Genomes:
Gespeichert in:
1. Verfasser: | |
---|---|
Format: | Buch |
Sprache: | English |
Veröffentlicht: |
New York [u.a.]
Garland Science
2007
|
Ausgabe: | 3. ed. |
Schlagworte: | |
Online-Zugang: | Inhaltsverzeichnis |
Beschreibung: | CD-ROM-Beil. u.d.T.: The art of genomes 3 |
Beschreibung: | XXII, 713 S. zahlr. Ill., graph. Darst. CD-ROM (12 cm) |
ISBN: | 0815341385 |
Internformat
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246 | 1 | 3 | |a Genomes 3 |
246 | 1 | 3 | |a The art of genomes 3 |
250 | |a 3. ed. | ||
264 | 1 | |a New York [u.a.] |b Garland Science |c 2007 | |
300 | |a XXII, 713 S. |b zahlr. Ill., graph. Darst. |e CD-ROM (12 cm) | ||
336 | |b txt |2 rdacontent | ||
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338 | |b nc |2 rdacarrier | ||
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Datensatz im Suchindex
_version_ | 1804135419856551936 |
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adam_text | Contents
Preface
A Note to the Reader
Contents in Brief
Abbreviations
v
vii
xi
xix
PART
Chapter
and Proteomes
1.1 DNA
1.1.1
1.1.2
Nucleotides and polynucleotides
The evidence that led to the double helix
The key features of the double helix
The double helix has structural flexibility
1.2
1.2.1
1.2.2
1.2.3
1.2.4
1.3
1.3.1
The four levels of protein structure
Amino
1.3.2
The link between the
the proteome
The genetic code is not universal
The link between the proteome and the
biochemistry of the cell
Study Aids
Chapter
2.1
2.1.1 DNA polymerases
Technical Note
The mode of action of a template-dependent
polymerase
The types of
2.1.2
Restriction endonucleases enable the
molecules to be cut at defined positions
Technical Note
Examining the results of a restriction digest
2.1.3 DNA
2.1.4
5
5
8
8
9
11
12
14
15
15
17
17
18
18
18
19
20
21
22
23
26
31
33
34
34
35
36
37
38
40
41
42
42
2.2 DNA
2.2.1
Vectors based on
Technical Note
Cloning vectors based on
bacteriophage genomes
Vectors for longer pieces of
Cloning in organisms other than
2.3
2.3.1
Technical Note
2.3.2
Study Aids
Chapter
3.1
3.2
3.2.1
3.2.2 DNA
Restriction fragment length polymorphisms
Simple sequence length polymorphisms
Single nucleotide polymorphisms
Technical Note
3.2.3
The principles of inheritance and the
discovery of linkage
Partial linkage is explained by the behavior
of chromosomes during meiosis
From partial linkage to genetic mapping
3.2.4
Linkage analysis when planned breeding
experiments are possible
Gene mapping by human pedigree analysis
Genetic mapping in bacteria
3.3
3.3.1
The basic methodology for restriction mapping
The scale of restriction mapping is limited
by the sizes of the restriction fragments
Direct examination of
restriction sites
3.3.2
In situ hybridization with radioactive or
fluorescent probes
FISH in action
3.3.3
Any unique
43
44
45
46
48
51
53
55
55
56
57
59
63
65
65
66
67
67
68
69
71
72
72
74
77
77
78
80
81
82
84
84
86
87
89
89
90
91
Contents xiii
Fragments
A clone library can also be used as the
mapping reagent for STS analysis
Study Aids
Chapter
4.1
4.1.1
4.1.2
4.2
4.2.1
4.2.2
4.2.3
The Methodology for
Technical Note
gel electrophoresis
Chain termination
Chain termination sequencing in outline
Chain termination sequencing requires a
single-stranded
DNA polymerases
sequencing
The primer determines the region of the
template
Thermal cycle sequencing offers an
alternative to the traditional methodology
Alternative methods for
Chemical degradation sequencing
Pyrosequencing is used for rapid
determination of very short sequences
97
103
104
104
105
105
107
108
108
109
109
110
111
Assembly of a Contiguous
Sequence assembly by the shotgun method
The potential of the shotgun method was proven
by the Haemophilus influenzae sequence
Sequence assembly by the clone contig
method
Clone contigs can be built up by chromosome
walking, but the method is laborious
More rapid methods for clone contig assembly
Whole-genome shotgun sequencing
Key features of whole-genome shotgun
sequencing
4.3
4.3.1
Project
4.3.2
4.3.3
Study Aids
Chapter
Sequence
5.1
5.1.1
The coding regions of genes are open
reading frames
Simple
DNA
Locating genes for functional
Homology searches and comparative genomics
give an extra dimension to sequence inspection
Automatic annotation of genome sequences
5.1.2
5.2
5.2.1
5.2.2
121
5.3.1
122
5.3.2
123
6.1
134
6.1.1
134
6.1.2
134
135
137
138
6.2
140
6.2.1
141
Hybridization tests can determine if a
fragment contains transcribed sequences
Technical Note
cDNA sequencing enables genes to be
mapped within
Methods are available for precise mapping
of the ends of transcripts
Exon-intron boundaries can also be located
with precision
Determining the Functions of Individual
Genes
Computer analysis of gene function
Homology reflects evolutionary relationships
Homology analysis can provide information
on the function of an entire gene or of
segments within it
Using homology searching to assign
functions to human disease genes
Assigning gene function by experimental
analysis
Functional analysis by gene inactivation
Individual genes can be inactivated by
homologous recombination
Gene inactivation without homologous
recombination
Gene overexpression can also be used to
assess function
The phenotypic effect of gene inactivation or
overexpression may be difficult to discern
More detailed studies of the activity of a
protein coded by an unknown gene
Directed mutagenesis can be used to probe
gene function in detail
Reporter genes and immunocytochemistry
can be used to locate where and when genes
are expressed
Technical Note
Case Study: Annotation of the Saccharomyces
cerevislae Genome Sequence
Annotation of the yeast genome sequence
Assigning functions to yeast genes
Study Aids
Chapter
Functions
Studying the
Studying
Studying
or chip analysis
Using a microarray or chip to study one
or more
Studies of the yeast
The human
Studying the Proteome
Protein profiling
identifying the proteins in a proteome
5.2.3
5.3
XIV
Contents
Separating the proteins in a proteome
Identifying the proteins in a proteome
6.2.2
another
Identifying pairs of interacting proteins by
phage display and two-hybrid studies
Identifying the components of multiprotein
complexes
Identifying proteins with functional
interactions
Protein interaction maps
6.3
6.3.1
6.3.2
Study Aids
PART
Chapter
7.1
Chromosomes
7.1.1
7.1.2
DNA-protein interactions in centromeres and
telomeres
7.2
Genomes
7.2.1
Technical Note
techniques
7.2.2
genome?
The genes make up only a small part of the
human genome
The yeast genome is very compact
Gene organization in other eukaryotes
7.2.3
functions?
The human gene catalog
Gene catalogs reveal the distinctive features
of different organisms
Families of genes
Pseudogenes and other evolutionary relics
7.2.4
nuclear genomes
Tandemly repeated
and elsewhere in eukaryotic chromosomes
Minisatellites
Interspersed repeats
216
Study Aids
220
Chapter
Eukaryotic Organelles
8.1
8.1.1
The traditional view of the prokaryotic
chromosome
Some bacteria have linear or multipartite
genomes
8.2
8.2.1
genome?
Gene organization in the
Opérons
prokaryotic genomes
8.2.2
functions?
8.2.3
8.3
8.3.1
8.3.2
8.3.3
Study Aids
Chapter
Genetic Elements
199
9.1
The Genomes of Bacteriophages and
Eukaryotic Viruses
250
202
9.1.1
Bacteriophage genomes
250
Bacteriophage genomes have diverse
structures and organizations
250
203
Replication strategies for bacteriophage
204
genomes
251
9.1.2
The genomes of eukaryotic viruses
253
205
Structures and replication strategies for
eukaryotic viral genomes
253
205
Genomes at the edge of life
254
206
9.2
Mobile Genetic Elements
256
207
9.2.1
Transposition via an
257
210
RNA
are related to viral retroelements
257
211
RNA
259
212
9.2.2
DNA
259
DNA
212
genomes
260
215
DNA
216
eukaryotic genomes
261
Study Aids
PART
Chapter
10.1
10.1.1
nucleus
The nucleus has a highly ordered internal
structure
Technical Note
after photobleaching (FRAP)
Contents xv
Each chromosome has its own territory
within the nucleus
10.1.2
Functional domains are defined by insulators
Some functional domains contain locus
control regions
10.2
Expression
10.2.1
Acetylation of histones influences many
nuclear activities including genome
expression
Histone deacetylation represses active regions
of the genome
Acetylation is not the only type of histone
modification
10.2.2
genome expression
10.3 DNA
10.3.1
DNA methyltransferases
of genome activity
Methylation is involved in genomic
imprinting and X inactivation
Study Aids
290
Chapter
Initiation Complex
11.1
Attachment Sites
11.1.1
The helix-turn-helix motif is present in
prokaryotic and eukaryotic proteins
Technical Note
and nuclear magnetic resonance spectroscopy
Zinc fingers are common in eukaryotic
proteins
Other nucleic acid-binding motifs
11.1.2
in a genome
Gel retardation identifies
bind to proteins
Protection assays pinpoint binding sites with
greater accuracy
Modification interference identifies
nucleotides central to protein binding
11.1.3
proteins
Direct readout of the nucleotide sequence
The nucleotide sequence has a number of
indirect effects on helix structure
Contacts between
11.2
Transcription Initiation
11.2.1
11.2.2
Bacterial
sequences
Eukaryotic promoters are more complex
11.2.3
complex
Transcription initiation in
Transcription initiation with
Transcription initiation with
polymerases I and III
11.3
11.3.1
initiation in bacteria
Promotor
level of transcription initiation
Regulatory control over bacterial
transcription initiation
11.3.2
Eukaryotic promoters contain regulatory
modules
Activators and coactivators of eukaryotic
transcription initiation
The mediator forms the contact between an
activator and the
preinitiation complex
Repressors of eukaryotic transcription initiation
Controlling the activities of activators and
repressors
Study Aids
Chapter
of
12.1
12.1.1
Elongation of a transcript by the bacterial
RNA
Termination of a bacterial transcript
12.1.2
and termination
Antitermination results in termination signals
being ignored
Attenuation results in premature termination
Transcript cleavage proteins can prevent
stalling of a backtracked polymerase
12.1.3
Cutting events release mature rRNAs and
tRNAs from their precursor molecules
Nucleotide modifications broaden the
chemical properties of tRNAs and rRNAs
12.1.4
Bacterial mRNAs are degraded in the
3 ->5 direction
12.2
12.2.1
polymerase II
Capping of
occurs immediately after initiation
Elongation of eukaryotic mRNAs
xvi Contents
Termination of synthesis of most mRNAs is
combined with polyadenylation
Regulation of mRNA synthesis in eukaryotes
12.2.2
Conserved sequence motifs indicate the key
sites in GU-AG
Outline of the splicing pathway for GU-AG
introns
snRNAs and their associated proteins are the
central components of the splicing apparatus
Alternative splicing is common in many
eukaryotes
Trans-splicing links exons from different
transcription units
AU-AC
but require a different splicing apparatus
12.2.3
12.2.4
Introns
autocatalytic
Removal of
Other types of
12.2.5
Small nucleolar RNAs act as guides for
chemical modification of eukaryotic rRNAs
RNA
12.2.6
Eukaryotes have diverse mechanisms for
degradation
RNA
of destroying invading viral
MicroRNAs regulate genome expression by
causing specific target mRNAs to be degraded
12.2.7
Study Aids
377
Chapter
Proteome
13.1
13.1.1
acids to tRNAs
All tRNAs have a similar structure
Aminoacyl-tRNA synthetases attach
acids to tRNAs
13.1.2
of tRNAs to mRNA
13.2
13.2.1
Ultracentrifugation was used to measure the
sizes of ribosomes and their components
Probing the fine structure of the ribosome
13.2.2
Initiation in bacteria requires an internal
ribosome binding site
Initiation in eukaryotes is mediated by the
cap structure and poly(A) tail
Initiation of eukaryotic translation without
scanning
Regulation of translation initiation
13.2.3
Elongation in bacteria and eukaryotes
Peptidyl transferase is a ribozyme
Frameshifting and other unusual events
during elongation
13.2.4
13.2.5
13.3
13.3.1
Not all proteins fold spontaneously in the
test tube
In cells, folding is aided by molecular
chaperones
13.3.2
Cleavage of the ends of polypeptides
Proteolytic processing of polyproteins
13.3.3
13.3.4
13.4
Study Aids
Chapter
14.1
14.1.1
extracellular signaling compound
Lactoferrin is an extracellular signaling
protein which acts as a transcription
activator
Some imported signaling compounds directly
influence the activity of preexisting
regulatory proteins
Some imported signaling compounds
influence genome activity indirectly
14.1.2
receptors
Signal transduction with one step between
receptor and genome
Signal transduction with many steps
between receptor and genome
Signal transduction via second messengers
Unraveling a signal transduction pathway
14.2
in Genome Activity
14.2.1
Yeast mating types are determined by gene
conversion events
Genome rearrangements are responsible
for immunoglobulin and T-cell receptor
diversities
14.2.2
14.2.3
14.3
Development
14.3.1
Contents xvii
Bacteriophage
between lysis and lysogeny
14.3.2
Sporulation
in two distinct cell types
Special a subunits control genome activity
during
14.3.3
С
eukaryotic development
Determination of cell fate during
development of the
14.3.4
Maternal genes establish protein gradients
in the Drosophila embryo
A cascade of gene expression converts positional
information into a segmentation pattern
Segment identity is determined by homeotic
selector genes
Homeotic selector genes are universal features
of higher eukaryotic development
Homeotic genes also underlie plant
development
Study Aids
PART
and Evolve
Chapter
15.1
15.1.1
scheme for
The Meselson-Stahl experiment
15.1.2 DNA topoisomerases
the topological problem
15.1.3
15.2
15.2.1
Initiation at the
Origins of replication in yeast have been
clearly defined
Replication origins in higher eukaryotes have
been less easy to identify
15.2.2
The
eukaryotes
Discontinuous strand synthesis and the
priming problem
Events at the bacterial replication fork
The eukaryotic replication fork: variations on
the bacterial theme
Genome replication in the archaea
15.2.3
Replication of the
within a defined region
Little is known about termination of
replication in eukaryotes
15.2.4
Telomeric
telomerase
Telomere length is implicated in cell
senescence and cancer
Telomeres in Drosophila
15.3
15.3.1
division
Establishment of the prereplication complex
enables genome replication to commence
Regulation of pre-RC assembly
15.3.2
Early and late replication origins
Checkpoints within
Study Aids
499
Chapter
16.1
16.1.1
Technical Note
Errors in replication are a source of point
mutations
Replication errors can also lead to insertion
and deletion mutations
Mutations are also caused by chemical and
physical mutagens
16.1.2
The effects of mutations on genomes
The effects of mutations on multicellular
organisms
The effects of mutations on microorganisms
16.1.3
programmed mutations
Hypermutation results form abnormal
repair processes
Programmed mutations appear to support the
Lamarckian theory of evolution
16.2 DNA
16.2.1
some types of nucleotide modification
16.2.2
Base excision repairs many types of damaged
nucleotide
Nucleotide excision repair is used to correct
more extensive types of damage
16.2.3
replication
16.2.4
16.2.5
replication
The SOS response is an emergency measure
for coping with a damaged genome
16.2.6
diseases, including cancers
Study Aids
535
xviii Contents
Chapter
17.1
17.1.1
The Holliday and Meselson-Radding models
for homologous recombination
The double-strand break model for
homologous recombination
17.1.2
The RecBCD pathway of Escherichia
Other homologous recombination pathways
in
Homologous recombination pathways in
eukaryotes
17.1.3
17.2
17.2.1
17.2.2
engineering
18.4
Million Years
Study Aids
586
589
595
17.3
Transposition
552
17.3.1
Replicative
of
553
17.3.2
Transposition of retroelements
553
17.3.3
How do cells minimize the harmful effect of
transposition?
556
Study
ids
558
Chapter
18.1
18.1.1
The first biochemical systems were centered
on
The first
How unique is life?
18.2
18.2.1
Genome sequences provide extensive
evidence of past gene duplications
A variety of processes could result in gene
duplication
Whole genome duplication is also possible
Analysis of modern genomes provides
evidence for past genome duplications
Smaller duplications can also be identified in
the human genome and other genomes
Genome evolution also involves
rearrangement of existing genes
18.2.2
18.3
18.3.1
18.3.2
Introns
two competing hypotheses
The current evidence disproves neither
hypothesis
Chapter
19.1
Phylogenetics
19.1.1
Phenetics and cladistics require large
Large
molecular characters
19.2
Phylogenetic Trees
19.2.1
trees
Gene trees are not the same as species trees
19.2.2
Sequence alignment is the essential
preliminary to tree reconstruction
Converting alignment data into a
phylogenetic tree
Technical Note
Assessing the accuracy of a reconstructed tree
Molecular clocks enable the time of divergence
of ancestral sequences to be estimated
Standard tree reconstruction is not
appropriate for all
19.3
19.3.1
DNA
evolutionary relationships between humans
and other primates
The origins of AIDS
19.3.2
of human prehistory
Studying genes in populations
The origins of modern humans
Africa or not?
Neandertals are not the ancestors of modern
Europeans
The patterns of more recent migrations into
Europe are also controversial
Prehistoric human migrations into the
NewWorld
Study Aids
Appendix
Glossary
Index
621
627
653
683
|
adam_txt |
Contents
Preface
A Note to the Reader
Contents in Brief
Abbreviations
v
vii
xi
xix
PART
Chapter
and Proteomes
1.1 DNA
1.1.1
1.1.2
Nucleotides and polynucleotides
The evidence that led to the double helix
The key features of the double helix
The double helix has structural flexibility
1.2
1.2.1
1.2.2
1.2.3
1.2.4
1.3
1.3.1
The four levels of protein structure
Amino
1.3.2
The link between the
the proteome
The genetic code is not universal
The link between the proteome and the
biochemistry of the cell
Study Aids
Chapter
2.1
2.1.1 DNA polymerases
Technical Note
The mode of action of a template-dependent
polymerase
The types of
2.1.2
Restriction endonucleases enable the
molecules to be cut at defined positions
Technical Note
Examining the results of a restriction digest
2.1.3 DNA
2.1.4
5
5
8
8
9
11
12
14
15
15
17
17
18
18
18
19
20
21
22
23
26
31
33
34
34
35
36
37
38
40
41
42
42
2.2 DNA
2.2.1
Vectors based on
Technical Note
Cloning vectors based on
bacteriophage genomes
Vectors for longer pieces of
Cloning in organisms other than
2.3
2.3.1
Technical Note
2.3.2
Study Aids
Chapter
3.1
3.2
3.2.1
3.2.2 DNA
Restriction fragment length polymorphisms
Simple sequence length polymorphisms
Single nucleotide polymorphisms
Technical Note
3.2.3
The principles of inheritance and the
discovery of linkage
Partial linkage is explained by the behavior
of chromosomes during meiosis
From partial linkage to genetic mapping
3.2.4
Linkage analysis when planned breeding
experiments are possible
Gene mapping by human pedigree analysis
Genetic mapping in bacteria
3.3
3.3.1
The basic methodology for restriction mapping
The scale of restriction mapping is limited
by the sizes of the restriction fragments
Direct examination of
restriction sites
3.3.2
In situ hybridization with radioactive or
fluorescent probes
FISH in action
3.3.3
Any unique
43
44
45
46
48
51
53
55
55
56
57
59
63
65
65
66
67
67
68
69
71
72
72
74
77
77
78
80
81
82
84
84
86
87
89
89
90
91
Contents xiii
Fragments
A clone library can also be used as the
mapping reagent for STS analysis
Study Aids
Chapter
4.1
4.1.1
4.1.2
4.2
4.2.1
4.2.2
4.2.3
The Methodology for
Technical Note
gel electrophoresis
Chain termination
Chain termination sequencing in outline
Chain termination sequencing requires a
single-stranded
DNA polymerases
sequencing
The primer determines the region of the
template
Thermal cycle sequencing offers an
alternative to the traditional methodology
Alternative methods for
Chemical degradation sequencing
Pyrosequencing is used for rapid
determination of very short sequences
97
103
104
104
105
105
107
108
108
109
109
110
111
Assembly of a Contiguous
Sequence assembly by the shotgun method
The potential of the shotgun method was proven
by the Haemophilus influenzae sequence
Sequence assembly by the clone contig
method
Clone contigs can be built up by chromosome
walking, but the method is laborious
More rapid methods for clone contig assembly
Whole-genome shotgun sequencing
Key features of whole-genome shotgun
sequencing
4.3
4.3.1
Project
4.3.2
4.3.3
Study Aids
Chapter
Sequence
5.1
5.1.1
The coding regions of genes are open
reading frames
Simple
DNA
Locating genes for functional
Homology searches and comparative genomics
give an extra dimension to sequence inspection
Automatic annotation of genome sequences
5.1.2
5.2
5.2.1
5.2.2
121
5.3.1
122
5.3.2
123
6.1
134
6.1.1
134
6.1.2
134
135
137
138
6.2
140
6.2.1
141
Hybridization tests can determine if a
fragment contains transcribed sequences
Technical Note
cDNA sequencing enables genes to be
mapped within
Methods are available for precise mapping
of the ends of transcripts
Exon-intron boundaries can also be located
with precision
Determining the Functions of Individual
Genes
Computer analysis of gene function
Homology reflects evolutionary relationships
Homology analysis can provide information
on the function of an entire gene or of
segments within it
Using homology searching to assign
functions to human disease genes
Assigning gene function by experimental
analysis
Functional analysis by gene inactivation
Individual genes can be inactivated by
homologous recombination
Gene inactivation without homologous
recombination
Gene overexpression can also be used to
assess function
The phenotypic effect of gene inactivation or
overexpression may be difficult to discern
More detailed studies of the activity of a
protein coded by an unknown gene
Directed mutagenesis can be used to probe
gene function in detail
Reporter genes and immunocytochemistry
can be used to locate where and when genes
are expressed
Technical Note
Case Study: Annotation of the Saccharomyces
cerevislae Genome Sequence
Annotation of the yeast genome sequence
Assigning functions to yeast genes
Study Aids
Chapter
Functions
Studying the
Studying
Studying
or chip analysis
Using a microarray or chip to study one
or more
Studies of the yeast
The human
Studying the Proteome
Protein profiling
identifying the proteins in a proteome
5.2.3
5.3
XIV
Contents
Separating the proteins in a proteome
Identifying the proteins in a proteome
6.2.2
another
Identifying pairs of interacting proteins by
phage display and two-hybrid studies
Identifying the components of multiprotein
complexes
Identifying proteins with functional
interactions
Protein interaction maps
6.3
6.3.1
6.3.2
Study Aids
PART
Chapter
7.1
Chromosomes
7.1.1
7.1.2
DNA-protein interactions in centromeres and
telomeres
7.2
Genomes
7.2.1
Technical Note
techniques
7.2.2
genome?
The genes make up only a small part of the
human genome
The yeast genome is very compact
Gene organization in other eukaryotes
7.2.3
functions?
The human gene catalog
Gene catalogs reveal the distinctive features
of different organisms
Families of genes
Pseudogenes and other evolutionary relics
7.2.4
nuclear genomes
Tandemly repeated
and elsewhere in eukaryotic chromosomes
Minisatellites
Interspersed repeats
216
Study Aids
220
Chapter
Eukaryotic Organelles
8.1
8.1.1
The traditional view of the prokaryotic
chromosome
Some bacteria have linear or multipartite
genomes
8.2
8.2.1
genome?
Gene organization in the
Opérons
prokaryotic genomes
8.2.2
functions?
8.2.3
8.3
8.3.1
8.3.2
8.3.3
Study Aids
Chapter
Genetic Elements
199
9.1
The Genomes of Bacteriophages and
Eukaryotic Viruses
250
202
9.1.1
Bacteriophage genomes
250
Bacteriophage genomes have diverse
structures and organizations
250
203
Replication strategies for bacteriophage
204
genomes
251
9.1.2
The genomes of eukaryotic viruses
253
205
Structures and replication strategies for
eukaryotic viral genomes
253
205
Genomes at the edge of life
254
206
9.2
Mobile Genetic Elements
256
207
9.2.1
Transposition via an
257
210
RNA
are related to viral retroelements
257
211
RNA
259
212
9.2.2
DNA
259
DNA
212
genomes
260
215
DNA
216
eukaryotic genomes
261
Study Aids
PART
Chapter
10.1
10.1.1
nucleus
The nucleus has a highly ordered internal
structure
Technical Note
after photobleaching (FRAP)
Contents xv
Each chromosome has its own territory
within the nucleus
10.1.2
Functional domains are defined by insulators
Some functional domains contain locus
control regions
10.2
Expression
10.2.1
Acetylation of histones influences many
nuclear activities including genome
expression
Histone deacetylation represses active regions
of the genome
Acetylation is not the only type of histone
modification
10.2.2
genome expression
10.3 DNA
10.3.1
DNA methyltransferases
of genome activity
Methylation is involved in genomic
imprinting and X inactivation
Study Aids
290
Chapter
Initiation Complex
11.1
Attachment Sites
11.1.1
The helix-turn-helix motif is present in
prokaryotic and eukaryotic proteins
Technical Note
and nuclear magnetic resonance spectroscopy
Zinc fingers are common in eukaryotic
proteins
Other nucleic acid-binding motifs
11.1.2
in a genome
Gel retardation identifies
bind to proteins
Protection assays pinpoint binding sites with
greater accuracy
Modification interference identifies
nucleotides central to protein binding
11.1.3
proteins
Direct readout of the nucleotide sequence
The nucleotide sequence has a number of
indirect effects on helix structure
Contacts between
11.2
Transcription Initiation
11.2.1
11.2.2
Bacterial
sequences
Eukaryotic promoters are more complex
11.2.3
complex
Transcription initiation in
Transcription initiation with
Transcription initiation with
polymerases I and III
11.3
11.3.1
initiation in bacteria
Promotor
level of transcription initiation
Regulatory control over bacterial
transcription initiation
11.3.2
Eukaryotic promoters contain regulatory
modules
Activators and coactivators of eukaryotic
transcription initiation
The mediator forms the contact between an
activator and the
preinitiation complex
Repressors of eukaryotic transcription initiation
Controlling the activities of activators and
repressors
Study Aids
Chapter
of
12.1
12.1.1
Elongation of a transcript by the bacterial
RNA
Termination of a bacterial transcript
12.1.2
and termination
Antitermination results in termination signals
being ignored
Attenuation results in premature termination
Transcript cleavage proteins can prevent
stalling of a backtracked polymerase
12.1.3
Cutting events release mature rRNAs and
tRNAs from their precursor molecules
Nucleotide modifications broaden the
chemical properties of tRNAs and rRNAs
12.1.4
Bacterial mRNAs are degraded in the
3'->5' direction
12.2
12.2.1
polymerase II
Capping of
occurs immediately after initiation
Elongation of eukaryotic mRNAs
xvi Contents
Termination of synthesis of most mRNAs is
combined with polyadenylation
Regulation of mRNA synthesis in eukaryotes
12.2.2
Conserved sequence motifs indicate the key
sites in GU-AG
Outline of the splicing pathway for GU-AG
introns
snRNAs and their associated proteins are the
central components of the splicing apparatus
Alternative splicing is common in many
eukaryotes
Trans-splicing links exons from different
transcription units
AU-AC
but require a different splicing apparatus
12.2.3
12.2.4
Introns
autocatalytic
Removal of
Other types of
12.2.5
Small nucleolar RNAs act as guides for
chemical modification of eukaryotic rRNAs
RNA
12.2.6
Eukaryotes have diverse mechanisms for
degradation
RNA
of destroying invading viral
MicroRNAs regulate genome expression by
causing specific target mRNAs to be degraded
12.2.7
Study Aids
377
Chapter
Proteome
13.1
13.1.1
acids to tRNAs
All tRNAs have a similar structure
Aminoacyl-tRNA synthetases attach
acids to tRNAs
13.1.2
of tRNAs to mRNA
13.2
13.2.1
Ultracentrifugation was used to measure the
sizes of ribosomes and their components
Probing the fine structure of the ribosome
13.2.2
Initiation in bacteria requires an internal
ribosome binding site
Initiation in eukaryotes is mediated by the
cap structure and poly(A) tail
Initiation of eukaryotic translation without
scanning
Regulation of translation initiation
13.2.3
Elongation in bacteria and eukaryotes
Peptidyl transferase is a ribozyme
Frameshifting and other unusual events
during elongation
13.2.4
13.2.5
13.3
13.3.1
Not all proteins fold spontaneously in the
test tube
In cells, folding is aided by molecular
chaperones
13.3.2
Cleavage of the ends of polypeptides
Proteolytic processing of polyproteins
13.3.3
13.3.4
13.4
Study Aids
Chapter
14.1
14.1.1
extracellular signaling compound
Lactoferrin is an extracellular signaling
protein which acts as a transcription
activator
Some imported signaling compounds directly
influence the activity of preexisting
regulatory proteins
Some imported signaling compounds
influence genome activity indirectly
14.1.2
receptors
Signal transduction with one step between
receptor and genome
Signal transduction with many steps
between receptor and genome
Signal transduction via second messengers
Unraveling a signal transduction pathway
14.2
in Genome Activity
14.2.1
Yeast mating types are determined by gene
conversion events
Genome rearrangements are responsible
for immunoglobulin and T-cell receptor
diversities
14.2.2
14.2.3
14.3
Development
14.3.1
Contents xvii
Bacteriophage
between lysis and lysogeny
14.3.2
Sporulation
in two distinct cell types
Special a subunits control genome activity
during
14.3.3
С
eukaryotic development
Determination of cell fate during
development of the
14.3.4
Maternal genes establish protein gradients
in the Drosophila embryo
A cascade of gene expression converts positional
information into a segmentation pattern
Segment identity is determined by homeotic
selector genes
Homeotic selector genes are universal features
of higher eukaryotic development
Homeotic genes also underlie plant
development
Study Aids
PART
and Evolve
Chapter
15.1
15.1.1
scheme for
The Meselson-Stahl experiment
15.1.2 DNA topoisomerases
the topological problem
15.1.3
15.2
15.2.1
Initiation at the
Origins of replication in yeast have been
clearly defined
Replication origins in higher eukaryotes have
been less easy to identify
15.2.2
The
eukaryotes
Discontinuous strand synthesis and the
priming problem
Events at the bacterial replication fork
The eukaryotic replication fork: variations on
the bacterial theme
Genome replication in the archaea
15.2.3
Replication of the
within a defined region
Little is known about termination of
replication in eukaryotes
15.2.4
Telomeric
telomerase
Telomere length is implicated in cell
senescence and cancer
Telomeres in Drosophila
15.3
15.3.1
division
Establishment of the prereplication complex
enables genome replication to commence
Regulation of pre-RC assembly
15.3.2
Early and late replication origins
Checkpoints within
Study Aids
499
Chapter
16.1
16.1.1
Technical Note
Errors in replication are a source of point
mutations
Replication errors can also lead to insertion
and deletion mutations
Mutations are also caused by chemical and
physical mutagens
16.1.2
The effects of mutations on genomes
The effects of mutations on multicellular
organisms
The effects of mutations on microorganisms
16.1.3
programmed mutations
Hypermutation results form abnormal
repair processes
Programmed mutations appear to support the
Lamarckian theory of evolution
16.2 DNA
16.2.1
some types of nucleotide modification
16.2.2
Base excision repairs many types of damaged
nucleotide
Nucleotide excision repair is used to correct
more extensive types of damage
16.2.3
replication
16.2.4
16.2.5
replication
The SOS response is an emergency measure
for coping with a damaged genome
16.2.6
diseases, including cancers
Study Aids
535
xviii Contents
Chapter
17.1
17.1.1
The Holliday and Meselson-Radding models
for homologous recombination
The double-strand break model for
homologous recombination
17.1.2
The RecBCD pathway of Escherichia
Other homologous recombination pathways
in
Homologous recombination pathways in
eukaryotes
17.1.3
17.2
17.2.1
17.2.2
engineering
18.4
Million Years
Study Aids
586
589
595
17.3
Transposition
552
17.3.1
Replicative
of
553
17.3.2
Transposition of retroelements
553
17.3.3
How do cells minimize the harmful effect of
transposition?
556
Study
\ids
558
Chapter
18.1
18.1.1
The first biochemical systems were centered
on
The first
How unique is life?
18.2
18.2.1
Genome sequences provide extensive
evidence of past gene duplications
A variety of processes could result in gene
duplication
Whole genome duplication is also possible
Analysis of modern genomes provides
evidence for past genome duplications
Smaller duplications can also be identified in
the human genome and other genomes
Genome evolution also involves
rearrangement of existing genes
18.2.2
18.3
18.3.1
18.3.2
"Introns
two competing hypotheses"
The current evidence disproves neither
hypothesis
Chapter
19.1
Phylogenetics
19.1.1
Phenetics and cladistics require large
Large
molecular characters
19.2
Phylogenetic Trees
19.2.1
trees
Gene trees are not the same as species trees
19.2.2
Sequence alignment is the essential
preliminary to tree reconstruction
Converting alignment data into a
phylogenetic tree
Technical Note
Assessing the accuracy of a reconstructed tree
Molecular clocks enable the time of divergence
of ancestral sequences to be estimated
Standard tree reconstruction is not
appropriate for all
19.3
19.3.1
DNA
evolutionary relationships between humans
and other primates
The origins of AIDS
19.3.2
of human prehistory
Studying genes in populations
The origins of modern humans
Africa or not?
Neandertals are not the ancestors of modern
Europeans
The patterns of more recent migrations into
Europe are also controversial
Prehistoric human migrations into the
NewWorld
Study Aids
Appendix
Glossary
Index
621
627
653
683 |
any_adam_object | 1 |
any_adam_object_boolean | 1 |
author | Brown, Terence A. 1953- |
author_GND | (DE-588)113251661 |
author_facet | Brown, Terence A. 1953- |
author_role | aut |
author_sort | Brown, Terence A. 1953- |
author_variant | t a b ta tab |
building | Verbundindex |
bvnumber | BV021625352 |
callnumber-first | Q - Science |
callnumber-label | QH447 |
callnumber-raw | QH447 |
callnumber-search | QH447 |
callnumber-sort | QH 3447 |
callnumber-subject | QH - Natural History and Biology |
classification_rvk | WG 1000 WG 2300 |
classification_tum | BIO 220f CHE 860f BIO 180f |
ctrlnum | (OCoLC)255314017 (DE-599)BVBBV021625352 |
dewey-full | 572.86 |
dewey-hundreds | 500 - Natural sciences and mathematics |
dewey-ones | 572 - Biochemistry |
dewey-raw | 572.86 |
dewey-search | 572.86 |
dewey-sort | 3572.86 |
dewey-tens | 570 - Biology |
discipline | Biologie Chemie |
discipline_str_mv | Biologie Chemie |
edition | 3. ed. |
format | Book |
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language | English |
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spelling | Brown, Terence A. 1953- Verfasser (DE-588)113251661 aut Genomes T. A. Brown Genomes 3 The art of genomes 3 3. ed. New York [u.a.] Garland Science 2007 XXII, 713 S. zahlr. Ill., graph. Darst. CD-ROM (12 cm) txt rdacontent n rdamedia nc rdacarrier CD-ROM-Beil. u.d.T.: The art of genomes 3 Genom Genomes Genetik (DE-588)4071711-2 gnd rswk-swf Genom (DE-588)4156640-3 gnd rswk-swf Molekulargenetik (DE-588)4039987-4 gnd rswk-swf 1\p (DE-588)4151278-9 Einführung gnd-content 2\p (DE-588)4123623-3 Lehrbuch gnd-content Genom (DE-588)4156640-3 s DE-604 Molekulargenetik (DE-588)4039987-4 s Genetik (DE-588)4071711-2 s 3\p DE-604 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014840343&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk 2\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk 3\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
spellingShingle | Brown, Terence A. 1953- Genomes Genom Genomes Genetik (DE-588)4071711-2 gnd Genom (DE-588)4156640-3 gnd Molekulargenetik (DE-588)4039987-4 gnd |
subject_GND | (DE-588)4071711-2 (DE-588)4156640-3 (DE-588)4039987-4 (DE-588)4151278-9 (DE-588)4123623-3 |
title | Genomes |
title_alt | Genomes 3 The art of genomes 3 |
title_auth | Genomes |
title_exact_search | Genomes |
title_exact_search_txtP | Genomes |
title_full | Genomes T. A. Brown |
title_fullStr | Genomes T. A. Brown |
title_full_unstemmed | Genomes T. A. Brown |
title_short | Genomes |
title_sort | genomes |
topic | Genom Genomes Genetik (DE-588)4071711-2 gnd Genom (DE-588)4156640-3 gnd Molekulargenetik (DE-588)4039987-4 gnd |
topic_facet | Genom Genomes Genetik Molekulargenetik Einführung Lehrbuch |
url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014840343&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
work_keys_str_mv | AT brownterencea genomes AT brownterencea genomes3 AT brownterencea theartofgenomes3 |