Biology: Chromosomes, Cell Cycle, and Mitosis

Chromosome Structure and Molecular Composition

Definition and Composition of Chromosomes:
- Chromosomes consist of a single, exceptionally long, and condensed DNA molecule.
- In eukaryotic cells, this DNA is associated with proteins to facilitate organization.
- The primary proteins present are histones, which are large, positively charged globular proteins.
- Histones serve to organize and condense DNA tightly so it can fit within the confines of the nucleus.
- Chromatin: This is the term for the tightly coiled combination of DNA and proteins. It is the material from which chromatids and chromosomes are constructed.
Chromatin vs. Chromatid:
- Chromatin: A loose, uncoiled mixture of DNA and proteins found in a cell during its non-dividing states.
- Chromatid: One exact copy of a newly replicated chromosome that remains joined to its partner during cell division.
Sister Chromatids and the Centromere:
- During the S phase of interphase, DNA replicates to create two identical strands called chromatids.
- These strands are joined at a narrow region called the centromere.
- The two chromatids forming a double structure are "sister chromatids."
- It is critical that sister chromatids are genetically identical (containing the same genes) to ensure that when they separate into two daughter cells during mitosis, the resulting cells are genetically identical.
- A single chromatid contains one very long, condensed DNA molecule composed of a series of genes.

The DNA Packaging Hierarchy and Histone Function

DNA and Histone Interactions:
- DNA is negatively charged due to the phosphate groups in its phosphate-sugar backbone.
- Histones are small, positively charged proteins (family members include $H1$ , $H2A$ , $H2B$ , $H3$ , and $H4$ ; Van Holde, 1988).
- The electrostatic interactions between the positive histones and negative DNA provide the energy for folding and packaging DNA into a significantly smaller volume than DNA alone.
The Levels of Folding:
- DNA Double Helix: The simplest level, a double-stranded helical structure with a width of $2\text{ nm}$ .
- Nucleosomes: DNA complexes with histones to form nucleosomes. Each nucleosome core consists of eight histone molecules around which DNA wraps $1.65$ times. The width is $11\text{ nm}$ .
- Chromatosome: This consists of a nucleosome plus an $H1$ histone.
- Linker DNA: A double-stranded segment of DNA connecting adjacent nucleosome core particles, behaving like the string in a "beads-on-a-string" model. It dictates the repeat length of nucleosomes.
- $30\text{-nm}$ Fiber: Nucleosomes fold to produce a fiber of $30\text{ nm}$ in width.
- Loooped Fibers: These fibers form loops averaging $300\text{ nm}$ in length.
- $250\text{-nm}$ Fiber: The $300\text{-nm}$ fibers are compressed and folded to create a fiber $250\text{ nm}$ wide.
- Chromatid and Chromosome: Tight coiling of the $250\text{-nm}$ fiber produces a chromatid ( $700\text{ nm}$ wide). A full chromosome (consisting of two chromatids) is $1400\text{ nm}$ wide.
Purpose of Histones:
- Condensation: Compacting DNA into a microscopic shape.
- Organization: Preventing DNA from becoming tangled.
- Access Control: Determining whether enzymes can reach DNA to trigger protein synthesis.

Telomeres

Composition and Location:
- Telomeres are protective structures that "seal" the ends of chromatids in chromosomes.
- They consist of non-coding DNA, meaning they do not contain genes.
- They are made of short base sequences repeated many times (multiple repeat sequences).
- One strand is rich in Guanine (G) ( $TTAGGGTTAGGG...$ ) and the other is rich in Cytosine (C) ( $AATCCCAATCCC...$ ).
Functional Importance:
- The DNA copying enzyme (DNA polymerase) cannot replicate a DNA molecule to the very end; it stops short.
- Telomeres act as a "buffer" region of non-essential DNA. They ensure that essential genetic information near the ends of the molecule is not lost during replication.
- Without telomeres, vital genes would be lost in every division, potentially leading to cell death.
- Telomeres allow for the continued replication of a cell.

Stem Cells and Potency

Definition: A stem cell is a cell capable of dividing via mitosis an unlimited number of times.
Telomerase: Unlike most cells, stem cells possess the enzyme telomerase, which rebuilds telomeres after each replication, allowing them to divide indefinitely.
Fate of Daughter Cells: New cells produced by stem cell division can either remain stem cells or undergo differentiation into specialized cells (e.g., blood cell, muscle cell).
Potency: The ability of stem cells to differentiate into specialized cell types.
Levels of Potency:
- Totipotent / Omnipotent: Can differentiate into any body cell type plus extra tissue required for growth (e.g., a first-day fertilized egg).
- Pluripotent: Can differentiate into any body cell type but cannot form extra-embryonic tissues (e.g., embryonic cells).
- Multipotent: Can differentiate into a few related cell types (e.g., blood stem cells in bone marrow).
- Unipotent: Can only differentiate into one specific cell type or renew their own specific type.
Types of Stem Cells:
- Embryonic Stem Cells: Derived from early embryos; can become almost any cell level.
- Adult Stem Cells: Multi-potent cells found in tissues like the bone marrow, skin, gut, heart, and brain for growth/repair. Bone marrow stem cells can differentiate into red blood cells, monocytes, neutrophils, and lymphocytes.
- Induced Pluripotent Stem Cells (iPS): Regular adult stem cells reprogrammed in a lab to behave like embryonic stem cells.

The Cell Cycle and Interphase

The Cell Cycle: A regulated sequence of events between one cell division and the next. It is triggered by chemical signals called cyclins.
Variation in Length:
- Onion root tip cells: Approximately $20\text{ hours}$ .
- Human intestine epithelial cells: Approximately $10\text{ hours}$ .
Phases of the Cell Cycle:

Interphase: The cell increases in mass/size and performs normal functions. It is composed of three sub-stages:
- $G_1$ Phase (Gap 1): Cells produce RNA, enzymes, and proteins necessary for growth. A signal to divide is received during this phase.
- S Phase (Synthesis): A relatively short phase where DNA replicates, resulting in chromosomes with two identical sister chromatids.
- $G_2$ Phase (Gap 2): The cell continues growing, checks newly synthesized DNA for errors (repairing them), and prepares for division (e.g., producing tubulin for spindle microtubules).
Nuclear Division (Mitosis / M Phase): The stage where growth stops and the nucleus divides into two genetically identical nuclei.
Cell Division (Cytokinesis): The division of the whole cell following the M phase.
- In animal cells, this involves the constriction of the cytoplasm.
- In plant cells, a new cell wall is formed.

The Stages of Mitosis

Overview: Mitosis is a continuous process divided into four main stages to produce two genetically identical daughter nuclei.

Prophase:
- Chromosomes condense and become visible when stained.
- Sister chromatids are joined at the centromere.
- Centrosomes (replicated during the $G_2$ phase) move to opposite poles.
- Spindle fibers (protein microtubules) emerge from centrosomes. (Note: Centrosomes in animal cells contain two centrioles).
- The nuclear envelope breaks down into small vesicles; the nucleolus also breaks down.
Metaphase:
- Centrosomes reach opposite poles.
- Chromosomes line up at the equator of the spindle (the metaphase plate), equidistant from the poles.
- Spindle fibers attach to the centromeres. Each sister chromatid attaches to a fiber from an opposite pole.
Anaphase:
- Sister chromatids separate at the centromere, which divides in two.
- Spindle fibers shorten.
- The separated chromatids (now considered individual chromosomes) are pulled centromere-first to opposite poles.
Telophase:
- Chromosomes arrive at opposite poles and decondense (uncoil).
- Nuclear envelopes reform around each set of chromosomes.
- The spindle fibers break down.

Biological Significance of Mitosis

Growth: Allows unicellular zygotes to grow into multicellular organisms by producing genetically identical clones. In plants, this is focused in meristems (e.g., just behind the root cap).
Cell Replacement and Tissue Repair: Continually replaces dead or damaged cells with identical ones. In humans, this is rapid in the skin and gut lining.
Asexual Reproduction: Production of offspring from a single parent.
- Unicellular: Amoeba cell division.
- Multicellular: Budding in Hydra and yeast; strawberry plant "runners" (stems that grow into new identical plants at nodes with adventitious roots).

Mitotic Index and Analysis

Mitotic Index: The proportion of cells in a sample undergoing mitosis.
Formula:
- $\text{mitotic index} = \frac{\text{number of cells with visible chromosomes}}{\text{total number of cells}}$
- Multiply by $100$ to express as a percentage.
Study Techniques: Meristems in plant root tips are studied using the squash technique, where stained root tips are flattened to spread cells into a thin sheet for visibility under a microscope.

Tumour Formation and Cancer

Cancer Mechanics: Cancer is caused by uncontrolled mitosis due to changes in genes regulating cell division.
Mutations and Oncogenes:
- Mutation: A change in any gene.
- Oncogene: A mutated gene that specifically causes cancer.
- Most mutations result in cell death or destruction by the immune system. Cancer cells evade these mechanisms and pass mutations to descendants.
Carcinogens: Agents that cause cancer (carcinogenic agents), such as ultraviolet (UV) light, asbestos, X-rays, and tar in tobacco smoke.
Types of Tumours:
- Benign: Do not spread from the original site (e.g., warts).
- Malignant: Invasive and destructive; they interfere with organ function (e.g., blocking lungs or vessels).
Metastasis: The process where malignant cells break off, travel through the blood or lymphatic system, and form secondary tumours elsewhere in the body. This is highly dangerous and difficult to treat.