Chapter 10 Lecture Outline Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
INTRODUCTION
•  Chromosomes are the structures that contain the
genetic material
–  They are complexes of DNA and proteins
•  The genome comprises all the genetic material
that an organism possesses
–  In bacteria, it is typically a single circular chromosome
–  In eukaryotes, it refers to one complete set of nuclear
chromosomes
–  Note:
•  Eukaryotes possess a mitochondrial genome
•  Plants also have a chloroplast genome
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10-2
INTRODUCTION
•  The main function of the genetic material is to store
the information required to produce an organism
–  The DNA molecule does that through its base sequence
•  DNA sequences are necessary for
–  1.
–  2.
–  3.
–  4.
Synthesis of RNA and cellular proteins
Replication of chromosomes
Proper segregation of chromosomes
Compaction of chromosomes
•  So they can fit within living cells
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10-3
10.1 VIRAL GENOMES
•  Viruses are small infectious particles containing
nucleic acid surrounded by a capsid of proteins
–  Refer to Figure 10.1
•  For replication, viruses rely on their host cells
–  ie., the cells they infect
•  Most viruses exhibit a limited host range
–  They typically infect only specific types of cells of one
host species
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10-4
n
Bacteriophages may also contain a sheath, base plate and
Lipid bilayer
tail fibers
n
Picked up when
virus leaves host cell
Refer to Figure 9.3
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Capsid"
(protein coat)"
Membrane
Nucleic"
acid
Spike"
proteins
(a) Nonenveloped virus
(b) Enveloped virus with spikes
Figure 10.1 General structure of viruses
10-5
Viral Genomes
•  A viral genome is the genetic material of the virus
–  Also termed the viral chromosome
•  The genome can be
–  DNA or RNA
–  Single-stranded or double-stranded
–  Circular or linear
•  Viral genomes vary in size from a few thousand to
more than a hundred thousand nucleotides
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10-6
10-7
•  During an infection process, mature viral particles
need to be assembled
Single-stranded"
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n
RNA molecule
Viruses with a
simple structure
may self-assemble
n
n
Genetic material
and capsid proteins
spontaneously bind
to each other
Capsid"
protein
Example: Tobacco
mosaic virus
Figure 10.2
Capsid composed of 2,130
identical protein subunits
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10-8
•  Complex viruses, such as T2 bacteriophages,
undergo a process called directed assembly
–  Virus assembly requires proteins that are not part of the
mature virus itself
•  The noncapsid proteins usually have two main
functions
–  1. Carry out the assembly process
•  Scaffolding proteins that are not part of the mature virus
–  2. Act as proteases that cleave viral capsid proteins
•  This yields smaller capsid proteins that assemble correctly
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10-9
10.2 BACTERIAL
CHROMOSOMES
•  The bacterial chromosome is found in a region of the
cell called the nucleoid
–  Refer to Figure 10.3
•  The nucleoid is not bounded by membrane
–  So the DNA is in direct contact with the cytoplasm
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10-10
•  Bacterial chromosomal DNA is usually a circular
molecule that is a few million nucleotides in length
–  Escherichia coli à ~ 4.6 million base pairs
–  Haemophilus influenzae à ~ 1.8 million base pairs
•  A typical bacterial chromosome contains a few
thousand different genes
–  Structural gene sequences (encoding proteins) account
for the majority of bacterial DNA
–  The nontranscribed DNA between adjacent genes are
termed intergenic regions
•  Figure 10.4 summarizes the key features of
bacterial chromosomes
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10-11
A few hundred
nucleotides in length
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Key features:
• Most, but not all, bacterial species"
contain circular chromosomal DNA.
Origin of"
replication
• A typical chromosome is a few"
million base pairs in length.
• Most bacterial species contain a"
single type of chromosome, but it"
may be present in multiple copies.
• Several thousand different genes are "
interspersed throughout the chromosome."
The short regions between adjacent genes"
are called intergenic regions.
• One origin of replication is required to"
initiate DNA replication.
Genes"
Intergenic regions"
Repetitive sequences
Figure 10.4
• Repetitive sequences may be interspersed"
throughout the chromosome.
These play roles in DNA folding,
DNA replication, gene regulation, and
genetic recombination
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10-12
•  To fit within the bacterial cell, the chromosomal
DNA must be compacted about a 1000-fold
–  This involves the formation of loop domains
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The looped structure compacts
the chromosome about 10-fold
Loop"
domains
Formation of"
loop domains
DNA-"
binding"
proteins
Figure 10.5
(a) Circular chromosomal DNA
n
(b) Looped chromosomal DNA with!
associated proteins
The number of loops varies according to the size of the
bacterial chromosome and the species
n
E. coli has 50-100 with 40,000 to 80,000 bp of DNA in each loop
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10-13
•  DNA supercoiling is a second important way to
compact the bacterial chromosome
Supercoiling within loops creates
a more compact DNA structure
Supercoiling"
Figure 10.6
(a) Looped chromosomal DNA!
n
(b) Looped and supercoiled DNA!
Figure 10.7 provides a schematic illustration of
DNA supercoiling
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10-14
Chromosome Function Is Influenced
by DNA Supercoiling
•  The chromosomal DNA in bacteria is negatively
supercoiled
–  In E. coli, there is one negative supercoil per 40 turns of
the double helix
•  Negative supercoiling has two major effects
–  1. Helps in the compaction of the chromosome
•  Refer to Figure 10.6
–  2. Creates tension that may be released by DNA
strand separation
•  Refer to Figure 10.8
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10-16
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Area of"
negative"
supercoiling
Strand"
separation"
Circular"
chromosome"
Figure 10.8
This enhances
DNA replication and
transcription
10-17
•  The control of supercoiling in bacteria is
accomplished by two main enzymes
–  1. DNA gyrase (also termed DNA topoisomerase II)
•  Introduces negative supercoils using energy from ATP
–  Refer to Figure 10.9
•  It can also relax positive supercoils when they occur
•  Can untangle intertwined DNA molecules
–  2. DNA topoisomerase I
•  Relaxes negative supercoils
•  The competing action of these two enzymes
governs the overall supercoiling of bacterial DNA
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10-18
•  The ability of gyrase to introduce negative supercoils
into DNA is crucial for bacteria to survive
–  Blocking the function of this enzyme is a way to cure or
alleviate bacterial diseases
•  Two main classes of drugs inhibit gyrase and other
bacterial topoisomerases
–  1. Quinolones
–  2. Coumarins
–  These do not inhibit eukaryotic topoisomerases
–  An example of a quinolone is Ciprofloxacin ( Cipro )
•  Used in the treatment of anthrax, among other diseases
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10-20
10.3 EUKARYOTIC
CHROMOSOMES
•  Eukaryotic species contain one or more sets of
chromosomes
–  Each set is composed of several different linear chromosomes
•  The total amount of DNA in eukaryotic species is
typically much greater than that in bacterial cells
•  Chromosomes in eukaryotes are located in the
nucleus
–  To fit within the nucleus, they must be highly compacted
•  This is accomplished by the binding of many proteins
•  The DNA-protein complex found in eukaryotic chromosomes is
termed chromatin
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10-21
•  Eukaryotic genomes vary substantially in size
–  Refer to Figure 10.10a
•  note that this is a log scale
•  In many cases, this variation is not related to the
complexity of the species
–  For example, there is a two fold difference in the size of
the genome in two closely related salamander species
–  Refer to Figure 10.10b
–  The difference in the size of the genome is not because
of extra genes
•  Rather, the accumulation of repetitive DNA sequences
–  These do not encode proteins
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10-22
Organization of Eukaryotic
Chromosomes
•  A eukaryotic chromosome contains a long, linear
DNA molecule
–  Refer to Figure 10.11
•  Three types of DNA sequences are required for
chromosomal replication and segregation
–  Origins of replication
–  Centromeres
–  Telomeres
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10-24
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Eukaryotic chromosomes
contain many origins of
replication approximately
100,000 bp apart
Telomere
• Eukaryotic chromosomes are usually linear.
• A typical chromosome is tens of millions to"
hundreds of millions of base pairs in length.
Origin of"
replication
Origin of"
replication
Required for proper
segregation during
mitosis and meiosis
• Genes are interspersed throughout the"
chromosome. A typical chromosome"
contains between a few hundred and several"
thousand different genes.
Centromere • Each chromosome contains a centromere"
that forms a recognition site for the"
kinetochore proteins.
• Telomeres contain specialized sequences"
located at both ends of the linear"
chromosome.
• Repetitive sequences are commonly found"
near centromeric and telomeric regions, but"
they may also be interspersed throughout"
the chromosome.
Prevent chromosome
translocations and shortening
Origin of"
replication
Telomere
Figure 10.11
• Eukaryotic chromosomes occur in sets."
Many species are diploid, which means that"
somatic cells contain 2 sets of chromosomes.
• Each chromosome contains many origins of"
replication that are interspersed about every"
Kinetochore"
100,000 base pairs.
proteins
Origin of"
replication
Kinetochore proteins
link the centromere to
the spindle apparatus
Key features:
Genes
Repetitive sequences
10-25
•  Genes are located between the centromeric and
telomeric regions along the entire chromosome
–  A single chromosome usually has a few hundred to
several thousand genes
•  In lower eukaryotes (such as yeast)
–  Genes are relatively small
•  They primarily contain the sequences that encode the amino
acid sequences within proteins
•  i.e.: Very few, short introns are present
•  In higher eukaryotes (such as mammals)
–  Genes are long
•  They tend to have many introns (noncoding intervening
sequences)
•  Intron lengths from less than 100 to more than 10,000 bp
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10-26
Repetitive Sequences
•  Sequence complexity refers to the number of
times a particular base sequence appears in
the genome
•  There are three main types of repetitive
sequences
–  Unique or non-repetitive
–  Moderately repetitive
–  Highly repetitive
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10-27
Repetitive Sequences
•  Unique or non-repetitive sequences
–  Found once or a few times in the genome
–  Includes structural genes as well as intergenic areas
–  In humans, make up roughly 41% of the genome
•  Moderately repetitive
–  Found a few hundred to several thousand times
–  Includes
•
•
•
•
Genes for rRNA and histones
Origins of replication
Sequences that regulate gene expression and translation
Transposable elements
–  Discussed in detail in Chapter 17
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10-28
Repetitive Sequences
•  Highly repetitive
–  Found tens of thousands to millions of times
–  Each copy is relatively short (a few nucleotides to several
hundred in length)
–  Some sequences are interspersed throughout the genome
•  Example: Alu family in humans
–
–
–
–
Approximately 300 bp long
Represents 10% of human genome
Found every 5000-6000 bp
Discussed in detail in Chapter 17
–  Other sequences are clustered together in tandem arrays
•  Example: AATAT and AATATAT sequences in Drosophila
•  These are commonly found in the centromeric regions
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10-29
Renaturation Experiments
n
n
Renaturation studies have proven useful in
understanding genome complexity
A renaturation study involves the following steps:
n
n
n
n
1. Double-stranded DNA is broken into small pieces
several hundred bp in length
2. The pieces are melted into single strands by heat
treatment
3. The temperature is lowered, allowing the renaturation
of complementary DNA strands
Refer to Figure 10.13a
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10-30
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Denaturation"
(high temperature)"
Renaturation"
(lower temperature)"
(a) Renaturation of DNA strands
Figure 10.13
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10-31
Renaturation Experiments
n
n
The rate of renaturation of complementary DNA
strands provides a way to distinguish the three
different types of repetitive sequences
The renaturation rate of a given category of DNA
sequences depends on the concentration of its
complementary partner
n
Highly repetitive DNA will be the fastest to renature
n
n
Because there are many copies of complementary sequences
Unique sequences will be the slowest to renature
n
It takes added time for these sequences to find each other
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10-32
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0
Intermediate:"
moderately"
repetitive DNA
Percent DNA reassociated
20
40
Fast:"
highly"
repetitive"
DNA
40% of human
DNA are unique
sequences
60
Slow:"
unique DNA"
80
100
10–3
10–1
101
10
C 0t
(b) Human chromosomal DNA C0t curve
Figure 10.13
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10-35
Eukaryotic Chromatin Compaction
n
If stretched end to end, a single set of human
chromosomes would be over 1 meter long!
n
Yet the cell s nucleus is only 2 to 4 µm in diameter
n
n
Therefore, the DNA must be tightly compacted to fit within the
nucleus
The compaction of linear DNA in eukaryotic
chromosomes involves interactions between DNA
and several different proteins
n
Proteins bound to DNA are subject to change during the
life of the cell
n
These changes affect the degree of chromatin compaction
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10-36
Nucleosomes
n
n
The repeating structural unit within eukaryotic
chromatin is the nucleosome
It is composed of a double-stranded segment of DNA
wrapped around an octamer of histone proteins
n
n
n
A histone octamer is composed of two copies each of four
different histone proteins
146 bp of DNA make 1.65 negative superhelical turns
around the octamer
Refer to Figure 10.14a
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10-37
Vary in length between 20 to 100 bp,
depending
on species and cell type
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H2A
H2A
Linker region
H3
H2B
H4
Figure 10.14
n
11 nm
DNA
H2B
H3
Diameter of the
nucleosome
H4
Amino"
terminal"
tail
Histone"
protein"
(globular"
domain)
Nucleosome—"
8 histone proteins +"
146 or 147 base"
pairs of DNA
(a) Nucleosomes showing core histone proteins
Overall structure of connected nucleosomes resembles beads on a
string
n  This structure shortens the DNA length about seven-fold
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10-38
n
Histone proteins are basic
n
They contain many positively-charged amino acids
n
n
n
n
Lysine and arginine
These bind to the phosphates along the DNA backbone
Histone proteins have a globular domain and a flexible,
charged amino terminus or tail
There are five types of histones
n
H2A, H2B, H3 and H4 are the core histones
n
n
H1 is called the linker histone
n
n
n
n
Two of each make up the octamer
Binds to DNA in the linker region
Less tightly bound to DNA than core histones
May help compact adjacent nucleosomes
Refer to Figure 10.14
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10-39
Play a role in the
organization and compaction
of the chromosome
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Histone"
octamer
Nonhistone"
proteins
Histone H1
Linker"
DNA
(c) Nucleosomes showing linker histones!
and nonhistone proteins
Figure 10.14
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10-40
Nucleosome core particle
Figure 10.14
(b) Molecular model for nucleosome structure
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10-41
Nucleosomes Join to Form a 30 nm
Fiber
n
n
Nucleosomes associate with each other to form a
more compact structure termed the 30 nm fiber
Histone H1 plays a role in this compaction
n
At moderate salt concentrations, H1 is removed
n
n
At low salt concentrations, H1 remains bound
n
n
The result is the classic beads-on-a-string morphology
Beads associate together into a more compact morphology
Refer to Figure 10.16
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10-48
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(a)  H1 histone not bound—!
beads on a string
© This article was published in Cell. 12(1). Thoma , F. & Koller, T. Influence of histone
H1 on chromatin structure. P. 103. f. 2a&c, Copyright Elsevier, 1977. Reproduced with permission
(b)  H1 histone bound to!
linker region—nucleosomes!
more compact
© This article was published in Cell. 12(1). Thoma , F. & Koller, T. Influence of histone
H1 on chromatin structure. P. 103. f. 2a&c, Copyright Elsevier, 1977. Reproduced with permission
Figure 10.16
10-49
n
n
n
Fig. 10.17a shows a micrograph of the 30 nm fiber
The 30 nm fiber shortens the total length of DNA
another seven-fold
Its structure has proven difficult to determine
n
n
The DNA conformation may be substantially altered when
extracted from living cells
Two models have been proposed
n
n
n
Solenoid model
Three-dimensional zigzag model
Refer to Figure 10.17b and c
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10-50
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30 nm
30 nm
Core"
histone"
proteins
Irregular
configuration
where
nucleosomes
have little faceto-face contact
Regular, spiral
configuration
containing six
nucleosomes
per turn
(b) Solenoid model
Figure 10.17
(c) Zigzag model
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10-51
Further Compaction of the
Chromosome
n
n
n
The two events we have discussed so far have
shortened the DNA about 50-fold
A third level of compaction involves interaction
between the 30 nm fiber and the nuclear matrix
The nuclear matrix is composed of two parts
n
Nuclear lamina
n
n
Fibers that line the inner nuclear membrane
Internal matrix proteins
n
n
Connected to nuclear lamina and fills interior of nucleus
Structural and functional role remains controversial
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10-52
The nuclear matrix is
hypothesized to be an
intricate fine network of
irregular protein fibers plus
many other proteins bound to
these fibers. This structure is
very dynamic and complex.
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Protein bound"
to internal"
nuclear matrix"
fiber
Internal"
nuclear"
matrix
Nuclear"
lamina
Outer"
nuclear"
membrane
Inner"
nuclear"
membrane
Nuclear"
pore
(a) Proteins that form the nuclear matrix
Figure 10.18
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10-53
Further Compaction of the
Chromosome
n
The attachment of radial loops to the nuclear matrix
is important in two ways
n
1. It plays a role in gene regulation
n
n
Discussed in Chapter 15
2. It serves to organize the chromosomes within the
nucleus
n
n
Each chromosome in the nucleus is located in a discrete and
nonoverlapping chromosome territory
Refer to Figure 10.19
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10-55
Further Compaction of the
Chromosome
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1
1
1
2
3
2
3
2
4
4
5
5
6
6
3
6
Z
5
2
4
Z
(a) Metaphase chromosomes
Figure 10.19
3
Z
5
1
2µm
(b) Chromosomes in the cell nucleus during interphase
Each of seven types of chicken chromosomes is labeled a
different color. Each occupies a specific territory during
interphase.
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10-56
Heterochromatin vs. Euchromatin
n
The compaction level of interphase chromosomes
is not completely uniform
n
Euchromatin
n
n
n
n
Less condensed regions of chromosomes
Transcriptionally active
The 30 nm fiber forms radial loop domains
Heterochromatin
n
n
n
Tightly compacted regions of chromosomes
Transcriptionally inactive (in general)
Radial loop domains compacted even further
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10-57
Figure 10.20
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Telomere"
Centromere"
Telomere"
Euchromatin (30 nm fiber"
anchored in radial loops)"
Heterochromatin (greater"
compaction of the radial loops)"
n
There are two types of heterochromatin
n
Constitutive heterochromatin
n
n
n
n
Regions that are always heterochromatic
Permanently inactive with regard to transcription
Usually contain highly repetitive sequences
Facultative heterochromatin
n
n
Regions that can interconvert between euchromatin and
heterochromatin
Example: Barr body formation during development in female
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10-58
The levels of
compaction
leading to a
metaphase
chromosome
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2 nm
DNA double helix
Histone H1
Wrapping of DNA around"
a histone octamer
11 nm
Histone"
octamer
Nucleosome
(a) Nucleosomes ( beads on a string )
Formation of a three-dimensional zigzag structure"
via histone H1 and other DNA-binding proteins
30 nm
(b) 30 nm fiber
Figure 10.21
Nucleosome
Anchoring of radial loops to the"
nuclear matrix
10-59
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During interphase
most chromosomal
regions are
euchromatic
300 nm
(c) Radial loop domains
Compaction level
in euchromatin
Protein scaffold
Further compaction of"
radial loops
700 nm
Compaction level
in heterochromatin
Formation of a scaffold from the nuclear matrix"
and further compaction of all radial loops
1400 nm
Figure 10.21
(d) Metaphase chromosome
10-60
Metaphase Chromosomes
n
As cells enter M phase, the level of compaction
changes dramatically
n
n
n
By the end of prophase, sister chromatids are entirely
heterochromatic
Two parallel chromatids have an overall diameter of
1,400 nm
These highly condensed metaphase chromosomes
undergo little gene transcription
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10-61
Metaphase Chromosomes
n
In metaphase chromosomes the radial loops are
highly compacted and stay anchored to a scaffold
n
n
n
The scaffold is formed from the nuclear matrix
Histones are needed for the compaction of radial
loops
Refer to Figure 10.22
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10-62
Metaphase Chromosomes
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DNA strand
Scaffold
2 μm
© Peter Engelhardt/Department of Virology, Haartman Institue
(a) Metaphase chromosome
© Dr. Donald Fawcett/Visuals Unlimited
(b) Metaphase chromosome treated with high salt to remove histone proteins
Figure 10.22
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10-63
n
Two multiprotein complexes help to form and
organize metaphase chromosomes
n
Condensin
n
n
Cohesin
n
n
Plays a critical role in chromosome condensation
Plays a critical role in sister chromatid alignment
Both contain a category of proteins called SMC
proteins
n
n
Acronym = Structural Maintenance of Chromosomes
SMC proteins use energy from ATP to catalyze changes
in chromosome structure
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10-64
The number of loops has not changed
However, the diameter of each loop is smaller
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During interphase,
condensin is in the
cytoplasm
300 nm radial loops — euchromatin
700 nm — heterochromatin
Condensin
Condesin binds to
chromosomes and
compacts the
radial loops
Condensin
Decondensed"
chromosome
Condensed"
chromosome
G1, S, and G2 phases
Condesin travels
into the nucleus
Start of M phase
Figure 10.24 The condensation of a metaphase chromosome by condensin
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10-65
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Cohesin at"
centromere"
is degraded.
Cohesins along
chromosome arms are
released
Cohesin
Centromere"
region
Cohesin"
remains at"
centromere.
Chromatid
End of S phase"
G2 phase"
(decondensed sister"
chromatids, arms"
are cohered)
Beginning of"
prophase"
(condensed"
sister"
chromatids,"
arms are cohered)
Middle of"
prophase"
(condensed"
sister"
chromatids,"
arms are free)
Anaphase"
(condensed sister"
chromatids have"
separated)
Figure 10.25 The alignment of sister chromatids via cohesin
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10-66