Intracellular Compartments

Much of what we know about cells comes from studies of simple organisms that consist of one cell. But humans are much more complex, with trillions of cells in their bodies. It has been estimated that there are more than 200 different types of cells in the human body, each cell type with its own characteristic structure and function.

During development, cells specialize and take on specific shapes and functions. Each cell in the body inherits identical genetic information in its DNA, but no one cell uses all this information. During differentiation, only selected genes become active, transforming the cell into a specialized unit. In most cases, the final shape and size of a cell and its contents reflect its function. Figure 3.1b shows five representative cells in the human body. These mature cells look very different from one another, but they all started out alike in the early embryo, and they retain many features in common.

Cells Are Divided into Compartments

We can compare the structural organization of a cell to that of a medieval walled city. The city is separated from the surrounding countryside by a high wall, with entry and exit strictly controlled through gates that can be opened and closed. The city inside the walls is divided into streets and a diverse collection of houses and shops with varied functions. Within the city, a ruler in the castle oversees the everyday comings and goings of the city’s inhabitants. Because the city depends on food and raw material from outside the walls, the ruler negotiates with the farmers in the countryside. Foreign invaders are always a threat, so the city ruler communicates and cooperates with the rulers of neighboring cities.

In the cell, the outer boundary is the cell membrane. Like the city wall, it controls the movement of material between the cell interior and the outside by opening and closing “gates” made of protein. The inside of the cell is divided into compartments rather than into shops and houses. Each of these compartments has a specific purpose that contributes to the function of the cell as a whole. In the cell, DNA in the nucleus is the “ruler in the castle,” controlling both the internal workings of the cell and its interaction with other cells. Like the city, the cell depends on supplies from its external environment. It must also communicate and cooperate with other cells to keep the body functioning in a coordinated fashion.

Figure 3.4a is an overview map of cell structure. The cells of the body are surrounded by the dilute salt solution of the extracellular fluid. The cell membrane separates the inside environment of the cell (the intracellular fluid) from the extracellular fluid.

Internally the cell is divided into the cytoplasm and the nucleus. The cytoplasm consists of a fluid portion, called cytosol; insoluble particles called inclusions; insoluble protein fibers; and membrane-bound structures collectively known as organelles. Figure 3.4 shows a typical cell from the lining of the small intestine. It has most of the structures found in animal cells.

The Cytoplasm Includes Cytosol, Inclusions, Fibers, and Organelles

The cytoplasm includes all material inside the cell membrane except for the nucleus. The cytoplasm has four components:

  1. Cytosol {cyto-, cell + sol(uble)}, or intracellular fluid: The cytosol is a semi-gelatinous fluid separated from the extracellular fluid by the cell membrane. The cytosol contains dissolved nutrients and proteins, ions, and waste products. The other components of the cytoplasm—inclusions, fibers, and organelles—are suspended in the cytosol.

  2. Inclusions are particles of insoluble materials. Some are stored nutrients. Others are responsible for specific cell functions. These structures are sometimes called the nonmembranous organelles.

  3. Insoluble protein fibers form the cell’s internal support system, or cytoskeleton.

  4. Organelles—“little organs”—are membrane-bound compartments that play specific roles in the overall function of the cell. For example, the organelles called mitochondria (singular, mitochondrion) generate most of the cell’s ATP, and the organelles called lysosomes act as the digestive system of the cell. The organelles work in an integrated manner, each organelle taking on one or more of the cell’s functions.

Inclusions Are in Direct Contact with the Cytosol

The inclusions of cells do not have boundary membranes and so are in direct contact with the cytosol. Movement of material between inclusions and the cytosol does not require transport across a membrane. Nutrients are stored as glycogen granules and lipid droplets. Most inclusions with functions other than nutrient storage are made from protein or combinations of RNA and protein.

Ribosomes (Fig. 3.4i) are small, dense granules of RNA and protein that manufacture proteins under the direction of the cell’s DNA [see Chapter 4 for details]. Fixed ribosomes attach to the cytosolic surface of organelles. Free ribosomes are suspended free in the cytosol. Some free ribosomes form groups of 10 to 20 known as polyribosomes. A ribosome that is fixed one minute may release and become a free ribosome the next. Ribosomes are most numerous in cells that synthesize proteins for export out of the cell.

Cytoplasmic Protein Fibers Come in Three Sizes

The three families of cytoplasmic protein fibers are classified by diameter and protein composition (TBL. 3.2). All fibers are polymers of smaller proteins. The thinnest are actin fibers, also called microfilaments. Somewhat larger intermediate filaments may be made of different types of protein, including keratin in hair and skin, and neurofilament in nerve cells. The largest protein fibers are the hollow microtubules, made of a protein called tubulin. A large number of accessory proteins are associated with the cell’s protein fibers.

Table 3.2 Diameter of Protein Fibers in the Cytoplasm

Diameter Type of Protein Functions
Microfilaments 7 nm Actin (globular) Cytoskeleton; associates with myosin for muscle contraction
Intermediate Filaments 10 nm Keratin, neurofilament protein (filaments) Cytoskeleton, hair and nails, protective barrier of skin
Microtubules 25 nm Tubulin (globular) Movement of cilia, flagella, and chromosomes; intracellular transport of organelles; cytoskeleton

The insoluble protein fibers of the cell have two general purposes: structural support and movement. Structural support comes primarily from the cytoskeleton. Movement of the cell or of elements within the cell takes place with the aid of protein fibers and a group of specialized enzymes called motor proteins. These functions are discussed in more detail in the sections that follow.

Microtubules Form Centrioles, Cilia, and Flagella

The largest cytoplasmic protein fibers, the microtubules, create the complex structures of centrioles, cilia, and flagella, which are all involved in some form of cell movement. The cell’s microtubule-organizing center, the centrosome, assembles tubulin molecules into microtubules. The centrosome appears as a region of darkly staining material close to the cell nucleus. In most animal cells, the centrosome contains two centrioles, shown in the typical cell of Figure 3.4e.

Each centriole is a cylindrical bundle of 27 microtubules, arranged in nine triplets. In cell division, the centrioles direct the movement of DNA strands. Cells that have lost their ability to undergo cell division, such as mature nerve cells, lack centrioles.

Cilia are short, hair-like structures projecting from the cell surface like the bristles of a brush {singular, cilium, Latin for eyelash}. Most cells have a single short cilium, but cells lining the upper airways and part of the female reproductive tract are covered with cilia. In these tissues, coordinated ciliary movement creates currents that sweep fluids or secretions across the cell surface.

The surface of a cilium is a continuation of the cell membrane. The core of motile, or moving, cilia contains nine pairs of microtubules surrounding a central pair (Fig. 3.5b). The microtubules terminate just inside the cell at the basal body. These cilia beat rhythmically back and forth when the microtubule pairs in their core slide past each other with the help of the motor protein dynein.

Flagella have the same microtubule arrangement as cilia but are considerably longer {singular, flagellum, Latin for whip}. Flagella are found on free-floating single cells, and in humans the only flagellated cell is the male sperm cell. A sperm cell has only one flagellum, in contrast to ciliated cells, which may have one surface almost totally covered with cilia (Fig. 3.5a). The wavelike movements of the flagellum push the sperm through fluid, just as undulating contractions of a snake’s body push it headfirst through its environment. Flagella bend and move by the same basic mechanism as cilia.

FIG. 3.5 Cilia and flagella

The Cytoskeleton Is a Changeable Scaffold

The cytoskeleton is a flexible, changeable three-dimensional scaffolding of actin microfilaments, intermediate filaments, and microtubules that extends throughout the cytoplasm. Some cytoskeleton protein fibers are permanent, but most are synthesized or disassembled according to the cell’s needs. Because of the cytoskeleton’s changeable nature, its organizational details are complex and we will not discuss the details.

The cytoskeleton has at least five important functions.

  1. Cell shape. The protein scaffolding of the cytoskeleton provides mechanical strength to the cell and in some cells plays an important role in determining the shape of the cell. Figure  3.4b shows how cytoskeletal fibers help support microvilli {micro-, small + villus, tuft of hair}, fingerlike extensions of the cell membrane that increase the surface area for absorption of materials.

  2. Internal organization. Cytoskeletal fibers stabilize the positions of organelles. Figure 3.4b illustrates organelles held in place by the cytoskeleton. Note, however, that this figure is only a snapshot of one moment in the cell’s life. The interior arrangement and composition of a cell are dynamic, changing from minute to minute in response to the needs of the cell, just as the inside of the walled city is always in motion. One disadvantage of the static illustrations in textbooks is that they are unable to represent movement and the dynamic nature of many physiological processes.

  3. Intracellular transport. The cytoskeleton helps transport materials into the cell and within the cytoplasm by serving as an intracellular “railroad track” for moving organelles. This function is particularly important in cells of the nervous system, where material must be transported over intracellular distances as long as a meter.

  4. Assembly of cells into tissues. Protein fibers of the cytoskeleton connect with protein fibers in the extracellular space, linking cells to one another and to supporting material outside the cells. In addition to providing mechanical strength to the tissue, these linkages allow the transfer of information from one cell to another.

  5. Movement. The cytoskeleton helps cells move. For example, the cytoskeleton helps white blood cells squeeze out of blood vessels and helps growing nerve cells send out long extensions as they elongate. Cilia and flagella on the cell membrane are able to move because of their microtubule cytoskeleton. Special motor proteins facilitate movement and intracellular transport by using energy from ATP to slide or step along cytoskeletal fibers.

Motor Proteins Create Movement

Motor proteins are proteins that convert stored energy into directed movement. Three groups of motor proteins are associated with the cytoskeleton: myosins, kinesins, and dyneins. All three groups use energy stored in ATP to propel themselves along cytoskeleton fibers.

Myosins bind to actin fibers and are best known for their role in muscle contraction [Chapter 12]. Kinesins and dyneins assist the movement of vesicles along microtubules. Dyneins also associate with the microtubule bundles of cilia and flagella to help create their whiplike motion.

Concept Check

  1. Name the three sizes of cytoplasmic protein fibers.

  2. How would the absence of a flagellum affect a sperm cell?

  3. What is the difference between cytoplasm and cytosol?

  4. What is the difference between a cilium and a flagellum?

  5. What is the function of motor proteins?

Most motor proteins are made of multiple protein chains arranged into three parts: two heads that bind to the cytoskeleton fiber, a neck, and a tail region that is able to bind “cargo,” such as an organelle that needs to be transported through the cytoplasm (Fig. 3.6). The heads alternately bind to the cytoskeleton fiber, then release and “step” forward using the energy stored in ATP.

FIG. 3.6 Motor proteins

Organelles Create Compartments for Specialized Functions

Organelles are subcellular compartments separated from the cytosol by one or more phospholipid membranes similar in structure to the cell membrane. The compartments created by organelles allow the cell to isolate substances and segregate functions. For example, an organelle might contain substances that could be harmful to the cell, such as digestive enzymes. Figures 3.4g, 3.4h, and 3.4i show the four major groups of organelles: mitochondria, the Golgi apparatus, the endoplasmic reticulum, and membrane-bound spheres called vesicles {vesicula, bladder}.


Mitochondria {singular, mitochondrion; mitos, thread+chondros, granule} are unique organelles in several ways. First, they have an unusual double wall that creates two separate compartments within the mitochondrion (Fig. 3.4g). In the center, inside the inner membrane, is a compartment called the mitochondrial matrix {matrix, female animal for breeding}. The matrix contains enzymes, ribosomes, granules, and surprisingly, its own unique DNA. This mitochondrial DNA has a different nucleotide sequence from that found in the nucleus. Because mitochondria have their own DNA, they can manufacture some of their own proteins.

Why do mitochondria contain DNA when other organelles do not? This question has been the subject of intense scrutiny. According to the prokaryotic endosymbiont theory, mitochondria are the descendants of bacteria that invaded cells millions of years ago. The bacteria developed a mutually beneficial relationship with their hosts and soon became an integral part of the host cells. Supporting evidence for this theory is the fact that our mitochondrial DNA, RNA, and enzymes are similar to those in bacteria but unlike those in our own cell nuclei.

The second compartment inside a mitochondrion is the intermembrane space, which lies between the outer and inner mitochondrial membranes. This compartment plays an important role in mitochondrial ATP production, so the number of mitochondria in a cell is directly related to the cell’s energy needs. For example, skeletal muscle cells, which use a lot of energy, have many more mitochondria than less active cells, such as adipose (fat) cells.

Another unusual characteristic of mitochondria is their ability to replicate themselves even when the cell to which they belong is not undergoing cell division. This process is aided by the mitochondrial DNA, which allows the organelles to direct their own duplication. Mitochondria replicate by budding, during which small daughter mitochondria pinch off from an enlarged parent. For instance, exercising muscle cells that experience increased energy demands over a period of time may meet the demand for more ATP by increasing the number of mitochondria in their cytoplasm.

The Endoplasmic Reticulum

The endoplasmic reticulum, or ER, is a network of interconnected membrane tubes with three major functions: synthesis, storage, and transport of biomolecules (Fig. 3.4i). The name reticulum comes from the Latin word for net and refers to the netlike arrangement of the tubules. Electron micrographs reveal that there are two forms of endoplasmic reticulum: rough endoplasmic reticulum (RER) and smooth endoplasmic reticulum (SER).

The rough endoplasmic reticulum is the main site of protein synthesis. Proteins are assembled on ribosomes attached to the cytoplasmic surface of the rough ER, then inserted into the rough ER lumen, where they undergo chemical modification.

The smooth endoplasmic reticulum lacks attached ribosomes and is the main site for the synthesis of fatty acids, steroids, and lipids [here]. Phospholipids for the cell membrane are produced here, and cholesterol is modified into steroid hormones, such as the sex hormones estrogen and testosterone. The smooth ER of liver and kidney cells detoxifies or inactivates drugs. In skeletal muscle cells, a modified form of smooth ER stores calcium ions (Ca2+) to be used in muscle contraction.

The Golgi Apparatus

The Golgi apparatus (also known as the Golgi complex) was first described by Camillo Golgi in 1898 (Fig. 3.4h). For years, some investigators thought that this organelle was just a result of the fixation process needed to prepare tissues for viewing under the light microscope. However, we now know from electron microscope studies that the Golgi apparatus is indeed a discrete organelle. It consists of a series of hollow curved sacs, called cisternae, stacked on top of one another like a series of hot water bottles and surrounded by vesicles. The Golgi apparatus receives proteins made on the rough ER, modifies them, and packages them into the vesicles.

Cytoplasmic Vesicles

Membrane-bound cytoplasmic vesicles are of two kinds: secretory and storage. Secretory vesicles contain proteins that will be released from the cell. The contents of most storage vesicles, however, never leave the cytoplasm.

Lysosomes {lysis, dissolution + soma, body} are small storage vesicles that appear as membrane-bound granules in the cytoplasm (Fig. 3.4d). Lysosomes act as the digestive system of the cell. They use powerful enzymes to break down bacteria or old organelles, such as mitochondria, into their component molecules. Those molecules that can be reused are reabsorbed into the cytosol, while the rest are dumped out of the cell. As many as 50 types of enzymes have been identified from lysosomes of different cell types.

Because lysosomal enzymes are so powerful, early workers puzzled over the question of why these enzymes do not normally destroy the cell that contains them. What scientists discovered was that lysosomal enzymes are activated only by very acidic conditions, 100 times more acidic than the normal acidity level in the cytoplasm. When lysosomes first pinch off from the Golgi apparatus, their interior pH is about the same as that of the cytosol, 7.0–7.3. The enzymes are inactive at this pH. Their inactivity serves as a form of insurance. If the lysosome breaks or accidentally releases enzymes, they will not harm the cell.

However, as the lysosome sits in the cytoplasm, it accumulates H+ in a process that uses energy. Increasing concentrations of H+ decrease the pH inside the vesicle to 4.8–5.0, and the enzymes are activated. Once activated, lysosomal enzymes can break down biomolecules inside the vesicle. The lysosomal membrane is not affected by the enzymes.

The digestive enzymes of lysosomes are not always kept isolated within the organelle. Occasionally, lysosomes release their enzymes outside the cell to dissolve extracellular support material, such as the hard calcium carbonate portion of bone. In other instances, cells allow their lysosomal enzymes to come in contact with the cytoplasm, leading to self-digestion of all or part of the cell. When muscles atrophy (shrink) from lack of use or the uterus diminishes in size after pregnancy, the loss of cell mass is due to the action of lysosomes.

The inappropriate release of lysosomal enzymes has been implicated in certain disease states, such as the inflammation and destruction of joint tissue in rheumatoid arthritis. In the inherited conditions known as lysosomal storage diseases, lysosomes are ineffective because they lack specific enzymes. One of the best-known lysosomal storage diseases is the fatal inherited condition known as Tay-Sachs disease. Infants with Tay-Sachs disease have defective lysosomes that fail to break down glycolipids. Accumulation of glycolipids in nerve cells causes nervous system dysfunction, including blindness and loss of coordination. Most infants afflicted with Tay-Sachs disease die in early childhood.

Peroxisomes are storage vesicles that are even smaller than lysosomes (Fig. 3.4c). For years, they were thought to be a kind of lysosome, but we now know that they contain a different set of enzymes. Their main function appears to be to degrade long-chain fatty acids and potentially toxic foreign molecules.

Peroxisomes get their name from the fact that the reactions that take place inside them generate hydrogen peroxide (H2O2), a toxic molecule. The peroxisomes rapidly convert this peroxide to oxygen and water using the enzyme catalase. Peroxisomal disorders disrupt the normal processing of lipids and can severely disrupt neural function by altering the structure of nerve cell membranes.

Concept Check

  1. What distinguishes organelles from inclusions?

  2. What is the anatomical difference between rough endoplasmic reticulum and smooth endoplasmic reticulum? What is the functional difference?

  3. How do lysosomes differ from peroxisomes?

  4. Apply the physiological theme of compartmentation to organelles in general and to mitochondria in particular.

  5. Microscopic examination of a cell reveals many mitochondria. What does this observation imply about the cell’s energy requirements?

  6. Examining tissue from a previously unknown species of fish, you discover a tissue containing large amounts of smooth endoplasmic reticulum in its cells. What is one possible function of these cells?

The Nucleus Is the Cell’s Control Center

The nucleus of the cell contains DNA, the genetic material that ultimately controls all cell processes. Figure 3.4j illustrates the structure of a typical nucleus. Its boundary, or nuclear envelope, is a two-membrane structure that separates the nucleus from the cytoplasmic compartment. Both membranes of the envelope are pierced here and there by round holes, or pores.

Communication between the nucleus and cytosol occurs through the nuclear pore complexes, large protein complexes with a central channel. Ions and small molecules move freely through this channel when it is open, but transport of large molecules such as proteins and RNA is a process that requires energy. Specificity of the transport process allows the cell to restrict DNA to the nucleus and various enzymes to either the cytoplasm or the nucleus.

In electron micrographs of cells that are not dividing, the nucleus appears filled with randomly scattered granular material, or chromatin, composed of DNA and associated proteins. Usually a nucleus also contains from one to four larger dark-staining bodies of DNA, RNA, and protein called nucleoli {singular, nucleolus, little nucleus}. Nucleoli contain the genes and proteins that control the synthesis of RNA for ribosomes.

The process of protein synthesis, modification, and packaging in different parts of the cell is an excellent example of how compartmentation allows separation of function, as shown in Figure 3.7. RNA for protein synthesis is made from DNA templates in the nucleus , then transported to the cytoplasm through the nuclear pores . In the cytoplasm, proteins are synthesized on ribosomes that may be free inclusions or attached to the rough endoplasmic reticulum . The newly made protein is compartmentalized in the lumen of the rough ER , where it is modified before being packaged into a vesicle . The vesicles fuse with the Golgi apparatus, allowing additional modification of the protein in the Golgi lumen . The modified proteins leave the Golgi packaged in either storage vesicles or secretory vesicles whose contents will be released into the extracellular fluid . The molecular details of protein synthesis are discussed elsewhere [see Chapter 4].

FIG. 3.7 Protein synthesis demonstrates subcellular compartmentation