Chromosome Structure and DNA Sequence Organization

General Characteristics of Viral and Bacterial Chromosomes:
- Usually consist of a single nucleic acid molecule devoid of associated proteins.
- Much smaller than eukaryotic chromosomes.
- Chromosomes of viruses can consist of single- or double-stranded DNA or RNA and can be linear or circular.
Phage λ Example:
- Composed of double-stranded DNA.
- The DNA is linear before infection and circular after infection.
- Length of DNA molecule: 17 µm.
- Size of phage head: <0.1 µm on any side.
- DNA is inert when packaged in the phage head.
Phage T2 Example:
- Composed of double-stranded DNA.
- Linear molecule: 52 µm.
- Size of phage head: 0.1 µm.
Bacterial Chromosomes:
- Composed of double-stranded DNA, compacted into a nucleoid.
- In E. coli, the DNA is associated with binding proteins such as HU and H1 (positively charged).
- Circular DNA molecule length: 1200 µm, bacteria size: 2 µm.
- Unlike viruses, bacterial DNA is active even when highly compacted within the cell.

Mitochondria:
- Contain mitochondrial DNA (mtDNA), which is double-stranded and lacks chromosomal proteins.
- Introns are typically absent from mitochondrial genes and gene repetition is seldom seen.
- Replication of mtDNA relies on enzymes coded by nuclear DNA.
Chloroplasts:
- Contain chloroplast DNA (cpDNA) which shares characteristics with prokaryotic DNA.
- cpDNA is circular, double-stranded, and free from associated proteins normally found in eukaryotic DNA.
- It is larger than mtDNA and contains a higher number of genes, having both introns and duplications.

Eukaryotic Chromosomes:
- Larger and more complex (chromatin structure) than prokaryotic chromosomes.
- Composed of chromatin that is much more compacted.
- Specialized chromosomes, like polytene and lampbrush chromosomes, provided early insights into chromosome structure.
Polytene Chromosomes:
- Very large and can be visualized by light microscopy, found in salivary glands and guts of certain flies, protozoans, and plants (somatic cells).
- Distinctive banding patterns reflect paired homologs, though they are somatic, not from germ-line cells.
- Composed of multiple DNA strands along with many rounds of replication without strand separation or cytoplasmic division.
- Puff regions indicate areas of uncoiled DNA, representing high gene activity.
Lampbrush Chromosomes:
- Large structures with extensive DNA looping, discovered in vertebrate oocytes during Prophase I of meiosis.
- Considered extended and uncoiled versions of typical meiotic chromosomes and are transcriptionally active.
DNA Coiling and Gene Activity:
- Uncoiling is often associated with gene activity.
- However, in general, DNA in cells remains highly coiled and compact.

Definition of Chromatin:
- In a human cell, if unwound, DNA would be approximately 2 meters long. The nucleus's diameter is between 5–10 µm (5 × 10^-6 m).
- Eukaryotic chromosomes are structured in a nucleoprotein framework known as chromatin.
Nucleosome Structure:
- Nucleosomes are composed of histones (specifically H2A, H2B, H3, and H4).
- Nucleosomes condense multiple times to form chromatids.
- The nucleosome core particle has been analyzed through X-ray crystallography, showing double-helical DNA wrapped around four pairs of histones.
Chromatin Remodeling:
- Fundamental for allowing DNA to be accessible to binding proteins.
- Histone tails play an important role in histone modifications, such as acetylation, methylation, and phosphorylation.
- These modifications are essential for gene regulation, though specifics are still being researched.
Types of Chromatin:
- Euchromatin: Less coiled, transcriptionally active.
- Heterochromatin: Highly condensed, transcriptionally inactive; includes:
- Centromeres
- Telomeres
- Mammalian Y chromosome (inactive)
- Barr Body (inactive mammalian X chromosome)

Repetitive DNA Characteristics:
- Repetitive DNA sequences are extensively repeated within eukaryotic chromosomes and can be categorized in several ways.
Various Kinds of Repetitive DNA:
- Multi-copy Genes: Some coding genes exist in multiple copies (e.g., ribosomal RNA genes). Most repetitive DNA is non-coding.
- Highly Repetitive DNA (Satellite DNA):
- Found in centromeres, consists of short tandem repeats that contribute to chromosome stability and integrity.
- In vertebrates, the sequence 5’-TTAGGGG-3’ can be repeated many times, often exceeding 1,000 repeats in some species.
- Moderately Repetitive DNA:
- Includes:
  - Minisatellites: Variable number tandem repeats (VNTRs) consisting of sequences ranging from 15–100 bp, repeated hundreds of times.
  - Microsatellites: Sequences of 2–4 bp repeated 5–100 times. Often used in genetic identity and paternity analysis due to their variability among individuals.
- Repetitive Transposed Sequences:
- SINEs (Short Interspersed Elements): Approximately 500 bp, can occur more than 500,000 times in the human genome.
- LINEs (Long Interspersed Elements): Approximately 6,000 bp, can occur up to 850,000 times in the human genome. LINEs function as retrotransposons, encoding RNAs that reverse-transcribe back to DNA, integrating into the genome at new locations.

Eukaryotic Genome Composition:
- A small fraction (2-10%) of the eukaryotic genome consists of protein-encoding genes.
- Additionally, numerous single-copy noncoding regions are present, which often include pseudogenes.
- Pseudogenes:
- Originally functional genes that acquired mutations resulting in their non-functionality.
- They are evolutionary remnants of genes which once played active roles but have since become inactive.