Chromosome Structure and DNA Sequence Organization

Chromosome Structure in Viruses, Bacteria, and Eukaryotes

Abbreviations for DNA/RNA Length

Understanding the length of DNA and RNA molecules is fundamental in genetics. The following abbreviations are commonly used:

• bp: base pair – one bp corresponds to approximately 3.4 Å (340 pm) of length along the strand.

• kb (or kbp): kilo–base-pair = 1,000 bp.

• Mb (or Mbp): mega–base-pair = 1,000,000 bp.

• Gb (or Gbp): giga–base-pair = 1,000,000,000 bp.

Viral and Bacterial Chromosomes

Viral and bacterial chromosomes are structurally distinct from eukaryotic chromosomes. They are typically single nucleic acid molecules, largely devoid of associated proteins, and much smaller in size.

• Viral genomes can be either RNA or DNA, single- or double-stranded.

• Bacterial genomes are usually circular, double-stranded DNA compacted into a region called the nucleoid.

• Contain less genetic information compared to eukaryotes.

Example: The chromosome of bacteriophage T2 is 52 μm long and ~170 Kbp.

Bacterial Chromosome Structure

Bacterial chromosomes are organized in a compact manner within the cell.

• Structure: Circular, double-stranded DNA compacted into the nucleoid.

• DNA binding proteins (HU and H-NS) fold and bend DNA, creating coils for compaction.

• Most bacterial chromosomes have a single type, but may be present in multiple copies.

• Several thousand genes are interspersed throughout the chromosome.

• Intergenic regions exist between adjacent genes.

• One origin of replication is required to initiate DNA replication.

• Repetitive sequences may be interspersed throughout the chromosome.

Example: The chromosome of E. coli is 1200 μm long and ~5 Mbp.

The bacterial chromosome is found in the nucleoid, a region not surrounded by a membrane.

Mitochondria and Chloroplasts

Mitochondria and chloroplasts contain their own DNA, which is inherited through the maternal cytoplasm in most organisms. Their DNA is similar to that of viruses and bacteria, supporting the endosymbiotic theory.

Organization of Eukaryotic Chromosomes

Key Structural Features

Eukaryotic chromosomes are long, linear DNA molecules organized within the nucleus. Three types of DNA sequences are required for chromosomal replication and segregation:

• Origins of replication: Sites where DNA replication begins.

• Centromeres: Regions that form recognition sites for kinetochore proteins, essential for proper segregation during mitosis and meiosis.

• Telomeres: Specialized sequences at the ends of chromosomes that prevent sticky ends and chromosome shortening.

Eukaryotic chromosomes contain many origins of replication, approximately 100,000 bp apart.

General Properties of Eukaryotic Chromosomes

• Length: Tens of millions to hundreds of millions of bp.

• Occur in sets (e.g., diploid organisms have pairs).

• Genes are interspersed throughout the chromosome.

• Many origins of replication per chromosome.

• Centromere forms a recognition site for kinetochore proteins.

• Telomeres are located at the ends of linear chromosomes.

• Repetitive sequences are commonly found near centromeric and telomeric regions, but may also be interspersed.

Genome Size Variation Among Eukaryotes

Genome sizes vary widely among eukaryotic organisms, from fungi to mammals and salamanders.

Example: The genome of Plethodon larselli is more than twice as large as that of Plethodon richmondi.

Classes of DNA Sequences in the Human Genome

The human genome contains various classes of DNA sequences:

• Exons: Regions of genes that encode proteins (2%).

• Introns and other parts of genes: 24%.

• Unique noncoding DNA: 15%.

• Repetitive DNA: 59%.

Chromatin Structure and Compaction

Chromatin and Nucleosomes

DNA must be tightly compacted to fit in the nucleus, involving interactions with various proteins. The DNA-protein complex is known as chromatin. The basic subunit is the nucleosome, composed of double-stranded DNA wrapped around an octamer of histone proteins (two copies each of H2A, H2B, H3, and H4).

• 146 bp of DNA make 1.65 negative superhelical turns around the octamer.

• Histones contain many positively-charged amino acids, facilitating DNA binding.

Example: Nucleosomes appear as "beads on a string" along chromatin strands.

Higher-Order Chromatin Structure

Nucleosomes associate to form a more compact structure called the 30-nm fiber, which shortens the total length of DNA seven-fold. The structure of the 30-nm fiber has been difficult to determine.

Together, nucleosomes and the 30-nm fiber shorten DNA about 50-fold.

Further Compaction: Nuclear Matrix and Radial Loop Domains

A third level of compaction involves interaction between the 30-nm fiber and the nuclear matrix, which is composed of the nuclear lamina and internal nuclear matrix. This compacts DNA into radial loop domains.

Matrix-attachment regions (MARs) or Scaffold-attachment regions (SARs) are DNA sequences interspersed in the genome that anchor to the nuclear matrix, forming radial loops of 25,000 to 200,000 bp.

Euchromatin vs. Heterochromatin

Chromatin can exist in two main forms:

• Euchromatin: Less condensed, transcriptionally active, regions where the 30-nm fiber forms radial loop domains.

• Heterochromatin: Tightly compacted, transcriptionally inactive, radial loop domains compacted even further.

Metaphase Chromosome Compaction

As cells enter M phase, chromatin compaction increases dramatically. By the end of prophase, sister chromatids are entirely heterochromatic.

Levels of Chromatin Packaging

The most tightly packed chromatin is found in metaphase chromosomes. The levels of packaging include:

• Naked DNA

• DNA packaged in nucleosomes

• 30-nm fiber

• Metaphase chromosomes

Chromatin Remodeling and Chemical Modifications

Chromatin packaging can be modified by chromatin remodeling and chemical modifications on histone tails, including acetylation, methylation, phosphorylation, and DNA methylation (e.g., 5-methyl cytosine).

Summary Table: Comparison of Chromosome Structure

Feature	Bacterial Chromosome	Eukaryotic Chromosome
Shape	Circular	Linear
DNA Content	Few million bp	Tens to hundreds of millions bp
Associated Proteins	Few (HU, H-NS)	Many (histones, nonhistone proteins)
Origins of Replication	One	Many
Compaction	Nucleoid	Chromatin (nucleosomes, 30-nm fiber, radial loops)
Telomeres	Absent	Present

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