BackChromosome Structure and DNA Sequence Organization
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Chromosome Structure in Viruses, Bacteria, and Eukaryotes
Abbreviations for DNA/RNA Length
In genetics, the length of DNA or RNA molecules is commonly described using specific abbreviations:
bp: base pair – one bp corresponds to approximately 3.4 Å (340 pm) of length along the strand.
kb (kbp): kilo–base-pair = 1,000 bp.
Mb (Mbp): mega–base-pair = 1,000,000 bp.
Gb (Gbp): giga–base-pair = 1,000,000,000 bp.
Viral and Bacterial Chromosomes
Viral and bacterial chromosomes are fundamentally different from eukaryotic chromosomes in both structure and content.
Single nucleic acid molecules (either DNA or RNA).
Largely devoid of associated proteins.
Much smaller than eukaryotic chromosomes.
Contain less genetic information.
Most bacterial genomes are circular, double-stranded DNA compacted into a region called the nucleoid. Viral genomes may be either DNA or RNA, and can be single- or double-stranded.
Bacterial Chromosome Structure
Bacterial chromosomes are typically circular and are compacted into the nucleoid region of the cell, which is not surrounded by a membrane.
Associated DNA-binding proteins: HU and H-NS (Histone-like Nucleoid Structuring Protein) help fold and bend DNA, creating coils for compaction.
Key features:
Most are circular.
Usually a few million base pairs.
Most have a single type of chromosome, but it may be present in multiple copies.
Several thousand different genes interspersed throughout the chromosome.
Regions between adjacent genes are called intergenic regions.
One origin of replication is required to initiate DNA replication.
Repetitive sequences may be interspersed throughout the chromosome.
Bacterial Chromosome Localization
The bacterial chromosome is found in a region of the cell called the nucleoid, which is 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 remarkably similar to that of viruses and bacteria, supporting the endosymbiotic theory.
Organization of Eukaryotic Chromosomes
Types of DNA Sequences Required for Chromosomal Replication and Segregation
Origins of replication: Sites where DNA replication begins.
Centromeres: Regions required for proper segregation during mitosis and meiosis; form recognition sites for kinetochore proteins.
Telomeres: Specialized sequences located at the ends of linear chromosomes; prevent chromosome sticky ends and shortening.
Features of Eukaryotic Chromosomes
Length: Tens of millions to hundreds of millions of base pairs.
Occur in sets (e.g., diploid organisms have pairs).
Genes are interspersed throughout the chromosome.
Each chromosome contains many origins of replication, about every 100,000 base pairs.
Contains a centromere for kinetochore protein recognition.
Telomeres at chromosome ends.
Repetitive sequences commonly found near centromeric and telomeric regions, but also interspersed.
Genome Size Variation Among Eukaryotes
Eukaryotic genome sizes vary widely among different groups, from fungi to mammals and salamanders.
Examples of Genome Size Differences
Some species, such as certain salamanders, have genomes that are much larger than others, even within the same genus.
Classes of DNA Sequences in the Human Genome
The human genome contains a variety of DNA sequence types:
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 in Eukaryotes
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 interaction with negatively-charged DNA.
Nucleosome Arrangement and Compaction
Nucleosomes appear as "beads on a string" along chromatin strands, shortening the DNA length about seven-fold.
Formation of the 30-nm Fiber
Nucleosomes associate with each other to form a more compact structure called the 30-nm fiber, further shortening the total length of DNA.
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/SARs)
MARs (Matrix-attachment regions) or SARs (Scaffold-attachment regions) 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 major 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, the level of 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, followed by DNA packaged in nucleosomes, the 30-nm fiber, and naked DNA.
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 Features
Feature | Prokaryotic Chromosomes | Eukaryotic Chromosomes |
|---|---|---|
Structure | Circular, double-stranded DNA | Linear, double-stranded DNA |
Associated Proteins | Few, histone-like proteins | Many, histones and nonhistone proteins |
Genome Size | Few million bp | Tens to hundreds of millions bp |
Origins of Replication | One | Many |
Compaction | Nucleoid | Chromatin (nucleosomes, 30-nm fiber, radial loops) |
Telomeres | Absent | Present |
Key Equations
Length of DNA:
Genome size abbreviations: , ,
