Welcome Each of
You to My
Molecular Biology
Class
Molecular Biology of the Gene,
5/E --- Watson et al,(2004)
Part I,Chemistry and Genetics
Part II,Maintenance of the Genome
Part III,Expression of the Genome
Part IV,Regulation
Part V,Methods
3/11/05
Part II,Maintenance of the Genome
Dedicated to the structure of
DNA and the processes that
propagate,maintain and alter it
from one cell generation to the
next
Ch 6,The structures of DNA and RNA
Ch 7,Chromosomes,chromatins and
the nucleosome
Ch 8,The replication of DNA
Ch 9,The mutability and repair of
DNA
Ch 10,Homologous recombination at
the molecular level
Ch 11,Site-specific recombination
and transposition of DNA
3/11/05
CHAPTER 7,Chromosomes,
chromatin,and the
nucleosome
Consider the structure of DNA
within the cell,and the biological
relevance of the structure.
?DNA is associated with proteins in
cells,both prokaryotes and eukaryotes,
even viruses
?Each DNA and its associated
proteins is called a chromosome
Nucleus,细胞核 ; Nucleolus,核仁
Nucleoid,类核
Mitosis,有丝分裂； Meiosis：减数分裂
interphase：分裂间期
Histone,组蛋白； Nucleosome,核小体
Chromotasome,染色小体
Chromosome,染色体；
Chromatin,染色质； eu-; hetero-
Centromere (中心粒） Telomere（端粒）
Repetitive DNA (重复 DNA)
Tandem gene cluster（串联基因 簇）
Vocabulary
The importance of packing of DNA into
chromosomes
?Chromosome is a compact form of the
DNA that readily fits inside the cell
?To protect DNA from damage
?DNA in a chromosome can be
transmitted efficiently to both daughter
cells during cell division
?Chromosome confers an overall
organization to each molecule of DNA,
which facilitates gene expression as
well as recombination
Half of the molecular mass of eukaryotic
chromosome is protein
?In eukaryotic cells a given region of DNA
with its associated proteins is called
chromatin
?The majority of the associated proteins are
small,basic proteins called histones.
?Other proteins associated with the
chromosome are referred to as non-histone
proteins,including numerous DNA binding
proteins that regulate the transcription,
replication,repair and recombination of DNA.
Proteins in chromosome (1)
?Nucleosomes,regular association of
DNA with histones to form a structure
effectively compacting DNA
Proteins in chromosome (2)
1,What is the cost (challenge) of
compaction of DNA into
chromosome?
2,How the challenge could be
resolved?
3,What are the advantage of the
challenge?
CHAPTER 7,Chromosomes,chromatin,and the nucleosome
OUTLINE
? Chromosome sequence & diversity
? Chromosome duplication & segregation
? The nucleosome
? Higher-order chromatin structure
? Regulation of chromatin structure
? Nucleosome assembly
CHAPTER 7,Chromosomes,chromatin,and the nucleosome
Chromosome sequence & diversity
CHAPTER 7,Chromosomes,chromatin,and the nucleosome
Chromosomes
? Shape,circular or linear
? Number in an organism is
characteristic
? Copy,haploid,diploid,polyploid
Genomes
3/15/05
Difference in the structures of
eukaryotic and prokaryotic cells
is a key to better understand the
molecular processes of genome
maintenance and expression,as
well as the differences in these
processes between eukaryotes
and prokaryotes
Ch
ro
mo
so
me
se
qu
en
ce
&
di
ve
rs
ity
3/15/05
Ch
ro
mo
so
me
se
qu
en
ce
&
di
ve
rs
ity
Figure 7-1*
Ch
ro
mo
so
me
se
qu
en
ce
&
di
ve
rs
ity
? Genome size,the length of DNA
associated with one haploid
complement of chromosomes
? Gene number,the number of genes
included in a genome
? Gene density,the average number
of genes per Mb of genomic DNA
Genome & the complexity of
the organism
See Table 7-2 to find the relationship3/15/05
Table 7-2
Ch
ro
mo
so
me
se
qu
en
ce
&
di
ve
rs
ity
? Increases in gene size,(1) increase
in the sequence of regulatory
sequence; (2) presence of introns
(splicing)
? Increases in the DNA between
genes (intergenic sequences),(1)
unique; (2) repeated
Genes make up only a small
proportion of the eukaryotic genome
See Figure 7-2,3,4,5; Table 7-3
3/15/05
Table 7-3
Figure 7-2
Figure 7-4*
Chromosome
duplication &
segregation
CHAPTER 7,Chromosomes,chromatin,and the nucleosome
(1) Critical DNA elements
? Origins of replication
? Centromeres
? Telomeres
These elements are not involved
in gene expression
3/15/05
Sites at which the DNA replication
machinery assembles to initiate
replication; required fro replication
? 30-40 kb apart on each eukaryotic
chromosome
? Only one origin for prokaryotic
chromosome
Origins of replication
Ch
ro
mo
so
me
du
pli
ca
tio
n
&
se
gr
eg
ati
on
Required for the correct segregation of
the chromosomes after replication
? Direct the formation of kinetochore
(an elaborate protein complex)
essential for chrom,segregation
? One chromosome,one centromere
? The size varies (200 bp- >40 kb)
? Composed of largely repetitive DNA
sequences
Centromeres
Ch
ro
mo
so
me
du
pli
ca
tio
n
&
se
gr
eg
ati
on
Figure 7-6 Centromeres,origin of
replication and telomere are required for
eukaryotic chrom,maintenance
Cell cycle,a single round of cell
division
Mitotic cell division,the chrom,
Number is maintained during cell
division
(2) Eukaryotic chromosome
duplication & segregation occur in
separate phases of the cell cycle
Ch
ro
mo
so
me
du
pli
ca
tio
n
&
se
gr
eg
ati
on
Figure 7-10 The eukaryotic mitotic cell cycle
Figure 7-11 The events of S phase
Figure 7-11 The events of M phase
Mitotic spindle
M phase,condensed state,completely
disentangled from each other
G1,S,G2 phases,diffused,
significantly less compact,The
structure of chrom,changes,e.g,
DNA replication requires the nearly
complete disassembly and
reassembly of the proteins
associated with each chromosome
(3) Chromosome structure changes
as eukaryotic cells divide
Ch
ro
mo
so
me
du
pli
ca
tio
n
&
se
gr
eg
ati
on
Chromosome condensation
Figure 7-13 Changes in chromatin structure
REMEMBER,chromosome is a
consistently changing structure
(dynamics)
Think of the regulatory
mechanisms might be involved
to CHECK the cell condition
(4) The gap phase of the cell cycle
allow time to prepare for the next
cell cycle stage while also checking
that the previous stage is finished
correctly.
Ch
ro
mo
so
me
du
pli
ca
tio
n
&
se
gr
eg
ati
on
(5) Different levels of chromosome
structure can be observed by
microscopy
Ch
ro
mo
so
me
du
pli
ca
tio
n
&
se
gr
eg
ati
on
Figure 7-13 Forms of chromotin structure
seen in EM (electron microscopy)
The nucleosome
CHAPTER 7,Chromosomes,chromatin,and the nucleosome
Nucleosome & histone
structures
3/15/05
(1) Nucleosomes are the building
blocks of chromosomesT
he
nu
cle
os
om
e
? The nucleosome is composed of a
core of eight histone proteins and
the DNA (core DNA,147 bp)
wrapped around them,The DNA
between each nucleosome is called
a linker DNA,Each eukaryote has a
characteristic average linker DNA
length (20-60 bp)
Figure 7-18 DNA
packaged into
nucleosome
Six-fold DNA compaction
? Five abundant histones are H1
(linker histone,20 kd),H2A,H2B,
H3 and H4 (core histones,11-15 kd),
? The core histones share a common
structural fold,called histone-fold
domain
? The core histones each have an N-
terminal,tail”,the sites of
extensive modifications
(2) Histones are small,positively
charged (basic) proteins
Th
e n
uc
leo
so
me
Figure 7-19 The core histones share a
common structural fold
(1)(2)
(3) Many DNA sequence-
independent contacts (?) mediate
interaction between between the
core histones and DNA The
nu
cle
os
om
e
Figure 7-25
(4) The histone N-terminal tails
stabilize DNA wrapping around the
octamer
Figure 7-26 The histone tails emerge from
the core of the nucleosome at specific
positions,serving as the grooves of a screw
to direct the DNA wrapping around the
Higher-order chromatin
structure
CHAPTER 7,Chromosomes,chromatin,and the nucleosome
How does it form?
3/15/05
(1) Histone H1 binds to the linker
DNA between nucleosome,inducing
tighter DNA wrapping around the
nucleosome
Hig
her
-o
rd
er
ch
ro
mat
in
str
uct
ur
e
Figures 7-28,29
(2) Nuclear arrays can form more
complex structures,the 30-nm fiber
(“zigzag model”)
Hig
her
-o
rd
er
ch
ro
mat
in
str
uct
ur
e
Figures 7-30
(40-fold compaction)
(3) Further compaction of DNA
involves large loops of nucleosomal
DNA
Hig
her
-o
rd
er
ch
ro
mat
in
str
uct
ur
e
?Additional 103-104-fold
compaction is required,but the
mechanism is unclear
?The nuclear scaffold model is
proposed
Figures 7-32 The higher-
order structure of
chromatin,(a) A
transmission electron
micrograph,(b) A model
(3) Histone variants alter
nucleosome function
Hig
her
-o
rd
er
ch
ro
mat
in
str
uct
ur
e
?Several histone variants are
found in enkaryotes
?This variants can replace one
of the 4 standard histones to
form alternate nucleosomes
Figures 7-33 Alteration of chromatin
by incorporation of histone variants
CENP-A is associated with the nucleosomes
containing centromeric DNA
Regulation of chromatin
structure
CHAPTER 7,Chromosomes,chromatin,and the nucleosome
How?
3/15/05
The interaction of DNA with the
histone octamer is dynamic
Reg
ula
tio
n o
f c
hr
om
atin
st
ru
ctu
re
?There are factors acting on the
nucleosome to increase or
decrease the dynamic nature
?The dynamic nature of DNA-
binding to the histone core is
important for access of DNA by
other proteins essential genome
expression etc.
Figures 7-34 A model for gaining
access to core DNA
Nucleosome remodeling complexes
facilitate nucleosome movement
Reg
ula
tio
n o
f c
hr
om
atin
st
ru
ctu
re
?A large protein complexes
facilitate changes in nucleosome
location or interaction with the
DNA using the energy of ATP
hydrolysis.
Figures 7-35 Nucleosome movement
catalyzed by nucleosome remodeling
complexes
Modification of the N-terminal tails
of the histones alters chromatin
accessibility,and specific enzymes
are responsible for histone
modification
Reg
ula
tio
n o
f c
hr
om
atin
st
ru
ctu
re
Figures 7-38 Modification of the
histone N-terminal tails alters the
function of chromatin
Nucleosome assembly
CHAPTER 7,Chromosomes,chromatin,and the nucleosome
?Nucleosomes are assembled
immediately after DNA
replication,and the assembly
requires histone chaperones
3/15/05
Figures 7-41 The inheritance of
histones after DNA replication
Try to complete all the
excises on your study
CD
Homework
You to My
Molecular Biology
Class
Molecular Biology of the Gene,
5/E --- Watson et al,(2004)
Part I,Chemistry and Genetics
Part II,Maintenance of the Genome
Part III,Expression of the Genome
Part IV,Regulation
Part V,Methods
3/11/05
Part II,Maintenance of the Genome
Dedicated to the structure of
DNA and the processes that
propagate,maintain and alter it
from one cell generation to the
next
Ch 6,The structures of DNA and RNA
Ch 7,Chromosomes,chromatins and
the nucleosome
Ch 8,The replication of DNA
Ch 9,The mutability and repair of
DNA
Ch 10,Homologous recombination at
the molecular level
Ch 11,Site-specific recombination
and transposition of DNA
3/11/05
CHAPTER 7,Chromosomes,
chromatin,and the
nucleosome
Consider the structure of DNA
within the cell,and the biological
relevance of the structure.
?DNA is associated with proteins in
cells,both prokaryotes and eukaryotes,
even viruses
?Each DNA and its associated
proteins is called a chromosome
Nucleus,细胞核 ; Nucleolus,核仁
Nucleoid,类核
Mitosis,有丝分裂； Meiosis：减数分裂
interphase：分裂间期
Histone,组蛋白； Nucleosome,核小体
Chromotasome,染色小体
Chromosome,染色体；
Chromatin,染色质； eu-; hetero-
Centromere (中心粒） Telomere（端粒）
Repetitive DNA (重复 DNA)
Tandem gene cluster（串联基因 簇）
Vocabulary
The importance of packing of DNA into
chromosomes
?Chromosome is a compact form of the
DNA that readily fits inside the cell
?To protect DNA from damage
?DNA in a chromosome can be
transmitted efficiently to both daughter
cells during cell division
?Chromosome confers an overall
organization to each molecule of DNA,
which facilitates gene expression as
well as recombination
Half of the molecular mass of eukaryotic
chromosome is protein
?In eukaryotic cells a given region of DNA
with its associated proteins is called
chromatin
?The majority of the associated proteins are
small,basic proteins called histones.
?Other proteins associated with the
chromosome are referred to as non-histone
proteins,including numerous DNA binding
proteins that regulate the transcription,
replication,repair and recombination of DNA.
Proteins in chromosome (1)
?Nucleosomes,regular association of
DNA with histones to form a structure
effectively compacting DNA
Proteins in chromosome (2)
1,What is the cost (challenge) of
compaction of DNA into
chromosome?
2,How the challenge could be
resolved?
3,What are the advantage of the
challenge?
CHAPTER 7,Chromosomes,chromatin,and the nucleosome
OUTLINE
? Chromosome sequence & diversity
? Chromosome duplication & segregation
? The nucleosome
? Higher-order chromatin structure
? Regulation of chromatin structure
? Nucleosome assembly
CHAPTER 7,Chromosomes,chromatin,and the nucleosome
Chromosome sequence & diversity
CHAPTER 7,Chromosomes,chromatin,and the nucleosome
Chromosomes
? Shape,circular or linear
? Number in an organism is
characteristic
? Copy,haploid,diploid,polyploid
Genomes
3/15/05
Difference in the structures of
eukaryotic and prokaryotic cells
is a key to better understand the
molecular processes of genome
maintenance and expression,as
well as the differences in these
processes between eukaryotes
and prokaryotes
Ch
ro
mo
so
me
se
qu
en
ce
&
di
ve
rs
ity
3/15/05
Ch
ro
mo
so
me
se
qu
en
ce
&
di
ve
rs
ity
Figure 7-1*
Ch
ro
mo
so
me
se
qu
en
ce
&
di
ve
rs
ity
? Genome size,the length of DNA
associated with one haploid
complement of chromosomes
? Gene number,the number of genes
included in a genome
? Gene density,the average number
of genes per Mb of genomic DNA
Genome & the complexity of
the organism
See Table 7-2 to find the relationship3/15/05
Table 7-2
Ch
ro
mo
so
me
se
qu
en
ce
&
di
ve
rs
ity
? Increases in gene size,(1) increase
in the sequence of regulatory
sequence; (2) presence of introns
(splicing)
? Increases in the DNA between
genes (intergenic sequences),(1)
unique; (2) repeated
Genes make up only a small
proportion of the eukaryotic genome
See Figure 7-2,3,4,5; Table 7-3
3/15/05
Table 7-3
Figure 7-2
Figure 7-4*
Chromosome
duplication &
segregation
CHAPTER 7,Chromosomes,chromatin,and the nucleosome
(1) Critical DNA elements
? Origins of replication
? Centromeres
? Telomeres
These elements are not involved
in gene expression
3/15/05
Sites at which the DNA replication
machinery assembles to initiate
replication; required fro replication
? 30-40 kb apart on each eukaryotic
chromosome
? Only one origin for prokaryotic
chromosome
Origins of replication
Ch
ro
mo
so
me
du
pli
ca
tio
n
&
se
gr
eg
ati
on
Required for the correct segregation of
the chromosomes after replication
? Direct the formation of kinetochore
(an elaborate protein complex)
essential for chrom,segregation
? One chromosome,one centromere
? The size varies (200 bp- >40 kb)
? Composed of largely repetitive DNA
sequences
Centromeres
Ch
ro
mo
so
me
du
pli
ca
tio
n
&
se
gr
eg
ati
on
Figure 7-6 Centromeres,origin of
replication and telomere are required for
eukaryotic chrom,maintenance
Cell cycle,a single round of cell
division
Mitotic cell division,the chrom,
Number is maintained during cell
division
(2) Eukaryotic chromosome
duplication & segregation occur in
separate phases of the cell cycle
Ch
ro
mo
so
me
du
pli
ca
tio
n
&
se
gr
eg
ati
on
Figure 7-10 The eukaryotic mitotic cell cycle
Figure 7-11 The events of S phase
Figure 7-11 The events of M phase
Mitotic spindle
M phase,condensed state,completely
disentangled from each other
G1,S,G2 phases,diffused,
significantly less compact,The
structure of chrom,changes,e.g,
DNA replication requires the nearly
complete disassembly and
reassembly of the proteins
associated with each chromosome
(3) Chromosome structure changes
as eukaryotic cells divide
Ch
ro
mo
so
me
du
pli
ca
tio
n
&
se
gr
eg
ati
on
Chromosome condensation
Figure 7-13 Changes in chromatin structure
REMEMBER,chromosome is a
consistently changing structure
(dynamics)
Think of the regulatory
mechanisms might be involved
to CHECK the cell condition
(4) The gap phase of the cell cycle
allow time to prepare for the next
cell cycle stage while also checking
that the previous stage is finished
correctly.
Ch
ro
mo
so
me
du
pli
ca
tio
n
&
se
gr
eg
ati
on
(5) Different levels of chromosome
structure can be observed by
microscopy
Ch
ro
mo
so
me
du
pli
ca
tio
n
&
se
gr
eg
ati
on
Figure 7-13 Forms of chromotin structure
seen in EM (electron microscopy)
The nucleosome
CHAPTER 7,Chromosomes,chromatin,and the nucleosome
Nucleosome & histone
structures
3/15/05
(1) Nucleosomes are the building
blocks of chromosomesT
he
nu
cle
os
om
e
? The nucleosome is composed of a
core of eight histone proteins and
the DNA (core DNA,147 bp)
wrapped around them,The DNA
between each nucleosome is called
a linker DNA,Each eukaryote has a
characteristic average linker DNA
length (20-60 bp)
Figure 7-18 DNA
packaged into
nucleosome
Six-fold DNA compaction
? Five abundant histones are H1
(linker histone,20 kd),H2A,H2B,
H3 and H4 (core histones,11-15 kd),
? The core histones share a common
structural fold,called histone-fold
domain
? The core histones each have an N-
terminal,tail”,the sites of
extensive modifications
(2) Histones are small,positively
charged (basic) proteins
Th
e n
uc
leo
so
me
Figure 7-19 The core histones share a
common structural fold
(1)(2)
(3) Many DNA sequence-
independent contacts (?) mediate
interaction between between the
core histones and DNA The
nu
cle
os
om
e
Figure 7-25
(4) The histone N-terminal tails
stabilize DNA wrapping around the
octamer
Figure 7-26 The histone tails emerge from
the core of the nucleosome at specific
positions,serving as the grooves of a screw
to direct the DNA wrapping around the
Higher-order chromatin
structure
CHAPTER 7,Chromosomes,chromatin,and the nucleosome
How does it form?
3/15/05
(1) Histone H1 binds to the linker
DNA between nucleosome,inducing
tighter DNA wrapping around the
nucleosome
Hig
her
-o
rd
er
ch
ro
mat
in
str
uct
ur
e
Figures 7-28,29
(2) Nuclear arrays can form more
complex structures,the 30-nm fiber
(“zigzag model”)
Hig
her
-o
rd
er
ch
ro
mat
in
str
uct
ur
e
Figures 7-30
(40-fold compaction)
(3) Further compaction of DNA
involves large loops of nucleosomal
DNA
Hig
her
-o
rd
er
ch
ro
mat
in
str
uct
ur
e
?Additional 103-104-fold
compaction is required,but the
mechanism is unclear
?The nuclear scaffold model is
proposed
Figures 7-32 The higher-
order structure of
chromatin,(a) A
transmission electron
micrograph,(b) A model
(3) Histone variants alter
nucleosome function
Hig
her
-o
rd
er
ch
ro
mat
in
str
uct
ur
e
?Several histone variants are
found in enkaryotes
?This variants can replace one
of the 4 standard histones to
form alternate nucleosomes
Figures 7-33 Alteration of chromatin
by incorporation of histone variants
CENP-A is associated with the nucleosomes
containing centromeric DNA
Regulation of chromatin
structure
CHAPTER 7,Chromosomes,chromatin,and the nucleosome
How?
3/15/05
The interaction of DNA with the
histone octamer is dynamic
Reg
ula
tio
n o
f c
hr
om
atin
st
ru
ctu
re
?There are factors acting on the
nucleosome to increase or
decrease the dynamic nature
?The dynamic nature of DNA-
binding to the histone core is
important for access of DNA by
other proteins essential genome
expression etc.
Figures 7-34 A model for gaining
access to core DNA
Nucleosome remodeling complexes
facilitate nucleosome movement
Reg
ula
tio
n o
f c
hr
om
atin
st
ru
ctu
re
?A large protein complexes
facilitate changes in nucleosome
location or interaction with the
DNA using the energy of ATP
hydrolysis.
Figures 7-35 Nucleosome movement
catalyzed by nucleosome remodeling
complexes
Modification of the N-terminal tails
of the histones alters chromatin
accessibility,and specific enzymes
are responsible for histone
modification
Reg
ula
tio
n o
f c
hr
om
atin
st
ru
ctu
re
Figures 7-38 Modification of the
histone N-terminal tails alters the
function of chromatin
Nucleosome assembly
CHAPTER 7,Chromosomes,chromatin,and the nucleosome
?Nucleosomes are assembled
immediately after DNA
replication,and the assembly
requires histone chaperones
3/15/05
Figures 7-41 The inheritance of
histones after DNA replication
Try to complete all the
excises on your study
CD
Homework
