Comprehensive Study Notes on Cell Histology and Organelle Function

Cell Histology and the Structure of the Plasma Membrane

The cell is surrounded by a specialized barrier known as the plasma membrane. This membrane structure is not unique to the cell's outer boundary; the nucleus and various other organelles within the cell are also enclosed by similar membrane architectures. These membranes are primarily composed of proteins, lipids, and carbohydrates. Proteins represent the largest molecular component by weight, making up approximately $\sim 50\%$ of the membrane's mass. However, this ratio can vary based on the cell type's specific function. For instance, cells that form the myelin sheath, such as oligodendrocytes and Schwann cells, possess a higher proportion of lipids. Conversely, the inner mitochondrial membrane exhibits the highest protein content found in any cellular membrane.

Organelles within the cell are categorized by the presence or absence of a membrane. Membranous organelles include mitochondria, both granular (rough) and smooth endoplasmic reticulum, the Golgi complex, lysosomes, and peroxisomes. Non-membranous organelles and structures include ribosomes, proteasomes (which are enzymatic complexes), microtubules, intermediate filaments, microfilaments (which constitute the cytoskeleton), coated vesicles, centrioles, and secretory granules.

Membrane Lipids and the Phospholipid Bilayer

Phospholipids are the primary lipids involved in membrane structure. These molecules are amphipathic, meaning they possess both a hydrophilic (water-attracting) head and a hydrophobic (water-repelling) tail. In an aqueous environment, these molecules arrange themselves into a bilayer where the hydrophobic tails point inward toward each other, away from water, while the hydrophilic heads face the external and internal cellular environments. The major phospholipids found in the membrane are phosphatidylcholine (also known as lecithin), phosphatidylinositol, phosphatidylethanolamine, sphingomyelin, and phosphatidylserine. Among these, phosphatidylethanolamine and phosphatidylcholine are the most abundant.

The distribution of these phospholipids is asymmetric between the inner and outer leaflets of the bilayer. Phosphatidylethanolamine, phosphatidylserine, and phosphatidylinositol are found more frequently in the inner leaflet. In contrast, phosphatidylcholine and sphingomyelin are more prevalent in the outer leaflet; indeed, almost the entire outer layer is comprised of phosphatidylcholine. This asymmetry is vital for several physiological processes. For example, during platelet activation and the clotting process, phosphatidylserine must move to the outer layer. Furthermore, the presence of high levels of phosphatidylserine on the outer leaflet serves as a biological marker indicating that a cell is undergoing apoptosis (programmed cell death).

Membrane Fluidity, Cholesterol, and Lipid Rafts

Cholesterol is another essential lipid component of the cell membrane, where it exists in its free form rather than as cholesterol esters. Cholesterol serves as a stabilizing agent, and its presence, along with several other factors, dictates membrane fluidity. Fluidity is decreased by long-chain fatty acids, high cholesterol content, and the presence of saturated fatty acids. Additionally, a "trans" configuration of lipids and a high number of intercellular junctions also reduce fluidity. Conversely, an increase in temperature increases membrane fluidity.

Specific regions within the membrane, known as lipid rafts, are characterized by high concentrations of cholesterol and glycosphingolipids (such as cerebrosides and gangliosides) and are rich in long, saturated fatty acids. These regions are significantly less fluid than the surrounding membrane. Lipid rafts serve as specialized platforms where proteins related to cell signaling mechanisms are concentrated, effectively segregating different signaling pathways from one another. When the walls of these rafts are coated with a protein called caveolin, they form structures known as caveolae. In endothelial cells, caveolae are responsible for the transcytosis of various nutrients from the blood into the cell.

Membrane Proteins and Carbohydrates

Proteins within the membrane are classified as either integral or peripheral based on their positioning. Integral proteins are embedded within the phospholipid bilayer through hydrophobic interactions; those that span the entire membrane from one side to the other are called transmembrane proteins. These can function as channels, transporters, receptors, or enzymes, and provide structural support to the cytoskeleton. Peripheral proteins do not enter the lipid bilayer but are localized to either the inner or outer surface, often binding to the phosphate heads of phospholipids. One common method of attachment for these proteins is through glycosylphosphatidylinositol (GPI) anchors.

Membrane carbohydrates are located exclusively on the extracellular surface, forming glycolipids and glycoproteins. These carbohydrates carry a negative charge and act as the "identity card" for the cell. They are responsible for determining antigenic structures, such as blood group antigens. When viewed under an electron microscope, this carbohydrate-rich layer is visible as a thin coating called the glycocalyx. The glycocalyx is crucial for cell-to-cell recognition, cellular relationships, and providing receptor sites for certain hormones. It also plays a role in preventing platelets from adhering to the endothelium and contributes to the filtration barrier in the kidneys by preventing negatively charged proteins from entering kidney cells.

Mitochondria Structure and Genetics

Mitochondria are the organelles responsible for oxidative phosphorylation, providing ATP to the cell. While nearly all cells contain mitochondria, exceptions include erythrocytes (red blood cells) and terminal keratinocytes. These organelles possess their own mitochondrial DNA, which encodes 13 protein subunits. Enzyme complexes involved in oxidative phosphorylation result from the interaction between nuclear and mitochondrial genomes. Because the DNA repair systems in mitochondria are inefficient, the mutation rate of mitochondrial DNA is more than 10 times higher than that of nuclear DNA. Mitochondria also contain their own ribosomes, which are smaller than those found in the cytoplasm. Interestingly, mitochondrial replication is not synchronized with the cell cycle; they are the only organelles capable of dividing independently due to their genetic material.

Structurally, a mitochondrion consists of an outer membrane, an inner membrane, an intermembrane space, and a central matrix. The inner membrane folds into structures called cristae to increase surface area. In cells that produce steroid hormones, these cristae are organized into a tubular shape. Fatty acids enter the mitochondria with the assistance of a molecule called carnitine, which is a quaternary ammonium cation synthesized from the amino acids lysine and methionine. This process is essential for energy production. A specific phospholipid called cardiolipin is found in the inner membrane; it is unique for being the only antigenic human phosphoglycerite and is highly concentrated in heart muscle. Cardiolipin is highly negatively charged and is required for the activity of cytochrome oxidase and the function of phosphate transporters, as well as making the membrane impermeable to ions.

Mitochondrial Compartmentalization and Cellular Pathology

Different mitochondrial functions are localized to specific structures within the organelle. The outer membrane contains porins (voltage-dependent anion channels), through which ATP leaves to enter the cytoplasm. It is also the site for enzymes like phospholipase $A_2$ (PLP $A_2$), acetyl-CoA synthase, and monoamine oxidase (MAO), which breaks down catecholamines. The outer membrane also houses the translocase of the outer membrane (TOM). The intermembrane space contains cytochrome C, creatine kinase, and adenylate kinase. The inner membrane contains cardiolipin, the electron transport chain, enzymes for oxidative phosphorylation, the inner membrane translocase (TIM), and succinate dehydrogenase, which is the only component of the TCA cycle located in the inner membrane. The matrix serves as a storage site for large amounts of calcium and contains the enzymes for the tricarboxylic acid (TCA) cycle, fatty acid beta-oxidation enzymes, enzymes for porphyrin and urea metabolism, and genetic material.

Cells rich in mitochondria stain acidophilic (eosinophilic) and are referred to as oxyphilic cells. Tumors originating from these cells are called oncocytomas. In these tumors, the mitochondria-rich cells are specifically termed Hürthle cells or oncocytes. Such oncocytomas can occur in the parathyroid, thyroid, salivary glands, kidneys, and pituitary gland.

Ribosomes and the Endoplasmic Reticulum

Ribosomes are non-membranous organelles measuring approximately $22 \times 32\,\text{nm}$ where protein synthesis occurs. They consist of two subunits, 40S and 60S. When two ribosomes work together, they are called a diplosome; larger groups are called polysomes. Ribosomes synthesize different proteins depending on their location. Ribosomes attached to the endoplasmic reticulum synthesize all transmembrane proteins, most secreted proteins, Golgi complex proteins, and lysosomal enzymes. Free ribosomes in the cytoplasm synthesize the protein portion of hemoglobin, nuclear proteins, peroxisomal proteins, mitochondrial proteins, and general cytoplasmic proteins.

The endoplasmic reticulum (ER) is composed of tubules and cisternae. It is classified as Granular Endoplasmic Reticulum (GER or Rough ER) when ribosomes are attached to its cytoplasmic side, and Smooth Endoplasmic Reticulum (DER or Smooth ER) when ribosomes are absent. The GER is involved in synthesizing proteins for export, membrane proteins, and lysosomal enzymes. It also performs post-translational modifications such as central glycosylation and the formation of disulfide and hydrogen bonds, as well as protein folding to create tertiary structures. In active protein-synthesizing cells, the GER and its associated RNA stain basophilic; these regions are known as ergastoplasm or Nissl bodies in neurons. This basophilic staining is also prominent in pancreatic acinar cells.

Protein Synthesis and Vesicular Traffic

Protein synthesis on GER-bound ribosomes begins with a hydrophobic signal sequence. This sequence is recognized by a signal recognition particle (SRP) in the cytoplasm, which binds to the growing protein and halts further elongation. The SRP-ribosome complex then moves to the ER membrane and binds to an SRP receptor. The ribosome then attaches to a channel called a translocon, through which the protein enters the GER lumen. This entire process is GTP-dependent. Before the protein is finished, a signal peptidase enzyme removes the signal sequence. Completed proteins are then transported to the Golgi complex via COP II-coated vesicles. A failure in the process of sending proteins from the GER to the Golgi results in Alpha1-antitrypsin deficiency.

Vesicular traffic is regulated by SNARE proteins. Specifically, v-SNAREs on the vesicle interact with t-SNAREs on the target membrane in a key-lock mechanism to ensure correct delivery. Transport between the Golgi and GER is managed by coatomers (COP). COP I facilitates retrograde transport (Golgi to GER), while COP II facilitates anterograd transport (GER to Golgi). Additionally, vesicles traveling from the Golgi to lysosomes are marked with AP-1 (assembly protein 1), and those going to endosomes are marked with AP-2.

Smooth Endoplasmic Reticulum, Golgi, and Lysosomes

The Smooth Endoplasmic Reticulum (DER) lacks ribosomes and its cytoplasm stains eosinophilic (acidophilic). It is highly developed in cells that secrete steroid hormones and in liver cells (hepatocytes), where its volume increases upon exposure to lipophilic drugs. In muscle cells, it is called the sarcoplasmic reticulum and acts as a calcium reservoir essential for contraction. The DER's primary functions include steroid synthesis, detoxification, glycogen metabolism, membrane phospholipid synthesis, and methylation.

The Golgi complex acts as a packaging station and does not stain with standard Hematoxylin-Eosin (H&E), appearing as a clear area (negative staining). Specialized silver staining is required for visualization. It is polarized with a "cis" face (entry from GER) and a "trans" face (exit to cytoplasm). The Golgi performs post-translational modifications including glycosylation, phosphorylation, and sulfation. It is also responsible for proteolysis (cleaving preprohormones), creating secretory vesicles, and synthesizing carbohydrates like hyaluronic acid and chondroitin sulfate.

Lysosomes are the cell's digestive centers, containing acid hydrolases such as proteases, nucleases, glycosidases, lipases, and phospholipases. These enzymes function optimally at an acidic pH. Lysosomes degrade damaged cellular components and external materials like bacteria.