The Cell Cytoplasm

The cytoplasm occupies the space between the nucleus and the cell membrane. It usually stains acidophilic. It has three components: the matrix, cytoplasmic organelles and cytoplasmic inclusions. The cytoplasmic matrix (cytosol or ground substance) is amorphous. It contains electrolytes, enzymes and metabolites, and exhibits sol-gel properties. Cytoplasmic inclusions are non-living; they are stored nutrients, secretory product or pigment granules. Cytoplasmic organelles are small living structures; some of them can be seen by the light microscope (LM); others can only be seen by the electron microscope (EM). Some are membrane bound; others are not. They perform specific functions; They include:

1. Ribosomes

2. Rough endoplasmic reticulum (rER)

3. Golgi apparatus

4. Lysosomes

5. Smooth endoplasmic reticulum (sER)

6. Mitochondria

7. Microtubules

8. Filaments

9. Centrioles

10. Cilia

11. Peroxisomes

Organelles are categorized into membranous and non-membranous organelles. Membranous organelles include rough endoplasmic reticulum, Golgi apparatus, lysosomes, smooth endoplasmic reticulum, and mitochondria. Non-membranous organelles include ribosomes and centrioles.

Fig C1. Illustration of a cell showing the nucleus and the surrounding cytoplasm containing representative organelles including a mitochondrion, s Golgi apparatus and rough endoplasmic reticulum (rER).

Cytoplasmic Organelles

Ribosomes and Polysomes

Ribosomes are small organelles that can only be seen with the electron microscope (EM), where they appear as dark tiny particles (about 20nm). Ribosomes are made of ribonucleic acid (RNA) and protein. They are sites for protein synthesis, namely, site for mRNA translation. They read the genetic information coded on mRNA (messenger RNA) and accordingly build a string of amino acids to form a specific protein molecule. Ribosomes are present in the cytoplasm in two forms: free ribosomes or ribosomes attached to the rough endoplasmic reticulum (rER). Free ribosomes are present either as solitary ribosomes or as small groups of ribosomes called polysomes. Each ribosome has two subunits: a small subunit and a large one. Free ribosomes (not associated with rER) synthesize protein for use inside the cell itself (cytoplasmic proteins). Since ribosomes contain acid (rRNA), a cytoplasm rich in ribosomes stains basophilic.  

Fig. C2. Electron micrograph (on the left) showing part of the cytoplasm of a cell studded with free ribosomes that appear as small dense particles. This cell is active in producing proteins for utilization within the cell. The illustration on the right shows 15 ribosomes attached to a single strand of mRNA forming a polysome (in a process of translation). Each ribosome consists of two subunits: a small one and a large one.

Rough Endoplasmic Reticulum (RER)

Rough endoplasmic reticulum (RER) is a membranous cytoplasmic organelle. It consists of sacs called cisternae. This organelle cannot be seen with the light microscope; it can be seen only with the electron microscope. RER membranous cisterns are studded with ribosomes; thus, a cytoplasm rich in RER is basophilic. RER functions in synthesis of secretory protein, integral plasma membrane proteins and lysosomal enzymes. Protein synthesized in RER is carried to Golgi apparatus via small vesicles called transfer vesicles. RER is well developed in cells which secrete large amounts of proteins such as plasma cells which secrete immunoglobulins; the cytoplasm of plasma cells is fully packed with cisternae of RER.

Fig. C3. Electron micrograph (on the left) and two illustrations showing cisternae of rough endoplasmic reticulum and associated ribosomes and transfer vehicles.

Golgi Apparatus (Complex)

Golgi apparatus is membranous organelles. It is one of the few organelles that can be depicted with the light microscope, but only in sections stained by special methods such as the silver staining methods; it cannot be seen in H&E sections. Nevertheless, in cells which are highly basophilic such as plasma cells, the area occupied by Golgi appears pale. This pale area constitutes what is known as the Golgi negative image.

Fig. C4. Light micrograph showing a group of plasma cells. The nucleus (N) is dense basophilic, the cytoplasm is basophilic except for a pale region (G) close to the nucleus. This is where the Golgi apparatus resides forming a negative image for its presence.

1.      Under the electron microscope the Golgi apparatus appears as a stack of membranous sacs. These sacs are known as Golgi saccules. Several vesicles and tubules are associated with the Golgi saccules. All Golgi elements (saccules, vesicles and tubules) are devoid of ribosomes, and thus do not stain basophilic in route histology sections. The stack of Golgi saccules is often curved. The convex surface of stack is called immature (forming) face, whereas the concave one is called maturing face of Golgi apparatus. Golgi apparatus is sometimes referred to as the Golgi body or the Golgi complex. Golgi apparatus is not a static organelle; it is all the time gaining and losing elements. New saccules are formed at the immature (cis) face by merging of transfer vesicles. The newly formed saccules dip into the complex and gradually move towards the mature (trans) face, where they lost. Meanwhile, the saccule contents become more concentrated. The Golgi apparatus has several functions which include:

1.      Packaging secretory proteins and lysosomal enzymes.

2.      Modification of proteins.

3.      Conjugation of lipid and carbohydrates.

Fig. C5. Showing: (A) Golgi apparatus as seen under TEM and (B) an illustration for the Golgi complex. In both, the Golgi appears as a stack of tubular structures (the Golgi saccules). The stack is curved; the convex surface is the immature forming face and the concave surface is the maturing face. Transfer vesicles and secretory vesicles are seen.

Lysosomes

Lysosomes are membranous organelles containing hydrolytic enzymes. They contain more than fifty different acid hydrolases capable breaking down all sorts of organic matter, including proteins, lips nucleic acids and carbohydrates. Lysosomes shapes: different shapes; some are spherical, others are oval or irregular. Some of are quite electron dense, appearing uniformly dark other are uniformly moderately electron dense and have heterogenous contents. Lysosomes are of different types, which include primary lysosomes, secondary lysosomes, tertiary lysosomes and residual bodies.  Lysosomes can be seen by both EM and LM. By LM they need special staining techniques to be visualized. Lysosomes are a characteristic feature of phagocytic cells such as neutrophils and macrophages. Such cells contain large numbers of different types of lysosomes.

Primary lysosomes are produced by the Golgi apparatus. They enzymes are synthesized within RER and packaged by Golgi. Primary lysosomes appear under the transmission electron microscope as moderately dense spherical bodies. They are packages of hydrolytic enzymes that can digest organic matter. They fuse with foreign engulfed organisms, organic matter and degenerate own cytoplasmic organelles, forming secondary lysosomes. Secondary lysosomes have different sizes and a heterogenous content. The process of digestion ends by forming tertiary lysosomes which are dense bodies called residual bodies. Residual bodies may be conjugated with lipids forming lipofuscin granules which are usually numerous in neurons of old people. Lysosomal storage diseases are inborn diseases associated with malfunctioning of lysosomes. They cause accumulation of substrates (lipoproteins, mucolipids, mucopolysaccharides. oligosaccharides) in cells of some organs causing ill functioning of those organs.

Fig. C6. Illustration showing the origin and fate of lysosomes. Lysosomal hydrolytic enzyme genes in the nucleus are transcribed forming mRNA, which passes into the cytoplasm for rER to synthesize the coded lysosomal enzymes. The enzymes (proteins) are taken by transfer vesicles to the Golgi. There they are packed to form primary lysosomes, which fuse with phagocytosed particulate matter forming heterophagosomes, or with worn out organelles forming autophagosome. Lysosomal enzymes digest organic matter in both types of phagosomes yielding residual bodies which exocytosed. Fluids containing particulate matter can be pinocytosed and similarly form heterophagosomes and residual bodies.     

Protein Synthesis

Proteins are large complex molecules made up of amino acids. They are key players in the normal functioning of the human body and its tissues and cells providing building blocks and acting as hormones and enzymes. They are required for preserving the structure and function of tissues and organs of the body. Proteins synthesis is needed for making new building blocks and for replacement of proteins lost due to degradation and degeneration. It is evident then that protein synthesis is a crucially important biological process. The process has two phases: transcription and translation. Transcription takes place within the nucleus. It is a process of copying the code (gene) present in a segment of the DNA strand into a strand messenger RNA (mRNA). The process of copying is carried out by enzymes known as RNA polymerases. The mRNA strand leaves nucleus via the nuclear pores into the cytoplasm. Translation is the process whereby peptide chains are made by ribosomes in accordance with information encoded in the mRNA strand. Amino acids are brought into the location where a ribosome is attached to the mRNA strand to be conjoined in the sequence dictated by mRNA forming a specific peptide chain. Peptide chains formed by polyribosomes (polysomes) remain free in the cytoplasm, whereas those produced by ribosomes attached to rER cisterns pass into the lumen of cisterns isolated from the rest of the cytoplasm. They could enzymes, hormones, hydrolases. They carried from rER to Golgi complex to packed into secretory vesicles or primary lysosomes. Secretory vesicles pass towards the cell plasma membrane to be secreted by exocytosis (merocrine secretion).

Fig C7. Diagram illustrating both phases of protein synthesis. Transcription takes place within the nucleus whereas translation takes place in the cytoplasm.

Smooth Endoplasmic Reticulum (SER)

Smooth endoplasmic reticulum (sER) is also a membranous organelle. It cannot be seen by the light microscope; It can only be seen with the electron microscope. sER consists of interconnected short branching tubules and vesicles. There are no ribosomes associated to sER; sER is devoid of ribosomes.  The main functions of sER are

1.      Detoxification of noxious substances and drugs

2.      Synthesis of steroid hormones

3.      Lipid and glycogen metabolism

4.      Transport of Ca++

sER is abundant in liver cells (detoxification), adrenal cortex cells (steroid hormone synthesis) and muscle fibers (Ca++ transport).

Fig. C8. The illustration shows the 3D appearance of the branching tubules of smooth endoplasmic reticulum (sER). Below the electron microscopic appearance of sER.

Mitochondria

Mitochondria are membranous cytoplasmic organelles. They are clearly visible under the electron microscope and can also be seen with the light microscope using special staining techniques. Mitochondria are tiny sausage-like structures of variable length and thickness, 0.5-3 um. Electron microscopy shows that each mitochondrion is surrounded by two membranes; the outer membrane is smooth, whereas the inner one is folded forming shelf like structures known as cristae or ridges. The lumen of the mitochondrion is occupied by the mitochondrial matrix, which contains enzymes for oxidative phosphorylation, DNA strands, RNA strands, ribosomes and matrix granules. Matrix granules are thought to regulate ions and supply components of the inner mitochondrial membrane. The space between the outer and inner mitochondrial membranes is called the intermembranous space. Mitochondria reproduce by binary division.

Fig. C9. Two illustrations showing the structure of mitochondria. The left one is 3D showing the mitochondrion as hollow sausage-like structure with prominent internal ridges (cristae). The illustration on the right shows details of the contents (matrix, DNA strands, ribosomes, ridges / cristae, outer and inner membranes, and intermembrane space)

Mitochondria are present in all body cells except RBCs and dead keratinocytes. They are responsible for energy production. Thus, they are present in large numbers in cells that generate and utilize large amounts of energy such heart muscle cells and neurons. Mitochondria constitute up to 40% of the volume of cardiac muscle cells. Mitochondria contain Krebs cycle and phosphorylation enzymes (for cell respiration and ATP production). Enzymes for oxidative phosphorylation are present on membranes of mitochondrial cristae whereas Krebs cycle enzymes are present in the mitochondrial matrix, along with mitochondrial DNA, RNA. Mitochondria also play a significant role in apoptosis (programmed cell death). Mitochondrial DNA (mtDNA) is less protected than nuclear DNA from the surrounding environment, and accordingly mtDNA is more prone to mutation. Several diseases are related to mutations in the mitochondrial DNA. These are known as mitochondrial diseases. Everybody gets his/her mitochondria from the mother (from the oocyte), so mtDNA is passed down from the mother to children.

Fig C10. Transmission electron micrographs of two mitochondria. They have different shapes but have the same components: matrix, cristae, inner and outer membranes.

Microtubules and Filament

Microtubules are tiny hollow cylindrical structures that can only be seen with the electron microscope. They are about 25nm in diameter but comparatively long, reaching about 15um in length. Occasional, microtubules are present in groups, in such situations they can be seen with the light microscope using special methods. Microtubules contribute to formation of cilia, centrioles, the mitotic spindle and the cytoskeleton. Microtubules function in cell motility, intra-cytoplasmic transport of organelles & chromosomes (mitosis). They are polymers of tubulin subunits. These subunits join each other end to end forming new microtubules or increase the length of already existing microtubules. Microtubules can dismantle causing shortening of microtubules or their disappearance. The filaments are thinner than microtubules but are solid thread-like structures. There are different types of filaments. These include actin and myosin filaments present in muscle cells. Cell contraction depends on actin and myosin filaments. Filaments also include intermediate filaments such as keratin and vimentin which are present in both the cytoplasm and nucleoplasm giving shape and support to the nucleus and the cell itself. Intermediate filaments also include neurofilaments of neurons and spectrin of blood cells. Intermediate filaments are generally supportive.

Fig. C11. Illustrations showing microtubules of the mitotic spindle (left) and α and  β tubulin subunits building up a microtubule.

Fig. C12. A. Image of two fibroblasts taken by a confocal microscope showing the cytoskeleton made up of microtubules (yellow) and filaments (violet). B. Transmission electron micrograph two microtubules running horizontally parallel to each other.

Centrioles

Centrioles are a pair of cylindrical structures oriented perpendicular to each other seen in non-dividing cells (cells not undergoing cells division).  The pair occupies a region close to the nucleus called the centrosome. The centrosome can be seen by the light microscope and the centrioles can be seen with electron microscope. Centrioles control formation and disintegration of microtubules. As thus, they participated in the formation of the mitotic spindle, movement of chromosomes, change of cell shape cell motility and cell division. Each centriole is a short cylinder having a wall made of 9 triplets of microtubules. Of the triplet microtubules, the one in the middle is complete and the other two are incomplete.  

Fig. C13. Electron micrograph (on the left) showing a cross of a centriole characterized by the nine triplets (27 microtubules).The illustration on the right shows the 3D appearance of the centriole and its triplets.

Cilia

Cilia are motile organelles that project from the cell surface covered by the cell membrane. Many cilia can be seen on the surface of certain cells e.g. epithelial cells of the trachea. Cilia are characterized by what is known as the 9+2 pattern (9 peripheral microtubule doublets and 2 central singlet microtubules). Cilia have basal bodies that resemble centrioles (9 triplets). Cilia are a characteristic feature of epithelial cells of the respiratory passages and parts of the female genital tract. In the respiratory passages they participate in the formation of the muciliary apparatus which plats a significant role in defending the body against airborne organisms and particles. In genital tracts cilia play a significant role in propulsion of ova and zygotes.

Fig C14. Light micrograph of an H&E section of a ciliated epithelium. The hair-like are covering the apical surface of the cells. The basal bodies form a dark pinkish line beneath the cilia. On the right is an illustration of the cross-sectional appearance of a cilium showing the 9 (doublets) + 2 arrangements.

Cytoplasmic Inclusions

These are non-living structures seen in the cytoplasm of eukaryotic cells. The inclusions include stored food, pigments and crystals. Stored food includes glycogen and fat. Glycogen particles can be seen with light microscope after special stain (Best’s carmine staining method) in liver cells and muscle fibers. Lipid droplets are present in many cells (liver, adrenal cells. They can be seen by special stains (e.g. OsO4). Pigments include melanin (in the skin and eye for instance) and hemoglobin (RBCs). Pigments have natural colour. Crystals are made of protein. They have regular shape. They may be seen free in the cytoplasm (Leydig cells of testis) or within granules (eosinophils).

Fig. C15. A liver section stained by Best’s carmine method showing hepatocytes rich in glycogen.

Fig. C16. Basal cell of the epidermis of the skin showing brownish melanin pigment in their cytoplasm.

Cytoplasmic Matrix

Cytoplasmic matrix is the ground substance of the cytoplasm; it is also called cytosol. It has no visible structure. It contains metabolites and electrolytes, as well as synthesized proteins and enzymes. The cytoskeleton is embedded in the matrix. The cytoskeleton is made of networks of microtrabeculae where most cytoplasmic organelles are kept anchored.

Cell membrane

The cell membrane acts as a barrier between the cell and its environment. It has a trilaminar (3-layer) appearance under EM (2 dense layers and a light layer in-between) made of phospholipids, cholesterol and protein. The two dense layers are primarily made of lipids (phospholipids, fatty acid chains and cholesterol

Fig. C17. Illustration showing the lipid bilayer and transmembranous proteins.

The cell membrane proteins include integral proteins and peripheral proteins. Integral proteins have important functions. They act as receptors (e.g. for hormones), ion channels and pumps (e.g. for Na+), transducers (coupling receptors with cytoplasmic enzymes).

Fig. C18. A 3D illustration showing the lipid bilayer and transmembranous proteins

Fig. C19. Illustration of the role of the cell membrane in endocytosis and exocytosis

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