11.3Eukaryotic Structures

  • 11.3.2

Unlike prokaryotes, eukaryotes develop membrane compartments such as the nuclear membrane and endoplasmic reticulum (ER). These structures are not static; rather, their shape and distribution is in a constant flux during which they perform different functions. The cytoplasm also contains structures such as mitochondria and plastids, which have their own DNA and protein synthetic pathway. These structures are called organelles, and each organelle has a specialized function. A fibrous structure called the cytoskeleton is also laid out through the cell like a mesh.
Eukaryotes can be found as unicellular or multicellular organisms. Multicellular organisms are produced when the cells form a group. In such multicellular organisms, intercellular adhesion and joining of cells through cellular secretions called ECM lead to the formation of functional units called tissues or organs.

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In eukaryotes, the nuclear membrane encloses chromatin (Fig. 11-8A). It is composed of two separate lipid bilayers. Many different pathways are formed in the nuclear membrane for the exchange of materials between the nucleus and cytoplasm. These pathways are called nuclear pores and are composed of a complicated structure called the nuclear pore complex (see Selection 3 of Chapter 12, Fig. 12-11). This complex forms a very complicated structure because it is completely involved in the selective transport of substances between the nucleus and cytoplasm.
Electron microscope photographs of cross-sections of the nucleus generally show blackened areas with condensed chromatin (heterochromatin) and transparent areas with dispersed chromatin (euchromatin). The former is the region observed around the nuclear membrane, where transcription is inactive. On the other hand, the latter is the region where transcription is active (see Selection 4 of Chapter 10). Chromatin is found in a folded state of approximately 11 or 30 nm (see Selection 3 of Chapter 10, Fig. 10-6) when the nucleus is in interphase and not M phase of the cell cycle (see Selection 0f Chapter 13,Fig 13-2). The chromatin binds to fibrous structures called nuclear lamina, which line the interior of the nuclear membrane. Chromosomes are believed to be divided into regions in which they are housed within the nucleus. How the chromatin is organized and housed in the interior of the narrow nucleus remains unclear.
The nucleus also contains a noticeable structure called the nucleolus. The nucleolus is the site where large quantities of transcribed rRNA and ribosome precursors are stored. Therefore, a large nucleolus is generally observed in cells that are actively metabolizing or proliferating and are synthesizing large amounts of proteins.

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ER is classified into rough ER (Fig. 11-8B) and smooth ER depending on its structure. The rough ER synthesizes proteins when multiple ribosomes bind to its membrane surface, and the synthesized proteins are packed inside this part of the reticulum. Ribosomes do not bind to the smooth ER. The smooth ER is involved in various functions such as phospholipid synthesis, glycogen metabolism, calcium ion regulation, and intracellular digestion.

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Golgi Body

The Golgi body*3 is an organelle shaped like stacks of several layers of flat smooth ER (Fig. 11-8C). It modifies the saccharide chains of proteins exported from the rough ER. This structure has two sides: the cis side that takes in the proteins synthesized by the rough ER and the trans side that processes the proteins received and that then sends them out for later processing. Moreover, the middle part of the Golgi body is called medial.

*3 Also known as the Golgi apparatus or Golgi complex.

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Vesicles called lysosomes contain many different acidic hydrolases. These enzymes can degrade every type of biomolecule, including proteins, lipids, carbohydrates, and nucleic acid (Fig. 11-8D), and are transported from the Golgi body (see Column Selection 2 of Chapter 12). Lysosomes degrade foreign bodies and nutrients that enter the cell and anything within the cell itself that is no longer needed (see Selection 6 of Chapter 12 Fig. 12-14,see Selection 8 of Chapter Fig. 12-16). They are also responsible for autodigestion of cells during apoptosis (see Column Selection 3 of Chapter14). To increase the activity of catabolic enzymes, the internal of lysosomes is maintained in an acidic state that is suitable for enzymatic reactions.

*3 Also known as the Golgi apparatus or Golgi complex.

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Peroxisomes are small-sized (0.1–2 μm) vesicles (Fig. 11-8E) containing oxidases such as catalase, D-amino acid oxidase, and urate oxidase. These oxidases are involved in activities such as β-oxidation of long-chain fatty acids, synthesis of cholesterol and bile acid, and amino acid metabolism. These metabolic processes undergo oxidation reactions using O2 and produce hydrogen peroxide (H2O2), which is toxic.
In hepatic and renal cells of animals, H2O2 produced by oxidation reactions is used to oxidize and detoxify poisonous substances such as phenol, formic acid, formaldehyde, and alcohol. Peroxisomes in plants also play a role in β-oxidation and help chloroplasts and mitochondria in the photorespiration pathway (see Selection 4 of Chapter 16). Glyoxysomes, in which the glyoxylate cycle occurs, are a type of organelle similar to peroxisomes*4, and both of these organelles can be classified as microbodies.

*4 Some plants and bacteria possess a metabolic pathway called the glyoxylate cycle that produces carbohydrates by breaking down fatty acids. For example, this pathway functions in the seeds of germinating plants.

Fig. 11-8 Electron microscope photographs showing organelles

(A) Nucleus. Condensed heterochromatin is observed around the nuclear membrane, and diffused euchromatin is observed within the nucleus. Nucleoli are observed inside the nucleus. (B) Rough endoplasmic reticulum. Numerous ribosomes (dark spots) bind to the surface. The inner cavity of ribosomes is darkly colored as a result of synthesized proteins. (C) Golgi body. The top is the cis side and the bottom is the trans side. (D) Lysosome. Material being degraded is observed on the inside of this organelle. (E) Peroxisome. A crystalline, dark region is observed at the center. (F) Mitochondria. The dark granules contain calcium. (G) Chloroplast. Grana are the membrane structures observed in the dark.

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Mitochondria and Plastids—Organelles with Their Own DNA

Eukaryotes possess mitochondria and plastids, which contain systems to synthesize their own DNA and proteins. Mitochondria are found in almost all eukaryotic cells, while plastids are found only in plants, algae, secondary symbiotic algae such as Euglena, and malarial parasites. Both these structures have a bilayer membrane and synthesis systems for DNA and proteins that are similar to those of prokaryotes, leading to the belief that these features were originated in ancient prokaryotes and later incorporated into primordial eukaryotic cells (Refer to Chapter 24-1 for archaic proteobacteria and archaic cyanobacteria).


Mitochondria (Fig. 11-8F) are organelles that produce energy. They house both the citric acid cycle and electron transport system and are involved in ATP production via enzymatic respiration (see Chapter 16). Mitochondria are composed of a two-layer membrane comprising inner and outer layers. These vary in both size and shape depending on the cell type, but lengthwise, they are in the order of half a micrometer to several micrometers. The outer membrane has a comparatively higher permeability to substances than the inner membrane. When the inner membrane collapses inward, it forms structures called cristae and the membrane has an increased surface area. The membrane of the cristae has an electron transport system through which redox reactions form an H+ concentration gradient across the membrane and synthesize ATP. The interior enclosed by the inner membrane of the mitochondria is called the matrix. The citric acid cycle occurs in the matrix.
The matrix contains mitochondrial DNA, RNA polymerase, and ribosomes, and it is the place where mitochondrial proteins are synthesized. These proteins are only a part of what the mitochondria requires for itself, and much of the remaining proteins is utilized by taking into account the proteins encoded by the genes on the nuclear genome (see Selection 3 of Chapter 12, Fig. 12-12). Mitochondria also autoproliferate by binary fission, similar to prokaryotic cells.


Plastids (including chloroplasts (Fig. 11-8G), amyloplasts, and leucoplasts) are organelles required by plants, algae, and also other prokaryotes. They perform a broad range of functions including photosynthesis, fatty acid biosynthesis, amino acid synthesis, nitrogen and sulfur assimilation, and pigment synthesis. Plastids are surrounded by the biological membrane with two layers (outer and inner membranes), each of which has different characteristics. Of these, chloroplasts are plastids that are the center of photosynthesis, and their lengthwise diameter is in the order of 5 μm. Their inner membrane encloses a structure known as the stroma, which contains vesicles called thylakoids. Stacks of thylakoids are known as grana. These thylakoid membranes contain a series of enzymes that catalyze photosynthesis, beginning with the enzyme related to the pigment chlorophyll, which receives light (Chapter 16, Chapter 16, Fig. 16-8, Column Fig. 16-5). The stroma also contains the chloroplast DNA, RNA polymerase, and ribosomes and synthesizes approximately 100 different types of chloroplast proteins. However, for the many other types of proteins required by the chloroplast, it must rely on those that are encoded by the genes on the nuclear genome.

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Plant cells contain large membranous structures called vacuoles that account for most of the volume of the cytoplasm. Vacuoles are responsible for various functions that include storing nutrients, secondary metabolites, and phytotoxins; catabolism by hydrolases (the same function as lysosomes); isolation and detoxification of toxic substances; and filling the intercellular space (participating in growth and increased volume).

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