Cytoplasm

The cytoplasm is the material inside a cell, bounded by the cell membrane. In eukaryotic cells, it includes the organelles but not the nucleus—the material inside the nucleus is called the nucleoplasm. The cytoplasm is roughly 80% water and typically colorless. Its main parts are the cytosol (a gel-like substance), the cell’s internal structures, and various inclusions. Many essential processes happen here, including metabolic pathways like glycolysis and photosynthesis, as well as cell division.

The cytosol, also called the cytoplasmic matrix or groundplasm, is what remains after removing the organelles and inclusions. Under a microscope, it appears as a complex, polyphasic system where all visible cytoplasmic elements are suspended, including larger organelles such as ribosomes, mitochondria, plant plastids, lipid droplets, and vacuoles. The inner, denser region is the endoplasm, while the outer layer is the cell cortex or ectoplasm. Calcium ions moving into and out of the cytoplasm serve as a signaling mechanism for metabolic activities. In larger animal and plant cells, amoebae, and slime molds, the cytoplasm can stream around organelles and vacuoles—a process known as cytoplasmic streaming.

The term “cytoplasm” was introduced by Rudolf von Kölliker in 1863, originally as a synonym for protoplasm, but later came to mean the cell substance and organelles outside the nucleus. There has been some disagreement over the definition, with some authors choosing to exclude certain organelles, particularly vacuoles and sometimes plastids.

How the cytoplasm’s components interact to allow organelle movement while maintaining cell structure is still not fully understood. The flow of cytoplasmic parts is important for many functions that depend on the cytoplasm’s permeability, such as cell signaling. Small signaling molecules like calcium ions diffuse easily, but larger molecules and subcellular structures often need help moving through the cytoplasm. The irregular motion of these particles has led to various theories about the cytoplasm’s nature.

One theory is that the cytoplasm behaves like a sol-gel. At times, its molecules and structures act like a disordered colloidal solution (sol); at other times, they form an integrated network like a solid mass (gel). This suggests the cytoplasm exists in distinct fluid and solid phases depending on how its components interact, which may explain why different particles move through it at different rates. A study suggested that at scales smaller than 100 nanometers, the cytoplasm acts like a liquid, but at larger scales, it acts like a gel.

Another model describes the cytoplasm as a biphasic material using poroelastic theory. This treats it as a porous, elastic solid framework (including the cytoskeleton, organelles, and macromolecules) immersed in a fluid called cytosol. The cytosol and the solid framework—called the intracellular cytomatrix (CMX)—are chemically separated from each other and from the nucleus. Research found that the CMX compartmentalizes the transcriptome, proteome, and metabolome, and that ribosomes attached to the CMX have a different mRNA profile than those in the cytosol. This compartmentalization boosts biocatalysis by sequestering metabolome enzymes, overcoming spatial barriers to biochemical reactions. The study also showed distinct responses in the cytosol and CMX during drug-induced protein deficiency, highlighting the flexibility of protein translation in the cytomatrix.

A third proposal is that the cytoplasm behaves like a glass-forming liquid near the glass transition. The more concentrated its components, the less it acts like a liquid and the more like a solid glass, freezing larger structures in place. The cell’s metabolic activity can fluidize the cytoplasm to allow movement of these components. In dormant periods, when metabolic activity stops, the cytoplasm may vitrify, which could be a defense strategy: a solid glass cytoplasm would freeze subcellular structures to prevent damage while still allowing tiny proteins and metabolites to pass through, helping the cell restart growth upon revival.

Other research has examined particle motion in the cytoplasm without focusing on its physical nature. In this view, the aggregate random forces from motor proteins explain why cytoplasmic particles move in a non-Brownian manner.

The three major elements of the cytoplasm are the cytosol, organelles, and inclusions. The cytosol is the part of the cytoplasm not inside membrane-bound organelles, making up about 70% of the cell’s volume. It is a complex mixture of cytoskeleton filaments (such as actin filaments and microtubules), dissolved molecules, and water. It also contains soluble proteins and small structures like ribosomes, proteasomes, and vault complexes. The inner, granular, and more fluid part of the cytoplasm is the endoplasm.