Cell Nucleus and the Cytoskeleton

The Nucleus

  • The nucleus contains DNA, a key molecule for life.
  • DNA is packaged within the nucleus in eukaryotic cells.

Prokaryotic vs. Eukaryotic Cells

  • Prokaryotic Cells:
    • Do not have a nucleus.
    • Have a single, circular chromosome of DNA.
    • Duplicate through fission, where DNA is replicated and segregated to daughter cells.
    • DNA molecule remains attached to the plasma membrane during replication.
    • New plasma membrane is created to accommodate new DNA molecules.
    • Cytokinesis separates the two new cells, each with one chromosome.
  • Eukaryotic Cells:
    • Divide through mitosis or meiosis.
    • Mitosis: Same amount of DNA is segregated to daughter cells (somatic cells).
    • Meiosis: Half the amount of DNA is transferred (gamete cells involved in reproduction).
    • Contain multiple chromosomes; the number depends on the species.
      • Humans have 46 chromosomes.
      • Mitosis transfers 46 chromosomes.
      • Gamete cells contain half the amount (23 chromosomes) and undergo meiosis.

Nucleus Structure and Function

  • The nucleus is the largest organelle in the cell and contains DNA.
  • DNA replication and the first step in protein production (transcription) occur inside the nucleus.
  • Components:
    • Two plasma membranes (nuclear envelope).
    • Nuclear pores.
    • Nucleolus.
    • Chromatin.
  • The nucleus is close to the rough endoplasmic reticulum (RER), where ribosomes are located.
  • RNA, transcribed from DNA, moves from the nucleus to the RER for protein synthesis.
    • DNA itself is too precious to leave the nucleus.
    • RNA contains the information for protein synthesis and is decoded at the RER.

Nuclear Pores

  • Nuclear pores are composed of different subunits and facilitate the exchange of materials between the nucleus and cytoplasm.
  • Outward Transport (Nucleus to Cytoplasm):
    • RNA.
    • Ribosomal proteins.
  • Inward Transport (Cytoplasm to Nucleus):
    • Proteins (e.g., DNA polymerase).
    • Carbohydrates (sugars for energy).
    • Signaling molecules.
    • Lipids involved in nuclear processes.

Nucleus Size and DNA Packaging

  • The diameter of a nucleus is typically between 5 and 10 micrometers (1μm=10−6m)(1 \mu m = 10^{-6} m).
  • The nucleolus occupies 25% of the nucleus volume.
  • The DNA molecule inside the nucleus is approximately two meters long.
  • DNA is packaged into thread-like structures called chromosomes.
  • Chromosomes are visible only when the cell is dividing.
  • DNA, when not condensed into chromosomes, exists as chromatin filaments.

Chromosome Structure

  • Each chromosome has a central part called the centromere, which divides it into arms.
  • The shorter arm is referred to as the P arm, and the longer arm is the Q arm.
  • A karyogram is a way to classify chromosomes based on their shape.
  • Humans have 22 pairs of chromosomes plus two sex chromosomes (X and Y).
  • Each chromosome contains approximately 50,000,000 to 250,000,000 base pairs.
  • Every cell in the body contains a copy of the entire DNA sequence.
  • 99% of the DNA sequence is the same across all cells; minor differences account for specialized cell functions.

DNA Packaging and Histones

  • DNA is compressed and packaged into the small volume of the nucleus with the help of proteins called histones.
  • DNA plus histones form chromatin.
  • The coiling mechanism requires energy, which is provided by electrostatic interactions rather than ATP.
  • Histones are small, positively charged proteins that facilitate DNA packaging.
  • Core histone proteins include H1, H2A, H2B, H3, and H4.
  • Histones offer a positively charged environment for the negatively charged DNA molecule.
  • DNA wraps around histones to form a nucleosome.
  • DNA is composed of bases (adenine, thymine, cytosine, guanine), a sugar (deoxyribose), and a phosphate group (PO4−−)(PO_4^{--}). Phosphate groups give DNA its negative charge.
  • A nucleosome consists of nine proteins, including a histone core, and 166 bases of DNA wrapped around it.
  • Packaging DNA into nucleosomes shortens the DNA length by seven times.
  • Further twisting and coiling of DNA through histones leads to a more compressed form, resulting in a 30-nanometer fiber.

Chromatin Structure: Heterochromatin vs. Euchromatin

  • Chromatin exists in two forms: heterochromatin (more packed and dense) and euchromatin (less packed).
  • Heterochromatin: Densely packed, less accessible.
  • Euchromatin: Less dense, more accessible; allows for DNA duplication and gene activation.
  • The difference in density is due to the need for access to the DNA molecule for transcriptional replication.

Transcriptional Replication and DNA Accessibility

  • DNA needs to be temporarily accessible for duplication and transcription.
  • The formation of nucleosomes and 30-nanometer fibers creates barriers for the enzymes involved in DNA replication and transcription.
  • Histones must be transiently removed or modified to allow access to the DNA molecule.
  • Mechanisms for Access:
    • Enzymatic modification of histones.
    • Temporary removal of histones from chromatin.
  • These processes are reversible; once the task is completed, the DNA returns to its initial packaged state.

Chromosome Visibility and DNA Remodeling

  • Chromosomes are visible during cell division when DNA is most compressed.
  • DNA remodeling involves transitioning from a double helix to a chromosome through the addition of histones and subsequent compression into fibers of increasing thickness.
  • A chromosome has a diameter of 1,400 nanometers, and DNA is inaccessible when in this form.

Cytoskeleton

  • Prokaryotic cells do not have a cytoskeleton.
  • Eukaryotic cells have a cytoskeleton that organizes and compartmentalizes the cytoplasm.

Cytoskeleton Functionality

  • The cytoskeleton gives eukaryotic cells the ability to create compartments within the cytoplasm and maintain a relatively stable organization.

Cytoskeleton Structure

  • Composed of microfilaments; various filaments are composed within the cytoskeleton.
  • An intricate network of filaments is created and maintained through a process called polymerization, where small subunits of proteins are added together.

Types of Filaments

  • Microtubules (25 nm):
    • Provide a rigid intracellular skeleton for cells.
    • Serve as highways for motor proteins.
  • Microfilaments.
  • Intermediate filaments.

Microtubules

  • Located around the nucleus and nearby.
  • Formed through polymerization of tubulin monomers (alpha and beta tubulin).
  • Have a polar structure with a minus end (where polymerization starts) and a plus end (the head).
  • Created in a structure called the centrosome.
  • Centrosomes are there producing microfilaments.
  • Centrosomes located in the middle of the cells have to be segregated in the daughter cells.
  • A visual example of elongation is present in Donnie Darko, where a tube comes out of of the body. Watch the movie as homework.

Dynamic Nature of Microtubules

  • Microtubules are dynamic structures that can be created on demand and removed when not needed.
  • Microtubules grow and shrink on demand from the minus end to the plus end.

Microtubules in Action

  • Microtubules reorganize the topography of the cell cytoplasm.

Microtubules and Cell Division

  • Microtubules help segregate chromosomes during cell division.

Drugs Affecting Microtubules

  • Colchicine:
    • Binds to tubulin molecules.
    • Prevents polymerization.
    • Prevents the formation of microtubules and mitotic spindle.
  • Taxol:
    • Promotes the formation of microtubules.
    • Promotes polymerization.

Motor Proteins

  • Use microtubules as a network to position organelles.
  • Move along microtubules in two directions:
    • Retrograde (toward the minus end).
    • Toward the plus end.
  • Movement requires energy provided by ATP hydrolysis.
  • Main families of motor proteins on microtubules:
    • Kinesins: Move toward the plus end.
    • Dyneins: Move toward the minus end.
  • Organelles can send messages to motor proteins via receptors.
    • The endoplasmic reticulum is sensible to the Kinases.
    • The godly apparatus is sensible to the Dynasins.

Kinesins

  • Promote organelle movement.
  • Transport RNA and protein.
  • Involved in the assembly of cilia and flagella.
  • Involved in signaling pathways.
  • Involved in mitotic spindle formation and chromosome movement.

Dynein

  • Cytoplasmic dynein: Found within the cytoplasm.
  • Ciliary dynein: Important for the movement of cilia and flagella.

Cilia and Flagella

  • Involved in the locomotion of cells.
  • Made of microtubules.
  • Flagella are longer than cilia.
  • Sperms cells have flagella.
  • Highway cells have cilia.
  • The ultrastructure of cilia and flagella has an array of nine pairs of microtubules plus two in the middle (9 + 2 arrangement).
  • Motor proteins interact to allow movement.
  • Can either:
    • Move through locomotion (Sperm cells)
    • Move to create a flux of something (Highway cells).

Mircofilaments

  • Actin (7nm)
  • May be:
    • Single filament.
    • Bundle.
    • Network.
  • Stabilize cell shape.
  • Help the cell or part of a cell to move.
  • In the cytoplasm.
  • Involved in the formation of pseudopodia (fake foot).

Microfilaments in Action

  • Can be involved in the movement of the cell, or by internal movement of organs within the cell.
  • Movie demonstrating microfilaments involved in movement of a keratocyte cell.

Microfilaments and Bacteria

  • Bacteria hijack functions of microfilaments.
  • Listeria monocytogenes penetrates a cell by using actin microfilaments for movement, which allows it to penetrate the cell, move within the cell, and transfer itself to another cell.

Microfilaments and Myosin

  • Myosin is involved in muscle contraction.
  • Can be found in a Sarcoma
  • Myosin and actin interact with each other to create the movement of muscle cells

Cytoskeleton Interactions

  • Cytoskeleton filaments need to interact each other to make a specific function.
  • Actin and microtubules interact with cytotoxic T cells (white blood cells).
  • T cytotoxic cells can reorganizing microtubules and microfilaments internally to move them.

Intermediate Filaments

  • 8-12 nanometers in size.
  • Found in multicellular organisms only.
  • Tough, rope-like structures.
  • Mostly expressed by cells exposed to mechanical stress, such as muscle cells and epithelial cells
  • Filaments are also involved in keeping the nucleus and other organoids in their own position.
  • Stabilize cells and resist tension.

Types of Intermediate Filaments

  • Keratins and keratin like proteins are the proteins involved in the structure of intermediate filaments.
  • In monomers
  • Made of fibrous molecule
  • Create dimers in anti parallel.
  • There is no polymerization process involved in this filaments as it's present in others but they join through fibrous molecules.

Keratins

  • Epithelial cells contain more than 20 different kinds of keratins.
  • The toughest keratin proteins can be found in hair and nails.

Vimentin

  • They can form polymers.
  • The widely distributed microfilm intermediate filaments that can be found in the cytoplasm (fibroblasts, and leucocytes).
  • Keratin and Vimentin do not polymerize but can be found on the same cells.

Dysfunction of Intermediate Filaments

  • If the intermediate filament doesn't work and it doesn't provide the mechanical supports, the function will be affected.
  • Epidermolysis bullosa simplex is a genetic disease caused by a mutation of a specific keratin gene that disrupts the created protein network, and it makes them really soft.