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5.1: Characteristics of Eukaryotic Cells

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    Learning Objectives

    • Identify and describe structures and organelles unique to eukaryotic cells
    • Compare and contrast similar structures found in prokaryotic and eukaryotic cells

    Eukaryotic organisms include protozoans, algae, fungi, plants, and animals. Some eukaryotic cells are independent, single-celled microorganisms, whereas others are part of multicellular organisms. The cells of eukaryotic organisms have several distinguishing characteristics. Above all, eukaryotic cells are defined by the presence of a nucleus surrounded by a complex nuclear membrane. Also, eukaryotic cells are characterized by the presence of membrane-bound organelles in the cytoplasm. Organelles such as mitochondria, the endoplasmic reticulum (ER), Golgi apparatus, lysosomes, and peroxisomes are held in place by the cytoskeleton, an internal network that supports transport of intracellular components and helps maintain cell shape (Figure \(\PageIndex{1}\)). The genome of eukaryotic cells is packaged in multiple, rod-shaped chromosomes as opposed to the single, circular-shaped chromosome that characterizes most prokaryotic cells. Table \(\PageIndex{1}\) compares the characteristics of eukaryotic cell structures with those of bacteria and archaea.

    A diagram of a large cell. The outside of the cell is a thin line labeled plasma membrane. A long projection outside of the plasma membrane is labeled flagellum. Shorter projections outside the membrane are labeled cilia. Just under the plasma membrane are lines labeled microtubules and microfilaments. The fluid inside the plasma membrane is labeled cytoplasm. In the cytoplasm are small dots labeled ribosomes. These dots are  either floating in the cytoplasm or attached to a webbed membrane labeled rough endoplasmic reticulum. Some regions of the webbed membrane do not have dots; these regions of the membrane are called smooth endoplasmic reticulum. Other structures in the cytoplasm include an oval with a webbed line inside of it; this is labeled the mitochondrion. Spheres in the cytoplasm are labeled peroxisome and lysosome. A pancake stack of membranes is labeled golgi complex. Two short tubes are labeled centrosomes. A large sphere in the cell is labeled nucleus. The outer membrane of this sphere is the nuclear envelope. Holes in the nuclear envelope are called nuclear pores. A smaller sphere in the nucleus is labeled nucleolus.
    Figure \(\PageIndex{1}\): An illustration of a generalized, single-celled eukaryotic organism. Note that cells of eukaryotic organisms vary greatly in terms of structure and function, and a particular cell may not have all of the structures shown here.


    Table \(\PageIndex{1}\): Summary of Cell Structures.

    Cell Structure Prokaryotes Eukaryotes
    Bacteria Archaea
    Size ~0.5–1 μM ~0.5–1 μM ~5–20 μM
    Surface area-to-volume ratio High High Low
    Nucleus No No Yes
    Genome characteristics
    • Single chromosome
    • Circular
    • Haploid
    • Lacks histones
    • Single chromosome
    • Circular
    • Haploid
    • Contains histones-like proteins
    • Multiple chromosomes
    • Linear
    • Haploid or diploid
    • Contains histones
    Cell division Binary fission Binary fission Mitosis, meiosis
    Membrane lipid composition
    • Ester-linked
    • Straight-chain fatty acids
    • Bilayer
    • Ether-linked
    • Branched isoprenoids
    • Bilayer or monolayer
    • Ester-linked
    • Straight-chain fatty acids
    • Sterols
    • Bilayer
    Cell wall composition
    • Peptidoglycan, or
    • None
    • Pseudopeptidoglycan, or
    • Glycopeptide, or
    • Polysaccharide, or
    • Protein (S-layer), or
    • None
    • Cellulose (plants, some algae)
    • Chitin (molluscs, insects, crustaceans, and fungi)
    • Silica (some algae)
    • Most others lack cell walls
    Motility structures Rigid spiral flagella composed of flagellin Rigid spiral flagella composed of archaeal flagellins Flexible flagella and cilia composed of microtubules, membrane-bound
    Membrane-bound organelles No No Yes
    Endomembrane system No No Yes (ER, Golgi, lysosomes)
    Ribosomes 70S 70S
    • 80S in cytoplasm and rough ER
    • 70S in mitochondria, chloroplasts

    Exercise \(\PageIndex{1}\)

    Identify two differences between eukaryotic and prokaryotic cell.

    Clinical Focus: part 1

    Upon arriving home from school, 7-year-old Sarah complains that a large spot on her arm will not stop itching. She keeps scratching at it, drawing the attention of her parents. Looking more closely, they see that it is a red circular spot with a raised red edge (Figure \(\PageIndex{2}\)).


    Figure \(\PageIndex{2}\): Ringworm presents as a raised, red ring on the skin. (credit: Centers for Disease Control and Prevention)

    The next day, Sarah’s parents take her to their doctor, who examines the spot using a Wood’s lamp. A Wood’s lamp produces ultraviolet light that causes the spot on Sarah’s arm to fluoresce, which confirms what the doctor already suspected: Sarah has a case of ringworm. Sarah’s mother is mortified to hear that her daughter has a “worm.” How could this happen?

    Exercise \(\PageIndex{2}\)

    What are some likely ways that Sarah might have contracted ringworm?

    Inside the cell:


    Unlike prokaryotic cells, in which DNA is loosely contained in the nucleoid region, eukaryotic cells possess a nucleus (plural = nuclei), which is surrounded by a complex nuclear membrane that houses the DNA genome (Figure \(\PageIndex{3}\)). By containing the cell’s DNA, the nucleus ultimately controls all activities of the cell and also serves an essential role in reproduction and heredity. Eukaryotic cells typically have their DNA organized into multiple linear chromosomes. The DNA within the nucleus is highly organized and condensed to fit inside the nucleus, which is accomplished by wrapping the DNA around proteins called histones.

    A micrograph of a portion of an oval cell. In the center is a darker spherical structure.
    Figure \(\PageIndex{3}\): Eukaryotic cells have a well-defined nucleus. The nucleus of this mammalian lung cell is the large, dark, oval-shaped structure in the lower half of the image.

    Although most eukaryotic cells have only one nucleus, exceptions exist. For example, protozoans of the genus Paramecium typically have two complete nuclei: a small nucleus that is used for reproduction (micronucleus) and a large nucleus that directs cellular metabolism (macronucleus). Additionally, some fungi transiently form cells with two nuclei, called heterokaryotic cells, during sexual reproduction. Cells whose nuclei divide, but whose cytoplasm does not, are called coenocytes.

    The nucleus is bound by a complex nuclear membrane, often called the nuclear envelope, that consists of two distinct lipid bilayers that are contiguous with each other (Figure \(\PageIndex{4}\)). Despite these connections between the inner and outer membranes, each membrane contains unique lipids and proteins on its inner and outer surfaces. The nuclear envelope contains nuclear pores, which are large, rosette-shaped protein complexes that control the movement of materials into and out of the nucleus. The overall shape of the nucleus is determined by the nuclear lamina, a meshwork of intermediate filaments found just inside the nuclear envelope membranes. Outside the nucleus, additional intermediate filaments form a looser mesh and serve to anchor the nucleus in position within the cell.

    A micrograph showing an oval cell with a large oval nucleus. The nucleus is red with a bright green outline labeled nuclear lamina. Green lines criss-cross the rest of the cell outside the nucleus.
    Figure \(\PageIndex{4}\): In this fluorescent microscope image, all the intermediate filaments have been stained with a bright green fluorescent stain. The nuclear lamina is the intense bright green ring around the faint red nuclei.


    The nucleolus is a dense region within the nucleus where ribosomal RNA (rRNA) biosynthesis occurs. In addition, the nucleolus is also the site where assembly of ribosomes begins. How does it do this? Some chromosomes have sections of DNA that encode ribosomal RNA. Pre-ribosomal complexes are assembled from rRNA and proteins into the ribosomal subunits in the nucleolus; these are then transported out to the cytoplasm, where ribosome assembly is completed (Figure \(\PageIndex{5}\)).

    a) A diagram showing the nucleus. A sphere in the center of the nucleus is labeled nucleolus. Lines within the nucleus are labeled chromatin. The fluid of the nucleus is labeled nucleoplasm. The outer region just inside the nuclear envelope is labeled nuclear lamina. The outside of the nucleus is labeled nuclear envelop and pores in the envelope are labeled nuclear pores.  The nuclear envelope is continuous with and becomes the endoplasmic reticulum; a webbing of membranes outside the nucleus. B) A micrograph showing these same structures. The nucleolus is a dark region inside the nucleus which is composed of many lighter lines. The nuclear envelop forms the outside of the nucleus and a pore is seen as a light region in the envelope. Outside the envelope are many lines labeled rough endoplasmic reticulum. A smaller set of lines is labeled mitochondrion overlaying part of the RER.
    Figure \(\PageIndex{5}\): (a) The nucleolus is the dark, dense area within the nucleus. It is the site of rRNA synthesis and preribosomal assembly. (b) Electron micrograph showing the nucleolus.

    Chromatin and Chromosomes

    Between the nucleolus and the nuclear envelope is the chromatin. To understand chromatin, it is helpful to first consider chromosomes. Chromosomes are structures within the nucleus that are made up of DNA, the hereditary material, and carry information (genes) that are required. You may remember that in prokaryotes, DNA is organized into a single circular chromosome. Eukaryotic chromosomes are typically linear, and eukaryotic cells contain multiple distinct chromosomes. Many eukaryotic cells contain two copies of each chromosome and, therefore, are diploid. The length of a even a single chromosome greatly exceeds the length of the cell, so a chromosome needs to be packaged into a very small space to fit within the cell. For example, the combined length of all of the DNA of the human genome would measure approximately 2 meters if completely stretched out, and some eukaryotic genomes are many times larger than the human genome. Every eukaryotic species has a specific number of chromosomes in the nuclei of its body’s cells. For example, in humans, the chromosome number is 46, while in fruit flies, it is eight. Chromosomes are only visible and distinguishable from one another when the cell is getting ready to divide. When the cell is in the growth and maintenance phases of its life cycle, proteins are attached to chromosomes, and they resemble an unwound, jumbled bunch of threads. These unwound protein-chromosome complexes are called chromatin (Figure \(\PageIndex{6}\)); chromatin describes the material that makes up the chromosomes both when condensed and decondensed.


    Figure \(\PageIndex{6}\): (a) This image shows various levels of the organization of chromatin (DNA and protein). (b) This image shows paired chromosomes. (credit b: modification of work by NIH; scale-bar data from Matt Russell)


    Cytoplasmic ribosomes in eukaryotic cells are 80S ribosomes, composed of a 40S small subunit and a 60S large subunit. In terms of size and composition, this makes them distinct from the ribosomes of prokaryotic cells. The two types of cytoplasmic eukaryotic ribosomes are defined by their location in the cell: free ribosomes and membrane-bound ribosomes. Free ribosomes are found floating in the cytoplasm and serve to synthesize water-soluble proteins; membrane-bound ribosomes are found attached to the cytoplasmic side of the rough endoplasmic reticulum and make proteins for insertion into the cell membrane or proteins destined for export from the cell.

    In contrast, ribosomes found in eukaryotic organelles such as mitochondria or chloroplasts have 70S ribosomes—the same size as prokaryotic ribosomes. The differences between eukaryotic and prokaryotic ribosomes are clinically relevant because certain antibiotic drugs are designed to target one or the other. For example, cycloheximide targets eukaryotic action, whereas chloramphenicol targets prokaryotic ribosomes.1 Since human cells are eukaryotic, they generally are not harmed by antibiotics that destroy the prokaryotic ribosomes in bacteria. However, sometimes negative side effects may occur because mitochondria in human cells contain prokaryotic ribosomes.

    Endomembrane System

    The endomembrane system, unique to eukaryotic cells, is a series of membranous tubules, sacs, and flattened disks that synthesize many cell components and move materials around within the cell (Figure \(\PageIndex{7}\)). Because of their larger cell size, eukaryotic cells require this system to transport materials that cannot be dispersed by diffusion alone. The endomembrane system comprises several organelles and connections between them, including the endoplasmic reticulum, Golgi apparatus, lysosomes, and vesicles.

    A diagram showing the nucleus. A sphere in the center of the nucleus is labeled nucleolus. Lines within the nucleus are labeled chromatin. The fluid of the nucleus is labeled nucleoplasm. The outer region just inside the nuclear envelope is labeled nuclear lamina. The outside of the nucleus is labeled nuclear envelop and pores in the envelope are labeled nuclear pores.  The nuclear envelope is continuous with and becomes the endoplasmic reticulum; a webbing of membranes outside the nucleus. Regions of the endoplasmic reticulum with dots are labeled rough endoplasmic reticulum (RER) and regions without dots are labeled smooth endoplasmic reticulum (SER). The RER and SER are continuous with each other.
    Figure \(\PageIndex{7}\): The endomembrane system is composed of a series of membranous intracellular structures that facilitate movement of materials throughout the cell and to the cell membrane.

    Endoplasmic Reticulum

    The endoplasmic reticulum (ER) is an interconnected array of tubules and cisternae (flattened sacs) with a single lipid bilayer (Figure \(\PageIndex{7}\)). The spaces inside of the cisternae are called lumen of the ER. There are two types of ER, rough endoplasmic reticulum (RER) and smooth endoplasmic reticulum (SER). These two different types of ER are sites for the synthesis of distinctly different types of molecules. RER is studded with ribosomes bound on the cytoplasmic side of the membrane. These ribosomes make proteins destined for the plasma membrane (Figure \(\PageIndex{8}\)). Following synthesis, these proteins are inserted into the membrane of the RER. Small sacs of the RER containing these newly synthesized proteins then bud off and move either to the Golgi apparatus for further processing, directly to the plasma membrane, to the membrane of another organelle, or out of the cell. SER does not have ribosomes and, therefore, appears “smooth.” It is involved in biosynthesis of lipids, carbohydrate synthesis and degradation, and detoxification of medications and poisons; and storage of calcium ions.

    a) A small diagram of the cell highlighting the nucleus and endoplasmic reticulum. The nucleus is a large sphere in the cell and the endoplasmic reticulum is a series of webbed membranes just outside the nucleus. B) A micrograph showing these same structures. Outside the nuclear envelope are many lines labeled rough endoplasmic reticulum. A smaller set of lines is labeled mitochondrion overlaying part of the RER.
    Figure \(\PageIndex{8}\): The rough endoplasmic reticulum is studded with ribosomes for the synthesis of membrane proteins (which give it its rough appearance).

    Golgi Apparatus

    The Golgi apparatus was discovered within the endomembrane system in 1898 by Italian scientist Camillo Golgi (1843–1926), who developed a novel staining technique that showed stacked membrane structures within the cells of Plasmodium, the causative agent of malaria. The Golgi apparatus is composed of a series of membranous disks called dictyosomes, each having a single lipid bilayer, that are stacked together (Figure \(\PageIndex{9}\)).

    Modification, sorting, tagging, packaging, and distribution of lipids and proteins takes place in the Golgi apparatus. Enzymes in the Golgi apparatus modify lipids and proteins transported from the ER to the Golgi, often adding carbohydrate components to them, producing glycolipids, glycoproteins, or proteoglycans. Glycolipids and glycoproteins are often inserted into the plasma membrane and are important for signal recognition by other cells or infectious particles. Different types of cells can be distinguished from one another by the structure and arrangement of the glycolipids and glycoproteins contained in their plasma membranes. These glycolipids and glycoproteins commonly also serve as cell surface receptors.

    Vesicles and Vacuoles

    Vesicles and vacuoles are single-lipid, bilayer, membranous spheres with hollow interiors that function in storage and transport. Other than the fact that vacuoles are somewhat larger than vesicles, there is a very subtle distinction between them: The membranes of vesicles can fuse with either the plasma membrane or other membrane systems within the cell. Additionally, some agents such as enzymes within plant vacuoles break down macromolecules. The membrane of a vacuole does not fuse with the membranes of other cellular components making them great storage units.

    Transport vesicles leaving the ER with proteins, carbohydrates and other goods or waste fuse with a Golgi apparatus on its receiving, or cis, face. The proteins are processed within the Golgi apparatus, and then additional transport vesicles containing the modified proteins and lipids pinch off from the Golgi apparatus on its outgoing, or trans, face. These outgoing vesicles move to and fuse with the plasma membrane (through exocytosis) or the membrane of other organelles (Figure \(\PageIndex{9}\)).

    A small diagram of the cell outlining the Golgi complex which is a series of stacked membranes in the cell. A more detailed diagram shows the stacked membranes labeled cisternae and the inner regions of the stacks labeled lumen. Small spheres on the top are show transport vesicles from ER fuse with the cis face of the golgi. Small spheres on the bottom show newly formed secretory vesicles emerging from the trans face of the golgi. A micrograph shows the golgi in the cell as a stack of lines forming a semi-circle.
    Figure \(\PageIndex{9}\): A transmission electron micrograph (left) of a Golgi apparatus in a white blood cell. The illustration (right) shows the cup-shaped, stacked disks and several transport vesicles. The Golgi apparatus modifies lipids and proteins, producing glycolipids and glycoproteins, respectively, which are commonly inserted into the plasma membrane.


    In the 1960s, Belgian scientist Christian de Duve (1917–2013) discovered lysosomes, membrane-bound organelles of the endomembrane system that contain digestive enzymes. Certain types of eukaryotic cells use lysosomes to break down various particles, such as food, damaged organelles or cellular debris, microorganisms, or immune complexes. Compartmentalization of the digestive enzymes within the lysosome allows the cell to efficiently digest matter without harming the cytoplasmic components of the cell.

    Exercise \(\PageIndex{3}\)

    Name the components of the endomembrane system and describe the function of each component.


    Christian de Duve is also credited with the discovery of peroxisomes, membrane-bound organelles that are not part of the endomembrane system (Figure \(\PageIndex{10}\)). Peroxisomes form independently in the cytoplasm from the synthesis of peroxin proteins by free ribosomes and the incorporation of these peroxin proteins into existing peroxisomes. Growing peroxisomes then divide by a process similar to binary fission.

    Peroxisomes were first named for their ability to produce hydrogen peroxide, a highly reactive molecule that helps to break down molecules such as uric acid, amino acids, and fatty acids. Peroxisomes also possess the enzyme catalase, which can degrade hydrogen peroxide. Along with the SER, peroxisomes also play a role in lipid biosynthesis. Like lysosomes, the compartmentalization of these degradative molecules within an organelle helps protect the cytoplasmic contents from unwanted damage.

    The peroxisomes of certain organisms are specialized to meet their particular functional needs. For example, glyoxysomes are modified peroxisomes of yeasts and plant cells that perform several metabolic functions, including the production of sugar molecules. Similarly, glycosomes are modified peroxisomes made by certain trypanosomes, the pathogenic protozoans that cause Chagas disease and African sleeping sickness.

    A diagram of the cell outlines the peroxisomes which are small spheres in the cell. A micrograph shows a close-up of the peroxisome which is a sphere within the cell.
    Figure \(\PageIndex{10}\): A transmission electron micrograph (left) of a cell containing a peroxisome. The illustration (right) shows the location of peroxisomes in a cell. These eukaryotic structures play a role in lipid biosynthesis and breaking down various molecules. They may also have other specialized functions depending on the cell type. (credit “micrograph”: modification of work by American Society for Microbiology).


    Eukaryotic cells have an internal cytoskeleton made of microfilaments, intermediate filaments, and microtubules. This matrix of fibers and tubes provides structural support as well as a network over which materials can be transported within the cell and on which organelles can be anchored (Figure \(\PageIndex{11}\)). For example, the process of exocytosis involves the movement of a vesicle via the cytoskeletal network to the plasma membrane, where it can release its contents.

    A micrograph shows many lines emminating from the nucleus and extending throughout the cell. These are shown in diagram form as small spheres forming the outside of a long tube. Each pair of spheres is a tubulin dimer and columns of these dimers can be seen on the outside of the large tube they form. The diameter of the tube is 25 µm. The same micrograph shows lines throughout the cell; these are drawn as spheres forming a braided structures (a double helix). The diameter of the helix is 7 nm. The spheres are labeled actin subunit. Another micrograph shows many lines forming a webbing in the cell. These are drawn as a rope; each strand of the rope is labeled fibrous subunit (keratins coiled together). The diameter of the rope is 8 – 12 nm.Figure \(\PageIndex{11}\): The cytoskeleton is a network of microtubules, microfilaments, and intermediate filaments found throughout the cytoplasm of a eukaryotic cell. In these fluorescently labeled animal cells, the microtubules are green, the actin microfilaments are red, the nucleus is blue, and keratin (a type of intermediate filament) is yellow.

    Microfilaments are composed of two intertwined strands of actin, each composed of actin monomers forming filamentous cables 6 nm in diameter2 (Figure \(\PageIndex{11}\)). The actin filaments work together with motor proteins, like myosin, to effect muscle contraction in animals or the amoeboid movement of some eukaryotic microbes. In ameboid organisms, actin can be found in two forms: a stiffer, polymerized, gel form and a more fluid, unpolymerized soluble form. Actin in the gel form creates stability in the ectoplasm, the gel-like area of cytoplasm just inside the plasma membrane of ameboid protozoans. Temporary extensions of the cytoplasmic membrane called pseudopodia (meaning “false feet”) are produced through the forward flow of soluble actin filaments into the pseudopodia, followed by the gel-sol cycling of the actin filaments, resulting in cell motility. Once the cytoplasm extends outward, forming a pseudopodium, the remaining cytoplasm flows up to join the leading edge, thereby creating forward locomotion. Beyond amoeboid movement, microfilaments are also involved in a variety of other processes in eukaryotic cells, including cytoplasmic streaming (the movement or circulation of cytoplasm within the cell), cleavage furrow formation during cell division, and muscle movement in animals (Figure \(\PageIndex{12}\)). These functions are the result of the dynamic nature of microfilaments, which can polymerize and depolymerize relatively easily in response to cellular signals, and their interactions with molecular motors in different types of eukaryotic cells.

    a) A diagram of the plasma membrane shows the filaments of the cytoskeleton as thin lines on the cytoplasmic side of the membrane. B) A closeup of the filaments shows spheres labeled actin subunits forming into a long chain labeled actin filaments. C)examples of how actin is used in various cells. Some cells use actin for amoeboid movement. This is done when actin polymerizes and depolymerizes to allow a portion of the cell to project out, attach to a surface and pull the rest of the cell behind it. Cytoplasmic streaming is the movement of cytoplasm due to the actions of actin. Contractile ring formation during cytokinesis is when actin pinches a dividing cell off into two separate cells. Muscle contraction in animals is when actin strands are pulled together by myosin; this shortens the length of the muscle cell and contracts the muscle.
    Figure \(\PageIndex{12}\): (a) A microfilament is composed of a pair of actin filaments. (b) Each actin filament is a string of polymerized actin monomers. (c) The dynamic nature of actin, due to its polymerization and depolymerization and its association with myosin, allows microfilaments to be involved in a variety of cellular processes, including ameboid movement, cytoplasmic streaming, contractile ring formation during cell division, and muscle contraction in animals.

    Intermediate filaments (Figure \(\PageIndex{13}\)) are a diverse group of cytoskeletal filaments that act as cables within the cell. They are termed “intermediate” because their 10-nm diameter is thicker than that of actin but thinner than that of microtubules.They are composed of several strands of polymerized subunits that, in turn, are made up of a wide variety of monomers. Intermediate filaments tend to be more permanent in the cell and maintain the position of the nucleus. They also form the nuclear lamina (lining or layer) just inside the nuclear envelope. Additionally, intermediate filaments play a role in anchoring cells together in animal tissues. The intermediate filament protein desmin is found in desmosomes, the protein structures that join muscle cells together and help them resist external physical forces. The intermediate filament protein keratin is a structural protein found in hair, skin, and nails.

    a) Intermediate filaments are shown as a rope-like structure. B) These are found in the nuclear lamina (lamina intermediate filaments) which are just under the nuclear envelope. C) Intermediate filaments are also found in desmosomes. Desmosomes are connections between two cells (shown here as two small regions of plasma membranes next to each other. The intermediate filaments connect these two membranes together across the extracellular space. A micrograph shows these as dark lines running across the membranes between two cells.
    Figure \(\PageIndex{13}\): (a) Intermediate filaments are composed of multiple strands of polymerized subunits. They are more permanent than other cytoskeletal structures and serve a variety of functions. (b) Intermediate filaments form much of the nuclear lamina. (c) Intermediate filaments form the desmosomes between cells in some animal tissues. (credit c “illustration”: modification of work by Mariana Ruiz Villareal)

    Microtubules (Figure \(\PageIndex{14}\)) are a third type of cytoskeletal fiber composed of tubulin dimers (α tubulin and β tubulin). These form hollow tubes 23 nm in diameter that are used as girders within the cytoskeleton.4 Like microfilaments, microtubules are dynamic and have the ability to rapidly assemble and disassemble. Microtubules also work with motor proteins (such as dynein and kinesin) to move organelles and vesicles around within the cytoplasm. Additionally, microtubules are the main components of eukaryotic flagella and cilia, composing both the filament and the basal body components (Figure \(\PageIndex{21}\)). Microtubules are also involved in cell division, forming the mitotic spindle that serves to separate chromosomes during mitosis and meiosis. The mitotic spindle is produced by two centrosomes, which are essentially microtubule-organizing centers, at opposite ends of the cell.

    A) a computer simulation shows micrtububles as spheres forming a rube structure. This can be drawn as spheres forming a ring; stacks of these rings form the tube. Each ring is 13 polymerized dimers of alpha-tubulin and beta-tubulin. C) The long tubes that are formed create a structure similar to a railroad track; motor proteins move along the microtubule track to carry vesicles throughout the cell.
    Figure \(\PageIndex{14}\): (a) Microtubules are hollow structures composed of polymerized tubulin dimers. (b) They are involved in several cellular processes, including the movement of organelles throughout the cytoplasm. Motor proteins carry organelles along microtubule tracks that crisscross the entire cell. (credit b: modification of work by National Institute on Aging)

    Exercise \(\PageIndex{4}\)

    Compare and contrast the three types of cytoskeletal structures described in this section.


    Endosymbiotic Theory

    As scientists were making progress toward understanding the role of cells in plant and animal tissues, others were examining the structures within the cells themselves. In 1831, Scottish botanist Robert Brown (1773–1858) was the first to describe observations of nuclei, which he observed in plant cells. Then, in the early 1880s, German botanist Andreas Schimper (1856–1901) was the first to describe the chloroplasts of plant cells, identifying their role in starch formation during photosynthesis and noting that they divided independent of the nucleus.

    Based upon the chloroplasts’ ability to reproduce independently, Russian botanist Konstantin Mereschkowski (1855–1921) suggested in 1905 that chloroplasts may have originated from ancestral photosynthetic bacteria living symbiotically inside a eukaryotic cell. He proposed a similar origin for the nucleus of plant cells. This was the first articulation of the endosymbiotic hypothesis, and would explain how eukaryotic cells evolved from ancestral bacteria.

    Mereschkowski’s endosymbiotic hypothesis was furthered by American anatomist Ivan Wallin (1883–1969), who began to experimentally examine the similarities between mitochondria, chloroplasts, and bacteria—in other words, to put the endosymbiotic hypothesis to the test using objective investigation. Wallin published a series of papers in the 1920s supporting the endosymbiotic hypothesis, including a 1926 publication co-authored with Mereschkowski. Wallin claimed he could culture mitochondria outside of their eukaryotic host cells. Many scientists dismissed his cultures of mitochondria as resulting from bacterial contamination. Modern genome sequencing work supports the dissenting scientists by showing that much of the genome of mitochondria had been transferred to the host cell’s nucleus, preventing the mitochondria from being able to live on their own.6 7

    Wallin’s ideas regarding the endosymbiotic hypothesis were largely ignored for the next 50 years because scientists were unaware that these organelles contained their own DNA. However, with the discovery of mitochondrial and chloroplast DNA in the 1960s, the endosymbiotic hypothesis was resurrected. Lynn Margulis (1938–2011), an American geneticist, published her ideas regarding the endosymbiotic hypothesis of the origins of mitochondria and chloroplasts in 1967.8 In the decade leading up to her publication, advances in microscopy had allowed scientists to differentiate prokaryotic cells from eukaryotic cells. In her publication, Margulis reviewed the literature and argued that the eukaryotic organelles such as mitochondria and chloroplasts are of prokaryotic origin. She presented a growing body of microscopic, genetic, molecular biology, fossil, and geological data to support her claims.

    Diagram of the endosymbiotic theory. Step 1 shows a cell labeled proto-eukaryote; the cell contains an outer membrane and DNA inside. The text reads: infoldings in the plasm amembrane of an ancestral cell gave rise to endomembrane components, including a nucleus and endoplasmic reticulum. The cell now contains DNA within a membrane (the nucleus). Outside are many folds labeled endoplasmic reticulum. Step 2 reads: In a first endosymbiotic event, the ancestral eukaryote consumed aerobic bacteria that evolved into mitochondria. The cell how shows a small oval entering the larger cell; the small oval is labeled aerobic bacterium. Once the small oval is in the cell, it is now labeled mitochondrion. The larger cell is now labeled modern heterotrophic eukaryote.  Step 3 reads: in a second endosymbiotic event, the early eukaryote consumed photosynthetic bacteria that evolved into chloroplast. The cell is shown engulfing another small oval labeled photosynthetic bacterium.  Once the oval is inside the larger cell is now labeled modern photosynthetic eukaryote.
    Figure \(\PageIndex{15}\): According to the endosymbiotic theory, mitochondria and chloroplasts are each derived from the uptake of bacteria. These bacteria established a symbiotic relationship with their host cell that eventually led to the bacteria evolving into mitochondria and chloroplasts.

    Again, this hypothesis was not initially popular, but mounting genetic evidence due to the advent of DNA sequencing supported the endosymbiotic theory, which is now defined as the theory that mitochondria and chloroplasts arose as a result of prokaryotic cells establishing a symbiotic relationship within a eukaryotic host (Figure \(\PageIndex{15}\)). With Margulis’ initial endosymbiotic theory gaining wide acceptance, she expanded on the theory in her 1981 book Symbiosis in Cell Evolution. In it, she explains how endosymbiosis is a major driving factor in the evolution of organisms. More recent genetic sequencing and phylogenetic analysis show that mitochondrial DNA and chloroplast DNA are highly related to their bacterial counterparts, both in DNA sequence and chromosome structure. However, mitochondrial DNA and chloroplast DNA are reduced compared with nuclear DNA because many of the genes have moved from the organelles into the host cell’s nucleus. Additionally, mitochondrial and chloroplast ribosomes are structurally similar to bacterial ribosomes, rather than to the eukaryotic ribosomes of their hosts. Last, the binary fission of these organelles strongly resembles the binary fission of bacteria, as compared with mitosis performed by eukaryotic cells. Since Margulis’ original proposal, scientists have observed several examples of bacterial endosymbionts in modern-day eukaryotic cells. Examples include the endosymbiotic bacteria found within the guts of certain insects, such as cockroaches,9 and photosynthetic bacteria-like organelles found in protists.10

    Exercise \(\PageIndex{5}\)

    1. What does the modern endosymbiotic theory state?
    2. What evidence supports the endosymbiotic theory?


    Mitochondria (singular = mitochondrion) are often called the “powerhouses” or “energy factories” of a cell because they are responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule. ATP represents the short-term stored energy of the cell. Cellular respiration is the process of making ATP using the chemical energy found in glucose and other nutrients. In mitochondria, this process uses oxygen and produces carbon dioxide as a waste product. In fact, the carbon dioxide that you exhale with every breath comes from the cellular reactions that produce carbon dioxide as a byproduct (Figure \(\PageIndex{16}\)). The term “mitochondrion” was first coined by German microbiologist Carl Benda in 1898 and was later connected with the process of respiration by Otto Warburg in 1913.

    Each mitochondrion has two lipid membranes. The outer membrane is a remnant of the original host cell’s membrane structures. The inner membrane was derived from the bacterial plasma membrane. The electron transport chain for aerobic respiration uses integral proteins embedded in the inner membrane. The mitochondrial matrix, corresponding to the location of the original bacterium’s cytoplasm, is the current location of many metabolic enzymes. It also contains mitochondrial DNA and 70S ribosomes. Invaginations of the inner membrane, called cristae, evolved to increase surface area for the location of biochemical reactions. The folding patterns of the cristae differ among various types of eukaryotic cells and are used to distinguish different eukaryotic organisms from each other.

    The mitochondria is shown as a long oval structure. The outside of the structure is an outer membrane. Inside of that is an inner membrane that folds back and forth filling most of the inner part of the mitochondrion. The folds of the inner membrane are labeled cristae and the fluid inside the inner membrane is the mitochondrial matrix. The space between the inner and outer membranes is the inner membrane space. Inside the mitochondrial matrix are found DNA, ribosomes and granules.

    Figure \(\PageIndex{16}\): Each mitochondrion is surrounded by two membranes, the inner of which is extensively folded into cristae and is the site of the intermembrane space. The mitochondrial matrix contains the mitochondrial DNA, ribosomes, and metabolic enzymes. The transmission electron micrograph of a mitochondrion, on the right, shows both membranes, including cristae and the mitochondrial matrix. (credit “micrograph”: modification of work by Matthew Britton; scale-bar data from Matt Russell)


    Plant cells and algal cells contain chloroplasts, the organelles in which photosynthesis occurs (Figure \(\PageIndex{17}\)). Photosynthesis is the series of reactions that use carbon dioxide, water, and light energy to make glucose and oxygen. All chloroplasts have at least three membrane systems: the outer membrane, the inner membrane, and the thylakoid membrane system. Inside the outer and inner membranes is the chloroplast stroma, a gel-like fluid that makes up much of a chloroplast’s volume, and in which the thylakoid system floats. The thylakoid system is a highly dynamic collection of folded membrane sacs. It is where the green photosynthetic pigment chlorophyll is found and the light reactions of photosynthesis occur. In most plant chloroplasts, the thylakoids are arranged in stacks called grana (singular: granum), whereas in some algal chloroplasts, the thylakoids are free floating.

    The cholorplast is shown as an oval structure with an outer membrane. The inner membrane folds into pancake like stacks called grana (stacks of thylakoids). One individual stack from the grana is called a thylakoid. The space inside the thylakoid is called the thylakoid lumen. The aqueous fluid outside the thylakoids but inside the inner membrane is the stroma. The space between the inner and outer membranes is the intermembrane space.

    Figure \(\PageIndex{17}\): Photosynthesis takes place in chloroplasts, which have an outer membrane and an inner membrane. Stacks of thylakoids called grana form a third membrane layer.

    Other organelles similar to mitochondria have arisen in other types of eukaryotes, but their roles differ. Hydrogenosomes are found in some anaerobic eukaryotes and serve as the location of anaerobic hydrogen production. Hydrogenosomes typically lack their own DNA and ribosomes. Kinetoplasts are a variation of the mitochondria found in some eukaryotic pathogens. In these organisms, each cell has a single, long, branched mitochondrion in which kinetoplast DNA, organized as multiple circular pieces of DNA, is found concentrated at one pole of the cell.

    Mitochondria-related Organelles in Protozoan Parasites

    Many protozoans, including several protozoan parasites that cause infections in humans, can be identified by their unusual appearance. Distinguishing features may include complex cell morphologies, the presence of unique organelles, or the absence of common organelles. The protozoan parasites Giardia lamblia and Trichomonas vaginalis are two examples.

    G. lamblia, a frequent cause of diarrhea in humans and many other animals, is an anaerobic parasite that possesses two nuclei and several flagella. Its Golgi apparatus and endoplasmic reticulum are greatly reduced, and it lacks mitochondria completely. However, it does have organelles known as mitosomes, double-membrane-bound organelles that appear to be severely reduced mitochondria. This has led scientists to believe that G. lamblia’s ancestors once possessed mitochondria that evolved to become mitosomes. T. vaginalis, which causes the sexually transmitted infection vaginitis, is another protozoan parasite that lacks conventional mitochondria. Instead, it possesses hydrogenosomes, mitochondrial-related, double-membrane-bound organelles that produce molecular hydrogen used in cellular metabolism. Scientists believe that hydrogenosomes, like mitosomes, also evolved from mitochondria.5

    The Boundary Layer: the Cellular Envelope

    Plasma Membrane

    The plasma membrane structure of most bacterial and eukaryotic cell types is a bilayer composed mainly of phospholipids formed with ester linkages and proteins. Proteins on the cell’s surface are important for a variety of functions. (review chapter 3 section 3 for more detail, will be described more in chapter 8) Unlike the prokaryotic membrane, eukaryotic membranes contain sterols, including cholesterol, that alter membrane fluidity. Additionally, many eukaryotic cells contain some specialized lipids, including sphingolipids, which are thought to play a role in maintaining membrane stability as well as being involved in signal transduction pathways and cell-to-cell communication.

    Cell Wall

    In addition to a plasma membrane, some eukaryotic cells have a cell wall. Cells of fungi, algae, plants, and even some protists have cell walls. Depending upon the type of eukaryotic cell, cell walls can be made of a wide range of materials, including cellulose (fungi and plants); biogenic silica, calcium carbonate, agar, and carrageenan (protists and algae); or chitin (fungi). In general, all cell walls provide structural stability for the cell and protection from environmental stresses such as desiccation, changes in osmotic pressure, and traumatic injury.6

    Outside the Cell

    Extracellular Matrix

    Cells of animals and some protozoans do not have cell walls to help maintain shape and provide structural stability. Instead, many of these types of eukaryotic cells produce an extracellular matrix for this purpose. They secrete a sticky mass of carbohydrates and proteins into the spaces between adjacent cells (Figure \(\PageIndex{18}\)). Some protein components assemble into a basement membrane to which the remaining extracellular matrix components adhere. Proteoglycans typically form the bulky mass of the extracellular matrix while fibrous proteins, like collagen, provide strength. Both proteoglycans and collagen are attached to fibronectin proteins, which, in turn, are attached to integrin proteins. These integrin proteins interact with transmembrane proteins in the plasma membranes of eukaryotic cells that lack cell walls. This makes them both similar and different to the glycocalyx found in prokaryote cells.

    A drawing of the plasma membrane with proteins shown in the membrane. One of these proteins is labeled integrin. Attached to this and other proteins are long strands made of a chain of hexagons labeled polysaccharides. Branches off this chain of hexagons are labeled proteins and branches of the proteins are labeled carbohydrates. These proteoglycan complexes (made of polysaccharides, proteins, and carbohydrates) are attached to proteins in the membranes via fibronectins. Larger chains on the outside of the membrane are not visibly attached to the membrane and are labeled collagen fibers. Smaller chains on the inside surface of the membrane are labeled microfilaments of cytoskeleton.
    Figure \(\PageIndex{18}\): The extracellular matrix is composed of protein and carbohydrate components. It protects cells from physical stresses and transmits signals arriving at the outside edges of the tissue to cells deeper within the tissue.

    In animal cells, the extracellular matrix allows cells within tissues to withstand external stresses and transmits signals from the outside of the cell to the inside. The amount of extracellular matrix is quite extensive in various types of connective tissues, and variations in the extracellular matrix can give different types of tissues their distinct properties. In addition, a host cell’s extracellular matrix is often the site where microbial pathogens attach themselves to establish infection. For example, Streptococcus pyogenes, the bacterium that causes strep throat and various other infections, binds to fibronectin in the extracellular matrix of the cells lining the oropharynx (upper region of the throat).

    Flagella and Cilia

    Some eukaryotic cells use flagella for locomotion; however, eukaryotic flagella are structurally distinct from those found in prokaryotic cells. Whereas the prokaryotic flagellum is a stiff, rotating structure, a eukaryotic flagellum is more like a flexible whip composed of nine parallel pairs of microtubules surrounding a central pair of microtubules. This arrangement is referred to as a 9+2 array (Figure \(\PageIndex{19}\)). The parallel microtubules use dynein motor proteins to move relative to each other, causing the flagellum to bend.

    Cilia (singular: cilium) are a similar external structure found in some eukaryotic cells. Unique to eukaryotes, cilia are shorter than flagella and often cover the entire surface of a cell; however, they are structurally similar to flagella (a 9+2 array of microtubules) and use the same mechanism for movement. A structure called a basal body is found at the base of each cilium and flagellum. The basal body, which helps connect the cilium or flagellum to the cell, is composed of an array of triplet microtubules similar to that of a centriole but embedded in the plasma membrane. Because of their shorter length, cilia use a rapid, flexible, waving motion. In addition to motility, cilia may have other functions such as sweeping particles past or into cells. For example, ciliated protozoans use the sweeping of cilia to move food particles into their mouthparts, and ciliated cells in the mammalian respiratory tract beat in synchrony to sweep mucus and debris up and out of the lungs (Figure \(\PageIndex{19}\)).

    a) A micrograph of a cross section of a flagellum showing a ring of 9 sets of structures that are made of smaller rings. In the center are two more complete smaller rings. B)  A micrograph showing a flagellum. This shows a star shaped structure in the cell attached to the long lines that make up the filament of the flagellum. A diagram shows the triplet centriole in the cell as part of the basal body that attaches the filament to the cell. The diagram also shows a cross section of the filament. The outer ring is made of 9 sets of the following: a ring labeled subfiber A, a ring labeled subfiber B, a projection labeled radial spoke with a small end labeled spoke head, a projection towards the center labeled inner dynein, and a projection towards the outside labeled outer dynein. Each of these 9 sets are connected to the ones next to it via a line called nexin. These 9 sets form a ring; in the center of this ring are 2 small circles labeled central singlet microtubule. These two are attached to each other by a line labeled central bridge. C) A cell with flagella on either end. D) A cell with many small cilia along the outside and an indentation labeled mouth.
    Figure \(\PageIndex{19}\): (a) Eukaryotic flagella and cilia are composed of a 9+2 array of microtubules, as seen in this transmission electron micrograph cross-section. (b) The sliding of these microtubules relative to each other causes a flagellum to bend. (c) An illustration of Trichomonas vaginalis, a flagellated protozoan parasite that causes vaginitis. (d) Many protozoans, like this Paramecium, have numerous cilia that aid in locomotion as well as in feeding. Note the mouth opening shown here. (credit d: modification of work by University of Vermont/National Institutes of Health)

    Exercise \(\PageIndex{6}\)

    1. Explain how the cellular envelope of eukaryotic cells compares to that of prokaryotic cells.
    2. Explain the difference between eukaryotic and prokaryotic flagella.

    Key Concepts and Summary

    • Eukaryotic cells are defined by the presence of a nucleus containing the DNA genome and bound by a nuclear membrane (or nuclear envelope) composed of two lipid bilayers that regulate transport of materials into and out of the nucleus through nuclear pores.
    • Eukaryotic cell morphologies vary greatly and may be maintained by various structures, including the cytoskeleton, the cell membrane, and/or the cell wall
    • The nucleolus, located in the nucleus of eukaryotic cells, is the site of ribosomal synthesis and the first stages of ribosome assembly.
    • Eukaryotic cells contain 80S ribosomes in the rough endoplasmic reticulum (membrane bound-ribosomes) and cytoplasm (free ribosomes). They contain 70s ribosomes in mitochondria and chloroplasts.
    • Eukaryotic cells have evolved an endomembrane system, containing membrane-bound organelles involved in transport. These include vesicles, the endoplasmic reticulum, and the Golgi apparatus.
    • The smooth endoplasmic reticulum plays a role in lipid biosynthesis, carbohydrate metabolism, and detoxification of toxic compounds. The rough endoplasmic reticulum contains membrane-bound 80S ribosomes that synthesize proteins destined for the cell membrane
    • The Golgi apparatus processes proteins and lipids, typically through the addition of sugar molecules, producing glycoproteins or glycolipids, components of the plasma membrane that are used in cell-to-cell communication.
    • Lysosomes contain digestive enzymes that break down small particles ingested by endocytosis, large particles or cells ingested by phagocytosis, and damaged intracellular components.
    • The cytoskeleton, composed of microfilaments, intermediate filaments, and microtubules, provides structural support in eukaryotic cells and serves as a network for transport of intracellular materials.
    • Centrosomes are microtubule-organizing centers important in the formation of the mitotic spindle in mitosis.
    • Endosymbiotic theory states that mitochondria and chloroplasts, organelles found in many types of organisms, have their origins in bacteria. Significant structural and genetic information support this theory.
    • Mitochondria are the site of cellular respiration. They have two membranes: an outer membrane and an inner membrane with cristae. The mitochondrial matrix, within the inner membrane, contains the mitochondrial DNA, 70S ribosomes, and metabolic enzymes.
    • Chloroplasts are used by plants and some protists to help collect solar energy and transform it into sugars for food, structural components or other uses.
    • The plasma membrane of eukaryotic cells is structurally similar to that found in prokaryotic cells, and membrane components move according to the fluid mosaic model. However, eukaryotic membranes contain sterols, which alter membrane fluidity, as well as glycoproteins and glycolipids, which help the cell recognize other cells and infectious particles
    • Cells of fungi, algae, plants, and some protists have a cell wall, whereas cells of animals and some protozoans have a sticky extracellular matrix that provides structural support and mediates cellular signaling.
    • Eukaryotic flagella are structurally distinct from prokaryotic flagella but serve a similar purpose (locomotion). Cilia are structurally similar to eukaryotic flagella, but shorter; they may be used for locomotion, feeding, or movement of extracellular particles.


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    • Nina Parker, (Shenandoah University), Mark Schneegurt (Wichita State University), Anh-Hue Thi Tu (Georgia Southwestern State University), Philip Lister (Central New Mexico Community College), and Brian M. Forster (Saint Joseph’s University) with many contributing authors. Original content via Openstax (CC BY 4.0; Access for free at

    This page titled 5.1: Characteristics of Eukaryotic Cells is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.