPOSITORIES OF GENETIC INFORMATION 171 Our understanding of the nature of genes is constantly evolving 171 The central dogma states that information flows from DNA to protein 172 It was necessary to separate cellular RNAs to seek the adaptors 174 Messenger RNA, tRNA, and ribosomes constitute the protein factories of the cell 174 7.2 RELATING PROTEIN SEQUENCE TO DNA SEQUENCE IN THE GENETIC CODE 175 The first task was to define the nature of the code 175 7.3 SURPRISES FROM THE EUKARYOTIC CELL: INTRONS AND SPLICING Eukaryotic genes usually contain interspersed noncoding sequences 7.4 GENES FROM A NEW AND BROADER PER SPECTIVE Protein-coding genes are complex Genome sequencing has revolutionized the gene concept Mutations, pseudogenes, and alternative splicing all con tribute togene diversity 7.5 COMPARING WHOLE GENOMES AND NEW PERSPECTIVES ON EVOLUTION Genome sequencing reveals puzzling features of genomes How are DNA sequence types and functions
distributed in eukaryotes? Key concepts Further reading Videos on the Internet Chapter 8: Physical Structure ofthe Genomic Material 179 179 180 180 180 181 HIGHER-ORDER CHROMATIN STRUCTURE Nucleosomes along the DNA form a chromatin fiber The chromatin fiber is folded, but its structure remains controversial The organization of chromosomes in the interphase nucleus is still obscure 191 8.2 CHROMOSOMES OF VIRUSES AND BACTERIA 192 192 200 213 214 216 217 217 218 219 221 225 225 226 Chapter 9: Transcription in Bacteria 227 9.1 228 INTRODUCTION 9.2 OVERVIEW OF TRANSCRIPTION 228 There are aspects of transcription common to all organisms Transcription requires the participation of many proteins Transcription is rapid but is often interrupted by pauses Transcription can be visualized by electron microscopy 228 229 232 233 RNA POLYMERASES AND TRANSCRIPTION CATALYSIS 235 9.3 RNA polymerases are a large family of enzymes that pro duce RNA transcripts of polynucleotide templates Initiation requires a multisubunit polymerase complex, termed the holoenzyme The initiation phase of bacterial transcription is frequent ly aborted Elongation in bacteria must overcome topological problems There are several mechanisms for transcription termina tion in bacteria Antisense transcription in bacteria is widespread and might have numerous functions Understanding transcription in bacteria is useful in clini cal practice Key concepts Further reading Videos on the Internet INTRODUCTION 213 Chromosomes condense and separate in mitosis A number of proteins are needed to form and maintain mitotic
chromosomes Centromeres and telomeres are chromosome regions with special functions There are a number of models of mitotic chromosome structure Key concepts Further reading Videos on the Internet 182 191 201 8.5 MITOTIC CHROMOSOMES 182 184 188 189 189 201 Eukaryotic chromosomes are highly condensed DNA-protein complexes segregated into a nucleus 201 The nucleosome is the basic repeating unit of eukaryotic chromatin 203 Histone nonallelic variants and postsynthetic modifica tions create a heterogeneous population of nucleosomes 206 The nucleosome family is dynamic 211 Nucleosome assembly in vivo uses histone chaperones 212 9.4 MECHANICS OF TRANSCRIPTION IN BACTERIA 8.1 Generally, viruses are packages for minimal genomes Bacterial chromosomes are organized structures in the cytoplasm 8.3 EUKARYOTIC CHROMATIN 8.4 162 Key concepts Further reading Videos on the Internet 7.1 DNA-bending proteins and DNA-bridging proteins help to pack bacterial DNA 235 237 237 241 242 244 246 247 249 250 250 ix
x Contents Chapter 10: Transcription in Eukaryotes 251 10.1 INTRODUCTION Transcription in eukaryotes is a complex, highly regulated process Eukaryotic cells contain multiple RNA polymerases, each specific for distinct functional subsets of genes 10.2 TRANSCRIPTION BY RNA POLYMERASE II The yeast Pol II structure provides insights into transcrip tional mechanisms The structure of Pol II is more evolutionarily conserved than its sequence Nucleotide addition during transcription elongation is cyclic Transcription initiation depends on multisubunit protein complexes that assemble at core promoters An additional protein complex is needed to connect Pol II to regulatory proteins Termination of eukaryotic transcription is coupled to polyadenylation of the RNA transcript 10.3 TRANSCRIPTION BY RNA POLYMERASE I 10.4 TRANSCRIPTION BY RNA POLYMERASE III RNA polymerase III specializes in transcription of small genes 10.5 TRANSCRIPTION IN EUKARYOTES: PERVA SIVE AND SPATIALLY ORGANIZED Control of the trp operon involves both repression and attenuation 291 շ5շ The same protein can serve as an activator or a repressor: the ara operon 294 252 11.5 OTHER MODES OF GENE REGULATION IN BACTERIA 295 DNA supercoiling is involved in both global and local regulation of transcription 299 DNA methylation can provide specific regulation 29θ 11.6 COORDINATION OF GENE EXPRESSION IN BACTERIA 297 252 շ53 255 257 262 Networks of transcription factors form the basis of coordi nated gene expression 2Э8 Key concepts Further reading Videos on the Internet 2θ2 Chapter 12: Regulation ofTranscription in
Eukaryotes 301 263 12.1 INTRODUCTION 302 257 264 264 Most of the eukaryotic genome is transcribed Transcription in eukaryotes is not uniform within the nucleus Active and inactive genes are spatially separated in the nucleus 285 288 269 270 10.6 METHODS FOR STUDYING EUKARYOTIC TRANSCRIPTION 2γ1 12.2 REGULATION OF TRANSCRIPTION INITIATION: REGULATORY REGIONS AND TRANSCRIPTION FACTORS Core and proximal promoters are needed for basal and regulated transcription Enhancers, silencers, insulators, and locus control regions are all distal regulatory elements Some eukaryotic transcription factors are activators, others are repressors, and still others can be either, depending on context Regulation can use alternative components of the basal transcriptional machinery Mutations in gene regulatory regions and in transcriptional machinery components lead to human diseases 299 299 300 302 302 303 306 A battery of methods is available for the study of transcription Key concepts Further reading Videos on the Internet 271 277 277 շ78 Chapter 11: Regulation ofTranscription in Bacteria 279 11.1 INTRODUCTION 230 11.2 GENERAL MODELS FOR REGULATION OF TRANSCRIPTION 2θθ The polymerase may stall close to the promoter Transcription elongation rate can be regulated by elongation factors 280 12.4 TRANSCRIPTION REGULATION AND CHROMATIN STRUCTURE 309 What happens to nucleosomes during transcription? 309 Regulation can occur via differences in promoter strength or use of alternative σ factors Regulation through ligand binding to RNA polymerase is called stringent control 11.3 SPECIFIC REGULATION
OFTRANSCRIPTION Regulation of specific genes occurs through cis-trans interactions with transcription factors Transcription factors are activators and repressors whose own activity is regulated in a number of ways Several transcription factors can act synergistically or in opposition to activate or repress transcription 11.4 TRANSCRIPTIONAL REGULATION OF OPERONS IS IMPORTANT TO BACTERIAL PHYSIOLOGY The lac operon is controlled by a dissociable repressor and an activator 281 282 282 284 285 2g5 285 12.3 REGULATION OF TRANSCRIPTIONAL ELONGATION 307 308 308 308 309 12.5 REGULATION OF TRANSCRIPTION BY HISTONE MODIFICATIONS AND VARIANTS Modification of histones provides epigenetic control of transcription Gene expression is often regulated by histone post-translational modifications Readout of histone post-translational modification marks involves specialized protein molecules Post-translational histone marks distinguish transcrip tionally active and inactive chromatin regions Some genes are specifically silenced by post-translational modification in some cell lines Polycomb protein complexes silence genes through H3K27 trimethylation and H2AK119 ubiquitylation 311 311 312 313 314 315 316
Contents Heterochromatin formation at telomeres in yeast silences genes through H4K16 deacetylation 318 HPl-mediated gene repression in the majority of eukary otic organisms involves H3K9 methylation 318 Poly(ADP)ribosylation of proteins is involved in tran scriptional regulation 319 Histone variants H2A.Z, H3.3, and H2A.Bbd are present in active chromatin 319 MacroH2A is a histone variant prevalent in inactive chromatin 321 Problems caused by chromatin structure can be fixed by remodeling 321 Endogenous metabolites can exert rheostat control of transcription 323 12.6 DNA METHYLATION DNA methylation patterns in genomic DNA may partici pate in regulation of transcription Carcinogenesis alters the pattern of CpG methylation DNA methylation changes during embryonic development DNA methylation is governed by complex enzymatic machinery There are proteins that read the DNA methylation mark 12.7 LONG NONCODING RNAS IN TRANSCRIP TIONAL REGULATION Noncoding RNAs play surprising roles in regulating tran scription The sizes and genomic locations of noncoding transcripts are remarkably diverse 324 325 327 327 328 328 329 329 330 12.8 METHODS FOR MEASURING THE ACTIVITY OF TRANSCRIPTIONAL REGULATORY ELE MENTS 333 Key concepts Further reading Vidoes on the Internet 334 335 336 Chapter 13: Transcription Regulation in the Human Genome 339 13.1 INTRODUCTION 340 Rapid full-genome sequencing allows deep analysis 340 13.2 BASIC CONCEPTS OF ENCODE 340 ENCODE depends on high-throughput, massively proces sive sequencing and sophisticated computer algo rithms for analysis The ENCODE
project integrates diverse data relevant to transcription in the human genome 13.3 REGULATORY DNA SEQUENCE ELEMENTS Seven classes of regulatory DNA sequence elements make up the transcriptional landscape 13.4 SPECIFIC FINDINGS CONCERNING CHRO MATIN STRUCTURE FROM ENCODE Millions of DNase I-hypersensitive sites mark regions of accessible chromatin DNase I signatures at promoters are asymmetric and stereotypic Nucleosome positioning at promoters and around TFbinding sites is highly heterogeneous 340 342 342 342 343 343 344 345 The chromatin environment at regulatory elements and in gene bodies is also heterogeneous and asymmetric 13.5 ENCODE INSIGHTS INTO GENE REGULATION Distal control elements are connected to promoters in a complex network Transcription factor binding defines the structure and function of regulatory regions Transcription factors interact in a huge network TF-binding sites and TF structure co-evolve DNA methylation patterns show a complex relationship with transcription 13.6 ENCODE OVERVIEW 346 346 346 348 349 351 352 353 What have we learned from ENCODE, and where is it leading? 353 Certain methods are essential to ENCODE project studies 354 13.7 BEYOND THE ENCODE PROJECT 356 Key concepts Further reading Videos on the Internet 357 357 358 Chapter 14: RNA Processing 359 14.1 INTRODUCTION 360 Most RNA molecules undergo post-transcriptional processing 360 There are four general categories of processing 360 Eukaryotic RNAs exhibit much more processing than bacterial RNAs 360 14.2 PROCESSING OF TRNAS AND RRNAS 361 tRNA processing is similar in all organisms All
three mature ribosomal RNA molecules are cleaved from a single long precursor RNA 361 361 14.3 PROCESSING OF EUKARYOTIC MRNA: END MODIFICATIONS 364 Eukaryotic mRNA capping is co-transcriptional Polyadenylation at the З'-end serves a number of functions Chemical modifications of eukaryotic RNAs and their roles 364 364 366 14.4 PROCESSING OF EUKARYOTIC MRNA: SPLICING 368 The splicing process is complex and requires great precision 368 Splicing is carried out by spliceosomes 368 Splicing can produce alternative mRNAs 369 Tandem chimerism links exons from separate genes 371 Trans-splicing combines exons residing in the two complementary DNA strands 376 14.5 REGULATION OF SPLICING AND ALTERNA TIVE SPLICING 376 Splice sites differ in strength Exon-intron architecture affects splice-site usage Cis-trans interactions may stimulate or inhibit splicing RNA secondary structure can regulate alternative splicing Sometimes alternative splicing regulation needs no auxiliary regulators The rate of transcription and chromatin structure may help regulate splicing 376 376 377 379 379 379 14.6 SELF-SPLICING: INTRONS AND RIBOZYMES 381 A fraction of introns is excised by self-splicing RNA There are two classes of self-splicing introns 381 381
χϋ Contents 14.7 OVERVIEW: THE HISTORY OF AN MRNA MOLECULE 382 Proceeding from the primary transcript to a functioning mRNA requires a number of steps mRNA is exported from the nucleus to the cytoplasm through nuclear pore complexes RNA sequence can be edited by enzymatic modification even after transcription 382 383 383 14.8 RNA QUALITY CONTROL AND DEGRADATION Bacteria, archaea, and eukaryotes all have mechanisms for RNA quality control Archaea and eukaryotes utilize specific pathways to deal with different RNA defects 14.9 BIOGENESIS AND FUNCTIONS OF SMALL SILENCING RNAS 385 385 386 386 386 390 393 394 Chapter 15: Translation: The Players 395 15.1 INTRODUCTION 396 15.2 A BRIEF OVERVIEW OF TRANSLATION 396 Three participants are needed for translation to occur 396 15.3 TRANSFER RNA 398 tRNA molecules fold into four-arm cloverleaf structures tRNAs are aminoacylated by a set of specific enzymes, aminoacyl-tRNA synthetases Aminoacylation of tRNA is a two-step process Quality control or proofreading occurs during the amino acylation reaction Insertion of noncanonical amino acids into polypeptide chains is guided by stop codons 398 400 400 401 402 407 The Shine-Dalgarno sequence in bacterial mRNAs aligns the message on the ribosome 407 Eukaryotic mRNAs do not have Shine-Dalgarno sequenc es but more complex 5'- and З'-untranslated regions 408 Overall translation efficiency depends on a number of factors 410 15.5 RIBOSOMES 410 The ribosome is a two-subunit structure comprising rRNAs and numerous ribosomal proteins 411 Functional ribosomes require both subunits, with specific
complements of RNA and protein molecules 411 The small subunit can accept mRNA but must join with the large subunit for peptide synthesis to occur 413 Ribosome assembly has been studied both in vivo and in vitro 414 The expanding "riboverse" 417 Key concepts 419 Further reading 420 Videos on the Internet 420 Chapter 16: Translation: The Process 421 16.1 INTRODUCTION 422 16.2 AN OVERVIEW OF TRANSLATION: HOW FAST AND HOW ACCURATE? 422 424 Cryo-EM allows visualization of discrete kinetic states of ribosomes X-ray crystallography provides the highest resolution Single-pair fluorescence resonance energy transfer allows dynamic studies at the single-particle level 424 425 427 16.4 INITIATION OF TRANSLATION 427 Initiation of translation begins on a free small ribosomal subunit Cryo-EM provides details of initiation complexes Start site selection in eukaryotes is complex 427 428 429 16.5 TRANSLATIONAL ELONGATION All ssRNAs are produced by processing from larger precursors Key concepts Further reading Videos on the Internet 15.4 MESSENGER RNA 16.3 ADVANCED METHODOLOGY FOR THE ANALYSIS OF TRANSLATION 430 Decoding means matching the codon to the anticodon carrying aminoacyl-tRNA Accommodation denotes a relaxation of distorted tRNA to allow peptide bond formation Peptide bond formation is accelerated by the ribosome The formation of hybrid states is an essential part of trans location Structural information on bacterial elongation factors provides insights into mechanisms There is an exit tunnel for the peptide chain in the ribosome Translation elongation in eukaryotes involves even
more factors Ribosome stalling during translation elongation 430 432 432 434 436 438 439 439 16.6 TERMINATION OF TRANSLATION 440 RF3 aids in removing RF1 andRF2 Ribosomes are recycled after termination Our views of translation continue to evolve Key concepts Further reading Videos on the Internet 441 442 443 443 444 445 Chapter 17: Regulation ofTranslation 447 17.1 INTRODUCTION 448 17.2 REGULATION OF TRANSLATION BY CON TROLLING RIBOSOME NUMBER 448 Ribosome numbers in bacteria are responsive to the environment 448 Ribosome numbers in eukaryotes: Control and conse quences of dysrégulation 449 Synthesis of ribosomal components in bacteria is coordinated 450 Regulation of the synthesis of ribosomal components in eukaryotes involves chromatin structure 451 17.3 REGULATION OF TRANSLATION INITIATION Regulation of translation initiation is ubiquitous and remarkably varied Regulation may depend on protein factors binding to the 5'- огЗ'-ends ofmRNA Cap-dependent regulation is the major pathway for con trolling initiation Initiation may utilize internal ribosome entry sites 5'-3'-UTR interactions provide a novel mechanism that regulates initiation in eukaryotes 454 454 454 455 455 457
xiii Contents Riboswitches are RNA sequence elements that regulate initiation in response to stimuli 457 Repeat-associated non-AUG translation 459 MicroRNAs can bind to mRNA, thereby regulating translation 460 17.4 REGULATION OF THE ELONGATION PROCESS 17.5 mRNA STABILITY AND DECAY IN EUKARYOTES 461 463 The two major pathways of decay for nonfaulty mRNA molecules start with mRNA deadenylation 464 The 5' - 3' pathway is initiated by the activities of the decapping enzyme Dcp2 465 The 3' - 5' pathway uses the exosome, followed by a dif ferent decapping enzyme, DcpS 466 There are additional pathways for mRNA degradation 468 Unused mRNA is sequestered in P bodies and stress granules 468 Cells have several mechanisms that destroy faulty mRNA molecules 471 mRNA molecules that contain premature stop codons are degraded through nonsense-mediated decay or NMD 472 No-go decay (NGD) functions when the ribosome stalls during elongation 473 Non-stop decay or NSD functions when mRNA does not contain a stop codon 473 493 Acetylation mainly modifies interactions Several classes of glycosylated proteins contain added sugar moieties Mechanisms of glycosylation depend on the type of modi fication Ubiquitylation adds single or multiple ubiquitin mol ecules to proteins through an enzymatic cascade Specificity of ubiquitin targeting is determined by a spe cial class of enzymes The structure of protein-ubiquitin conjugates determines the biological role of the modification Polyubiquitin marks proteins for degradation by the proteasome Sumoylation adds single or multiple SUMO molecules to
proteins 494 500 502 504 509 509 510 18.6 PROTEIN CO-TRANSLATIONAL FOLDING 512 18.7 THE GENOMIC ORIGIN OF PROTEINS 513 Key concepts Further reading Videos on the Internet 513 514 515 Chapter 19: DNA Replication in Bacteria 517 518 17.6 SUMMARY OF TRANSLATION REGULATION 474 19.1 INTRODUCTION Key concepts Further reading Videos on the Internet 474 474 476 19.2 FEATURES OF DNA REPLICATION SHARED BYALL ORGANISMS 518 Chapter 18: Protein Processing and Modification 477 18.1 INTRODUCTION 478 18.2 STRUCTURE OF BIOLOGICAL MEMBRANES 478 Biological membranes are protein-rich lipid bilayers Numerous proteins are associated with biomembranes 478 479 18.3 PROTEIN TRANSLOCATION THROUGH BIO LOGICAL MEMBRANES Protein translocation can occur during or after translation Membrane translocation in bacteria and archaea primar ily functions for secretion Membrane translocation in eukaryotes serves a multitude of functions Integral membrane proteins have special mechanisms for membrane insertion Vesicles transport proteins between compartments in eukaryotic cells 18.4 PROTEOLYTIC PROTEIN PROCESSING: CUT TING, SPLICING, AND DEGRADATION Proteolytic cleavage is sometimes used to produce mature proteins from precursors Some proteases can catalyze protein splicing Controlled proteolysis is also used to destroy proteins no longer needed 18.5 POST-TRANSLATIONAL CHEMICAL MODIFI CATIONS OF SIDE CHAINS Modification of side chains can affect protein structure and function Phosphorylation plays a major role in signaling 479 480 480 481 482 484 485 485 486 488 489 489 491 Replication on both strands
creates a replication fork Mechanistically, synthesis of new DNA chains requires a template, a polymerase, and a primer DNA replication requires the simultaneous action of two DNA polymerases Other protein factors are obligatory at the replication fork 518 520 520 521 19.3 DNA REPLICATION IN BACTERIA Bacterial chromosome replication is bidirectional, from a single origin of replication DNA polymerase III catalyzes replication in bacteria Sliding clamp ß, or processivity factor, is essential for processivity The clamp loader organizes the replisome The full complement of proteins in the replisome is orga nized in a complex and dynamic way DNA polymerase I is necessary for maturation of Okazaki fragments 523 523 523 523 523 524 528 19.4 THE PROCESS OF BACTERIAL REPLICATION 530 The replisome is a dynamic structure during elongation 530 19.5 INITIATION AND TERMINATION OF BACTE RIAL REPLICATION 532 Initiation involves both specific DNA sequence elements and numerous proteins Termination of replication also employs specific DNA sequences and protein factors that bind to them 532 534 19.6 DNA REPLICATION AND BACTERIAL CELL CYCLE 536 19.7 BACTERIOPHAGE AND PLASMID REPLICATION 540 Rolling-circle replication is an alternative mechanism Phage replication can involve both bidirectional and rolling-circle mechanisms 542 543
xiv Contents Key concepts Further reading Videos on the Internet 543 546 547 Chapter 20: DNA Replication in Eukaryotes 549 20.1 INTRODUCTION 550 20.2 REPLICATION INITIATION IN EUKARYOTES 550 Replication initiation in eukaryotes proceeds from mul tiple origins 550 Eukaryotic origins of replication have diverse DNA and chromatin structure depending on the biological species 553 There is a defined scenario for formation of initiation complexes 559 Re-replication must be prevented 561 Histone methylation regulates onset of replication licensing 561 20.3 REPLICATION ELONGATION IN EUKARYOTES 561 Eukaryotic replisomes both resemble and significantly differ from those of bacteria 561 Other components of the bacterial replisome have func tional counterparts in eukaryotes Eukaryotic elongation has some special dynamic features 564 565 20.4 REPLICATION OF CHROMATIN 565 Chromatin structure is dynamic during replication Histone chaperones may play multiple roles in replication Both old and newly synthesized histones are required in replication 565 566 567 Epigenetic information in chromatin must also be replicated 568 20.5 THE DNA END-REPLICATION PROBLEM AND ITS RESOLUTION Telomerase solves the end-replication problem Alternative lengthening of telomeres pathway is active in telomerase-deficient cells Holliday junctions are the essential intermediary struc tures in HR 21.4 HOMOLOGOUS RECOMBINATION IN EUKARYOTES Proteins involved in eukaryotic recombination resemble their bacterial counterparts HR malfunction is connected with many human diseases Meiotic recombination allows exchange
of genetic infor mation between homologous chromosomes in meiosis 21.5 NONHOMOLOGOUS RECOMBINATION Transposable elements or transposons are mobile DNA sequences that change positions in the genome Many transposons are transcribed but only a few have known functions There are several types of transposons DNA class II transposons can use either of two mecha nisms to transpose themselves Retrotransposons, or class I transposons, require an RNA intermediate 21.6 SITE-SPECIFIC RECOMBINATION Bacteriophage λ integrates into the bacterial genome by site-specific recombination Immunoglobulin gene rearrangements also occur through site-specific recombination Key concepts Further reading Videos on the Internet 590 590 591 593 596 596 596 598 601 602 602 603 603 616 616 617 570 Chapter 22: DNA Repair 619 570 22.1 INTRODUCTION 620 22.2 TYPES OF LESIONS IN DNA 622 572 20.6 MITOCHONDRIAL DNA REPLICATION 573 Natural agents, from both within and outside a cell, can change the information content of DNA Are circular mitochondrial genomes myth or reality? Models of mitochondrial genome replication are contentious 574 574 22.3 PATHWAYS AND MECHANISMS OF DNA REPAIR 20.7 REPLICATION IN VIRUSES THAT INFECT EUKARYOTES 575 Retroviruses use reverse transcriptase to copy RNA into DNA Key concepts Further reading Videos on the Internet 575 578 579 580 Chapter 21: DNA Recombination 581 21.1 INTRODUCTION 582 21.2 HOMOLOGOUS RECOMBINATION 582 Homologous recombination plays a number of roles in bacteria 583 Homologous recombination has multiple roles in mitotic cells 584 Meiotic exchange is essential to
eukaryotic evolution 584 21.3 HOMOLOGOUS RECOMBINATION IN BACTERIA 584 End resection requires the RecBCD complex 585 586 Strand invasion and strand exchange both depend on RecA Much concerning homologous recombination is still not understood 589 587 622 624 DNA lesions are countered by a number of mechanisms of repair 624 Thymine dimers are directly repaired by DNA photolyase 626 The enzyme Oe-alkylguanine alkyltransferase is involved in the repair of alkylated bases 628 Nucleotide excision repair is active on helix-distorting lesions 628 The role of TFIIH in NER 629 Base excision repair corrects damaged bases 630 Mismatch repair corrects errors in base pairing 630 Methyl-directed mismatch repair in bacteria uses meth ylation on adenines as a guide 631 Mismatch repair pathways in eukaryotes may be directed by strand breaks during DNA replication 632 Repair of double-strand breaks can be error-free or error-prone 633 Homologous recombination repairs double-strand breaks faithfully 633 Nonhomologous end-joining restores the continuity of the DNA double helix in an error-prone process 634 22.4 TRANSLESION SYNTHESIS 635 Many repair pathways utilize RecQ helicases 637
Contents 22.5 CHROMATIN AS AN ACTIVE PLAYER IN DNA REPAIR 637 Key concepts Further reading Videos on the Internet 652 653 654 Histone variants and their post-translational modifications are specifically involved in DNA repair 638 22.6 SUMMARY OF DNA REPAIR 644 Glossary 655 22.7 OVERVIEW: THE ROLE OF DNA REPAIR IN LIFE 645 Index 695 XV |
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| author | Zlatanova, Jordanka Van Holde, K. E. 1928- |
| author_GND | (DE-588)1195250983 (DE-588)120099993 |
| author_facet | Zlatanova, Jordanka Van Holde, K. E. 1928- |
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| callnumber-subject | QH - Natural History and Biology |
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| ctrlnum | (OCoLC)1379412280 (DE-599)BVBBV048852822 |
| dewey-full | 572.8 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.8 |
| dewey-search | 572.8 |
| dewey-sort | 3572.8 |
| dewey-tens | 570 - Biology |
| discipline | Biologie Chemie |
| discipline_str_mv | Biologie Chemie |
| edition | Second edition |
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| illustrated | Illustrated |
| index_date | 2024-07-03T21:40:40Z |
| indexdate | 2024-07-10T09:47:51Z |
| institution | BVB |
| isbn | 9780367678098 0367678098 9780367674083 0367674084 |
| language | English |
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| physical | xxi, 709 Seiten Illustrationen, Diagramme 28 cm |
| publishDate | 2023 |
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| publishDateSort | 2023 |
| publisher | CRC Press, Taylor & Francis Group |
| record_format | marc |
| spelling | Zlatanova, Jordanka Verfasser (DE-588)1195250983 aut Molecular biology structure and dynamics of genomes and proteomes Jordanka Zlatanova, Kensal E. van Holde Second edition Boca Raton ; London ; New York CRC Press, Taylor & Francis Group 2023 xxi, 709 Seiten Illustrationen, Diagramme 28 cm txt rdacontent n rdamedia nc rdacarrier Molecular biology Genomes Proteomics Molecular Biology / methods Genome / physiology Proteome / physiology Transcription, Genetic / genetics Genregulation (DE-588)4122166-7 gnd rswk-swf Genomik (DE-588)4776397-8 gnd rswk-swf Molekularbiologische Methode (DE-588)7650063-9 gnd rswk-swf Proteomanalyse (DE-588)4596545-6 gnd rswk-swf Molekularbiologische Methode (DE-588)7650063-9 s Proteomanalyse (DE-588)4596545-6 s Genomik (DE-588)4776397-8 s Genregulation (DE-588)4122166-7 s DE-604 Van Holde, K. E. 1928- Verfasser (DE-588)120099993 aut Erscheint auch als Online-Ausgabe 978-1-003-13292-9 Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=034118064&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Zlatanova, Jordanka Van Holde, K. E. 1928- Molecular biology structure and dynamics of genomes and proteomes Molecular biology Genomes Proteomics Molecular Biology / methods Genome / physiology Proteome / physiology Transcription, Genetic / genetics Genregulation (DE-588)4122166-7 gnd Genomik (DE-588)4776397-8 gnd Molekularbiologische Methode (DE-588)7650063-9 gnd Proteomanalyse (DE-588)4596545-6 gnd |
| subject_GND | (DE-588)4122166-7 (DE-588)4776397-8 (DE-588)7650063-9 (DE-588)4596545-6 |
| title | Molecular biology structure and dynamics of genomes and proteomes |
| title_auth | Molecular biology structure and dynamics of genomes and proteomes |
| title_exact_search | Molecular biology structure and dynamics of genomes and proteomes |
| title_exact_search_txtP | Molecular biology structure and dynamics of genomes and proteomes |
| title_full | Molecular biology structure and dynamics of genomes and proteomes Jordanka Zlatanova, Kensal E. van Holde |
| title_fullStr | Molecular biology structure and dynamics of genomes and proteomes Jordanka Zlatanova, Kensal E. van Holde |
| title_full_unstemmed | Molecular biology structure and dynamics of genomes and proteomes Jordanka Zlatanova, Kensal E. van Holde |
| title_short | Molecular biology |
| title_sort | molecular biology structure and dynamics of genomes and proteomes |
| title_sub | structure and dynamics of genomes and proteomes |
| topic | Molecular biology Genomes Proteomics Molecular Biology / methods Genome / physiology Proteome / physiology Transcription, Genetic / genetics Genregulation (DE-588)4122166-7 gnd Genomik (DE-588)4776397-8 gnd Molekularbiologische Methode (DE-588)7650063-9 gnd Proteomanalyse (DE-588)4596545-6 gnd |
| topic_facet | Molecular biology Genomes Proteomics Molecular Biology / methods Genome / physiology Proteome / physiology Transcription, Genetic / genetics Genregulation Genomik Molekularbiologische Methode Proteomanalyse |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=034118064&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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