Cell Organelles: Structure and Function of Ribosomes, ER, Golgi, Lysosomes, Mitochondria and Peroxisomes

Cytoplasmic Organelles

1. Ribosomes

Concept: Cytoplasmic organelles delimited by a membrane, which are particles composed of ribonucleoproteins and protein. Free ribosomes are found in the cytoplasm, or bound to the membrane of the endoplasmic reticulum. The association of ribosomes with the rough endoplasmic reticulum constitutes a group of ribosomes that are sometimes called clusters.

Structure: Ribosomes are made up of two subunits: a large subunit (containing 28S rRNA, 5.8S and 5S rRNA and about 49 proteins) and a small subunit (containing about 33 proteins and 18S rRNA).

Function: The ribosome is the organelle responsible for protein synthesis. It reads the sequences of nucleotides in the mRNA, a different codon in the DNA determines which amino acid each triplet codes for.

Three stages of protein synthesis:

• Initiation: The initiator tRNA binds to the small ribosomal subunit. Proteins called initiation factors help the small ribosomal subunit recognize the cap added to the mRNA transcript. The small subunit moves along the mRNA until it reaches the initiation codon, whose anticodon UAC complements it. The large ribosomal subunit then joins.
• Elongation: Another tRNA brings the next amino acid to the ribosome, which enters the site at the end. Its amino group links with the carboxyl group of methionine. After the first peptide bond is formed, the ribosome moves three nucleotides along the mRNA, so the methionine-bearing tRNA, now discharged, is displaced and the tRNA with the second amino acid moves into the vacant site. This allows the incorporation of a new tRNA with its amino acid. This process requires energy.
• Termination: A release factor enters the site when a stop codon is reached. The peptidyl transferase releases the peptidyl-tRNA, freeing the polypeptide chain. Release factors also determine the dissociation of the two ribosomal subunits.

Many mRNA molecules are translated simultaneously in the form of a polyribosome, which allows many protein molecules to be synthesized per unit of time. Proteins synthesized by free ribosomes have one or more amino acid sequences (signal peptides) that serve to classify them according to their final destination and determine where they are secreted. The absence of signal peptides means the protein remains in the cytoplasm.

Proteins are accompanied by machinery for repair and maintenance, such as chaperones, which correct their shape. Cells have specialized routes to degrade the amino acids that make up proteins, through the proteasome. Most cytosolic proteins are degraded by proteasomes. The proteasome contains a central cylinder formed by proteases and two complexes at its ends that feed the proteins into the cylinder. To recognize which proteins are targeted for degradation, they are marked by the addition of ubiquitin.

2. Endoplasmic Reticulum

Concept and types: The endoplasmic reticulum is a system of membranes organized into sacs, interconnected with tubules and vesicles, and has two types:

• Rough endoplasmic reticulum: Contains many ribosomes attached to it. Organized into piles of flattened sacs called cisternae. It synthesizes new membrane components and proteins destined for export.
• Smooth endoplasmic reticulum: Has no ribosomes attached. Organized as a network of tubules. It synthesizes new lipids.

Structure: Ribosomes are considered part of the different functional and morphological units of the ER. Its two structural components are the membranes: a central lipid bilayer with a limiting character, covered on each side by a protein layer, and the content: the space called the matrix, where synthesis, transport and storage of substances involved in its functions take place.

Function:

• Rough endoplasmic reticulum: Synthesizes proteins. The ribosome is guided to the membrane by a signal peptide recognized by the SRP receptor in the membrane of the ER. After the SRP is released, a channel in the membrane inserts the polypeptide chain into the matrix of the ER. To end synthesis, the signal peptide is cleaved by a signal peptidase located on the face of the ER membrane, and the protein is released into the cisterna. These proteins are stored in the ER and used for several purposes: training and secretion of cell membranes. Glycosylation: In the ER, proteins receive an oligosaccharide made of N-acetylglucosamine, mannose and glucose. At the entrance, the oligosaccharide is attached to a lipid in the ER, and then transferred to an asparagine amino acid of the protein. This process is catalyzed by a glycosyltransferase.
• Smooth endoplasmic reticulum:
  • Lipid synthesis: It synthesizes phospholipids and cholesterol for cell membranes, but does not synthesize fatty acids.
  • Lipid transport: Steroid hormones, chylomicrons from enterocytes, and lipoproteins and bile acids from hepatocytes.
  • Detoxification: Many toxic fat-soluble substances are degraded here, mainly in the liver. Toxic substances are made inactive through oxidation and conjugation reactions in the membrane. With drug administration, such as phenobarbital, the smooth ER increases in amount and returns to its normal level once the drug is eliminated, through lysosomal degradation.
  • Muscle contraction: The sarcoplasmic reticulum has a Ca²⁺ pump in its membrane, along with Ca²⁺ channels that allow the release of this ion involved in muscle contraction. Once the process ends, Ca²⁺ is stored in the sarcoplasmic reticulum, allowing the muscle to relax.

3. Golgi Complex

The Golgi complex is a membranous organelle made of flattened sacs and vesicles organized into two fundamental units: the dictyosomes.

• Function: Packing and transport of the products it manufactures.
• Structure: Flattened sacs bounded by a membrane, with smooth, disc-shaped surfaces, and vesicles of different sizes. Each set of flattened sacs and vesicles forms a dictyosome. The cis face is next to the nuclear envelope and has a convex form. The trans or maturing face is next to the plasma membrane, and has a concave form. Large vesicles called secretory granules migrate from this surface.

Main functions:

• Main circulation director: Directs the macromolecules within the cell.
• Concentration and packaging of proteins: The Golgi concentrates secretions and packages them into membrane-bound vesicles.
• Formation and sulfation of glycoproteins and sugars: Changes to protein macromolecules take place in the Golgi, forming glycoproteins. Some sugars are polymerized from various precursors.
• Lysosome formation: Participates in the formation of lysosomes, intervening in the aggregation, transport and packaging of enzymes.
• Formation of new membranes and the glycocalyx: Secretory products are transported in vesicles from the trans face of the Golgi complex to the plasma membrane, releasing their contents. This is an authentic membrane recycling process, dependent on exocytosis of secretory vesicles and endocytosis by clathrin-coated vesicles. Other partly indirect contributions to the glycocalyx also come from the Golgi complex.

4. Lysosomes

Concept: Cytoplasmic organelles that contain a mixture of hydrolytic enzymes.

Function: They break down complex structures and large molecules into simpler ones.

Structure: Always bounded by a typical membrane. They contain hydrolytic enzymes: acid hydrolases that degrade nucleic acids, proteins, carbohydrates, lipids and others. The acidic enzymes need a low pH, which protects the cytoplasm from their activity against damaged cell components, which could produce serious harm.

Types:

• Primary lysosomes: Their contents have a homogeneous appearance. They contain inactive hydrolytic enzymes.
• Secondary lysosomes: Not uniform in appearance. They result from the fusion of primary lysosomes with vacuoles of variable content and size, and contain the same macromolecular complexes. They contain hydrolytic formations and a substrate-susceptible enzyme that can be degraded. Several types of secondary lysosomes exist: multivesicular bodies, autolysosomes, phagolysosomes and residual bodies.

Functions: They break down macromolecular complexes into polymers or simple molecules that can enter metabolism, and rid the cell of old or worn-out organelles, and destroy or eliminate harmful materials of exogenous origin.

5. Mitochondria

Concept: Cytoplasmic organelles with a double membrane shell, present in aerobic eukaryotic cells.

Structure: Shaped like a peanut, with a diameter of about 0.5 microns and a length of 1-7 µm. Each mitochondrion is surrounded by cytoplasm and bounded by an outer membrane. Inside, it is bounded by an inner membrane. The inner membrane forms folds called cristae. The inner membrane, on its inner face, has projecting structures called elementary particles. The two membranes delimit two compartments: the first is the intermembrane space, located between the outer and inner membranes, which contains ADP and AMP molecules. The second is the mitochondrial matrix, bounded by the inner membrane, formed by a finely granular substance.

Functions:

• Respiratory oxidations: Occur in successive stages: formation of acetyl-CoA in the matrix through oxidation of pyruvic acid, which comes from glycolysis, and of fatty acids, from the hydrolysis of triglycerides.
• Oxidation of acetyl-CoA in the matrix: The Krebs cycle: degradation consists of the complete breakdown of acetyl radicals into CO₂ and hydrogen through decarboxylations and dehydrogenations.
• Electron transport: Electrons are transported by carriers to the inner membrane, with energy lost by the electrons.
• Oxidative phosphorylation in the inner membrane: The energy lost by electrons is partly recovered for the phosphorylation of ADP and ATP molecules, catalyzed by ATP synthase in the inner membrane (oxidative phosphorylation). The complete oxidation of one acetyl-CoA produces 12 ATP.
• Protein synthesis: Carried out by mitoribosomes in the matrix.

6. Peroxisomes

Concept: Dense cytoplasmic organelles, oval in shape, surrounded by a membrane and characterized by containing oxidase and catalase. They can be identified by specific cytochemical techniques, such as diaminobenzidine. They consist of a membrane and a nuclear matrix.

Function:

• Enzyme activity: Peroxisomes contain enzymes that use molecular oxygen to remove hydrogen atoms from specific substrates, through the reaction: R-H₂ + O₂ → R + H₂O₂. These enzymes catalyze oxidase reactions. The highly toxic product H₂O₂ is removed from the peroxisome by another enzyme, catalase, which decomposes it into H₂O and O₂, or it reacts directly with other substances it preferentially oxidizes.
• Purine catabolism: Old nucleic acids and nucleotides are degraded into purine and pyrimidine bases. In purine base degradation, peroxisomal enzymes take part.
• Lipid metabolism: Peroxisomes participate in the degradation process called β-oxidation of fatty acids, which leads to the formation of acetyl-CoA. The oxidation of acetyl-CoA produces molecular oxygen in the form of H₂O₂, which is decomposed by catalase.
• Other functions: The oxidative reactions carried out by peroxisomes are very important, especially in the liver and kidney, where peroxisomes detoxify many toxic molecules that enter the circulation.