Chromosome Structure and Organization

Molecular Structure of Chromosomes and Transposable Elements

• Chromosomes contain genetic material; they are made of DNA and proteins.

• Genome: the complete set of genetic material in an organism.

• Prokaryotic Chromosomes: single circular chromosome.

• Eukaryotic Chromosomes: nuclear chromosomes and separate mitochondrial and chloroplast genomes.

Introduction

• Chromosomes serve as structures for genetic material.

• Complexes of DNA and proteins.

• Prokaryotic genomes typically consist of a singular circular chromosome.

• Eukaryotic genomes comprise multiple linear chromosomes along with mitochondrial and chloroplast DNA.

Function of Genetic Material

• Main role: store information to produce organism traits.

• Accomplished mainly through protein-coding genes.

• DNA sequences necessary for:

  • RNA synthesis and cellular proteins.

  • Chromosome replication and segregation.

  • Chromosome compaction for fitting within cells.

Prokaryotic Chromosomes

• Discusses organization and transposition of chromosomes.

• Features of prokaryotic chromosomes:

  • Circular DNA, few million nucleotides long (e.g., E. coli ~4.6 million base pairs).

  • Thousands of genes, mostly protein-coding.

  • Intergenic regions: non-transcribed DNA between genes.

Prokaryotic Chromosomal DNA Organization

• Origin of replication, genes, and intergenic regions clearly mapped.

• Repetitive sequences interspersed throughout the DNA.

Key Features of Prokaryotic Chromosomes

• Most prokaryotes have circular DNA; may have multiple copies of a chromosome.

• Chromosome length: a few million base pairs.

• Interspersed genes and repetitive sequences; necessary for replication and function.

Nucleoid Structure

• Prokaryotic chromosomal DNA found in the nucleoid region, not membrane-bound.

• DNA contacts the cytoplasm directly.

Loop Domains in Bacterial Chromosome

• To fit within the cell, DNA compaction is required (~1000-fold).

• Loop domains (microdomains) of about 10,000 bp vary by species (e.g., E. coli has 400-500 microdomains).

• Adjacent microdomains organized into macrodomains.

Nucleoid-Associated Proteins (NAPs)

• DNA-binding proteins (NAPs) are crucial for:

  • Formation of microdomains.

  • Chromosome segregation and structure.

  • Gene regulation via DNA bending or bridging.

Features of Archaeal Chromosomes

• Varying structures; depend on DNA-binding protein types.

• Archaeal species may produce bacterial-like NAPs or eukaryotic histones.

• DNA wrapped around histones forms nucleosomes and loop domains.

DNA Supercoiling in Bacterial Chromosome

• Additional DNA twists (supercoiling) compact the chromosome further.

• Both underwinding and overwinding of DNA leads to different supercoiling forms.

Effects of DNA Supercoiling

• Bacterial DNA is negatively supercoiled; enhances compaction and segregation.

• Negative supercoiling creates regions of tension aiding in strand separation for replication and transcription.

Control of Supercoiling

• Regulated by two enzymes:

  • DNA gyrase: introduces negative supercoils; can untangle DNA.

  • DNA topoisomerase I: relaxes supercoiling tension by breaking one strand.

Eukaryotic Chromosome Organization

• Eukaryotic species have multiple linear chromosomes (e.g., humans: 2 sets of 23).

• Each chromosome composed of a single DNA molecule, with lengths varying from tens to hundreds of millions of base pairs.

• Eukaryotic chromosomes possess centromeres, telomeres and many origins of replication; repetitive sequences commonly found near centromeres.

Eukaryotic Chromosome Complexity

• Simpler eukaryotes (e.g., yeast) have shorter genes; complex eukaryotes (e.g., mammals) have longer genes with introns.

• Introns vary in length significantly among species.

Sizes of Eukaryotic Genomes

• Eukaryotic genomes generally more extensive than prokaryotic.

• Size variation in genomes not always related to species complexity.

• Example: salamander species show genome size variation due to repetitive DNA accumulation, not extra genes.

Repetitive Sequences in Genomes

• Genome sequence complexity defined by the frequency of base sequences:

  • Unique: Found infrequently (41% in humans).

  • Moderately repetitive: Multiple occurrences; includes rRNA genes and transposable elements.

  • Highly repetitive: Many copies, often short sequences.

Examples of Genomic Repetitive Sequences

• Alu family in humans (300 bp, 10% of human genome), found every 5000-6000 bp.

• Drosophila has AATAT and AATATAT sequences in centromeres.

Relative Amounts of Unique and Repetitive DNA in Human Genome

• Unique sequences: 24% accounts for protein coding regions.

• Repetitive DNA constitutes a significant part, influencing overall genomic structure.