The Nucleus

 The nucleus contains the cell’s genome. It is bounded by a membrane, which is composed of two lipid bilayer mem branes: the inner and the outer membrane. The inner membrane is usually a simple sac, but the outermost mem brane is, in many places, continuous with the endoplasmic reticulum (ER). The nuclear membrane exhibits selective permeability because of pores, which consist of a complex of several proteins whose function is to import substances into and export substances out of the nucleus. The chromosomes of eukaryotic cells contain linear DNA macromolecules arranged as a double helix. They are only visible with a light microscope when the cell is undergoing division and the DNA is in a highly condensed form; at other times, the chromosomes are not condensed and appear as in Figure 1. Eukaryotic DNA macromolecules are associated with basic proteins called histones that bind to the DNA by ionic interactions.

Fig1. Eukaryotic cells. A: Diagrammatic representation of an animal cell. B: Diagrammatic representation of a plant cell. C: Micrograph of an animal cell shows several membrane-bound structures, including mitochondria and a nucleus. (Fig. 2-3(A) and (B) Reproduced with permission from Nester EW, Anderson DG, Roberts CE, et al: Microbiology: A Human Perspective, 6th ed. McGraw-Hill, 2009. © McGraw-Hill Education. Fig. 2-3(C) Reproduced with permission from Thomas Fritsche, MD, PhD.)

A structure often visible within the nucleus is the nucleolus, an area rich in RNA that is the site of ribosomal RNA synthesis (see Figure 1). Ribosomal proteins synthesized in the cytoplasm are transported into the nucleolus and combine with ribosomal RNA to form the small and large subunits of the eukaryotic ribosome. These are then exported to the cytoplasm, where they associate to form an intact ribosome that can function in protein synthesis.

Cytoplasmic Structures

 The cytoplasm of eukaryotic cells is characterized by the presence of an ER, vacuoles, self-reproducing plastids, and an elaborate cytoskeleton composed of microtubules, microfilaments, and intermediate filaments.

The endoplasmic reticulum (ER) is a network of membrane-bound channels continuous with the nuclear mem brane. Two types of ER are recognized: rough, to which 80S ribosomes are attached; and smooth, which does not have attached ribosomes (see Figure 1). Rough ER is a major producer of glycoproteins as well as new membrane material that is transported throughout the cell; smooth ER participates in the synthesis of lipids and in some aspects of carbohydrate metabolism. The Golgi complex consists of a stack of membranes that function in concert with the ER to chemically modify and sort products of the ER into those destined to be secreted and those that function in other membranous structures of the cell.

The plastids include mitochondria and chloroplasts. Several lines of evidence suggest that mitochondria and chloroplasts arose from the engulfment of a prokaryotic cell by a larger cell (endosymbiosis). Current hypotheses, making use of mitochondrial genome and proteome data, suggest that the mitochondrial ancestor was most closely related to Alphaproteobacteria and that chloroplasts are related to nitrogen-fixing cyanobacteria. Mitochondria are of prokaryotic size (Figure 1), and its membrane, which lacks sterols, is much less rigid than the eukaryotic cell’s cytoplasmic mem brane, which does contain sterols. Mitochondria contain two sets of membranes. The outermost membrane is rather permeable, having numerous minute channels that allow passage of ions and small molecules (eg, adenosine triphosphate [ATP]). Invagination of the outer membrane forms a system of inner folded membranes called cristae. The cristae are the sites of enzymes involved in respiration and ATP production. Cristae also contain specific transport proteins that regulate passage of metabolites into and out of the mitochondrial matrix. The matrix contains a number of enzymes, particularly those of the citric acid cycle. Chloroplasts are the photosynthetic cell organelles that can convert the energy of sunlight into chemical energy through photosynthesis. Chlorophyll and all other components needed for photosynthesis are located in a series of flattened membrane discs called thylakoids. The size, shape, and number of chloroplasts per cell vary markedly; in contrast to mitochondria, chloroplasts are generally much larger than prokaryotes. Mitochondria and chloroplasts contain their own DNA, which exists in a covalently closed circular form and codes for some (not all) of their constituent proteins and transfer RNAs. Mitochondria and chloroplasts also contain 70S ribosomes, the same as those of prokaryotes.

Eukaryotic microorganisms that were previously thought to lack mitochondria (amitochondriate eukaryotes) have been recently shown to contain some mitochondrial remnants either through the maintenance of membrane-enclosed respiratory organelles called hydrogenosomes, mitosomes, or nuclear genes of mitochondrial origin. There are two types of amitochondriate eukaryotes: type II (eg, Trichomonas vaginalis) harbors a hydrogenosome, while type I (eg, Giardia lamblia) lacks organelles involved in core energy metabolism. Some amitochondrial parasites (eg, Entamoeba histolytica) are intermediate and appear to be evolving from a type II to type I. Some hydrogenosomes have been identified that contain DNA and ribosomes. The hydrogenosome, although similar in size to mitochondria, lacks cristae and the enzymes of the tricarboxylic acid cycle. Pyruvate is taken up by the hydrogenosome, and H₂ , CO₂ , acetate, and ATP are produced. The mitosome has only recently been discovered and named, and its function has not been well characterized.

Lysosomes are membrane-enclosed vesicles that contain various digestive enzymes that the cell uses to digest macromolecules such as proteins, fats, and polysaccharides. The lysosome allows these enzymes to be partitioned away from the cytoplasm proper, where they could destroy key cellular macromolecules if not contained. After the hydrolysis of macromolecules in the lysosome, the resulting monomers pass from the lysosome into the cytoplasm, where they serve as nutrients.

The peroxisome is a membrane-enclosed structure whose function is to produce H₂O₂ from the reduction of O₂ by various hydrogen donors. The H₂O₂ produced in the peroxisome is subsequently degraded to H₂O and O₂ by the enzyme catalase. Peroxisomes are believed to be of evolutionary origin unrelated to mitochondria.

The cytoskeleton is a three-dimensional structure that fills the cytoplasm. Eukaryotic cells contain three main kinds of cytoskeletal filaments: microfilaments, intermediate filaments, and microtubules. Each cytoskeletal filament type is formed by polymerization of a distinct type of protein subunit and has its own shape and intracellular distribution. Microfilaments are about 7 nm in diameter and are polymers composed of the protein actin. These fibers form scaffolds throughout the cell, defining and maintaining the shape of the cell. Microfilaments can also carry out intracellular transport/trafficking, and cellular movements, including gliding, contraction, and cytokinesis.

Microtubules are hollow cylinders about 23 nm in diameter (lumen is approximately 15 nm in diameter) most commonly comprising 13 protofilaments that, in turn, are polymers of alpha and beta tubulin. Microtubules assist microfilaments in maintaining cell structure, form the spindle fibers for separating chromosomes during mitosis, and play an important role in cell motility. Intermediate filaments are composed of various proteins (eg, keratin, lamin, and desmin) depending on the type of cell in which they are found. They are normally 8–12 nm in diameter and provide tensile strength for the cell. They are most commonly known as the support system or “scaffolding” for the cell and nucleus. All filaments react with accessory proteins (eg, Rho and dynein) that regulate and link the filaments to other cell components and each other.

Surface Layers

The cytoplasm is enclosed within a plasma membrane com posed of protein and phospholipid similar to the prokaryotic cell membrane illustrated later . Most animal cells have no other surface layers; however, plant cells have an outer cell wall composed of cellulose (Figure 1-B). Many eukaryotic microorganisms also have an outer cell wall, which may be composed of a polysaccharide such as cellulose or chitin or may be inorganic (eg, the silica wall of diatoms).

Motility Organelles

Many eukaryotic microorganisms have organelles called flagella (eg, T. vaginalis) or cilia (eg, Paramecium) that move with a wavelike motion to propel the cell through water. Eukaryotic flagella emanate from the polar region of the cell, and cilia, which are shorter than flagella, surround the cell (Figure 2).

Fig2. A paramecium moves with the aid of cilia on the cell surface. (© Manfred Kage.)

Both the flagella and the cilia of eukaryotic cells have the same basic structure and biochemical composition. Both consist of a series of microtubules, hollow protein cylinders composed of a protein called tubulin surrounded by a membrane. The arrangement of the microtubules is commonly referred to as the “9 + 2 arrangement” because it consists of nine doublets of microtubules surrounding two single central microtubules (Figure 3). Each doublet is connected to another by the protein dynein. The dynein arms attached to the microtubule function as the molecular motors.

Fig3. Cilia and flagella structure. A: An electron micrograph of a cilium cross section. Note the two central microtubles surrounded by nine microtubule doublets (160,000×). (Reproduced with permission. © Kallista Images/Visuals Unlimited, Inc.) B: A diagram of cilia and flagella structure. (Reproduced with permission from Willey JM, Sherwood LM, Woolverton CJ: Prescott, Harley, and Klein’s Microbiology, 7th ed. McGraw-Hill; 2008. © McGraw-Hill Education.)