Chromosomes

Mr. Arvind Kumar

Introduction

  • Chromosomes are thread-like structures present inside the nucleus of every living cell.
  • They are made up of DNA (deoxyribonucleic acid) and proteins, mainly histones, which help in packaging the long DNA molecules into a compact form.
  • Each chromosome carries genes, the units of heredity, that control the traits and functions of an organism.
  • In humans, chromosomes occur in pairs.
  • A normal human cell has 46 chromosomes (23 pairs), out of which 22 pairs are autosomes and 1 pair are sex chromosomes (XX in females and XY in males).
  • During cell division, chromosomes ensure the accurate distribution of genetic material from parent cells to daughter cells.
  • Thus, chromosomes play a central role in storing, protecting, and transmitting genetic information from one generation to the next.

 

Structure of Chromosomes

Chromosomes are highly condensed thread-like structures composed of DNA and proteins, found in the nucleus of eukaryotic cells, carrying genetic information.

  • Chemical composition:

    • DNA (~40%): double-helical molecule containing genes.

    • Histones (~50%): basic proteins (H1, H2A, H2B, H3, H4) that package DNA into nucleosomes.

    • Non-histone proteins (~10%): enzymes (polymerases, topoisomerases), regulatory proteins, scaffold proteins.

    • RNA molecules (small amount, regulatory).

  • Levels of organization:

    1. DNA double helix → 2 nm.

    2. Nucleosomes (DNA wrapped around histone octamer) → “beads-on-a-string” form (10 nm fiber).

    3. 30 nm solenoid fiber → coiling of nucleosomes.

    4. Chromatin loops (300 nm).

    5. Condensed metaphase chromosome (1400 nm).

  • Morphology of a metaphase chromosome:

    • Chromatid: Each duplicated chromosome has two identical chromatids.

    • Centromere: Constriction region dividing chromosome into short arm (p) and long arm (q).

    • Telomeres: Repetitive DNA at chromosome ends (TTAGGG in humans), protecting against degradation and fusion.

    • Secondary constrictions/NOR (Nucleolar Organizer Regions): Sites of ribosomal RNA (rRNA) synthesis.

    • Satellite bodies: Small chromatin masses attached to secondary constrictions.

  • Types of chromosomes (based on centromere position):

    • Metacentric: centromere in middle.

    • Submetacentric: centromere slightly off-center.

    • Acrocentric: centromere near one end (humans: 13,14,15,21,22).

    • Telocentric: centromere at extreme end (not in humans, common in rodents).

 

Number of Chromosomes

Each species has a constant diploid (2n) chromosome number.

Examples:

  • Humans → 46 (23 pairs).

  • Chimpanzee → 48.

  • Drosophila → 8.

  • Onion → 16.

  • Dog → 78.

Diploid (2n): complete set (somatic cells).

  • Haploid (n): half set (gametes).

  • Chromosomal abnormalities:

    • Aneuploidy (loss/gain of a chromosome) – e.g., Down syndrome (Trisomy 21), Turner syndrome (45,X), Klinefelter syndrome (47,XXY).

    • Polyploidy (extra complete sets) – common in plants, rare in humans.

 

Sex Chromosomes

  • Autosomes: non-sex chromosomes (22 pairs in humans).

  • Sex chromosomes: determine biological sex (XX in female, XY in male).

  • Y chromosome: smallest human chromosome; carries SRY gene → triggers male development.

  • Sex determination:

    • XX = female.

    • XY = male.

  • Disorders of sex chromosomes:

    • Turner syndrome (45,X).

    • Klinefelter syndrome (47,XXY).

    • Triple X syndrome (47,XXX).

    • XYY males (47,XYY).

 

Human Karyotype

Complete set of chromosomes of an organism, arranged in homologous pairs, decreasing in size.

  • Human karyotype:

    • Normal female: 46,XX.

    • Normal male: 46,XY.

  • Techniques for preparation:

    • Collect dividing cells (blood lymphocytes, bone marrow, amniotic fluid).

    • Arrest at metaphase (using colchicine).

    • Hypotonic treatment (swells cells).

    • Fixation, spreading, and staining.

  • Uses:

    • Identify numerical abnormalities (trisomy, monosomy).

    • Identify structural abnormalities (translocations, deletions).

    • Prenatal diagnosis (amniocentesis, chorionic villus sampling).

    • Cancer diagnosis (e.g., Philadelphia chromosome in CML).

 

Methods for Chromosome Analysis

  • Conventional cytogenetics:

    • Karyotyping.

    • Banding techniques.

  • Molecular cytogenetics:

    • FISH (Fluorescence In Situ Hybridization).

    • CGH (Comparative Genomic Hybridization).

    • Array-CGH (microarray based).

  • Flow cytometry: analysis of DNA content, ploidy, and cell cycle distribution.

  • Next-generation sequencing (NGS): genome-wide chromosomal studies.

 

Chromosome Banding

Developed to identify each chromosome uniquely.

  • Types of banding:

    • G-banding: Giemsa stain → alternating dark/light bands. AT-rich regions appear dark.

    • Q-banding: Quinacrine → fluorescent bands.

    • R-banding: reverse of G-banding (GC-rich areas).

    • C-banding: stains centromeric heterochromatin.

    • T-banding: highlights telomeric regions.

  • Applications:

    • Detecting structural abnormalities (deletions, duplications, translocations).

    • Genetic counseling and prenatal testing.

 

Fluorescence In Situ Hybridization

Principle: DNA probes labeled with fluorescent dyes hybridize to complementary chromosome regions.

  • Types of probes:

    • Locus-specific probes (for single genes).

    • Centromere-specific probes (detect aneuploidy).

    • Whole-chromosome painting probes (translocations).

  • Applications:

    • Detect microdeletions (e.g., DiGeorge syndrome 22q11).

    • Detect oncogene amplification (HER2 in breast cancer).

    • Identify cryptic chromosomal rearrangements.

    • Rapid prenatal diagnosis of trisomies.

 

Comparative Genomic Hybridization

Test DNA (patient) and reference DNA are labelled with different fluorescent dyes and hybridised to normal metaphase chromosomes or DNA microarrays.

  • Applications:

    • Detect genome-wide copy number variations (CNVs).

    • Detect gains/losses in tumor cells.

    • Array-CGH allows detection of very small deletions/duplications.

  • Limitations:

    • Cannot detect balanced rearrangements (translocations, inversions).

    • Requires specialized equipment.

 

Flow Cytometry

Cells stained with a DNA-binding fluorescent dye pass through a laser beam. Fluorescence intensity ∝ DNA content.

  • Applications:

    • Cell cycle analysis (proportion of G0/G1, S, G2/M cells).

    • Detect aneuploidy and polyploidy.

    • Immunophenotyping (with antibodies).

    • Used in oncology (tumor DNA content, prognosis).

Cell Cycle

  • Phases:

    • G1 phase: cell growth, protein synthesis.

    • S phase: DNA replication, centrosome duplication.

    • G2 phase: preparation for mitosis, repair of replication errors.

    • M phase: mitosis (prophase, metaphase, anaphase, telophase) + cytokinesis.

    • G0 phase: resting stage (non-dividing cells like neurons, muscle).

  • Regulation:

    • Controlled by cyclins and CDKs.

    • Checkpoints:

      • G1/S (DNA damage check).

      • G2/M (DNA replication completion).

      • Spindle checkpoint (chromosome alignment).

  • Dysregulation → cancer.

Mitosis

  • Purpose: Growth, repair, asexual reproduction.

  • Produces 2 identical diploid daughter cells.

  • Phases:

    • Prophase: chromosomes condense, spindle forms.

    • Metaphase: chromosomes align at equator.

    • Anaphase: sister chromatids separate.

    • Telophase: nuclear envelope reforms.

    • Cytokinesis: cytoplasm divides.

  • Significance:

    • Maintains genetic stability.

    • Errors may lead to cancer.

 

Meiosis

  • Purpose: Gamete formation, sexual reproduction.

  • Produces 4 haploid cells, genetically different.

  • Meiosis I (reductional division):

    • Homologous chromosomes pair (synapsis).

    • Crossing over occurs (genetic recombination at chiasmata).

    • Homologs separate → 2 haploid cells.

  • Meiosis II (equational division):

    • Sister chromatids separate → 4 haploid gametes.

  • Significance:

    • Maintains chromosome number across generations.

    • Introduces genetic diversity (crossing-over, independent assortment).

    • Errors cause nondisjunction → aneuploidy.