3.1.3: Eukaryotic Cells - Biology

3.1.3: Eukaryotic Cells - Biology

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At this point, it should be clear that eukaryotic cells have a more complex structure than do prokaryotic cells. Before discussing the functions of organelles within a eukaryotic cell, let us first examine two important components of the cell: the plasma membrane and the cytoplasm.


What structures does a plant cell have that an animal cell does not have? What structures does an animal cell have that a plant cell does not have?

The Plasma Membrane

Like prokaryotes, eukaryotic cells have a plasma membrane (Figure (PageIndex{2})) made up of a phospholipid bilayer with embedded proteins that separates the internal contents of the cell from its surrounding environment. A phospholipid is a lipid molecule composed of two fatty acid chains, a glycerol backbone, and a phosphate group. The plasma membrane regulates the passage of some substances, such as organic molecules, ions, and water, preventing the passage of some to maintain internal conditions, while actively bringing in or removing others. Other compounds move passively across the membrane.

The plasma membranes of cells that specialize in absorption are folded into fingerlike projections called microvilli (singular = microvillus). This folding increases the surface area of the plasma membrane. Such cells are typically found lining the small intestine, the organ that absorbs nutrients from digested food. This is an excellent example of form matching the function of a structure.

People with celiac disease have an immune response to gluten, which is a protein found in wheat, barley, and rye. The immune response damages microvilli, and thus, afflicted individuals cannot absorb nutrients. This leads to malnutrition, cramping, and diarrhea. Patients suffering from celiac disease must follow a gluten-free diet.

The Cytoplasm

The cytoplasm comprises the contents of a cell between the plasma membrane and the nuclear envelope (a structure to be discussed shortly). It is made up of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals (Figure (PageIndex{1})). Even though the cytoplasm consists of 70 to 80 percent water, it has a semi-solid consistency, which comes from the proteins within it. However, proteins are not the only organic molecules found in the cytoplasm. Glucose and other simple sugars, polysaccharides, amino acids, nucleic acids, fatty acids, and derivatives of glycerol are found there too. Ions of sodium, potassium, calcium, and many other elements are also dissolved in the cytoplasm. Many metabolic reactions, including protein synthesis, take place in the cytoplasm.

The Cytoskeleton

If you were to remove all the organelles from a cell, would the plasma membrane and the cytoplasm be the only components left? No. Within the cytoplasm, there would still be ions and organic molecules, plus a network of protein fibers that helps to maintain the shape of the cell, secures certain organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move independently. Collectively, this network of protein fibers is known as the cytoskeleton. There are three types of fibers within the cytoskeleton: microfilaments, also known as actin filaments, intermediate filaments, and microtubules (Figure (PageIndex{3})).

Microfilaments are the thinnest of the cytoskeletal fibers and function in moving cellular components, for example, during cell division. They also maintain the structure of microvilli, the extensive folding of the plasma membrane found in cells dedicated to absorption. These components are also common in muscle cells and are responsible for muscle cell contraction. Intermediate filaments are of intermediate diameter and have structural functions, such as maintaining the shape of the cell and anchoring organelles. Keratin, the compound that strengthens hair and nails, forms one type of intermediate filament. Microtubules are the thickest of the cytoskeletal fibers. These are hollow tubes that can dissolve and reform quickly. Microtubules guide organelle movement and are the structures that pull chromosomes to their poles during cell division. They are also the structural components of flagella and cilia. In cilia and flagella, the microtubules are organized as a circle of nine double microtubules on the outside and two microtubules in the center.

The centrosome is a region near the nucleus of animal cells that functions as a microtubule-organizing center. It contains a pair of centrioles, two structures that lie perpendicular to each other. Each centriole is a cylinder of nine triplets of microtubules.

The centrosome replicates itself before a cell divides, and the centrioles play a role in pulling the duplicated chromosomes to opposite ends of the dividing cell. However, the exact function of the centrioles in cell division is not clear, since cells that have the centrioles removed can still divide, and plant cells, which lack centrioles, are capable of cell division.

Flagella and Cilia

Flagella (singular = flagellum) are long, hair-like structures that extend from the plasma membrane and are used to move an entire cell, (for example, sperm, Euglena). When present, the cell has just one flagellum or a few flagella. When cilia (singular = cilium) are present, however, they are many in number and extend along the entire surface of the plasma membrane. They are short, hair-like structures that are used to move entire cells (such as paramecium) or move substances along the outer surface of the cell (for example, the cilia of cells lining the fallopian tubes that move the ovum toward the uterus, or cilia lining the cells of the respiratory tract that move particulate matter toward the throat that mucus has trapped).

The Endomembrane System

The endomembrane system (endo = within) is a group of membranes and organelles (Figure (PageIndex{3})) in eukaryotic cells that work together to modify, package, and transport lipids and proteins. It includes the nuclear envelope, lysosomes, and vesicles, the endoplasmic reticulum and Golgi apparatus, which we will cover shortly. Although not technically within the cell, the plasma membrane is included in the endomembrane system because, as you will see, it interacts with the other endomembranous organelles.

The Nucleus

Typically, the nucleus is the most prominent organelle in a cell (Figure (PageIndex{1})). The nucleus (plural = nuclei) houses the cell’s DNA in the form of chromatin and directs the synthesis of ribosomes and proteins. Let us look at it in more detail (Figure (PageIndex{4})).

The nuclear envelope is a double-membrane structure that constitutes the outermost portion of the nucleus (Figure (PageIndex{4})). Both the inner and outer membranes of the nuclear envelope are phospholipid bilayers.

The nuclear envelope is punctuated with pores that control the passage of ions, molecules, and RNA between the nucleoplasm and the cytoplasm.

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 proteins. This combination of DNA and proteins is called chromatin. In eukaryotes, chromosomes are linear structures. Every species has a specific number of chromosomes in the nucleus of its body cells. For example, in humans, the chromosome number is 46, whereas in fruit flies, the chromosome number 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, the chromosomes resemble an unwound, jumbled bunch of threads.

We already know that the nucleus directs the synthesis of ribosomes, but how does it do this? Some chromosomes have sections of DNA that encode ribosomal RNA. A darkly staining area within the nucleus, called the nucleolus (plural = nucleoli), aggregates the ribosomal RNA with associated proteins to assemble the ribosomal subunits that are then transported through the nuclear pores into the cytoplasm.

The Endoplasmic Reticulum

The endoplasmic reticulum (ER) (Figure (PageIndex{7})) is a series of interconnected membranous tubules that collectively modify proteins and synthesize lipids. However, these two functions are performed in separate areas of the endoplasmic reticulum: the rough endoplasmic reticulum and the smooth endoplasmic reticulum, respectively.

The hollow portion of the ER tubules is called the lumen or cisternal space. The membrane of the ER, which is a phospholipid bilayer embedded with proteins, is continuous with the nuclear envelope.

The rough endoplasmic reticulum (RER) is so named because the ribosomes attached to its cytoplasmic surface give it a studded appearance when viewed through an electron microscope.

The ribosomes synthesize proteins while attached to the ER, resulting in transfer of their newly synthesized proteins into the lumen of the RER where they undergo modifications such as folding or addition of sugars. The RER also makes phospholipids for cell membranes.

If the phospholipids or modified proteins are not destined to stay in the RER, they will be packaged within vesicles and transported from the RER by budding from the membrane (Figure (PageIndex{7})). Since the RER is engaged in modifying proteins that will be secreted from the cell, it is abundant in cells that secrete proteins, such as the liver.

The smooth endoplasmic reticulum (SER) is continuous with the RER but has few or no ribosomes on its cytoplasmic surface (see Figure (PageIndex{1})). The SER’s functions include synthesis of carbohydrates, lipids (including phospholipids), and steroid hormones; detoxification of medications and poisons; alcohol metabolism; and storage of calcium ions.

The Golgi Apparatus

We have already mentioned that vesicles can bud from the ER, but where do the vesicles go? Before reaching their final destination, the lipids or proteins within the transport vesicles need to be sorted, packaged, and tagged so that they wind up in the right place. The sorting, tagging, packaging, and distribution of lipids and proteins take place in the Golgi apparatus (also called the Golgi body), a series of flattened membranous sacs (Figure (PageIndex{5})).

The Golgi apparatus has a receiving face near the endoplasmic reticulum and a releasing face on the side away from the ER, toward the cell membrane. The transport vesicles that form from the ER travel to the receiving face, fuse with it, and empty their contents into the lumen of the Golgi apparatus. As the proteins and lipids travel through the Golgi, they undergo further modifications. The most frequent modification is the addition of short chains of sugar molecules. The newly modified proteins and lipids are then tagged with small molecular groups to enable them to be routed to their proper destinations.

Finally, the modified and tagged proteins are packaged into vesicles that bud from the opposite face of the Golgi. While some of these vesicles, transport vesicles, deposit their contents into other parts of the cell where they will be used, others, secretory vesicles, fuse with the plasma membrane and release their contents outside the cell.

The amount of Golgi in different cell types again illustrates that form follows function within cells. Cells that engage in a great deal of secretory activity (such as cells of the salivary glands that secrete digestive enzymes or cells of the immune system that secrete antibodies) have an abundant number of Golgi.

In plant cells, the Golgi has an additional role of synthesizing polysaccharides, some of which are incorporated into the cell wall and some of which are used in other parts of the cell.


In animal cells, the lysosomes are the cell’s “garbage disposal.” Digestive enzymes within the lysosomes aid the breakdown of proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles. In single-celled eukaryotes, lysosomes are important for digestion of the food they ingest and the recycling of organelles. These enzymes are active at a much lower pH (more acidic) than those located in the cytoplasm. Many reactions that take place in the cytoplasm could not occur at a low pH, thus the advantage of compartmentalizing the eukaryotic cell into organelles is apparent.

Lysosomes also use their hydrolytic enzymes to destroy disease-causing organisms that might enter the cell. A good example of this occurs in a group of white blood cells called macrophages, which are part of your body’s immune system. In a process known as phagocytosis, a section of the plasma membrane of the macrophage invaginates (folds in) and engulfs a pathogen. The invaginated section, with the pathogen inside, then pinches itself off from the plasma membrane and becomes a vesicle. The vesicle fuses with a lysosome. The lysosome’s hydrolytic enzymes then destroy the pathogen (Figure (PageIndex{6})).

Vesicles and Vacuoles

Vesicles and vacuoles are membrane-bound sacs that function in storage and transport. Vacuoles are somewhat larger than vesicles, and the membrane of a vacuole does not fuse with the membranes of other cellular components. Vesicles can fuse with other membranes within the cell system. Additionally, enzymes within plant vacuoles can break down macromolecules.


Why does the cis face of the Golgi not face the plasma membrane?


Ribosomes are the cellular structures responsible for protein synthesis. When viewed through an electron microscope, free ribosomes appear as either clusters or single tiny dots floating freely in the cytoplasm. Ribosomes may be attached to either the cytoplasmic side of the plasma membrane or the cytoplasmic side of the endoplasmic reticulum (Figure (PageIndex{7})). Electron microscopy has shown that ribosomes consist of large and small subunits. Ribosomes are enzyme complexes that are responsible for protein synthesis.

Because protein synthesis is essential for all cells, ribosomes are found in practically every cell, although they are smaller in prokaryotic cells. They are particularly abundant in immature red blood cells for the synthesis of hemoglobin, which functions in the transport of oxygen throughout the body.


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. The formation of ATP from the breakdown of glucose is known as cellular respiration. Mitochondria are oval-shaped, double-membrane organelles (Figure (PageIndex{8})) that have their own ribosomes and DNA. Each membrane is a phospholipid bilayer embedded with proteins. The inner layer has folds called cristae, which increase the surface area of the inner membrane. The area surrounded by the folds is called the mitochondrial matrix. The cristae and the matrix have different roles in cellular respiration.

In keeping with our theme of form following function, it is important to point out that muscle cells have a very high concentration of mitochondria because muscle cells need a lot of energy to contract.


Peroxisomes are small, round organelles enclosed by single membranes. They carry out oxidation reactions that break down fatty acids and amino acids. They also detoxify many poisons that may enter the body. Alcohol is detoxified by peroxisomes in liver cells. A byproduct of these oxidation reactions is hydrogen peroxide, H2O2, which is contained within the peroxisomes to prevent the chemical from causing damage to cellular components outside of the organelle. Hydrogen peroxide is safely broken down by peroxisomal enzymes into water and oxygen.

Animal Cells versus Plant Cells

Despite their fundamental similarities, there are some striking differences between animal and plant cells (see Table). Animal cells have centrioles, centrosomes (discussed under the cytoskeleton), and lysosomes, whereas plant cells do not. Plant cells have a cell wall, chloroplasts, plasmodesmata, and plastids used for storage, and a large central vacuole, whereas animal cells do not.

The Cell Wall

In Figure (PageIndex{1})b, the diagram of a plant cell, you see a structure external to the plasma membrane called the cell wall. The cell wall is a rigid covering that protects the cell, provides structural support, and gives shape to the cell. Fungal and protist cells also have cell walls.

While the chief component of prokaryotic cell walls is peptidoglycan, the major organic molecule in the plant cell wall is cellulose, a polysaccharide made up of long, straight chains of glucose units. When nutritional information refers to dietary fiber, it is referring to the cellulose content of food.


Like mitochondria, chloroplasts also have their own DNA and ribosomes. Chloroplasts function in photosynthesis and can be found in eukaryotic cells such as plants and algae. In photosynthesis, carbon dioxide, water, and light energy are used to make glucose and oxygen. This is the major difference between plants and animals: Plants (autotrophs) are able to make their own food, like glucose, whereas animals (heterotrophs) must rely on other organisms for their organic compounds or food source.

Like mitochondria, chloroplasts have outer and inner membranes, but within the space enclosed by a chloroplast’s inner membrane is a set of interconnected and stacked, fluid-filled membrane sacs called thylakoids (Figure (PageIndex{9})). Each stack of thylakoids is called a granum (plural = grana). The fluid enclosed by the inner membrane and surrounding the grana is called the stroma.

The chloroplasts contain a green pigment called chlorophyll, which captures the energy of sunlight for photosynthesis. Like plant cells, photosynthetic protists also have chloroplasts. Some bacteria also perform photosynthesis, but they do not have chloroplasts. Their photosynthetic pigments are located in the thylakoid membrane within the cell itself.


We have mentioned that both mitochondria and chloroplasts contain DNA and ribosomes. Have you wondered why? Strong evidence points to endosymbiosis as the explanation.

Symbiosis is a relationship in which organisms from two separate species live in close association and typically exhibit specific adaptations to each other. Endosymbiosis (endo-= within) is a relationship in which one organism lives inside the other. Endosymbiotic relationships abound in nature. Microbes that produce vitamin K live inside the human gut. This relationship is beneficial for us because we are unable to synthesize vitamin K. It is also beneficial for the microbes because they are protected from other organisms and are provided a stable habitat and abundant food by living within the large intestine.

Scientists have long noticed that bacteria, mitochondria, and chloroplasts are similar in size. We also know that mitochondria and chloroplasts have DNA and ribosomes, just as bacteria do. Scientists believe that host cells and bacteria formed a mutually beneficial endosymbiotic relationship when the host cells ingested aerobic bacteria and cyanobacteria but did not destroy them. Through evolution, these ingested bacteria became more specialized in their functions, with the aerobic bacteria becoming mitochondria and the photosynthetic bacteria becoming chloroplasts.

The Central Vacuole

Previously, we mentioned vacuoles as essential components of plant cells. If you look at Figure (PageIndex{1}), you will see that plant cells each have a large, central vacuole that occupies most of the cell. The central vacuole plays a key role in regulating the cell’s concentration of water in changing environmental conditions. In plant cells, the liquid inside the central vacuole provides turgor pressure, which is the outward pressure caused by the fluid inside the cell. Have you ever noticed that if you forget to water a plant for a few days, it wilts? That is because as the water concentration in the soil becomes lower than the water concentration in the plant, water moves out of the central vacuoles and cytoplasm and into the soil. As the central vacuole shrinks, it leaves the cell wall unsupported. This loss of support to the cell walls of a plant results in the wilted appearance. Additionally, this fluid has a very bitter taste, which discourages consumption by insects and animals. The central vacuole also functions to store proteins in developing seed cells.

Most animal cells release materials into the extracellular space. The primary components of these materials are glycoproteins and the protein collagen. Collectively, these materials are called the extracellular matrix (Figure (PageIndex{10})). Not only does the extracellular matrix hold the cells together to form a tissue, but it also allows the cells within the tissue to communicate with each other.

Blood clotting provides an example of the role of the extracellular matrix in cell communication. When the cells lining a blood vessel are damaged, they display a protein receptor called tissue factor. When tissue factor binds with another factor in the extracellular matrix, it causes platelets to adhere to the wall of the damaged blood vessel, stimulates adjacent smooth muscle cells in the blood vessel to contract (thus constricting the blood vessel), and initiates a series of steps that stimulate the platelets to produce clotting factors.

Intercellular Junctions

Cells can also communicate with each other by direct contact, referred to as intercellular junctions. There are some differences in the ways that plant and animal cells do this. Plasmodesmata (singular = plasmodesma) are junctions between plant cells, whereas animal cell contacts include tight and gap junctions, and desmosomes.

In general, long stretches of the plasma membranes of neighboring plant cells cannot touch one another because they are separated by the cell walls surrounding each cell. Plasmodesmata are numerous channels that pass between the cell walls of adjacent plant cells, connecting their cytoplasm and enabling signal molecules and nutrients to be transported from cell to cell (Figure (PageIndex{11})a).

A tight junction is a watertight seal between two adjacent animal cells (Figure (PageIndex{11})b). Proteins hold the cells tightly against each other. This tight adhesion prevents materials from leaking between the cells. Tight junctions are typically found in the epithelial tissue that lines internal organs and cavities, and composes most of the skin. For example, the tight junctions of the epithelial cells lining the urinary bladder prevent urine from leaking into the extracellular space.

Also found only in animal cells are desmosomes, which act like spot welds between adjacent epithelial cells (Figure (PageIndex{11})c). They keep cells together in a sheet-like formation in organs and tissues that stretch, like the skin, heart, and muscles.

Gap junctions in animal cells are like plasmodesmata in plant cells in that they are channels between adjacent cells that allow for the transport of ions, nutrients, and other substances that enable cells to communicate (Figure (PageIndex{11})d). Structurally, however, gap junctions and plasmodesmata differ.

Table (PageIndex{1}): This table provides the components of prokaryotic and eukaryotic cells and their respective functions.
Cell ComponentFunctionPresent in Prokaryotes?Present in Animal Cells?Present in Plant Cells?
Plasma membraneSeparates cell from external environment; controls passage of organic molecules, ions, water, oxygen, and wastes into and out of the cellYesYesYes
CytoplasmProvides structure to cell; site of many metabolic reactions; medium in which organelles are foundYesYesYes
NucleoidLocation of DNAYesNoNo
NucleusCell organelle that houses DNA and directs synthesis of ribosomes and proteinsNoYesYes
RibosomesProtein synthesisYesYesYes
MitochondriaATP production/cellular respirationNoYesYes
PeroxisomesOxidizes and breaks down fatty acids and amino acids, and detoxifies poisonsNoYesYes
Vesicles and vacuolesStorage and transport; digestive function in plant cellsNoYesYes
CentrosomeUnspecified role in cell division in animal cells; organizing center of microtubules in animal cellsNoYesNo
LysosomesDigestion of macromolecules; recycling of worn-out organellesNoYesNo
Cell wallProtection, structural support and maintenance of cell shapeYes, primarily peptidoglycan in bacteria but not ArchaeaNoYes, primarily cellulose
Endoplasmic reticulumModifies proteins and synthesizes lipidsNoYesYes
Golgi apparatusModifies, sorts, tags, packages, and distributes lipids and proteinsNoYesYes
CytoskeletonMaintains cell’s shape, secures organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move independentlyYesYesYes
FlagellaCellular locomotionSomeSomeNo, except for some plant sperm.
CiliaCellular locomotion, movement of particles along extracellular surface of plasma membrane, and filtrationNoSomeNo


Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, cytoplasm, and ribosomes, but a eukaryotic cell is typically larger than a prokaryotic cell, has a true nucleus (meaning its DNA is surrounded by a membrane), and has other membrane-bound organelles that allow for compartmentalization of functions. The plasma membrane is a phospholipid bilayer embedded with proteins. The nucleolus within the nucleus is the site for ribosome assembly. Ribosomes are found in the cytoplasm or are attached to the cytoplasmic side of the plasma membrane or endoplasmic reticulum. They perform protein synthesis. Mitochondria perform cellular respiration and produce ATP. Peroxisomes break down fatty acids, amino acids, and some toxins. Vesicles and vacuoles are storage and transport compartments. In plant cells, vacuoles also help break down macromolecules.

Animal cells also have a centrosome and lysosomes. The centrosome has two bodies, the centrioles, with an unknown role in cell division. Lysosomes are the digestive organelles of animal cells.

Plant cells have a cell wall, chloroplasts, and a central vacuole. The plant cell wall, whose primary component is cellulose, protects the cell, provides structural support, and gives shape to the cell. Photosynthesis takes place in chloroplasts. The central vacuole expands, enlarging the cell without the need to produce more cytoplasm.

The endomembrane system includes the nuclear envelope, the endoplasmic reticulum, Golgi apparatus, lysosomes, vesicles, as well as the plasma membrane. These cellular components work together to modify, package, tag, and transport membrane lipids and proteins.

The cytoskeleton has three different types of protein elements. Microfilaments provide rigidity and shape to the cell, and facilitate cellular movements. Intermediate filaments bear tension and anchor the nucleus and other organelles in place. Microtubules help the cell resist compression, serve as tracks for motor proteins that move vesicles through the cell, and pull replicated chromosomes to opposite ends of a dividing cell. They are also the structural elements of centrioles, flagella, and cilia.

Animal cells communicate through their extracellular matrices and are connected to each other by tight junctions, desmosomes, and gap junctions. Plant cells are connected and communicate with each other by plasmodesmata.

Art Connections

Figure (PageIndex{1}) What structures does a plant cell have that an animal cell does not have? What structures does an animal cell have that a plant cell does not have?

Figure (PageIndex{1}) Plant cells have plasmodesmata, a cell wall, a large central vacuole, chloroplasts, and plastids. Animal cells have lysosomes and centrosomes.

Figure (PageIndex{7}) Why does the cis face of the Golgi not face the plasma membrane?

Figure (PageIndex{7}) Because that face receives chemicals from the ER, which is toward the center of the cell.

Multiple Choice

Which of the following is found both in eukaryotic and prokaryotic cells?

A. nucleus
B. mitochondrion
C. vacuole
D. ribosome


Which of the following is not a component of the endomembrane system?

A. mitochondrion
B. Golgi apparatus
C. endoplasmic reticulum
D. lysosome


Free Response

In the context of cell biology, what do we mean by form follows function? What are at least two examples of this concept?

“Form follows function” refers to the idea that the function of a body part dictates the form of that body part. As an example, organisms like birds or fish that fly or swim quickly through the air or water have streamlined bodies that reduce drag. At the level of the cell, in tissues involved in secretory functions, such as the salivary glands, the cells have abundant Golgi.


cell wall
a rigid cell covering made of cellulose in plants, peptidoglycan in bacteria, non-peptidoglycan compounds in Archaea, and chitin in fungi that protects the cell, provides structural support, and gives shape to the cell
central vacuole
a large plant cell organelle that acts as a storage compartment, water reservoir, and site of macromolecule degradation
a plant cell organelle that carries out photosynthesis
(plural: cilia) a short, hair-like structure that extends from the plasma membrane in large numbers and is used to move an entire cell or move substances along the outer surface of the cell
the entire region between the plasma membrane and the nuclear envelope, consisting of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals
the network of protein fibers that collectively maintains the shape of the cell, secures some organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move
the gel-like material of the cytoplasm in which cell structures are suspended
a linkage between adjacent epithelial cells that forms when cadherins in the plasma membrane attach to intermediate filaments
endomembrane system
the group of organelles and membranes in eukaryotic cells that work together to modify, package, and transport lipids and proteins
endoplasmic reticulum (ER)
a series of interconnected membranous structures within eukaryotic cells that collectively modify proteins and synthesize lipids
extracellular matrix
the material, primarily collagen, glycoproteins, and proteoglycans, secreted from animal cells that holds cells together as a tissue, allows cells to communicate with each other, and provides mechanical protection and anchoring for cells in the tissue
(plural: flagella) the long, hair-like structure that extends from the plasma membrane and is used to move the cell
gap junction
a channel between two adjacent animal cells that allows ions, nutrients, and other low-molecular weight substances to pass between the cells, enabling the cells to communicate
Golgi apparatus
a eukaryotic organelle made up of a series of stacked membranes that sorts, tags, and packages lipids and proteins for distribution
an organelle in an animal cell that functions as the cell’s digestive component; it breaks down proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles
(singular: mitochondrion) the cellular organelles responsible for carrying out cellular respiration, resulting in the production of ATP, the cell’s main energy-carrying molecule
nuclear envelope
the double-membrane structure that constitutes the outermost portion of the nucleus
the darkly staining body within the nucleus that is responsible for assembling ribosomal subunits
the cell organelle that houses the cell’s DNA and directs the synthesis of ribosomes and proteins
a small, round organelle that contains hydrogen peroxide, oxidizes fatty acids and amino acids, and detoxifies many poisons
plasma membrane
a phospholipid bilayer with embedded (integral) or attached (peripheral) proteins that separates the internal contents of the cell from its surrounding environment
(plural: plasmodesmata) a channel that passes between the cell walls of adjacent plant cells, connects their cytoplasm, and allows materials to be transported from cell to cell
a cellular structure that carries out protein synthesis
rough endoplasmic reticulum (RER)
the region of the endoplasmic reticulum that is studded with ribosomes and engages in protein modification
smooth endoplasmic reticulum (SER)
the region of the endoplasmic reticulum that has few or no ribosomes on its cytoplasmic surface and synthesizes carbohydrates, lipids, and steroid hormones; detoxifies chemicals like pesticides, preservatives, medications, and environmental pollutants, and stores calcium ions
tight junction
a firm seal between two adjacent animal cells created by protein adherence
a membrane-bound sac, somewhat larger than a vesicle, that functions in cellular storage and transport
a small, membrane-bound sac that functions in cellular storage and transport; its membrane is capable of fusing with the plasma membrane and the membranes of the endoplasmic reticulum and Golgi apparatus

6.1 – Eukaryotic Cells

By the end of this section, you will be able to do the following:

  • Describe the structure of eukaryotic cells
  • Compare animal cells with plant cells
  • State the role of the plasma membrane
  • Summarize the functions of the major cell organelles

Have you ever heard the phrase “form follows function?” It’s a philosophy that many industries follow. In architecture, this means that buildings should be constructed to support the activities that will be carried out inside them. For example, a skyscraper should include several elevator banks. A hospital should have its emergency room easily accessible.

Our natural world also utilizes the principle of form following function, especially in cell biology, and this will become clear as we explore eukaryotic cells ((Figure)). Unlike prokaryotic cells, eukaryotic cells have: 1) a membrane-bound nucleus 2) numerous membrane-bound organelles such as the endoplasmic reticulum, Golgi apparatus, chloroplasts, mitochondria, and others and 3) several, rod-shaped chromosomes. Because a membrane surrounds eukaryotic cell’s nucleus, it has a “true nucleus.” The word “organelle” means “little organ,” and, as we already mentioned, organelles have specialized cellular functions, just as your body’s organs have specialized functions.

At this point, it should be clear to you that eukaryotic cells have a more complex structure than prokaryotic cells. Organelles allow different functions to be compartmentalized in different areas of the cell. Before turning to organelles, let’s first examine two important components of the cell: the plasma membrane and the cytoplasm.

IB Biology 2 Cells 2 3 Eukaryotic Cells

IB Biology 2 Cells 2. 3 Eukaryotic Cells All syllabus statements ©IBO 2007 All images CC or public domain or link to original material. Jason de Nys http: //commons. wikimedia. org/wiki/File: Biological_cell. svg

2. 3. 1. Draw and label a diagram of the ultrastructure of a liver cell as an example of an animal cell

2. 3. 2 Annotate the diagram from 2. 3. 1 with the functions of each named structure. The Nucleus contains the chromosomes which comprise most of the DNA in a cell - It is the largest organelle - It has a double layer membrane - m. RNA, transcribed from the DNA in the nucleus, exits through pores more in 3. 3, 3. 4 and 7. 1 and 7. 2 - Some cells have multiple nuclei The bright blue stains are nuclei in He. La cells. Read “The Immortal Life of Henrietta Lacks” for a fascinating story of the origin of He. La cells http: //commons. wikimedia. org/wiki/File: He. La_cells_stained_with_Hoechst_33258. jpg

http: //commons. wikimedia. org/wiki/File: Diagram_human_cell_nucleus. svg

The Cell membrane is the boundary of the cell. • It acts as a “gatekeeper”, preventing the entry or exit of some molecules and facilitating the movement of others. • It is a phospholipid bilayer • It is permeable to oxygen and carbon dioxide • It is impermeable to water and charged particles, they must enter through special proteins embedded in the membrane More in 2. 4 http: //commons. wikimedia. org/wiki/File: Cell_membrane_detailed_diagram_en. svg

The Mitochondrion (pl. Mitochondria) • The ‘power house’ of the cell • Has a smooth outer membrane and a folded inner membrane • Where aerobic respiration occurs in the cell More in 3. 7 and 8. 1 Mitochondria in mammalian lung cells Remember: Where else do we see loops of DNA? How does the size of a mitochondrion compare with an average prokaryote? The implications of the answers to these questions are in Option D: Evolution http: //commons. wikimedia. org/wiki/File: Animal_mitochondrion_diagram_en. svg http: //commons. wikimedia. org/wiki/File: Mitochondria, _mammalian_lung_-_TEM. jpg

Rough Endoplasmic Reticulum Spot the difference? Smooth Endoplasmic Reticulum http: //images. wellcome. ac. uk/

The ‘spots’ are the difference! The Rough Endoplasmic Reticulum is peppered with ribosomes that give it the rough appearance It is where protein synthesis occurs more in 3. 5 and 7. 4

The (free) Ribosome, the molecular machine responsible for protein synthesis much, much more in 3. 5 and 7. 4 A ribosome on the sculpture “Waltz of the Polypeptides” at Cold Spring Harbor Laboratory http: //www. flickr. com/photos/cryo_mariena/6033827307/sizes/m/in/photostream/

I shall name it……… The internal reticular apparatus!! Pretty catchy… no? * Camillo Golgi *Everybody thought that was a terrible name, so they called it the Golgi apparatus instead http: //commons. wikimedia. org/wiki/File: C_Golgi. jpg http: //commons. wikimedia. org/wiki/File: Golgi_in_the_cytoplasm_of_a_macrophage_in_the_alveolus_(lung)_-_TEM. jpg

The Golgi Apparatus is a flattened stack of membranes responsible for the packaging and delivery of proteins http: //en. wikipedia. org/wiki/File: Nucleus_ER_golgi. svg

Lysosomes are simple, membrane-bound organelles full of enzymes that digest engulfed bacteria and viruses and large molecules for recycling. http: //commons. wikimedia. org/wiki/File: Lysosome. jpg

Image from an amazing site by teacher Andrew Brown http: //www. tokresource. org/tok_classes/biobiobio/biomenu/eukaryotic_cells/index. htm

2. 3. 3 Identify structures from 2. 3. 1 in electron micrographs of liver cells. Rough Endoplasmic Reticulum Mitochondrion Smooth Endoplasmic Reticulum

2. 3. 4 Compare prokaryotic and eukaryotic cells Compare Give an account of similarities and differences between two (or more) items, referring to both (all) of them throughout Prokaryotic Eukaryotic Small cells Relatively larger cells Always unicellular Some multicellular, some unicellular No nucleus: DNA a ‘naked’ loop in the nucleoid region DNA in chromosomes in a membranebound nucleus Ribosomes smaller (70 s) Ribosomes larger (80 s) No mitochondria, respiration in cell membrane and mesosomes Mitochondria, where aerobic respiration occurs Cell division by binary fission Cell division by meiosis or Mitosis Reproduction asexual (some gene exchange can occur via conjugation) Reproduction Sexual or asexual Table modified from Click 4 Biology

2. 3. 5 State three differences between plant and animal cells State: Give a specific name, value or other brief answer without explanation or calculation. Animals Plants Have a cell wall Don’t have a cell wall Have chloroplasts in photosynthetic cells Don’t have chloroplasts anywhere Carbohydrate stored as starch and plant oils V. Carbohydrate stored as glycogen and animal fat Rigid Shape (due to cell wall) Flexible shape Have a large permanent storage vacuole May have small, temporary vacuoles http: //www. flickr. com/photos/chubbybat/45407031/ http: //www. flickr. com/photos/powi/749366522/

2. 3. 6 Outline two roles of extracellular components Outline: Give a brief account or summary. Got a banana? Bone cells have an extracellular matrix in the interstitial spaces (between the cells)of collagen and calcium phosphate which together form the hard bone. http: //www. flickr. com/photos/limonada/14705232/

The other form of extracellular matrix is the basement membranes They exist in many tissue types as a form of support e. g. as the lining in blood vessels You may already know about the glomerulus in the kidney. A basement membrane is integral to ultrafiltration there. More in HL 11. 3 http: //commons. wikimedia. org/wiki/File: Gallbladder_cholesterolosis_low_mag. jpg

As well as extracellular matrices in animals, plant have extracellular components…. Cell Walls They are made of cellulose and provide structure, support and protection. They maintain cell shape and prevent turgor pressure from rupturing the cell http: //www. flickr. com/photos/ah_pao/2590017159/

Further information: Ag ood intr odu ctio n to wh at a cell i s an d th e fu nct ion s of org a Three of the best sites for IB-specific Biology information. The top link takes you to the PPT by Stephen Taylor nel les

AQA Trilogy B1.3 Eukaryotic and Prokaryotic Cells

pptx, 4.31 MB docx, 42.77 KB

AQA Trilogy B1.3-Eukaryotic and Prokaryotic Cells

Lesson objectives
1. Describe the differences between eukaryotic and prokaryotic cells.
2. Explain how the main sub-cellular structures of eukaryotic and prokaryotic cells are related to their functions.

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3.1.3: Eukaryotic Cells - Biology

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Cells are the building blocks of all organisms, and their size can vary, depending on the type. For instance, a bacterial cell is significantly smaller in diameter, a few micrometers, than say a plant one, which could range from 10 to a 100 micrometers.

The smallness of bacteria, and prokaryotes in general, allows nutrients and gases that enter to easily spread from one part to another. Equally, any waste produced inside can quickly defuse out.

However, larger plant cells, and more broadly, other eukaryotes, have evolved different structural adaptations to improve functions such as intercellular transport.

Such modifications highlight the important relationship between volume and surface area. The three-dimensional parameter, cubic capacity, increases much more quickly than its two-dimensional counterpart, surface area. Many types of cells need to maximize surface area and reduce volume in order to properly exchange gases and gather resources.

For this reason, plants may alter their shape, say by producing long, thin leaves and root hairs, and bacteria might stay small and divide. Thus, structural adaptations change the surface-to-volume ratio and are crucial for organisms to interface with their environment. Without such compensation for size, they would perish.

4.2: Cell Size

The size of cells varies widely among and within organisms. For instance, the smallest bacteria are 0.1 micrometers (&mum) in diameter&mdashabout a thousand times smaller than many eukaryotic cells. Most other bacteria are larger than these tiny ones&mdashbetween 1-10 &mum&mdashbut they still tend to be smaller than most eukaryotic cells, which typically range from 10-100 &mum.

Surface Area

Larger is not necessarily better when it comes to cells. For instance, cells need to take in nutrients and water through diffusion. The plasma membrane surrounding cells limits the rate at which these materials are exchanged. Smaller cells tend to have a higher surface area to volume ratio than larger cells. That is because changes in volume are not linear to changes in surface area. When a sphere increases in size, the volume grows proportional to the cube of its radius (r 3 ), while its surface area grows proportional to only the square of its radius (r 2 ). Therefore, smaller cells have relatively more surface area compared to their volume than larger cells of the same shape. A larger surface area means more area of the plasma membrane where materials can pass into and out of the cell. Substances also need to travel within cells. Hence the rate of diffusion may limit processes in large cells.


Prokaryotes are often small and divide before they face limitations due to cell size. Larger eukaryotic cells have organelles that facilitate intracellular transport. Also, structural changes help overcome limitations. Some cells that need to exchange large amounts of substances with the environment developed long, thin extrusions that maximize the surface area to volume ratio. An example of such structures are the root hairs of plant cells that facilitate the intake of water and nutrients. Therefore, cell size and surface area to volume ratio are crucial factors in the evolution of cellular characteristics.

Chien, An-Chun, Norbert S. Hill, and Petra Anne Levin. &ldquoCell Size Control in Bacteria.&rdquo Current Biology 22, no. 9 (May 8, 2012): R340&ndash49. [Source]

Sachs, Frederick, and Mettupalayam V. Sivaselvan. &ldquoCell Volume Control in Three Dimensions: Water Movement without Solute Movement.&rdquo The Journal of General Physiology 145, no. 5 (May 2015): 373&ndash80. [Source]


Bioinformatical sequence acquisition

Various nucleotide databases (Histone Sequence Database, GeneBank, RefSeq, TBestDB) were scanned for H3 sequences using Drosophila melanogaster H3.3 or CenpA protein sequence as query for tBlastn. H3-similar hits were virtually translated into proteins and used for alignment analyses. To identify phylogenetically distant H3 or CenH3 variants from putatively early branching eukaryotic clades we re-used more diverging H3 variants found before in some cases as query sequences for tBlastn. Sequence fragments were assembled to full-length sequences where sufficient fragment overlap was found.

Telomere suppression PCR and expression profiling

We fully characterized Stylonychia lemnae macronuclear genome encoded H3 variants using degenerate oligonucleotides in combination with telomere suppression PCR (TSP), a technique to amplify the 5'- or 3'-ends of Stylonychia nanochromosomes including their telomeric sequences [45]. Sexual reproduction of Stylonychia was initiated by mixing equal numbers of cells from different mating types. Samples for cDNA synthesis were taken periodically at time points as indicated. Total RNA was isolated as described earlier [46]. Subsequently, cDNA was synthesized using the Qiagen QuantiTect Reverse Transcription kit. Quantitative Real-Time PCR was performed on a Roche Light Cycler.


Aligments were performed using ClustalW included in MEGA 4.1 [47] and were subsequently manually refined.

Phylogenetic analyses and ancestral state reconstruction

Phylogenetic tree calculations were conducted using MEGA 4.1 [47] software.

The evolutionary history of 159 H3 and CenH3 variants (Figure ​ (Figure2A) 2A ) was inferred using the Neighbor-Joining method [48]. The bootstrap consensus tree inferred from 1.000 replicates [49] was taken to represent the evolutionary history of the taxa analyzed. Evolutionary distances were computed using the JTT matrix-based method [50] and are in the units of the number of amino acid substitutions per site. All positions containing alignment gaps and missing data were eliminated only in pairwise sequence comparisons. The final dataset contained a total of 100 positions.

The evolutionary relationship of 128 non-redundant histone H3 variants (Figure ​ (Figure2B) 2B ) was inferred as described above. The bootstrap consensus tree was inferred from 10.000 replicates [49]. Evolutionary distances were computed as described above. The final dataset contained a total of 358 positions.

Ancestral states represented by selected internal nodes from clades well supported by NJ tree topology were reconstructed (compare node markers in Figure ​ Figure2). 2 ). The putative ancestral sequences were subsequently inspected by eye and manually refined.

Immunofluorescence microscopy

Cells were fixed in 2% paraformaldehyde (Stylonychia, Trichomonas) or alternatively in methanol:acetic acid (3:1) (Euglena), washed twice with phosphate buffered saline (PBS), and immobilized onto poly-L-lysine coated coverslips. Subsequently immunostaining with PTM-specific antibodies and in some experiments peptide competition assays were performed as described earlier [29]. Cells were analyzed by confocal laser scanning microscopy (CLSM). Acquisition of serial sections was done with a Zeiss LSM 5 Pascal confocal laser scanning microscope equipped with a water objective lens (Plan-Neofluar 25/0.8, or in some cases C-Apochromat 63/1.2). Fluorochromes were visualized with an argon laser with excitation wavelengths of 488 nm for Alexa Fluor 488 and 514 nm for SYTOX Orange. Fluorochrome images were scanned sequentially generating 8 bit grayscale images. Image resolution was 512 × 512 pixels with variable pixel size depending on the selected zoom factor. The axial distance between light optical serial sections was 300 nm. To obtain an improved signal to noise ratio each section image was averaged from four successive scans. The 8 bit grayscale single channel images were overlaid to an RGB image assigning a false color to each channel and then assembled into tables using open source software ImageJ (Rasband, W.S., ImageJ, National Institutes of Health, Bethesda, Maryland, USA,, 1997-2004.) and Adobe Photoshop CS3 software.

SDS Page and Western Analyses

Cells were lysed, and subsequently total cellular proteins were resuspended in loading buffer [51], heated for 10 min at 100ଌ, and separated on 15% sodium dodecyl sulfate (SDS)-polyacrylamide gels. Proteins were then transferred onto a nylon membrane and probed with specific antibodies. Detection was done using the digoxigenin system (Roche).


The overexpression of authentically folded eukaryotic membrane proteins in milligramme quantities is a fundamental prerequisite for structural studies. One of the most commonly used expression systems for the production of mammalian membrane proteins is the baculovirus expression system in insect cells. However, a detailed analysis by radioligand binding and comparative Western blotting of G protein-coupled receptors and a transporter produced in insect cells showed that a considerable proportion of the expressed protein was misfolded and incapable of ligand binding. In contrast, production of the same membrane proteins in stable inducible mammalian cell lines suggested that the majority was folded correctly. It was noted that detergent solubilisation of the misfolded membrane proteins using either digitonin or dodecylmaltoside was considerably less efficient than using sodium dodecyl sulfate or foscholine-12, whilst these detergents were equally efficient at solubilising correctly folded membrane proteins. This provides a simple and rapid test to suggest whether heterologously expressed mammalian membrane proteins are indeed correctly folded, without requiring radioligand binding assays. This will greatly facilitate the high-throughput production of fully functional membrane proteins for structural studies.

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More. </a></p> Expression i

Gene expression databases

Bgee dataBase for Gene Expression Evolution

ExpressionAtlas, Differential and Baseline Expression

Genevisible search portal to normalized and curated expression data from Genevestigator

Organism-specific databases


We thank Christopher T. Brown for helpful discussions and Nicholas Bhattacharya for advice on statistical methods.


This research was supported by the National Institutes of Health (NIH) under award RAI092531A, the Alfred P. Sloan Foundation under grant APSF-2012-10-05, and National Science Foundation Graduate Research Fellowships to M.O. and P.W. under Grant No. DGE 1106400. This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 OD018174 Instrumentation Grant.

Availability of data and materials

The datasets supporting the conclusions of this article are available in the NCBI BioProeject repository, PRJNA471744, the Short Read Archive (SRA) SRR5420274 to SRR5420297, and GitHub,

Biology Questions and Answers – Eukaryotic Cells and it’s Organelles – 3

This set of Biology Multiple Choice Questions & Answers (MCQs) focuses on “Eukaryotic Cells and it’s Organelles – 3”.

1. Identify the structure.

a) Mitochondria
b) Nucleus
c) Golgi apparatus
d) Endoplasmic reticulum
View Answer

2. What is the space inside the endoplasmic reticulum called?
a) Tubular compartment
b) Extra – tubular compartment
c) Luminal compartment
d) Extra – luminal compartment
View Answer

3. Where are the ribosomes attached in rough endoplasmic reticulum?
a) In the lumen
b) On the folds towards the nucleus
c) On the surface
d) On the folds towards the cell membrane
View Answer

4. What is present on the surface of the rough endoplasmic reticulum?
a) Ribosomes
b) Peroxisomes
c) Lysosomes
d) Endosomes
View Answer

5. Endoplasmic reticulum without ribosomes is called ______
a) rough endoplasmic reticulum
b) smooth endoplasmic reticulum
c) non – ribosomal endoplasmic reticulum
d) nuclear endoplasmic reticulum
View Answer

6. Which of these cell organelles is involved in protein synthesis?
a) Lysosome
b) Smooth endoplasmic reticulum
c) Rough endoplasmic reticulum
d) Peroxisome
View Answer

7. Which of these statements is not true regarding rough endoplasmic reticulum?
a) The inner compartment is called the tubular compartment
b) It is involved in protein synthesis
c) Ribosomes are attached to its outer surface
d) Its membrane is continuous with the outer membrane of the nucleus
View Answer

8. What is the site of production of lipid-like steroidal hormones in animal cells?
a) Mitochondria
b) Nucleus
c) Peroxisomes
d) Smooth endoplasmic reticulum
View Answer

9. What is the diameter of cisternae of Golgi bodies?
a) 5&mum to 10&mum
b) 0.05&mum to 0.1&mum
c) 0.5&mum to 1.0&mum
d) 50&mum to 100&mum
View Answer

10. The forming face of the Golgi complex is convex. True or false?
a) True
b) False
View Answer

11. Which of these is not a function of the Golgi apparatus?
a) Packaging of proteins
b) Modification of proteins
c) Synthesis of glycoproteins and glycolipids
d) Synthesis of proteins
View Answer

12. Which of these is not a lysosomal enzyme?
a) Lipases
b) Protease
c) Kinases
d) carbohydrase
View Answer

13. Which of these statements is false regarding lysosomes?
a) They are bound by a single membrane
b) They contain hydrolytic enzymes
c) Lysosomal enzymes are active at a basic pH
d) They can digest nucleic acids
View Answer

14. What are the membranes of vacuoles called?
a) Tonoplast
b) Leucoplast
c) Amyloplast
d) Chromoplast
View Answer

15. Which of these is a function of the contractile vacuole in Amoeba?
a) Lipoprotein synthesis
b) Osmoregulation of the cell
c) Glycoprotein synthesis
d) Degradation of nucleic acids
View Answer

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