| Chapter 1 To the Cell and Beyond: The Realm of Molecular Biology |
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1 | (14) |
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1 | (1) |
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1.2 The Vital Role Of Microscopy In Biology |
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2 | (5) |
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The light microscope led to the first revolution in biology |
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2 | (3) |
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Biochemistry led to the discovery of the importance of macromolecules in life's structure and processes |
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5 | (1) |
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The electron microscope provided another order of resolution |
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6 | (1) |
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1.3 Fine Structure Of Cells And Viruses As Revealed By Microscopy |
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7 | (1) |
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1.4 Ultrahigh Resolution: Biology At The Molecular Level |
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8 | (4) |
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Fluorescence techniques allow for one approach to ultraresolution |
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8 | (1) |
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Confocal fluorescence microscopy allows observation of the fluorescence emitted by a particular substance in a cell |
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9 | (1) |
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FIONA provides ultimate optical resolution by use of fluorescence |
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10 | (1) |
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FRET allows distance measurements at the molecular level |
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10 | (1) |
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Single-molecule cryo-electron microscopy is a powerful new technique |
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10 | (1) |
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The atomic force microscope feels molecular structure |
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11 | (1) |
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X-ray diffraction and NMR provide resolution to the atomic level |
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11 | (1) |
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1.5 Molecular Genetics: Another Face Of Molecular Biology |
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12 | (1) |
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13 | (1) |
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14 | (1) |
| Chapter 2 From Classical Genetics to Molecular Genetics |
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15 | (16) |
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15 | (1) |
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2.2 Classical Genetics And The Rules Of Trait Inheritance |
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15 | (8) |
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Gregor Mendel developed the formal rules of genetics |
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15 | (5) |
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Mendel's laws have extensions and exceptions |
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20 | (1) |
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Genes are arranged linearly on chromosomes and can be mapped |
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21 | (1) |
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The nature of genes and how they determine phenotypes was long a mystery |
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22 | (1) |
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2.3 The Great Breakthrough To Molecular Genetics |
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23 | (3) |
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Bacteria and bacteriophage exhibit genetic behavior and serve as model systems |
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23 | (2) |
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Transformation and transduction allow transfer of genetic information |
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25 | (1) |
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The Watson-Crick model of DNA structure provided the final key to molecular genetics |
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25 | (1) |
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26 | (2) |
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28 | (1) |
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29 | (2) |
| Chapter 3 Proteins |
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31 | (34) |
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31 | (2) |
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Proteins are macromolecules with enormous variety in size, structure, and function |
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31 | (1) |
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Proteins are essential for the structure and functioning of all organisms |
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31 | (2) |
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33 | (2) |
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Amino acids are the building blocks of proteins |
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33 | (1) |
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In proteins, amino acids are covalently connected to form polypeptides |
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34 | (1) |
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3.3 Levels Of Structure In The Polypeptide Chain |
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35 | (18) |
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The primary structure of a protein is a unique sequence of amino acids |
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35 | (4) |
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A protein's secondary structure involves regions of regular folding stabilized by hydrogen bonds |
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39 | (3) |
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Each protein has a unique three-dimensional tertiary structure |
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42 | (2) |
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The tertiary structure of most proteins is divided into distinguishable folded domains |
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44 | (1) |
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Algorithms are now used to identify and classify domains in proteins of known sequence |
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45 | (4) |
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Some domains or proteins are intrinsically disordered |
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49 | (2) |
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Quaternary structure involves associations between protein molecules to form aggregated structures |
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51 | (2) |
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3.4 How Do Proteins Fold? |
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53 | (5) |
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53 | (2) |
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Chaperones help or allow proteins to fold |
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55 | (3) |
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3.5 How Are Proteins Destroyed? |
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58 | (2) |
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The proteasome is the general protein destruction system |
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58 | (2) |
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3.6 The Proteome And Protein Interaction Networks |
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60 | (3) |
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New technologies allow a census of an organism's proteins and their interactions |
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60 | (3) |
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63 | (1) |
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64 | (1) |
| Chapter 4 Nucleic Acids |
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65 | (28) |
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65 | (1) |
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Protein sequences are dictated by nucleic acids |
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65 | (1) |
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4.2 Chemical Structure Of Nucleic Acids |
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65 | (4) |
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DNA and RNA have similar but different chemical structures |
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65 | (3) |
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Nucleic acids (polynucleotides) are polymers of nucleotides |
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68 | (1) |
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4.3 Physical Structures Of DNA |
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69 | (13) |
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Discovery of the B-DNA structure was a breakthrough in molecular biology |
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69 | (2) |
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A number of alternative DNA structures exist |
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71 | (3) |
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Although the double helix is quite rigid, it can be bent by bound proteins |
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74 | (1) |
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DNA can also form folded tertiary structures |
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75 | (1) |
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Closed DNA circles can be twisted into supercoils |
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76 | (6) |
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4.4 Physical Structures Of RNA |
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82 | (2) |
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RNA can adopt a variety of complex structures but not the B-form helix |
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82 | (2) |
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4.5 One-Way Flow Of Genetic Information |
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84 | (1) |
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4.6 Methods Used To Study Nucleic Acids |
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84 | (7) |
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91 | (1) |
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92 | (1) |
| Chapter 5 Recombinant DNA: Principles I and Applications |
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93 | (34) |
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93 | (2) |
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Cloning of DNA involves several fundamental steps |
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94 | (1) |
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5.2 Construction Of Recombinant DNA Molecules |
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95 | (5) |
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Restriction endonucleases and ligases are essential tools in cloning |
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95 | (5) |
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100 | (6) |
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Genes coding for selectable markers are inserted into vectors during their construction |
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100 | (2) |
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Bacterial plasmids were the first cloning vectors |
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102 | (1) |
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Recombinant bacteriophages can serve as bacterial vectors |
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103 | (2) |
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Cosmids and phagemids expand the repertoire of cloning vectors |
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105 | (1) |
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5.4 Artificial Chromosomes As Vectors |
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106 | (2) |
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Bacterial artificial chromosomes meet the need for cloning very large DNA fragments in bacteria |
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106 | (1) |
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Eukaryotic artificial chromosomes provide proper maintenance and expression of very large DNA fragments in eukaryotic cells |
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107 | (1) |
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5.5 Expression Of Recombinant Genes |
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108 | (1) |
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Expression vectors allow regulated and efficient expression of cloned genes |
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108 | (1) |
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Shuttle vectors can replicate in more than one organism |
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109 | (1) |
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5.6 Introducing Recombinant DNA Into Host Cells |
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109 | (1) |
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Numerous host-specific techniques are used to introduce recombinant DNA molecules into living cells |
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109 | (1) |
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5.7 Polymerase Chain Reaction And Site-Directed Mutagenesis |
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110 | (2) |
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5.8 Sequencing Of Entire Genomes |
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112 | (3) |
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Genomic libraries contain the entire genome of an organism as a collection of recombinant DNA molecules |
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112 | (1) |
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There are two approaches for sequencing large genomes |
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113 | (2) |
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5.9 Manipulating The Genetic Content Of Eukaryotic Organisms |
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115 | (1) |
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Making a transgenic mouse involves numerous steps |
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115 | (1) |
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To inactivate, replace, or otherwise modify a particular gene, the vector must be targeted for homologous recombination at that particular site |
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115 | (1) |
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5.10 Practical Applications Of Recombinant DNA Technologies |
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116 | (9) |
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Hundreds of pharmaceutical compounds are produced in recombinant bacteria |
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116 | (2) |
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Plant genetic engineering is a huge but controversial industry |
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118 | (4) |
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Gene therapy is a complex multistep process aiming to correct defective genes or gene functions that are responsible for disease |
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122 | (1) |
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Delivering a gene into sufficient cells within a specific tissue and ensuring its subsequent long-term expression is a challenge |
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122 | (2) |
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Whole animals can be cloned by nuclear transfer |
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124 | (1) |
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125 | (1) |
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125 | (2) |
| Chapter 6 Protein-Nucleic Acid Interactions |
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127 | (18) |
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127 | (1) |
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6.2 DNA-Protein Interactions |
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128 | (8) |
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DNA-protein binding occurs by many modes and mechanisms |
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128 | (1) |
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Site-specific binding is the most widely used mode |
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129 | (2) |
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Most recognition sites fall into a limited number of classes |
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131 | (1) |
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Most specific binding requires the insertion of protein into a DNA groove |
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132 | (1) |
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Some proteins cause DNA looping |
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133 | (1) |
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There are a few major protein motifs of DNA-binding domains |
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134 | (1) |
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Helix-turn-helix motif interacts with the major groove |
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134 | (1) |
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Zinc fingers also probe the major groove |
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135 | (1) |
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Leucine zippers are especially suited for dimeric sites |
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135 | (1) |
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6.3 RNA-Protein Interactions |
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136 | (3) |
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6.4 Studying Protein-Nucleic Acid Interactions |
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139 | (5) |
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144 | (1) |
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144 | (1) |
| Chapter 7 The Genetic Code, Genes, and Genomes |
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145 | (18) |
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145 | (1) |
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7.2 Genes As Nucleic Acid Repositories Of Genetic Information |
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145 | (4) |
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Our understanding of the nature of genes is constantly evolving |
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145 | (2) |
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The central dogma states that information flows from DNA to protein |
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147 | (1) |
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It was necessary to separate cellular RNAs to seek the adaptors |
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147 | (1) |
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Messenger RNA, tRNA, and ribosomes constitute the protein factories of the cell |
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148 | (1) |
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7.3 Relating Protein Sequence To DNA Sequence In The Genetic Code |
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149 | (3) |
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The first task was to define the nature of the code |
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149 | (3) |
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7.4 Surprises From The Eukaryotic Cell: Introns And Splicing |
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152 | (1) |
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Eukaryotic genes usually contain interspersed noncoding sequences |
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152 | (1) |
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7.5 Genes From A New And Broader Perspective |
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153 | (3) |
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Protein-coding genes are complex |
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153 | (1) |
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Genome sequencing has revolutionized the gene concept |
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153 | (1) |
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Mutations, pseudogenes, and alternative splicing all contribute to gene diversity |
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154 | (2) |
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7.6 Comparing Whole Genomes And New Perspectives On Evolution |
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156 | (5) |
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Genome sequencing reveals puzzling features of genomes |
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156 | (2) |
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How are DNA sequence types and functions distributed in eukaryotes? |
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158 | (3) |
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161 | (1) |
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161 | (2) |
| Chapter 8 Physical Structure of the Genomic Material |
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163 | (30) |
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163 | (1) |
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8.2 Chromosomes Of Viruses And Bacteria |
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164 | (4) |
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Viruses are packages for minimal genomes |
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164 | (1) |
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Bacterial chromosomes are organized structures in the cytoplasm |
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165 | (1) |
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DNA-bending proteins and DNA-bridging proteins help to pack bacterial DNA |
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166 | (2) |
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168 | (10) |
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Eukaryotic chromosomes are highly condensed DNA-protein complexes segregated into a nucleus |
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168 | (1) |
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The nucleosome is the basic repeating unit of eukaryotic chromatin |
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168 | (3) |
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Histone nonallelic variants and postsynthetic modifications create a heterogeneous population of nucleosomes |
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171 | (5) |
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The nucleosome family is dynamic |
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176 | (1) |
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Nucleosome assembly in vivo uses histone chaperones |
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177 | (1) |
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8.4 Higher-Order Chromatin Structure |
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178 | (4) |
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Nucleosomes along the DNA form a chromatin fiber |
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178 | (2) |
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The chromatin fiber is folded, but its structure remains controversial |
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180 | (1) |
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The organization of chromosomes in the interphase nucleus is still obscure |
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181 | (1) |
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182 | (8) |
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Chromosomes condense and separate in mitosis |
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182 | (1) |
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A number of proteins are needed to form and maintain mitotic chromosomes |
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183 | (1) |
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Centromeres and telomeres are chromosome regions with special functions |
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184 | (3) |
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There are a number of models of mitotic chromosome structure |
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187 | (3) |
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190 | (1) |
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190 | (3) |
| Chapter 9 Transcription in Bacteria |
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193 | (22) |
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193 | (1) |
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9.2 Overview Of Transcription |
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193 | (8) |
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There are aspects of transcription common to all organisms |
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193 | (2) |
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Transcription requires the participation of many proteins |
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195 | (2) |
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Transcription is rapid but is often interrupted by pauses |
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197 | (1) |
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Transcription can be visualized by electron microscopy |
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198 | (3) |
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9.3 RNA Polymerases And Transcription Catalysis |
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201 | (1) |
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RNA polymerases are a large family of enzymes that produce RNA transcripts of polynucleotide templates |
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201 | (1) |
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9.4 Mechanics Of Transcription In Bacteria |
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202 | (10) |
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Initiation requires a multisubunit polymerase complex, termed the holoenzyme |
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202 | (4) |
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The initiation phase of bacterial transcription is frequently aborted |
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206 | (3) |
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Elongation in bacteria must overcome topological problems |
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209 | (1) |
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There are two mechanisms for transcription termination in bacteria |
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210 | (1) |
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Understanding transcription in bacteria is useful in clinical practice |
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211 | (1) |
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212 | (1) |
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213 | (2) |
| Chapter 10 Transcription in Eukaryotes |
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215 | (26) |
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215 | (2) |
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Transcription in eukaryotes is a complex, highly regulated process |
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215 | (1) |
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Eukaryotic cells contain multiple RNA polymerases, each specific for distinct functional subsets of genes |
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216 | (1) |
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10.2 Transcription By RNA Polymerase II |
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217 | (8) |
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The yeast Pol II structure provides insights into transcriptional mechanisms |
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217 | (2) |
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The structure of Pol II is more evolutionarily conserved than its sequence |
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219 | (1) |
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Nucleotide addition during transcription elongation is cyclic |
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219 | (3) |
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Transcription initiation depends on multisubunit protein complexes that assemble at core promoters |
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222 | (2) |
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An additional protein complex is needed to connect Pol II to regulatory proteins |
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224 | (1) |
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Termination of eukaryotic transcription is coupled to polyadenylation of the RNA transcript |
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224 | (1) |
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10.3 Transcription By RNA Polymerase I |
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225 | (2) |
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10.4 Transcription By RNA Polymerase III |
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227 | (1) |
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RNA polymerase III specializes in transcription of small genes |
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227 | (1) |
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10.5 Transcription In Eukaryotes: Pervasive And Spatially Organized |
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228 | (6) |
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Most of the eukaryotic genome is transcribed |
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228 | (4) |
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Transcription in eukaryotes is not uniform within the nucleus |
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232 | (1) |
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Active and inactive genes are spatially separated in the nucleus |
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233 | (1) |
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10.6 Methods For Studying Eukaryotic Transcription |
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234 | (4) |
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A battery of methods is available for the study of transcription |
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234 | (4) |
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238 | (1) |
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239 | (2) |
| Chapter 11 Regulation of Transcription in Bacteria |
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241 | (20) |
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241 | (1) |
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11.2 General Models For Regulation Of Transcription |
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242 | (2) |
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Regulation can occur via differences in promoter strength or use of alternative σ factors |
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242 | (1) |
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Regulation through ligand binding to RNA polymerase is called stringent control |
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243 | (1) |
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11.3 Specific Regulation Of Transcription |
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244 | (2) |
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Regulation of specific genes occurs through cis-trans interactions with transcription factors |
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244 | (1) |
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Transcription factors are activators and repressors whose own activity is regulated in a number of ways |
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244 | (1) |
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Several transcription factors can act synergistically or in opposition to activate or repress transcription |
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244 | (2) |
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11.4 Transcriptional Regulation Of Operons Important To Bacterial Physiology |
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246 | (9) |
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The lac operon is controlled by a dissociable repressor and an activator |
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246 | (4) |
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Control of the trp operon involves both repression and attenuation |
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250 | (2) |
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The same protein can serve as an activator or a repressor: the ara operon |
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252 | (3) |
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11.5 Other Modes Of Gene Regulation In Bacteria |
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255 | (1) |
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DNA supercoiling is involved in both global and local regulation of transcription |
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255 | (1) |
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DNA methylation can provide specific regulation |
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256 | (1) |
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11.6 Coordination Of Gene Expression In Bacteria |
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256 | (2) |
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Networks of transcription factors form the basis of coordinated gene expression |
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257 | (1) |
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258 | (1) |
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259 | (2) |
| Chapter 12 Regulation of Transcription in Eukaryotes |
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261 | (36) |
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261 | (1) |
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12.2 Regulation Of Transcription Initiation: Regulatory Regions And Transcription Factors |
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262 | (5) |
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Core and proximal promoters are needed for basal and regulated transcription |
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262 | (1) |
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Enhancers, silencers, insulators, and locus control regions are all distal regulatory elements |
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263 | (1) |
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Some eukaryotic transcription factors are activators, others are repressors, and still others can be either, depending on context |
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264 | (3) |
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Regulation can use alternative components of the basal transcriptional machinery |
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267 | (1) |
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Mutations in gene regulatory regions and in transcriptional machinery components lead to human diseases |
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267 | (1) |
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12.3 Regulation Of Transcriptional Elongation |
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267 | (1) |
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The polymerase may stall close to the promoter |
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267 | (1) |
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Transcription elongation rate can be regulated by elongation factors |
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268 | (1) |
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12.4 Transcription Regulation And Chromatin Structure |
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268 | (3) |
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What happens to nucleosomes during transcription? |
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268 | (3) |
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12.5 Regulation Of Transcription By Histone Modifications And Variants |
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271 | (14) |
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Modification of histones provides epigenetic control of transcription |
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271 | (1) |
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Gene expression is often regulated by histone post-translational modifications |
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272 | (1) |
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Readout of histone post-translational modification marks involves specialized protein molecules |
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272 | (3) |
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Post-translational histone marks distinguish transcriptionally active and inactive chromatin regions |
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275 | (1) |
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Some genes are specifically silenced by post-translational modification in some cell lines |
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275 | (1) |
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Polycomb protein complexes silence genes through H3K27 trimethylation and H2AK119 ubiquitylation |
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276 | (1) |
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Heterochromatin formation at telomeres in yeast silences genes through H4K16 deacetylation |
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277 | (1) |
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HP1=mediated gene repression in the majority of eukaryotic organisms involves H3K9 methylation |
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277 | (2) |
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Poly(ADP)ribosylation of proteins is involved in transcriptional regulation |
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279 | (1) |
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Histone variants H2A.Z, H3.3, and H2A.Bbd are present in active chromatin |
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280 | (2) |
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MacroH2A is a histone variant prevalent in inactive chromatin |
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282 | (1) |
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Problems caused by chromatin structure can be fixed by remodeling |
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282 | (2) |
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Endogenous metabolites can exert rheostat control of transcription |
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284 | (1) |
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285 | (4) |
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DNA methylation patterns in genomic DNA may participate in regulation of transcription |
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286 | (1) |
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Carcinogenesis alters the pattern of CpG methylation |
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287 | (1) |
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DNA methylation changes during embryonic development |
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288 | (1) |
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DNA methylation is governed by complex enzymatic machinery |
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288 | (1) |
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There are proteins that read the DNA methylation mark |
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289 | (1) |
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12.7 Long Noncoding RNAs In Transcriptional Regulation |
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289 | (4) |
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Noncoding RNAs play surprising roles in regulating transcription |
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289 | (1) |
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The sizes and genomic locations of noncoding transcripts are remarkably diverse |
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290 | (3) |
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12.8 Methods For Measuring The Activity Of Transcriptional Regulatory Elements |
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293 | (1) |
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294 | (1) |
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295 | (2) |
| Chapter 13 Transcription Regulation in the Human Genome |
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297 | (18) |
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297 | (1) |
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Rapid full-genome sequencing allows deep analysis |
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298 | (1) |
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13.2 Basic Concepts Of Encode |
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298 | (2) |
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ENCODE depends on high-throughput, massively processive sequencing and sophisticated computer algorithms for analysis |
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298 | (1) |
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The ENCODE project integrates diverse data relevant to transcription in the human genome |
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299 | (1) |
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13.3 Regulatory DNA Sequence Elements |
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300 | (1) |
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Seven classes of regulatory DNA sequence elements make up the transcriptional landscape |
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300 | (1) |
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13.4 Specific Findings Concerning Chromatin Structure From Encode |
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301 | (4) |
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Millions of DNase I hypersensitive sites mark regions of accessible chromatin |
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301 | (1) |
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DNase I signatures at promoters are asymmetric and stereotypic |
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302 | (1) |
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Nucleosome positioning at promoters and around TF-binding sites is highly heterogeneous |
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303 | (1) |
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The chromatin environment at regulatory elements and in gene bodies is also heterogeneous and asymmetric |
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303 | (2) |
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13.5 Encode Insights Into Gene Regulation |
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305 | (7) |
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Distal control elements are connected to promoters in a complex network |
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305 | (1) |
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Transcription factor binding defines the structure and function of regulatory regions |
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|
305 | (2) |
|
Transcription factors interact in a huge network |
|
|
307 | (2) |
|
TF-binding sites and TF structure co-evolve |
|
|
309 | (2) |
|
DNA methylation patterns show a complex relationship with transcription |
|
|
311 | (1) |
|
|
|
312 | (1) |
|
What have we learned from ENCODE, and where is it leading? |
|
|
312 | (1) |
|
Certain methods are essential to ENCODE project studies |
|
|
312 | (1) |
|
|
|
313 | (1) |
|
|
|
314 | (1) |
| Chapter 14 RNA Processing |
|
315 | (32) |
|
|
|
315 | (1) |
|
Most RNA molecules undergo post-transcriptional processing |
|
|
315 | (1) |
|
There are four general categories of processing |
|
|
315 | (1) |
|
Eukaryotic RNAs exhibit much more processing than bacterial RNAs |
|
|
316 | (1) |
|
14.2 Processing Of tRNAS And rRNAS |
|
|
316 | (2) |
|
tRNA processing is similar in all organisms |
|
|
316 | (1) |
|
All three mature ribosomal RNA molecules are cleaved from a single long precursor RNA |
|
|
316 | (2) |
|
14.3 Processing Of Eukaryotic mRNA: End Modifications |
|
|
318 | (3) |
|
Eukaryotic mRNA capping is co-transcriptional |
|
|
319 | (1) |
|
Polyadenylation at the 3'-end serves a number of functions |
|
|
320 | (1) |
|
14.4 Processing Of Eukaryotic mRNA: Splicing |
|
|
321 | (8) |
|
The splicing process is complex and requires great precision |
|
|
321 | (1) |
|
Splicing is carried out by spliceosomes |
|
|
322 | (1) |
|
Splicing can produce alternative mRNAs |
|
|
322 | (2) |
|
Tandem chimerism links exons from separate genes |
|
|
324 | (4) |
|
Trans-splicing combines exons residing in the two complementary DNA strands |
|
|
328 | (1) |
|
14.5 Regulation Of Splicing And Alternative Splicing |
|
|
329 | (5) |
|
Splice sites differ in strength |
|
|
329 | (1) |
|
Exon-intron architecture affects splice-site usage |
|
|
329 | (1) |
|
Cis-trans interactions may stimulate or inhibit splicing |
|
|
330 | (2) |
|
RNA secondary structure can regulate alternative splicing |
|
|
332 | (1) |
|
Sometimes alternative splicing regulation needs no auxiliary regulators |
|
|
332 | (1) |
|
The rate of transcription and chromatin structure may help regulate splicing |
|
|
332 | (2) |
|
14.6 Self-Splicing: Introns And Ribozymes |
|
|
334 | (1) |
|
A fraction of introns is excised by self-splicing RNA |
|
|
334 | (1) |
|
There are two classes of self-splicing introns |
|
|
334 | (1) |
|
14.7 Overview: The History Of An mRNA Molecule |
|
|
335 | (4) |
|
Proceeding from the primary transcript to a functioning mRNA requires a number of steps |
|
|
335 | (1) |
|
mRNA is exported from the nucleus to the cytoplasm through nuclear pore complexes |
|
|
335 | (1) |
|
RNA sequence can be edited by enzymatic modification even after transcription |
|
|
336 | (3) |
|
14.8 RNA Quality Control And Degradation |
|
|
339 | (3) |
|
Bacteria, archaea, and eukaryotes all have mechanisms for RNA quality control |
|
|
339 | (2) |
|
Archaea and eukaryotes utilize specific pathways to deal with different RNA defects |
|
|
341 | (1) |
|
14.9 Biogenesis And Functions Of Small Silencing RNAs |
|
|
342 | (2) |
|
All ssRNAs are produced by processing from larger precursors |
|
|
342 | (2) |
|
|
|
344 | (1) |
|
|
|
345 | (2) |
| Chapter 15 Translation: The Players |
|
347 | (24) |
|
|
|
347 | (1) |
|
15.2 A Brief Overview Of Translation |
|
|
347 | (2) |
|
Three participants are needed for translation to occur |
|
|
347 | (2) |
|
|
|
349 | (7) |
|
tRNA molecules fold into four-arm cloverleaf structures |
|
|
350 | (1) |
|
tRNAs are aminoacylated by a set of specific enzymes, aminoacyl-tRNA synthetases |
|
|
351 | (1) |
|
Aminoacylation of tRNA is a two-step process |
|
|
352 | (1) |
|
Quality control or proofreading occurs during the aminoacylation reaction |
|
|
353 | (1) |
|
Insertion of noncanonical amino acids into polypeptide chains is guided by stop codons |
|
|
354 | (2) |
|
|
|
356 | (5) |
|
The Shine-Dalgarno sequence in bacterial mRNAs aligns the message on the ribosome |
|
|
357 | (1) |
|
Eukaryotic mRNAs do not have Shine-Dalgarno sequences but more complex 5'- and 3'-untranslated regions |
|
|
358 | (2) |
|
Overall translation efficiency depends on a number of factors |
|
|
360 | (1) |
|
|
|
361 | (7) |
|
The ribosome is a two-subunit structure comprising rRNAs and numerous ribosomal proteins |
|
|
361 | (1) |
|
Functional ribosomes require both subunits, with specific complements of RNA and protein molecules |
|
|
362 | (2) |
|
The small subunit can accept mRNA but must join with the large subunit for peptide synthesis to occur |
|
|
364 | (1) |
|
Ribosome assembly has been studied both in vivo and in vitro |
|
|
365 | (3) |
|
|
|
368 | (1) |
|
|
|
369 | (2) |
| Chapter 16 Translation: The Process |
|
371 | (24) |
|
|
|
371 | (1) |
|
16.2 An Overview Of Translation: How Fast And How Accurate? |
|
|
371 | (2) |
|
16.3 Advanced Methodology For The Analysis Of Translation |
|
|
373 | (4) |
|
Cryo-EM allows visualization of discrete kinetic states of ribosomes |
|
|
373 | (1) |
|
X-ray crystallography provides the highest resolution |
|
|
374 | (2) |
|
Single-pair fluorescence resonance energy transfer allows dynamic studies at the single-particle level |
|
|
376 | (1) |
|
16.4 Initiation Of Translation |
|
|
377 | (2) |
|
Initiation of translation begins on a free small ribosomal subunit |
|
|
377 | (1) |
|
Cryo-EM provides details of initiation complexes |
|
|
377 | (1) |
|
Start site selection in eukaryotes is complex |
|
|
378 | (1) |
|
16.5 Translational Elongation |
|
|
379 | (9) |
|
Decoding means matching the codon to the anticodon-carrying aminoacyl-tRNA |
|
|
380 | (1) |
|
Accommodation denotes a relaxation of distorted tRNA to allow peptide bond formation |
|
|
381 | (1) |
|
Peptide bond formation is accelerated by the ribosome |
|
|
381 | (2) |
|
The formation of hybrid states is an essential part of translocation |
|
|
383 | (2) |
|
Structural information on bacterial elongation factors provides insights into mechanisms |
|
|
385 | (2) |
|
There is an exit tunnel for the peptide chain in the ribosome |
|
|
387 | (1) |
|
Translation elongation in eukaryotes involves even more factors |
|
|
388 | (1) |
|
16.6 Termination Of Translation |
|
|
388 | |
|
RF3 aids in removing RF1 and RF2 |
|
|
390 | (1) |
|
Ribosomes are recycled after termination |
|
|
390 | (1) |
|
Our views of translation continue to evolve |
|
|
391 | |
|
|
|
292 | (1) |
|
|
|
293 | (102) |
| Chapter 17 Regulation of Translation |
|
395 | (26) |
|
|
|
395 | (1) |
|
17.2 Regulation Of Translation By Controlling Ribosome Number |
|
|
395 | (5) |
|
Ribosome numbers in bacteria are responsive to the environment |
|
|
395 | (1) |
|
Synthesis of ribosomal components in bacteria is coordinated |
|
|
396 | (1) |
|
Regulation of the synthesis of ribosomal components in eukaryotes involves chromatin structure |
|
|
397 | (3) |
|
17.3 Regulation Of Translation Initiation |
|
|
400 | (7) |
|
Regulation of translation initiation is ubiquitous and remarkably varied |
|
|
400 | (1) |
|
Regulation may depend on protein factors binding to the 5'- or 3'-ends of mRNA |
|
|
400 | (1) |
|
Cap-dependent regulation is the major pathway for controlling initiation |
|
|
400 | (1) |
|
Initiation may utilize internal ribosome entry sites |
|
|
401 | (1) |
|
5'-3'-UTR interactions provide a novel mechanism that regulates initiation in eukaryotes |
|
|
402 | (2) |
|
Riboswitches are RNA sequence elements that regulate initiation in response to stimuli |
|
|
404 | (1) |
|
MicroRNAs can bind to mRNA, thereby regulating translation |
|
|
405 | (2) |
|
17.4 mRNA Stability And Decay In Eukaryotes |
|
|
407 | (11) |
|
The two major pathways of decay for nonfaulty mRNA molecules start with mRNA deadenylation |
|
|
407 | (1) |
|
The 5' 3' pathway is initiated by the activities of the decapping enzyme Dcp2 |
|
|
408 | (2) |
|
The 3' 5' pathway uses the exosome, followed by a different decapping enzyme, DcpS |
|
|
410 | (2) |
|
There are additional pathways for mRNA degradation |
|
|
412 | (1) |
|
Unused mRNA is sequestered in P bodies and stress granules |
|
|
412 | (4) |
|
Cells have several mechanisms that destroy faulty mRNA molecules |
|
|
416 | (1) |
|
mRNA molecules that contain premature stop codons are degraded through nonsense-mediated decay or NMD |
|
|
416 | (1) |
|
No-go decay or NGD functions when the ribosome stalls during elongation |
|
|
417 | (1) |
|
Non-stop decay or NSD functions when mRNA does not contain a stop codon |
|
|
417 | (1) |
|
17.5 Mechanisms Of Translation |
|
|
418 | (1) |
|
|
|
419 | (1) |
|
|
|
419 | (2) |
| Chapter 18 Protein Processing and Modification |
|
421 | (36) |
|
|
|
421 | (1) |
|
18.2 Structure Of Biological Membranes |
|
|
422 | (1) |
|
Biological membranes are protein-rich lipid bilayers |
|
|
422 | (1) |
|
Numerous proteins are associated with biomembranes |
|
|
422 | (1) |
|
18.3 Protein Translocation Through Biological Membranes |
|
|
423 | (6) |
|
Protein translocation can occur during or after translation |
|
|
423 | (1) |
|
Membrane translocation in bacteria and archaea primarily functions for secretion |
|
|
424 | (1) |
|
Membrane translocation in eukaryotes serves a multitude of functions |
|
|
424 | (2) |
|
Integral membrane proteins have special mechanisms for membrane insertion |
|
|
426 | (2) |
|
Vesicles transport proteins between compartments in eukaryotic cells |
|
|
428 | (1) |
|
18.4 Proteolytic Protein Processing: Cutting, Splicing, And Degradation |
|
|
429 | (4) |
|
Proteolytic cleavage is sometimes used to produce mature proteins from precursors |
|
|
430 | (1) |
|
Some proteases can catalyze protein splicing |
|
|
431 | (2) |
|
Controlled proteolysis is also used to destroy proteins no longer needed |
|
|
433 | (1) |
|
18.5 Post-Translational Chemical Modifications Of Side Chains |
|
|
433 | (22) |
|
Modification of side chains can affect protein structure and function |
|
|
433 | (2) |
|
Phosphorylation plays a major role in signaling |
|
|
435 | (1) |
|
Acetylation mainly modifies interactions |
|
|
436 | (1) |
|
Several classes of glycosylated proteins contain added sugar moieties |
|
|
436 | |
|
Mechanisms of glycosylation depend on the type of modification |
|
|
433 | (12) |
|
Ubiquitylation adds single or multiple ubiquitin molecules to proteins through an enzymatic cascade |
|
|
445 | (2) |
|
Specificity of ubiquitin targeting is determined by a special class of enzymes |
|
|
447 | (4) |
|
The structure of protein-ubiquitin conjugates determines the biological role of the modification |
|
|
451 | (1) |
|
Polyubiquitin marks proteins for degradation by the proteasome |
|
|
451 | (1) |
|
Sumoylation adds single or multiple SUMO molecules to proteins |
|
|
452 | (3) |
|
18.6 The Genomic Origin Of Proteins |
|
|
455 | (1) |
|
|
|
455 | (1) |
|
|
|
456 | (1) |
| Chapter 19 DNA Replication in Bacteria |
|
457 | (28) |
|
|
|
457 | (1) |
|
19.2 Features Of DNA Replication Shared By All Organisms |
|
|
457 | (4) |
|
Replication on both strands creates a replication fork |
|
|
457 | (2) |
|
Mechanistically, synthesis of new DNA chains requires a template, a polymerase, and a primer |
|
|
459 | (1) |
|
DNA replication requires the simultaneous action of two DNA polymerases |
|
|
459 | (1) |
|
Other protein factors are obligatory at the replication fork |
|
|
460 | (1) |
|
19.3 DNA Replication In Bacteria |
|
|
461 | (9) |
|
Bacterial chromosome replication is bidirectional, from a single origin of replication |
|
|
461 | (1) |
|
DNA polymerase III catalyzes replication in bacteria |
|
|
462 | (1) |
|
Sliding clamp (3, or processivity factor, is essential for processivity |
|
|
462 | (2) |
|
The clamp loader organizes the replisome |
|
|
464 | (1) |
|
The full complement of proteins in the replisome is organized in a complex and dynamic way |
|
|
465 | (3) |
|
DNA polymerase I is necessary for maturation of Okazaki fragments |
|
|
468 | (2) |
|
19.4 The Process Of Bacterial Replication |
|
|
470 | (2) |
|
The replisome is a dynamic structure during elongation |
|
|
470 | (2) |
|
19.5 Initiation And Termination Of Bacterial Replication |
|
|
472 | (6) |
|
Initiation involves both specific DNA sequence elements and numerous proteins |
|
|
473 | (3) |
|
Termination of replication also employs specific DNA sequences and protein factors that bind to them |
|
|
476 | (2) |
|
19.6 Bacteriophage And Plasmid Replication |
|
|
478 | (4) |
|
Rolling-circle replication is an alternative mechanism |
|
|
481 | (1) |
|
Phage replication can involve both bidirectional and rolling-circle mechanisms |
|
|
481 | (1) |
|
|
|
482 | (1) |
|
|
|
482 | (3) |
| Chapter 20 DNA Replication in Eukaryotes |
|
485 | (30) |
|
|
|
485 | (1) |
|
20.2 Replication Initiation In Eukaryotes |
|
|
485 | (10) |
|
Replication initiation in eukaryotes proceeds from multiple origins |
|
|
485 | (3) |
|
Eukaryotic origins of replication have diverse DNA and chromatin structure depending on the biological species |
|
|
488 | (5) |
|
There is a defined scenario for formation of initiation complexes |
|
|
493 | (2) |
|
Re-replication must be prevented |
|
|
495 | (1) |
|
Histone methylation regulates onset of licensing |
|
|
495 | (1) |
|
20.3 Replication Elongation In Eukaryotes |
|
|
495 | (4) |
|
Eukaryotic replisomes both resemble and significantly differ from those of bacteria |
|
|
495 | (4) |
|
Other components of the bacterial replisome have functional counterparts in eukaryotes |
|
|
499 | (1) |
|
Eukaryotic elongation has some special dynamic features |
|
|
499 | (1) |
|
20.4 Replication Of Chromatin |
|
|
499 | (5) |
|
Chromatin structure is dynamic during replication |
|
|
499 | (1) |
|
Histone chaperones may play multiple roles in replication |
|
|
500 | (1) |
|
Both old and newly synthesized histones are required in replication |
|
|
501 | (2) |
|
Epigenetic information in chromatin must also be replicated |
|
|
503 | (1) |
|
20.5 The DNA End-Replication Problem And Its Resolution |
|
|
504 | (3) |
|
Telomerase solves the end-replication problem |
|
|
504 | (2) |
|
Alternative lengthening of telomeres pathway is active in telomerase-deficient cells |
|
|
506 | (1) |
|
20.6 Mitochondrial DNA Replication |
|
|
507 | (2) |
|
Are circular mitochondrial genomes myth or reality? |
|
|
507 | (1) |
|
Models of mitochondrial genome replication are contentious |
|
|
508 | (1) |
|
20.7 Replication In Viruses That Infect Eukaryotes |
|
|
509 | (3) |
|
Retroviruses use reverse transcriptase to copy RNA into DNA |
|
|
509 | (3) |
|
|
|
512 | (1) |
|
|
|
513 | (2) |
| Chapter 21 DNA Recombination |
|
515 | (34) |
|
|
|
515 | (1) |
|
21.2 Homologous Recombination |
|
|
515 | (2) |
|
Homologous recombination plays a number of roles in bacteria |
|
|
516 | (1) |
|
Homologous recombination has multiple roles in mitotic cells |
|
|
517 | (1) |
|
Meiotic exchange is essential to eukaryotic evolution |
|
|
517 | (1) |
|
21.3 Homologous Recombination In Bacteria |
|
|
517 | (8) |
|
End resection requires the RecBCD complex |
|
|
518 | (2) |
|
Strand invasion and strand exchange both depend on RecA |
|
|
520 | (1) |
|
Much concerning homologous recombination is still not understood |
|
|
520 | (3) |
|
Holliday junctions are the essential intermediary structures in HR |
|
|
523 | (2) |
|
21.4 Homologous Recombination In Eukaryotes |
|
|
525 | (7) |
|
Proteins involved in eukaryotic recombination resemble their bacterial counterparts |
|
|
525 | (2) |
|
HR malfunction is connected with many human diseases |
|
|
527 | (2) |
|
Meiotic recombination allows exchange of genetic information between homologous chromosomes in meiosis |
|
|
529 | (3) |
|
21.5 Nonhomologous Recombination |
|
|
532 | (8) |
|
Transposable elements or transposons are mobile DNA sequences that change positions in the genome |
|
|
532 | (1) |
|
Many transposons are transcribed but only a few have known functions |
|
|
533 | (2) |
|
There are several types of transposons |
|
|
535 | (3) |
|
DNA class II transposons can use either of two mechanisms to transpose themselves |
|
|
538 | (1) |
|
Retrotransposons, or class I transposons, require an RNA intermediate |
|
|
539 | (1) |
|
21.6 Site-Specific Recombination |
|
|
540 | (7) |
|
Bacteriophage A. integrates into the bacterial genome by site-specific recombination |
|
|
540 | (2) |
|
Immunoglobulin gene rearrangements also occur through site-specific recombination |
|
|
542 | (5) |
|
|
|
547 | (1) |
|
|
|
548 | (1) |
| Chapter 22 DNA Repair |
|
549 | |
|
|
|
549 | (2) |
|
22.2 Types Of Lesions In DNA |
|
|
551 | (1) |
|
Natural agents, from both within and outside a cell, can change the information content of DNA |
|
|
551 | (1) |
|
22.3 Pathways And Mechanisms Of DNA Repair |
|
|
551 | (15) |
|
DNA lesions are countered by a number of mechanisms of repair |
|
|
551 | (4) |
|
Thymine dimers are directly repaired by DNA photolyase |
|
|
555 | (1) |
|
The enzyme 06-alkylguanine alkyltransferase is involved in the repair of alkylated bases |
|
|
556 | (1) |
|
Nucleotide excision repair is active on helix-distorting lesions |
|
|
556 | (1) |
|
Base excision repair corrects damaged bases |
|
|
557 | (1) |
|
Mismatch repair corrects errors in base pairing |
|
|
558 | (1) |
|
Methyl-directed mismatch repair in bacteria uses methylation on adenines as a guide |
|
|
559 | (1) |
|
Mismatch repair pathways in eukaryotes may be directed by strand breaks during DNA replication |
|
|
560 | (1) |
|
Repair of double-strand breaks can be error-free or error-prone |
|
|
560 | (1) |
|
Homologous recombination repairs double-strand breaks faithfully |
|
|
560 | (1) |
|
Nonhomologous end-joining restores the continuity of the DNA double helix in an error-prone process |
|
|
561 | (5) |
|
22.4 Translesion Synthesis |
|
|
566 | (2) |
|
Many repair pathways utilize RecQ helicases |
|
|
568 | (1) |
|
22.5 Chromatin As An Active Player In DNA Repair |
|
|
568 | (8) |
|
Histone variants and their post-translational modifications are specifically involved in DNA repair |
|
|
568 | (8) |
|
22.6 Overview: The Role Of DNA Repair In Life |
|
|
576 | (1) |
|
|
|
576 | (1) |
|
|
|
577 | |
