BIOCHEMISTRY - Textbook - Ostapchenko L. I. - 2012

Chapter 3. THE CELL AND THE EXTRACELLULAR MATRIX

3.1. Molecular and Supramolecular Organization of the Cell

3.1.2. Eukaryotic Cells

Organisms of the superkingdom Eukaryota consist of Eukaryotic Cells. Their principal distinction from Prokaryotic Cells is the presence of a nucleus—a membrane-bound compartment that contains the majority of the cellular DNA and is separated from the Cytoplasm by a double membrane (Fig. 3.2). The Nucleus is typically spherical, oval, or varied in shape, with diameters ranging from 0.5 µm (in Fungi) to 50 µm (in certain egg cells). The primary Functions of the Cell Nucleus are: 1) storing Genetic information in the form of DNA; 2) transferring information to the cytoplasm via METABOLISM/31.html">Transcription—the synthesis of RNA molecules that facilitate information transfer; 3) transmitting information to daughter cells during Replication—cell and nuclear division. The nucleus consists of: 1) nucleoplasm—the fluid ground substance, the nuclear matrix (a three-dimensional protein scaffold), and various inclusions; 2) Chromosomes, each containing two chromatids, which are nucleoprotein structures composed of a single DNA molecule and associated Proteins; 3) the nuclear envelope, comprising two membranes perforated by pores up to 100 nm in diameter, enclosing a perinuclear space (10–40 nm wide). The nucleolus is a dense subnuclear Structure where rRNA (ribosomal RNA) is synthesized on nucleolar DNA templates.

The cytoplasm houses numerous Organelles that perform specific, vital functions. One such structure is the mitochondrion, which is particularly fascinating because it closely resembles prokaryotic cells in shape and size, contains its own DNA and Ribosomes, synthesizes ATP (adenosine triphosphate)—the universal cellular energy currency—and reproduces by binary fission. Other mitochondrial functions include biosynthetic processes (such as protein and steroid hormone synthesis) and ion transport. Like the nucleus, Mitochondria are bounded by two membranes separated by an intermembrane (perimitochondrial) space, and enclose a matrix containing metabolic intermediates, Citric Acid Cycle Enzymes, and Fatty acid oxidation enzymes, among others.

Chloroplasts can similarly be viewed as "descendants" of prokaryotic cells; they carry out the Photosynthesis of Organic compounds utilizing solar energy absorbed by chlorophyll. In their dimensions, the Organization of their chlorophyll-bearing membranes, their mode of division, and their DNA nucleotide sequences, chloroplasts bear a striking resemblance to cyanobacteria (blue-green Algae). This strongly suggests that chloroplasts, much like mitochondria, share a prokaryotic ancestry.

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Fig. 3.2 Schematic representation of a Introduction/5.html">Eukaryotic Cell with its main organelles:

A - animal cell: 1 - Endoplasmic reticulum (rough/granular);

2 - nucleus; 3 - nucleolus; 4 - nuclear envelope; 5 - endoplasmic reticulum (smooth/agranular); 6 - Cytoskeleton; 7 - Golgi apparatus; 8 - microvilli; 9 - Plasma Membrane; 10 - centrioles; 11 - Lysosomes; 12 - ribosomes; 13 - mitochondria; 14 - cytoplasm.

B - plant cell: 1 - cytoplasm; 2 - endoplasmic reticulum (smooth); 3 - nucleolus; 4 - nucleus; 5 - free ribosomes; 6 - Golgi apparatus; 7 - mitochondria; 8 - central vacuole; 9 - Cell wall; 10 - chloroplasts; 11 - plasma membrane; 12 - plasmodesma; 13 - lysosomes; 14 - nuclear envelope; 15 - endoplasmic reticulum (rough)

Eukaryotic cells differ from prokaryotic cells (Table 3.1) in yet another key aspect: they contain an extensive network of intracellular membranes that partition The Cell into distinct compartments. As will be demonstrated subsequently, most—if not all—processes in a eukaryotic cell directly or indirectly involve membranes. This necessitates a substantial increase in the surface area of intracellular membranes through folds, invaginations, vesicles, and other morphological variations. The most abundant intracellular membranes belong to The endoplasmic reticulum (ER), where Lipids and Membrane Proteins are synthesized, providing material destined for "export" from the cell. Such export—the Transport of substances out of the cell—occurs via exocytosis, a process in which intracellular membrane-bound vesicles fuse with The Plasma Membrane to release their contents into the extracellular milieu. The reverse process, endocytosis, allows the cell to internalize substances from the Extracellular matrix. Some literature References microsomes; however, It is important to note that microsomes do not exist in intact cells. These vesicles form spontaneously, primarily from the endoplasmic reticulum, during the homogenization of Cells and Tissues. The ER consists of flattened cisternae that may be studded with ribosomes (rough or granular ER) or devoid of them (smooth or agranular ER).

A ribosome is composed of two ribonucleoprotein subunits, which may either drift freely in the Cytosol or attach to the ER via the proteins they are actively synthesizing. During Protein Synthesis, multiple ribosomes can simultaneously translate a single mRNA molecule; such chains of ribosomes are termed polyribosomes (or Polysomes). Intracellular membranes also give rise to the Golgi apparatus (discovered in 1898), which consists of stacks of flattened membrane-bound vesicles (dictyosomes) that likewise facilitate the synthesis and transport of organic molecules, including proteins, CARBOHYDRATES, and lipids. This function is particularly prominent in secretory cells. Another major function of the Golgi apparatus is The formation of lysosomes.

Lysosomes are membrane-enclosed vesicles (0.2–0.5 µm in diameter) containing enzymes necessary for intracellular Digestion. Lysosomal enzymes are synthesized by ribosomes on the rough ER, transported to the Golgi apparatus, and subsequently bud off as membrane vesicles containing "mature" enzymes, thereby forming endolysosomes (Fig. 3.3).

Fig. 3.3. Three pathways of lysosome formation (schematic):

1 - bacterium; 2 - phagosome; 3 - phagolysosome; 4 - endolysosome; 5 - lysosome; 6 - autophagolysosome; 7 - autophagosome; 8 - mitochondrion; 9 - endoplasmic reticulum; 10 - endosome; 11 - Golgi apparatus; 12 - plasma membrane

Lysosomes are formed by the fusion of endolysosomes with endocytic vesicles (endosomes). Another class of lysosomes is autophagolysosomes, which result from the fusion of an autophagosome with an endolysosome. The fusion of a phagosome with an endolysosome produces a phagolysosome. The digestion products from all Three types of lysosomes are assimilated into the Cell Cytoplasm, whereas lysosomes containing indigestible material are referred to as residual bodies. These structures may persist within certain cells (such as hepatocytes) or have their contents expelled via exocytosis. Until relatively recently, it was traditional to distinguish between Primary and secondary lysosomes (a Classification unfortunately still found in some modern textbooks). Experimental studies from recent decades indicate that lysosomal Hydrolases and membrane proteins are sorted via distinct receptors. They leave the Golgi apparatus in separate transport vesicles and first converge in the endolysosome, which already contains the substrate targeted for degradation.

Peroxisomes (Microbodies) are formed in an analogous manner; they serve to break down toxic peroxides generated during cellular Respiration:

These microbodies are spherical, with diameters ranging from 0.3 to 1.5 µm, and originate from the ER, with which they sometimes maintain a continuous connection. Plant peroxisomes are subdivided into glyoxysomes (which participate in Lipid Metabolism), leaf peroxisomes (which neutralize hydrogen peroxide—a byproduct of Photorespiration), and unspecialized peroxisomes found in other tissues. In plant cells, membranes also give rise to large, fluid-filled vacuoles, as well as other permanent and temporary membranous structures.

Collectively, these membrane-bound structures occupy nearly half of the cell's volume and constitute its distinct compartments. The region of the cytoplasm devoid of all organelles is known as the cytosol.

A particularly vital role among cellular membranes is played by the plasma membrane (PM). While generally resembling the plasma membrane of prokaryotic cells, it differs significantly in both MOLECULAR ORGANIZATION AND function. It is highly plausible that the advanced specialization of the eukaryotic plasma membrane began when the function of ATP generation shifted from the PM in prokaryotes to mitochondria in eukaryotes. The plasma membrane harbors ion pumps that enable the cell to alter the intracellular concentrations of key inorganic ions (K⁺, Na⁺, Ca²⁺) and its permeability within milliseconds, thereby shifting the Membrane Potential. This mechanism is critical for the propagation of electrical signals (such as along The Nervous system). Thanks to its unique molecular organization, the eukaryotic plasma membrane is the primary site for receiving, decoding, and transducing the energy of external stimuli (light, Temperature, Hormones, toxins, drugs) into the energy of biological excitation.

The positioning and movement of the aforementioned organelles are regulated by the cytoskeleton, which is composed of microtubules, microfilaments, and Intermediate filaments. Microtubules are fine tubes with an outer diameter of 24 nm, a wall thickness of 5 nm, and a length spanning several micrometres, built from the globular protein tubulin. Microtubules serve a structural role by forming the cell's internal scaffolding (hence the term cytoskeleton), maintaining cell shape (for instance, Treatment with colchicine, which disrupts microtubules, causes animal cells to round up into a spherical shape), and facilitating the Intracellular Transport of Golgi vesicles, lysosomes, and mitochondria. Centrioles are constructed from microtubules (consisting of small hollow cylinders 0.3–0.5 µm long and 0.2 µm in diameter). During Cell Division, centrioles replicate, and the resulting two pairs migrate to opposite poles of the mitotic spindle—a structure along whose equator the chromosomes align prior to segregation, which is also composed of microtubules. Basal bodies share a similar microtubular architecture and are located at the base of flagella and cilia. The movement of the mitotic spindle, cilia, and flagella is driven by the sliding of microtubules, which ensures proper chromosome segregation as well as the beating motion of Cilia and flagella.

Microfilaments are thin filaments with a diameter of 5-7 nm, formed from the protein Actin. Like microtubules, microfilaments form networks that frequently lie adjacent to the plasma membrane, participating in Endocytosis and Exocytosis as well as in the movement of other organelles. Microfilaments consist of Actin and Myosin. A clear example of this is the functioning of microvilli—finger-like projections of the plasma membrane in absorptive cells (such as the epithelium of the Small Intestine and the convoluted tubules of nephrons). At the base of each microvillus, bundles of actin filaments are linked to myosin filaments. As a result of sliding movements of actin filaments along myosin ones, the microvillus can alternately shorten and lengthen, which presumably facilitates the absorption of substances into the cell. Microfilaments and their associated proteins beneath the PM form the cell cortex, which provides structural strength to the cell surface and enables changes in cell shape and motility. The properties of the cell cortex are determined by the balance of cooperative and competitive interactions among actin-binding proteins (myosin, Tropomyosin, spectrin, etc.). The PM is so tightly bound to the actin cell cortex that they are considered a single functional (rather than structural) entity. Filaments also participate in Cell-to-Cell adhesion via adhesive junctions.

Intermediate filaments, with a diameter of 8-10 nm (occupying an intermediate position in thickness between actin microfilaments and microtubules), also contribute to the Formation of the cytoskeleton. These structures typically form a "basket" around the nucleus, from which they extend not only to the cell periphery but may also participate in connecting cells to one another via desmosomes (intercellular contact structures). Intermediate filaments are formed from Fibrillar Proteins, among which Keratins, desmins, and vimentin predominate.

In addition to organelles, cells contain inclusions. These include lipid granules or droplets containing various lipids. Ultimately, these granules are surrounded by a single layer of lipids. Upon excessive accumulation of neutral fats, the lipid granules enlarge and are then referred to as fat granules. In animal fat cells, the latter merge into a single large central droplet. The primary site of carbohydrate storage in animal cells is Glycogen granules. Membrane-enclosed starch grains perform analogous functions in plant cells. Secretory products ready for release are contained within secretory granules inside cells.

Secretory inclusions (secretion) are the product of the synthetic activity of specialized secretory cells and are usually released continuously or in response to an external stimulus acting on the cell. Excretory inclusions do not contain enzymes or other active substances; rather, they are Metabolic waste products destined for removal (excretion) from the cells. Pigment inclusions can be exogenous (carotene, colorants, etc.) and endogenous (Hemoglobin, hemosiderin, melanin, lipofuscin). Their presence in the cytoplasm can alter the color of a tissue or organ (temporarily or permanently). Often, tissue pigmentation serves as a diagnostic sign of certain pathologies.

Thus, the fundamental Structural and functional unit of living organisms is the cell (Fig. 3.2). It is an elementary living system capable of existing either as a distinct Organism or as part of a multicellular organism. The content of the cell is protoplasma (cytoplasm + nucleus). The genetic apparatus in eukaryotic cells is localized within the nucleus, whereas in prokaryotic cells it resides in the nucleoid (corresponding to a single DNA molecule anchored at a single point on the inner side of the plasma membrane). Cells are capable of self-reproduction through various mechanisms.

Cells vary significantly in size: ranging from 0.1–0.25 µm (in certain Bacteria) to 155 mm (an ostrich egg in its shell). However, the diameter of most cells ranges from 10 to 100 µm. The performance of numerous cellular functions is ensured by organelles, which include the nucleus, chromosomes, ribosomes, mitochondria, ER, Golgi apparatus, lysosomes, and the plasma membrane, among others. The shape of a living cell is maintained by the cytoskeleton, composed of microtubules, intermediate filaments, and microfilaments. A characteristic feature of cells is their spatiotemporal organization (compartmentalization) and THE PRINCIPLE OF compactness (for instance, the 10^-12 g of DNA in a human egg cell contains information encoding all of its proteins). Thanks to the plasma membrane, the cell maintains the constancy of its intracellular environment and possesses the capacity for exocytosis and endocytosis: it can engulf not only droplets containing large molecules (including proteins) but also Viruses. Certain cells (macrophages, neutrophils) even phagocytose bacteria.

Eukaryotic cells share a similar set of organelles, analogous mechanisms of Metabolic Regulation, synthesis and Hydrolysis of vital macromolecules, as well as energy storage and utilization. Prokaryotic and eukaryotic cells utilize genetic material for Protein synthesis in a similar manner, possess a functioning plasma membrane, and share many common features pointing to a unified origin. At the same time, different cells within the same organism vary in shape, size, organelle count, and enzyme profile, which is dictated by their specific functions. Differences among cells in a multicellular organism arise from differential Gene activity that dictates distinct Cell Differentiation. Consequently, some cells conduct electrical impulses (Nerve Cells), others acquire contractile properties (Muscle cells), others synthesize hormones and digestive enzymes (glandular cells), and yet others cover the body surface and line internal cavities (epithelial cells). Furthermore, many cells perform multiple functions and are classified as polyfunctional; hepatocytes serve as a prime example. They synthesize proteins and Bile acids, store glycogen, convert glycogen into glucose, neutralize toxins, and perform other tasks. Nevertheless, cells share more common features than specialized ones. Cells also exhibit varying lifespans. For instance, The Human Body consists of 10¹⁴ cells. Every day, out of this total, 7 · 10¹⁰ intestinal epithelial cells and 2 · 10⁹ erythrocytes perish and are newly formed. Thus, the lifespan of cells in a multicellular organism ranges from 1–2 days (intestinal epithelium) up to the entire lifetime of the organism (Neurons, Skeletal Muscle fibers).

As for unicellular organisms, structural differences are explained by their adaptations to their habitats. Moreover, different unicellular organisms may have evolved from distinct prokaryotic precursors. Numerous hypotheses exist regarding Cell Evolution, of which two are the most plausible. The symbiogenetic hypothesis posits that certain prokaryotes inside a host cell transformed into mitochondria, while others became chloroplasts, retaining The ability to self-reproduce not as independent cells, but as organelles. Another hypothesis Supports the gradual Development of the Prokaryotic Cell's own structures during its transformation into a eukaryotic cell. All cells possess a universal system of regulation and autoregulation: intracellular metabolites and inorganic ions act either upon genes or directly upon enzymes. Through this type of regulation, an optimal dynamic level of intracellular processes is maintained. A vast number of cells integrated by metabolic regulatory processes and intercellular contacts ensure the reliable functioning of tissues and Organs in a multicellular organism.

Regarding the organization of cells into tissues, it is important to highlight the crucial role of the extracellular matrix, which comprises diverse Polysaccharides and proteins organized into mesh-like structures. Such a matrix can form bone or tooth structures, shape the transparent substance of the cornea, form the basal lamina, and more. It influences cell development, migration, proliferation, shape, and metabolism. The latter is facilitated by the aqueous phase of the polysaccharide gel, which allows the diffusion of nutrients, metabolites, and hormones between Blood and tissue cells.

Thus, cells were first discovered by R. Hooke in 1665, and only a century and a half later did M. Schleiden and T. Schwann formulate the Cell Theory, stating that all organisms possess a cellular structure (1838–1839). Twenty years later (1858), R. Virchow established the principle of cellular continuity through division: "omnis cellula e cellula". Subsequent discoveries of major organelles, mitotic division, and milestones in molecular cell biology shaped the modern understanding of THE CELLULAR LEVEL of biological organization. Modern cell theory views the organism as a complexly organized integrated system composed of interacting cells. The organism exhibits specific properties that do not

merely equal the sum of the properties of its constituent cells. However, cell theory is supported not only by the structural similarities between prokaryotic and eukaryotic cells, but also by their Chemical Composition and analogous metabolic processes. The cells of all living systems are composed of structurally and functionally similar proteins, carbohydrates, Nucleic Acids, inorganic ions, and Water. The existence of viruses—unique cellular parasites—further demonstrates the universality of the Cellular Organization of life.

In summary, the cell is the structural and functional elementary unit of living organisms. All cells are bounded by a plasma membrane and contain cytoplasm and a nucleus (or a nuclear region in prokaryotes). Cell dimensions (Table 3.1) are ultimately determined by the sizes of the molecules from which they are built, The rate of Transmembrane Transport of nutrients and oxygen, and The ratio of surface area to volume.

To sustain life processes, a cell requires a minimum Complement of Biomolecules, which sets a lower limit on its size. Nor can cells be indefinitely large, because the rate of metabolic processes depends on the diffusion of substances within the cytosol. In large cells, this would severely constrain the REGULATION OF METABOLISM. On the other hand, because the surface area of the plasma membrane is relatively large compared to its volume, an adequate number of nutrient molecules can penetrate the cell. As cell diameter increases, the S/V ratio drops sharply (S = 4πr²; V = 4/3πr³).

There are two primary types of cells: prokaryotic and eukaryotic. The former are small, lack membrane-bound compartments, and their genetic material is not enclosed by a membrane. Prokaryotic cells grow and divide rapidly. A prime example of such cells is the bacterium E. coli, a typical constituent of the intestinal microflora of humans and animals. It has a rod-like shape with a length of ~ 2 µm, a diameter of ~ 0.8 µm, a volume of 1 µm³, a density of ~ 1.1 g/cm³, and a mass of ~ 700 · 10⁹ Da (1 · 10^-9 mg). It has been studied at THE MOLECULAR LEVEL more thoroughly than any other bacterium, making it extremely valuable for biochemical research.

Eukaryotic cells are significantly larger (Table 3.1), with volumes exceeding those of prokaryotic cells by 1,000 to 10,000 times. Mitochondria and chloroplasts are hypothesized to have originated from prokaryotes. A key feature of eukaryotic cells is the presence of lysosomes—where degradative enzymes are localized—along with peroxisomes.

Investigations of modern organisms and all biomolecules suggest that The Development of autolytic mechanisms in their cells began with the evolution of a group of RNA-like precursor molecules capable of catalyzing both their own replication and the synthesis of Polypeptides. Following the accumulation of additional catalytic proteins—which drove the evolution of more complex cells—DNA replaced RNA as the carrier of genetic information.

Table 3.1

Approximate sizes of selected atoms, molecules, and cellular structures

It is also significant that Selection of RNA molecules based on the number of proteins they encode could not begin until a bounded volume—a compartment—had formed; thus, The Emergence of a "precursor" to the plasma membrane was crucial for the Origin of the first cell. The primary role in the biochemical evolution of cell membranes belongs to a class of amphipathic molecules capable of spontaneous aggregation. Once an RNA molecule became trapped within a membrane-bound space, its nucleotide sequences could begin to influence the phenotypic traits of the entire cell.