06-Cytoplasm, Cytosol, and Organelles

The cytoplasm is defined as the contents of the cell bounded by the plasma membrane.
It constitutes the part of the cell located outside the largest organelle, which is the nucleus.
It refers specifically to the jelly-like, water-based material containing organelles.
Soluble Part: If the organelles were removed from the cytoplasm, the remaining soluble part is called the cytosol.

The cytoplasm is a fluid environment where cellular organelles are suspended.
It fills all the internal spaces of the cell that are not occupied by organelles.
The Three Residents of the Cytoplasm are:
- 1. Cytosol
- 2. Organelles
- 3. Cytoplasmic Inclusions

The cytosol is the fluid substance that fills the space between the cell membrane and the cellular organelles.
Physical Properties:
- It is a colloidal substance.
- It is usually colorless.
- It makes up approximately $70 \%$ of the total cell volume.
Chemical Composition:
- The cytosol is composed of $80 \%$ water and $20 \%$ organic and inorganic compounds.
- It contains a high concentration of proteins. Proteins constitute about $20\text{--}30 \%$ of the cytosol by weight.
- Between one-quarter and one-half ( $\frac{1}{4}$ to $\frac{1}{2}$ ) of the total protein content within a cell is located in the cytosol.
- It is a mixture of water, salt, cytoskeleton and protein filaments, soluble proteins, and other organic molecules.
Specific Ions Continued in the Cytosol:
- Potassium ( $K^+$ )
- Sodium ( $Na^+$ )
- Bicarbonate ( $HCO_3^-$ )
- Chloride ( $Cl^-$ )
- Calcium ( $Ca^{2+}$ )
- Magnesium ( $Mg^{2+}$ )
- Amino acids

Organelles (literally translated as "little organs") are usually membrane-bound structures inside the cell that perform specific functions.
Major Organelles suspended in the cytosol include:
- Mitochondria
- Endoplasmic reticulum (Smooth and Rough)
- Golgi apparatus (Golgi complex)
- Vacuoles
- Lysosomes
- Chloroplasts (found specifically in plant cells)
Other identified structures within the cell include:
- Centriole
- Nucleolus
- Chromatin
- Nuclear envelope and Nuclear pore
- Ribosomes
- Microfilaments and Microtubules
Visualization Techniques: Proteins in different cellular compartments can be tagged with green fluorescent protein (GFP) or specialized fluorescent dyes to identify specific organelles such as:
- Mitochondria
- Peroxisomes
- Beta-actin
- Alpha-tubulin ( $\alpha\text{-tubulin}$
- Golgi
- Cytosol
- Plasma membrane

Inclusions are defined as small particles of insoluble substances suspended in the cytosol, distinct from membrane-bound organelles.
They encompass a huge range of substances depending on the cell type:
- Plants: Crystals of calcium oxalate ( $CaC_2O_4$ ) or silicon dioxide ( $SiO_2$ ).
- Energy Storage Materials: Granules of starch in plants or glycogen in animals.
- Pigments: Various colored substances.
Specific Examples of Inclusions:
- Onion's tunic: Exhibits calcium oxalate crystals.
- Potato: Contains potato starch granules, often visualized at a scale of $10 \mu m$ .
- Lipid Droplets: Spherical droplets composed of lipids and proteins. These are used in both prokaryotes and eukaryotes to store lipids such as fatty acids and sterols.
Microscopy Example: A431 cells viewed at $40 \times$ magnification can be stained using DAPI for nuclei (blue) and Bodipy493/503 for lipid droplets (green).

The cytosol is the place where the cell expands and grows.
It provides the medium for organelles to remain suspended.
Without cytosol, a cell would be restricted to a flat and empty membrane. Together, the cytosol liquid and the cytoskeleton provide the cell's physical shape.

The cytoplasm is the site of many biochemical reactions.
It aids in the movement of various cellular elements and the transport of genetic material.
It is involved in the breakdown of macromolecules.
Importance of Liquid Volume: The liquid nature allows materials to transport between organelles easily.
Cytoplasmic Streaming: A process where the cytoplasm is in "slow motion," creating a flow through the cytosol. This allows nutrients, genetic information, and metabolites to pass from one organelle to another. It facilitates cooperation where one organelle produces a compound that is moved to the organelle that needs it.
Locomotion: Cytoplasmic streaming allows movement in certain organisms like the amoeba. Structures like cilia (tiny hair-like appendages outside the cell) also aid in movement.

The liquid space between organelles acts as a storage site for materials until they are needed.
Metabolic Waste: The cytoplasm stores metabolic waste, such as carbon cells, until disposal processes can be carried out.

The cytosol is a major site of cellular metabolism and contains a large number of different enzymes.
Protein complexes and enzymes in the cytosol carry out metabolic functions, allowing organelles to interact.

The cytoskeleton is a component of structural functions critical to cell motility.
Cells possess three types of filaments, distinguished by their diameter:
- Actin filaments (microfilaments): $5\text{--}9\,nm$ in diameter, consisting of twisted strands.
- Intermediate Filaments: Approximately $9\,nm$ in diameter.
- Microtubules: Hollow tube-like structures with a diameter of approximately $24\,nm$ .

Recommended Reference Materials:
- David L. Nelson and Michael M. Cox: LEHNINGER PRINCIPLES OF BIOCHEMISTRY, Sixth Edition.
- Lodish et al.: Molecular Cell Biology, Fifth Edition.
Course Details:
- University: University of Pécs, Faculty of Health Sciences.
- Subject: Cell Biology, Biochemistry, 6th Lecture.
- Editor: Veronika Vincze.
Related Curricular Topics:
- Introduction to cell biology and pro- and eukaryote cell structure.
- Biomolecules (Saccharides, Amino acids, Proteins, Enzymes).
- Biomembranes, Membrane transport, and ATP-powered pumps.
- Cell adhesion and junctions.
- Cytoplasma, cell skeleton, microfilaments, and microtubules.
- Endoplasmic reticulum (Rough and Smooth), Golgi body, Lysosomes.
- Mitochondria, Bioenergetics, and Glycolysis.
- Nucleus structure, DNA, and RNA (mRNA, tRNA, rRNA).
- Cell cycle (Mitosis and Meiosis), DNA replication, transcription, and translation.