Organelles (Figure 3.1) are most commonly defined as specialised structures within a cell that are enclosed by a membrane. The most prominent organelle of eukaryotic cells is the nucleus, which stores the maternally and paternally inherited DNA. The DNA in the nucleus is bound to proteins (histones) to form chromatin fibres, which help package the DNA into the nucleus. The DNA is used as a template for messenger RNA in a process called transcription (Chapter 16). The nucleus is separated from the cytoplasm by the nuclear envelope, a double membrane structure. Transport of proteins and nucleic acids (ribonucleic acid, RNA) between the nucleus and the cytoplasm is facilitated by the nuclear pore complex. The nucleoskeleton provides structure and rigidity to the nuclear compartment. One or several clearly distinct regions (nucleoli) are visible within the nucleus using light microscopy. The nucleoli are sites of ribosomal RNA production.

Mitochondria are the major sites of O₂ consumption. The majority of ATP (adenosine triphosphate), a central source of energy in cells, is produced by mitochondria. The outer membrane is smooth, while the inner membrane forms characteristic folds (cristae). While the initial stage of glycolysis, in which glucose is converted into pyruvate, takes place in the cytosol, mitochondrial enzymes associated with the cristae and present in the mitochondrial matrix transfer energy present in pyruvate and fats to ATP via the tricarboxylic acid (TCA) cycle and the electron transport chain (Chapter 10). Mitochondria contain specialised enzymes encoded by mitochondrial DNA, which resides in the mitochondrial matrix. Because mitochondria in the embryo are derived from the egg cell, mitochondrial DNA is maternally inherited.

The endoplasmic reticulum (ER) is membrane-containing structure surrounding the nucleus and attached to the nuclear envelope. Based on its appearance on electron micrographs, the endoplasmic reticulum is divided into the smooth endoplasmic reticulum and rough endoplasmic reticulum. The smooth endoplasmic reticulum is associated with phospholipid biosynthesis, storage of Ca²⁺ ions and other processes. The rough endoplasmic reticulum is associated with many ribosomes. Whereas ribosomes present in the cytosol produce soluble proteins that will function in the cytosol, ribosomes associated with the RER are involved in the synthesis of three classes of proteins.

• Membrane proteins, which contain hydrophobic regions and are inserted into the ER membrane during translation.
  
• Soluble proteins that contain a sorting signal resulting in the release of the protein into the lumen of the ER. These proteins will eventually be secreted into the extracellular space (secretory proteins).
  
• Proteins of other organelles.

Many proteins undergo post-translational modifications in the lumen of the ER. Branched sugar chains are attached to serine and asparagine residues (glycosylation). The formation of the covalent bond between two cysteine residues (disulfide bond) also occurs in the lumen of the ER.

Proteins synthesised by the RER are transported in transport vesicles to the Golgi complex, a network of membrane-enclosed compartments. Both proteins inserted in the ER membrane as well as proteins present in the lumen of the ER are transported in this manner to the cis-Golgi network. The proteins in the Golgi continue to be transported in membrane-enclosed vesicles to the trans-Golgi network. At least two processes are carried out in the Golgi network.

• Glycosylation initiated in the ER is modified and completed in the Golgi complex, where both addition and removal of sugar moieties take place.
  
• Protein sorting: membrane and soluble proteins are sorted into membrane-enclosed vesicles. During exocytosis, these vesicles will travel from the trans-Golgi network and fuse with the plasma membrane, resulting in the release of secretory proteins and the delivery of trans-membrane proteins to the plasma membrane. Vesicles with specific signals will not travel to the plasma membrane, but target specific organelles. The signals required for sorting to specific organelles may be sugar moieties (lysosome) or short amino acid sequences (peroxisome).

Endosomes are formed from endocytic vesicles, which are pinched off from the plasma membrane facilitating transport from the plasma membrane into the cell (endocytosis). Often, membrane receptors bound to their ligands are involved. The lumen of endosomes gradually becomes more acidic and the contents of endosomes are finally delivered to lysosomes.

The lysosome is a membrane-enclosed organelle specialised in the degradation and recycling of proteins, lipids, polysaccharides and nucleic acids. Many lysosomal enzymes catalyse hydrolysis reactions. The products of these reactions, such as simple sugars and amino acids, are re-used in the cytosol.

Peroxisomes are enclosed by membranes and consume significant amounts of O₂, which is used to form hydrogen peroxide (H₂O₂). The enzyme catalase uses H₂O₂ for oxidative degradation of diverse substrates, including large fatty acids and ethanol. Peroxisomes are also important for the synthesis of the main phospholipid components of myelin. This role of peroxisomes is especially relevant for the function of nerve cells.

The system containing the numerous vesicles involved in transport between the ER, Golgi, endosomes, lysosomes and peroxisomes is collectively referred to as the membrane trafficking network.

In addition, there are a number of structures that are not enclosed by membranes, but which have clearly identified roles. These structures are sometimes classified as non-membrane organelles.

• The cytoskeleton: structural support is provided by a network of filaments. This results in a shape characteristic for a specific cell type. The main kinds of filaments are:
  
  
  
  • actin filaments play a particularly important role in cellular movement (motility);
    
  • microtubules are formed by tubulin and are important for cell movement as well as the movement of vesicles inside the cell;
    
  • intermediate filaments are made from a collection of different proteins. These filaments are important for the basic shape of cells and provide mechanical strength.
  
  
• Cell junctions are involved in the organisation of cells in tissues. The main types are:
  
  
  
  • desmosomes, which are multi-protein complexes that join cells (e.g. connect epithelial cells) and lead to integrity. Hemidesmosomes adhere the basal membranes of epithelial cells to the basement membrane;
    
  • tight junctions, which prevent passage of small molecules and fluid between cells;
    
  • anchoring junctions, which are linked to cytoskeletal structures (mostly intermediate filaments) and provide rigidity in a group of cells;
    
  • gap junctions, which provide channels between cells thereby facilitating movement of small molecules between neighbouring cells.

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