Chromosome Organization
and Molecular Structure
Chromosomes & Genomes
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Chromosomes
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complexes of DNA and proteins – chromatin
Viral – linear, circular; DNA or RNA
Bacteria – single, circular
Eukaryotes – multiple, linear
Genome
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The genetic material that an organism possesses
Nuclear genome
Mitochondrial & chloroplasts genome
Viruses
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Genome is Infectious particles containing nucleic
acid surrounded by a protein capsid
Rely on host cell for replication, transcription,
translation
Exhibit a limited host range
Genomes vary from a few thousand to a
hundred thousand nucleotides
Some Virus Structures
Phage
Capsid
protein
TMV
Bacterial Chromosomes
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In a region called the
nucleoid
DNA in direct contact
with cytoplasm
Bacterial Chromosomes
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Chromosomal DNA is compacted ~ 1000 fold to
fit within cell
Bacterial Chromosomes
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Size
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Escherichia coli
~ 4.6 million bp
Haemophilus influenzae
~ 1.8 million bp
Composition
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E coli ~6000 genes
Genes encoding proteins
for related functions
arranged in operons
Intergenic regions
nontranscribed DNA
Single origin of replication
(Ori)
Prokaryotic Gene (Operon) Structure
+1
DNA
Regulatory
Elements
Promoter
& Operator
Stop Codon
TAA, TAG, TGA
ATG
Coding Sequence= ORF
Protein A
Cistron 1
Regulatory Sequences
Stop Codon
TAA, TAG, TGA
ATG
Coding Sequence= ORF
Protein B
Cistron 2
Structural or Coding Sequences
Regulatory and Coding Sequence Unit = Operon
Terminator
sequence
Eukaryotic Chromosomes
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Eukaryotic species contain one or more sets of
chromosomes (ploidy level)
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Each set is composed of several linear chromosomes
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DNA amount in eukaryotic species is greater than
that in bacteria
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Chromosomes in eukaryotes are located in the
nucleus
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To fit in there, they must be highly compacted
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This is accomplished by the binding of many proteins
The DNA-protein complex is termed chromatin
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10-21
Eukaryotic genomes
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vary substantially in size
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variation not related to complexity of the
species
i.e - a two fold difference in genome size
between two salamander species
Size difference due to accumulation of
repetitive DNA sequences
Variations in DNA Content
Figure 10.10
Eukaryotic Chromosome Organization
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Eukaryotic chromosomes are long, linear
DNA molecule
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Three types of DNA sequences are required
for chromosome replication and segregation
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Origins of replication (multiple)
Centromeres (1)
Telomeres (2)
Telomere
Origin of replication
Origin of replication
Kinetochore proteins
Centromere
Origin of replication
Origin of replication
Genes
Repetitive sequences
Telomere
Chromosome Organization
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Genes located between centromere & telomeres
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hundreds to thousands of genes
lower eukaryotes (i.e. yeast)
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higher eukaryotes (i.e. mammals)
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Genes are relatively small
Very few introns
Genes are long
Have many introns
Non-gene sequences
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Repetitive DNA
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Telomere
Centromere
Satellite
Eukaryotic Gene Structure
CisRegulatory
Elements
Promoter/
Enhancer
Stop Codon
TAA, TAG, TGA
Start Codon
ATG
Exon1
Exon2
Exon3
Repetitive Sequences
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Sequence complexity refers to the number of
times a particular base sequence appears in
the genome
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2 main types of sequences
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Moderately repetitive
Highly repetitive (low complexity)
Repetitive Sequences
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Unique or non-repetitive sequences
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Found once or a few times in the genome
Includes structural genes as well as intergenic areas
Moderately repetitive
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Found a few hundred to a few thousand times
Includes
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Genes for rRNA and histones
Origins of replication
Transposable elements
10-28
Repetitive Sequences
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Highly repetitive
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Found tens of thousands to millions of times
Each copy is relatively short (a few nucleotides to several
hundred in length)
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Some sequences are interspersed throughout the genome
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Example: Alu family in humans
Other sequences are clustered together in tandem arrays
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Example: centromeric satellite & telomeric regions
Eukaryotic Chromatin Compaction
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Stretched end to end, a single set of human
chromosomes will be over 1 meter long
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nucleus is only 2 to 4 mm in diameter
The compaction of linear DNA in eukaryotic
chromosomes involves interactions between DNA
and various proteins

Proteins bound to DNA are subject to change during the
life of the cell
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These changes affect the degree of chromatin compaction
Nucleosomes
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Histone proteins
basic (+ charged
lysine & arginine)
amino acids that
bind DNA backbone
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Four core histones in nucleosome
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Two of each of H2A, H2B, H3 & H4
Fifth histone, H1 is the linker histone
Figure 10.14
Nucleosomes
Figure 10.14
Beads on a String
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Overall structure of connected nucleosomes resembles “beads on a string”
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Shortens DNA length ~ seven-fold
Nucleosomes Join
to Form 30 nm Fiber
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Nucleosomes
associate to form more
compact structure - the
30 nm fiber
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Histone H1 plays a role
in this compaction
10-54
Further Compaction of the
Chromosome
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The two events we have discussed so far have
shortened the DNA about 50-fold
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A third level of compaction involves interaction
between the 30 nm fiber and the nuclear matrix
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10-57
Nuclear Matrix Association
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Nuclear matrix composed of two parts
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Nuclear lamina
Internal matrix proteins
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10 nm fiber and associated proteins
Figure 10.18
DNA Loops on Nuclear Matrix
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The third mechanism of DNA compaction involves the
formation of radial loop domains
Matrix-attachment
regions
or
25,000 to
200,000 bp
Scaffold-attachment
regions (SARs)
Figure 10.18
MARs are anchored to
the nuclear matrix,
thus creating radial
loops
Further Compaction of the
Chromosome
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The attachment of radial loops to the nuclear matrix
is important in two ways
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1. It plays a role in gene regulation
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Discussed in Chapter 15
2. It serves to organize the chromosomes within the
nucleus
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Each chromosome in the nucleus is located in a discrete and
nonoverlapping chromosome territory
Refer to Figure 10.19
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10-60
Heterochromatin vs Euchromatin
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Compaction level of interphase chromosomes is
not uniform
Euchromatin
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Less condensed regions of chromosomes
Transcriptionally active
Regions where 30 nm fiber forms radial loop domains
Heterochromatin
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Tightly compacted regions of chromosomes
Transcriptionally inactive (in general)
Radial loop domains compacted even further
Types of Heterochromatin
Figure 10.20
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Constitutive heterochromatin
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Always heterochromatic
Permanently inactive with regard to transcription
Facultative heterochromatin
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Regions that can interconvert between euchromatin
and heterochromatin
Example: Barr body
Figure 10.21
Compaction level
in euchromatin
During interphase
most chromosomal
regions are
euchromatic
Compaction level
in heterochromatin
Figure 10.21
10-64
Metaphase Chromosomes
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Condensed chromosomes are referred to as
metaphase chromosomes
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During prophase, the compaction level increases
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By the end of prophase, sister chromatids are
entirely heterochromatic
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These highly condensed metaphase chromosomes
undergo little gene transcription
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In metaphase chromosomes, the radial loops are
compacted and anchored to the nuclear matrix
scaffold
Chromosome Condensation
The number of loops has not changed
However, the diameter of each loop is smaller
During interphase,
condensin is in the
cytoplasm
Condensin binds
to chromosomes
and compacts the
radial loops
Condensin travels
into the nucleus
Figure 10.23 The condensation of a metaphase chromosome by condensin
Chromosomes During Mitosis
Cohesins along
chromosome arms are
released
Cohesin at
centromer is
degraded
Cohesin
remains at
centromere
Figure 10.24 The alignment of sister chromatids via cohesin