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

Genome The genetic material that an organism possesses Nuclear genome Mitochondrial & chloroplasts genome

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

Viruses

Some Virus StructuresPhage

Capsid protein

TMV

In a region called the nucleoid

DNA in direct contact with cytoplasm

Bacterial Chromosomes

Bacterial Chromosomes

Chromosomal DNA is compacted ~ 1000 fold to fit within cell

Size Escherichia coli

~ 4.6 million bp Haemophilus influenzae

~ 1.8 million bp Composition

E coli ~6000 genes Genes encoding proteins

for related functions arranged in operons

Intergenic regions nontranscribed DNA

Single origin of replication (Ori)

Bacterial Chromosomes

Prokaryotic Gene (Operon) Structure Stop Codon

TAA, TAG, TGARegulatoryElements

Cistron 1

Coding Sequence= ORF

+1 ATGStop Codon

TAA, TAG, TGA ATG

Coding Sequence= ORF

Cistron 2

Promoter& Operator

DNA

Terminatorsequence

Regulatory and Coding Sequence Unit = Operon

Protein A Protein B

Structural or Coding SequencesRegulatory Sequences

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

Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Eukaryotic Chromosomes

10-21

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

Eukaryotic genomes

Figure 10.10

Variations in DNA Content

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)

Eukaryotic Chromosome Organization

Centromere

Kinetochore proteins

Origin of replication

Origin of replication

Origin of replication

Origin of replication

Telomere

Telomere

GenesRepetitive sequences

Chromosome Organization Genes located between centromere & telomeres

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

Genes are relatively small Very few introns

higher eukaryotes (i.e. mammals) Genes are long Have many introns

Non-gene sequences Repetitive DNA

Telomere Centromere Satellite

Eukaryotic Gene Structure

Promoter/Enhancer

Cis-Regulatory Elements

Start Codon ATG

Exon1 Exon2 Exon3

Stop CodonTAA, TAG, TGA

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

Repetitive Sequences

10-28

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

Repetitive Sequences

Stretched end to end, a single set of human chromosomes will be over 1 meter long nucleus is only 2 to 4 m 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

Eukaryotic Chromatin Compaction

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

Four core histones in nucleosome Two of each of H2A, H2B, H3 & H4

Fifth histone, H1 is the linker histone

Figure 10.14

Nucleosomes

Figure 10.14

Nucleosomes

Beads on a String

Overall structure of connected nucleosomes resembles “beads on a string” Shortens DNA length ~ seven-fold

Nucleosomes associate to form more compact structure - the 30 nm fiber

Histone H1 plays a role in this compaction

Nucleosomes Join to Form 30 nm Fiber

10-54

Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

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

Further Compaction of the Chromosome

10-57

Figure 10.18

Nuclear Matrix Association Nuclear matrix composed of two parts

Nuclear lamina Internal matrix proteins

10 nm fiber and associated proteins

Figure 10.18

Matrix-attachment regions

Scaffold-attachment regions (SARs)

or

MARs are anchored to the nuclear matrix, thus creating radial

loops

25,000 to 200,000 bp

DNA Loops on Nuclear Matrix The third mechanism of DNA compaction involves the

formation of radial loop domains

Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

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

Further Compaction of the Chromosome

10-60

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

Heterochromatin vs Euchromatin

Types of Heterochromatin

Figure 10.20

Constitutive heterochromatin Always heterochromatic Permanently inactive with regard to transcription

Facultative heterochromatin Regions that can interconvert between euchromatin

and heterochromatin Example: Barr body

Figure 10.21

10-64Figure 10.21

Compaction level in euchromatin

Compaction level in heterochromatin

During interphase most chromosomal

regions are euchromatic

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

Metaphase Chromosomes

The condensation of a metaphase chromosome by condensinFigure 10.23

The number of loops has not changedHowever, the diameter of each loop is smaller

Condensin travels into the nucleus

Condensin binds to chromosomes and compacts the

radial loops

During interphase, condensin is in the cytoplasm

Chromosome Condensation

The alignment of sister chromatids via cohesinFigure 10.24

Cohesins along chromosome arms are

released

Cohesin remains at centromere

Cohesin at centromer is degraded

Chromosomes During Mitosis