Chromosome Organization and Molecular Structure

Chromosomes & Genomes

Chromosomes

complexes of DNA and proteins chromatin Viral linear, circular; DNA or RNA Bacteria single, circular Eukaryotes multiple, linear The genetic material that an organism possesses Nuclear genome Mitochondrial & chloroplasts genome

Genome

Viruses

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

In a region called the nucleoid DNA in direct contact with cytoplasm

Bacterial Chromosomes

Chromosomal DNA is compacted ~ 1000 fold to fit within cell

Bacterial Chromosomes

Size

Escherichia coli ~ 4.6 million bp Haemophilus influenzae ~ 1.8 million bp E coli ~6000 genes Genes encoding proteins for related functions arranged in operons Intergenic regions nontranscribed DNA Single origin of replication (Ori)

Composition

Prokaryotic Gene (Operon) Structure

+1 ATG Stop Codon TAA, TAG, TGA ATG Stop Codon TAA, TAG, TGA

DNA

Regulatory Elements

Coding Sequence= ORF

Coding Sequence= ORF

Promoter & Operator

Protein A

Protein B

Terminator sequence

Cistron 1

Cistron 2

Regulatory Sequences

Structural or Coding Sequences

Regulatory and Coding Sequence Unit = Operon

Eukaryotic Chromosomes

Eukaryotic species contain one or more sets of chromosomes (ploidy level)

Each set is composed of several linear chromosomes

DNA amount in eukaryotic species is greater than that in bacteria Chromosomes in eukaryotes are located in the nucleus

To fit in there, they must be highly compacted

This is accomplished by the binding of many proteins The DNA-protein complex is termed chromatin

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Eukaryotic genomes

vary substantially in size

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

Eukaryotic chromosomes are long, linear DNA molecule Three types of DNA sequences are required for chromosome replication and segregation

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

Genes located between centromere & telomeres

hundreds to thousands of genes lower eukaryotes (i.e. yeast)

Genes are relatively small Very few introns

Genes are long Have many introns

higher eukaryotes (i.e. mammals)

Non-gene sequences

Repetitive DNA

Telomere Centromere Satellite

Eukaryotic Gene Structure

CisRegulatory Elements Promoter/ Enhancer
Start Codon ATG Stop Codon TAA, TAG, TGA

Exon1

Exon2

Exon3

Repetitive Sequences

Sequence complexity refers to the number of times a particular base sequence appears in the genome

2 main types of sequences

Moderately repetitive Highly repetitive (low complexity)

Repetitive Sequences

Unique or non-repetitive sequences

Found once or a few times in the genome Includes structural genes as well as intergenic areas

Moderately repetitive

Found a few hundred to a few thousand times Includes

Genes for rRNA and histones Origins of replication Transposable elements

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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

Other sequences are clustered together in tandem arrays

Example: centromeric satellite & telomeric regions

Eukaryotic Chromatin Compaction

Stretched end to end, a single set of human chromosomes will be over 1 meter long

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

These changes affect the degree of chromatin compaction

Nucleosomes

Histone proteins basic (+ charged lysine & arginine) amino acids that bind DNA backbone

Four core histones in nucleosome

Figure 10.14

Two of each of H2A, H2B, H3 & H4

Fifth histone, H1 is the linker histone

Nucleosomes

Figure 10.14

Beads on a String

Overall structure of connected nucleosomes resembles beads on a string

Shortens DNA length ~ seven-fold

Nucleosomes Join to Form 30 nm Fiber

Nucleosomes associate to form more compact structure - the 30 nm fiber Histone H1 plays a role in this compaction

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Further Compaction of the Chromosome

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

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Nuclear Matrix Association

Nuclear matrix composed of two parts

Nuclear lamina Internal matrix proteins

10 nm fiber and associated proteins

Figure 10.18

DNA Loops on Nuclear Matrix

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

The attachment of radial loops to the nuclear matrix is important in two ways

1. It plays a role in gene regulation

Discussed in Chapter 15

2. It serves to organize the chromosomes within the nucleus

Each chromosome in the nucleus is located in a discrete and nonoverlapping chromosome territory Refer to Figure 10.19
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Heterochromatin vs Euchromatin

Compaction level of interphase chromosomes is not uniform Euchromatin

Less condensed regions of chromosomes Transcriptionally active Regions where 30 nm fiber forms radial loop domains

Heterochromatin

Tightly compacted regions of chromosomes Transcriptionally inactive (in general) Radial loop domains compacted even further

Types of Heterochromatin

Figure 10.20

Constitutive heterochromatin

Always heterochromatic Permanently inactive with regard to transcription Regions that can interconvert between euchromatin and heterochromatin Example: Barr body

Facultative heterochromatin

Figure 10.21

Compaction level in euchromatin

During interphase most chromosomal regions are euchromatic

Compaction level in heterochromatin

Figure 10.21

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Metaphase Chromosomes

Condensed chromosomes are referred to as metaphase chromosomes During prophase, the compaction level increases By the end of prophase, sister chromatids are entirely heterochromatic These highly condensed metaphase chromosomes undergo little gene transcription 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