Chapter 5: Organelles




Organelles are complex intracellular locations where processes necessary for eukaryotic cellular life occur. Most organelles are membrane-enclosed structures. Their membranes are composed of the same components as plasma membranes that form the outer boundaries of cells (see Chapter 3). Together with the cytosol (liquid portion of the cytoskeleton), the organelles help to form the cytoplasm, composed of all materials contained within the boundaries of the plasma membrane. Organelles do not float freely within the cytosol (liquid portion of cytoplasm) but are interconnected and joined by the framework established by proteins of the cytoskeleton (see Chapter 4).

Each organelle carries out a specific function although the activities of organelles can also sometimes be united. Cooperation between organelles is necessary for the expression of genes within nuclear DNA as proteins that function in various intracellular and extracellular locations. Organelles in this group include the nucleus, ribosomes, the endoplasmic reticulum (ER), and the Golgi complex. Members of this collection of organelles have a characteristic arrangement within the cell and proximity to each other that allows them to carry out their function in protein processing (Figure 5.1). Starting with the nucleus and working outward toward the plasma membrane, the ER with attached ribosomes is found next, followed by the Golgi complex which is in close proximity to the plasma membrane.

FIGURE 5.1.Diagram of a eukaryotic cell showing characteristic features and arrangements of organelles.

Diagram of a eukaryotic cell showing characteristic features and arrangements of organelles.

Other organelles are found in various locations within the cytoplasm and have functions equally important to those involved in protein processing. The main function of mitochondria is to harvest energy to power cells’ metabolic processes. Some other organelles are involved in digestion and detoxification. Lysosomes contain potent enzymes that break down macromolecules at the end of their lifespan while peroxisomes are responsible for detoxification of peroxides that would otherwise damage the cell.


The processes involved in the expression of DNA as functional proteins require cooperative actions by the nucleus, ribosomes, the ER, and the Golgi complex. The details of protein processing and trafficking or movement between organelles will be discussed in Chapter 11. The structure and function of each of these organelles are our present focus.


All eukaryotic cells except mature erythrocytes (red blood cells) contain a nucleus (plural = nuclei) where the cell’s genomic DNA resides. In cells that are not actively dividing, the DNA is contained within chromosomes (see also Chapter 22). Every normal human cell contains 23 pairs of chromosomes within the nucleus of every cell. The outermost structure of the nucleus is the nuclear envelope (Figure 5.2). This is a double-layered phospholipid membrane with nuclear pores to permit transfer of materials between the nucleus and the cytosol.

The interior of the nucleus contains the nucleoplasm, the fluid in which the chromosomes are found. It is organized by the nuclear lamina, the protein scaffolding of the nucleoplasm that is composed mainly of intermediate filaments (see also Chapter 4). The nuclear lamina forms associations between the DNA and the inner nuclear membrane. A prominent structure within the nucleus is a suborganelle called the nucleolus. The nucleolus is the site of ribosome production.

FIGURE 5.2.Structure of a cell’s nucleus.

Structure of a cell’s nucleus.


Ribosomes are the cellular machinery for protein synthesis (see also Chapter 9). They are composed of proteins and ribosomal RNA (rRNA) (Figure 5.3) with approximately 40% being protein and 60% rRNA. A complete ribosome has two subunits, one large and the other small. The large subunit contains three rRNA molecules and close to 50 proteins while the small subunit has one rRNA and approximately 30 proteins. Ribosomes assemble when needed for translation or protein synthesis from messenger RNA. They disassemble after completing the translation of a particular mRNA. Ribosomes are found within the cytosol either free or else bound to the ER.

FIGURE 5.3.A ribosome synthesizing protein from mRNA.

A ribosome synthesizing protein from mRNA.

Endoplasmic reticulum

Appearing like a series of interconnected, flattened tubes, the ER is often observed to surround the nucleus (Figure 5.4). The outer layer of the nuclear envelope is actually contiguous with the ER. In muscle cells, this organelle is known as the sarcoplasmic reticulum. The ER forms a maze of membrane-enclosed, interconnected spaces that constitute the ER lumen, which sometimes expand into sacs or cisternae. Regions of ER where ribosomes are bound to the outer membrane are called rough endoplasmic reticulum (rough ER or rER). Bound ribosomes and the associated ER are involved in the production and modification of proteins that will be inserted into the plasma membrane, function within lysosomes, Golgi complex, or ER, or else will be secreted outside the cell (see also Chapter 11). Smooth endoplasmic reticulum (sER) refers to the regions of ER without attached ribosomes. Both rER and sER function in the glycosylation (addition of carbohydrate) of proteins and in the synthesis of lipids.

FIGURE 5.4.ER forming a contiguous membrane structure with the nucleus.

ER forming a contiguous membrane structure with the nucleus.

Golgi complex

Working outward from the nucleus and the ER, the next organelle encountered is the Golgi complex. This organelle appears as flat, stacked, membranous sacs (Figure 5.5). Three regions are described within the Golgi complex: the cis, which is closest to the ER; the medial; and the trans Golgi, which is near the plasma membrane. Each region is responsible for performing distinct modifications, such as glycosylations (addition of carbohydrate), phosphorylations (addition of phosphate), or proteolysis (enzyme-mediated breakdown of protein), to the newly synthesized proteins being processed and converted into mature, functional proteins. The trans Golgi network sorts and packages the newly synthesized and modified proteins into distinct regions within the trans Golgi. These regions bud off from the main body of the Golgi complex and form structures called transport vesicles. Movement of these new proteins toward their final cellular or extracellular destination is facilitated in this manner.

FIGURE 5.5. Golgi complex.

Golgi complex.


Complex organelles, mitochondria (singular = mitochondrion) have several important functions in eukaryotic cells. Their unique membranes are used to generate ATP, greatly increasing the energy yield from the breakdown of carbohydrates and lipids. Mitochondria can self replicate and also contain their own DNA. Owing to these properties, mitochondria are believed to have bacterial origins. The very survival of individual cells depends on the integrity of their mitochondria. Programmed cell death or apoptosis occurs when pores are formed in the mitochondrial membrane allowing for the release of proteins that facilitate the apoptotic death process (see also Chapter 23). The unique structure of mitochondria is important in allowing them to perform these necessary cellular functions.

Function in energy production

One characteristic feature of mitochondria is the double phospholipid bilayer membranes that form the outer boundary of the organelle (Figure 5.6). The inner mitochondrial membrane forms folded structures called cristae that protrude into the mitochondrial lumen (space) known as the mitochondrial matrix. Protons (H+) are pumped out of the mitochondrial matrix, creating an electrochemical gradient of protons. The flow of protons back into the matrix drives the formation of ATP from carbohydrates and lipids in the process of oxidative phosphorylation (see also LIR Biochemistry, pp. 77–80). The presence of mitochondria within a cell enhances the amount of ATP produced from each glucose molecule that is broken down, as evidenced by human red blood cells that lack mitochondria. In red blood cells, only 2 ATP molecules are generated per glucose molecule. In contrast, in human cells with mitochondria, the yield of ATP is as high as 32 per glucose molecule.

FIGURE 5.6.A mitochondrion.

A mitochondrion.

Role as independent units within the eukaryotic cells

Mitochondria also contain DNA (mtDNA) and ribosomes for the production of RNA and some mitochondrial proteins. mtDNA is approximately 1% of total cellular DNA and exists in a circular arrangement within the mitochondrial matrix. Mutations or errors in some mitochondrial genes can result in disease. Most mitochondrial proteins, however, are encoded by the genomic DNA of the cell’s nucleus. Mitochondria self replicate or divide by fission, as do bacteria. Mitochondria are actually believed to have arisen from bacteria that were engulfed by ancestral eukaryotic cells.

Function in cell survival

Survival of eukaryotic cells depends on intact mitochondria. At times, the death of an individual cell is important for the benefit of the organism. During development, some cells must die to allow for proper tissue and organ formation. Death of abnormal cells, such as virally infected cells or cancerous cells, is also for the good of the organism. In all these cases, mitochondrial involvement is important to ensure cell survival when it is appropriate and also to facilitate programmed cell death when necessary. When the process of programmed cell death or apoptosis is stimulated in a cell, proapoptotic proteins insert into the mitochondrial membrane, forming pores. A protein known as cytochrome c can then leave the intermembrane space of the mitochondria through the pores, entering the cytosol (Figure 5.7). Cytochrome c in the cytosol stimulates a cascade of biochemical events resulting in apoptotic death of the cell (see also Chapter 23).

FIGURE 5.7.Mitochondria in apoptosis.

Mitochondria in apoptosis.

Mitochondrial diseases

Mitochondrial cytopathies are disorders that result in an inability of mitochondria to properly produce ATP. These disorders may result from mutations in mtDNA or from mutations in genomic genes that encode mitochondrial proteins and enzymes. Because mitochondria from sperm cells do not enter a fertilized egg, mitochondria are inherited exclusively from the mother. Therefore, disorders of mtDNA are also inherited from the mother only. Siblings share mitochondria with each other and with their mother, causing mitochondrial disorders that arise from mtDNA mutations to occur within families. Some individuals may be affected more or less severely even within a family. It is estimated that 1 in 4,000 children in the United States will develop a mitochondrial disorder by age 10. Some diseases of aging (type 2 diabetes, Parkinson disease, Alzheimer disease, atherosclerosis, etc.) may also result in part from decreased mitochondrial function.

More than 40 different mitochondrial disorders are described. They share the common feature of a reduced ability of mitochondria to completely oxidize or breakdown fuel sources such as carbohydrates. The buildup of intermediates can further damage mitochondria and mtDNA, which does not have an efficient repair mechanism. Mitochondrial diseases are categorized by the organ that is affected. Defects in oxidative phosphorylation will affect tissues with the greatest need for ATP. Brain, heart, liver, skeletal muscles, and eyes are examples of organs often affected in some mitochondrial cytopathies. Developmental delays, poor growth, loss of muscle coordination, and loss of vision are various signs of these disorders.

Kearns-Sayre syndrome is an example of a mitochondrial disorder caused by defective mtDNA. It is rare and results in paralysis of eye muscles and degeneration of the retina. A single large deletion of mtDNA is responsible for the development of this syndrome. Leber hereditary optic neuropathy results in blindness, primarily in young men. A single change (point mutation) in mtDNA causes this disorder. Deletions in mtDNA can result in Pearson syndrome, where there are bone marrow and pancreas dysfunctions. Cures are not presently available for mitochondrial cytopathies and treatments are designed to reduce symptoms or to prevent progression of disease.


Lysosomes are membrane-enclosed organelles of various sizes that have an acidic internal pH (pH 5) (Figure 5.8). They are formed from regions of the Golgi complex that pinch off when proteins destined for the lysosome reach the trans Golgi (see also Chapter 11). Lysosomes contain potent enzymes known collectively as acid hydrolases. These enzymes are synthesized on ribosomes bound to the ER. They function within the acidic environment of lysosomes to hydrolyze or break down macromolecules (proteins, nucleic acids, carbohydrates, and lipids). Lysosomes play a critical role in the normal turnover of macromolecules that have reached the end of their functional life.

Nonfunctional macromolecules build up to toxic levels if they are not degraded within lysosomes and properly recycled for reuse within the cell. This is exemplified by diseases known as lysosomal storage diseases. Such diseases are caused by defective acid hydrolases, resulting in accumulation of substrates of the defective acid hydrolases. Most are fatal at an early age. In infantile Tay Sachs disease, gangliosides accumulate in the brain and death occurs by age 4. In addition to degrading cellular macromolecules at the end of their lifespan, lysosomal enzymes also degrade materials that have been taken up by the cell through endocytosis or phagocytosis.

FIGURE 5.8. Lysosome structure and function.

Lysosome structure and function.

Lysosomal storage diseases

Lysosomal storage diseases are caused by defects in acid hydrolases. (An exception is I cell disease, in which acid hydrolases do not traffic properly to the lysosomes.) Over 40 different acid hydrolases exist within normal, healthy lysosomes. The absence of particular acid hydrolases can lead to the accumulation of particular macromolecule substrates within the lysosomes. Therefore, the lysosomes store these substances instead of degrading and recycling them. These diseases are categorized by the type of compound that builds up to toxic levels within the lysosomes. For example, mucopolysaccharides (also known as glycosaminoglycans) accumulate in mucopolysaccharidoses such as Hurler and Hunter syndromes.

Both are severe, with hearing loss and damage to the central nervous system. Children with Hurler syndrome usually stop developing between 2 and 4 years of age. In Farber disease, ceramide accumulates as a result of acid ceramidase deficiency and is fatal within the first year of life. Tay Sachs disease is characterized by the accumulation of gangliosides in the brain. The infantile form is the most common variant of Tay Sachs disease and is seen in approximately 1/3,600 births to Ashkenazi Jewish couples, but it is rare in the general population. Symptoms appear at about 6 months of age and death occurs by age 4.

Some other lysosomal storage diseases do not become evident until much later in life. The adult-onset form of Gaucher syndrome (type I) is the most common lysosomal storage disease. This disease results from a deficiency of glucosylceramidase and results in glucosylceramide lipidosis (excess of this particular type of lipid). Splenomegaly (enlargement of the spleen) and bone pain are characteristics. The infantile form of Gaucher syndrome (type II) is much more severe, with neurological impairment and death by age 3.


Peroxisomes resemble lysosomes in size and in structure. They have single membranes enclosing them and contain hydrolytic enzymes. However, they are formed from regions of the ER as opposed to regions of the Golgi complex. Enzymes that function in peroxisomes are synthesized on free ribosomes and are not modified in the ER or Golgi complex. Within peroxisomes, fatty acids and purines (AMP and GMP) are broken down (see also Chapter 7 and LIR Biochemistry, p. 195). Hydrogen peroxide, a toxic by-product of many metabolic reactions, is detoxified in peroxisomes. Within liver cells (hepatocytes), peroxisomes participate in cholesterol and bile acid synthesis (see also LIR Biochemistry, pp. 220–224).

Peroxisomes are also involved in the synthesis of myelin, the substance that forms a protective sheath around many neurons. Some rare inherited diseases are caused by impaired peroxisome function. They exert their effects from birth onward and life expectancy is short. For example, X-linked adrenoleukodystrophy (the disease of the young boy in the 1992 film, Lorenzo’s Oil) is characterized by the deterioration of myelin sheaths of neurons, owing to the failure of proper fatty acid metabolism. Zellweger syndrome is caused by a defect in the transporting of peroxisomal enzymes into the peroxisomes in liver, kidneys, and brain. Affected individuals do not usually survive beyond 6 months of age.

Chapter Summary

  • Organelles are intracellular structures within eukaryotic cells that are responsible for carrying out specific functions necessary for normal cellular life.
  • The nucleus, ribosomes, and endoplasmic reticulum function together in processing proteins that will function outside of the cell or within lysosomes.
  •  The nucleus is enclosed by a double membrane layer and houses the genomic DNA of the cell within the chromosomes.
  •  The nucleolus within the nucleus is the site of ribosome manufacture.
  •  Ribosomes function in protein translation and may be free or else bound to the endoplasmic reticulum.
  •  The endoplasmic reticulum is contiguous with the nuclear envelope and a series of membrane-enclosed spaces in which protein processing can occur.
  •  Rough endoplasmic reticulum has attached ribosomes while smooth endoplasmic reticulum does not.
  •  The Golgi complex appears like a series of flat, membrane-enclosed sacs with three distinct regions (cis, medial, and trans). It is involved in modifying and packaging the newly produced proteins.
  •  Mitochondria have double membranes that form folded cristae and surround a matrix.
  •  ATP is generated using an electrochemical gradient that exists across the matrix.
  •  Mitochondria can self replicate and contain their own DNA and ribosomes. They are believed to have arisen from bacteria engulfed by ancestral eukaryotic cells.
  •  Cell survival depends on the integrity of the mitochondrial membrane. When pores are placed in the membrane, cytochrome c is released into the cytosol, setting off a cascade of reactions that lead to programmed cell death.
  •  Lysosomes contain powerful digestive enzymes known as acid hydrolases that function within their acidic environment.
  •  Defects in lysosomal acid hydrolases can result in lysosomal storage diseases where accumulation of nonfunctional macromolecules causes cellular damage and can result in death at an early age.
  •  Peroxisomes contain hydrolytic enzymes, detoxify hydrogen peroxide, and participate in the breakdown of fatty acids. They are involved in liver synthesis of cholesterol and in the production of myelin sheaths that protect neurons.