Organelles that Process Energy

A cell uses energy to synthesize cell-specific materials that it can use for activities such as growth, reproduction and movement. Energy is transformed from one form to another in mitochondria (found in all eukaryotic cells) and in chloroplasts (found in eukaryotic cells that harvest energy from sunlight). In contrast, energy transformations in prokaryotic cells are associated with enzymes attached to the inner surface of the plasma membrane or extensions of the plasma membrane that protrude into the cytoplasm.

Mitochondria are energy transformers

In eukaryotic cells, the breakdown of fuel molecules such as glucose begins in the cytosol. The molecules that result from this partial degradation enter the mitochondria (singular, mitochondrion), whose primary function is to convert the potential chemical energy of those fuel molecules into a form that the cell can use: the energy-rich molecule ATP (adenosine triphosphate). The production of ATP in the mitochondria using fuel molecules and molecular oxygen (O₂) is called cellular respiration. Typical mitochondria are small—somewhat less than 1.5 µm in diameter and 2–8 µm in length—about the size of many bacteria. The number of mitochondria per cell ranges from one contorted giant in some unicellular protists to a few hundred thousand in large egg cells. An average human liver cell contains more than a thousand mitochondria. Cells that require the most chemical energy tend to have the most mitochondria per unit of volume. Mitochondria have two membranes. The outer membrane is smooth and protective, and it offers little resistance to the movement of substances into and out of the mitochondrion. Immediately inside the outer membrane is an inner membrane, which folds inward in many places, giving it a much greater surface area than that of the outer membrane. These folds tend to be quite regular, giving rise to shelflike structures called cristae.

The inner mitochondrial membrane contains many large protein molecules that participate in cellular respiration. The inner membrane exerts much more control over what enters and leaves the mitochondrion than does the outer membrane. The region enclosed by the inner membrane is referred to as the mitochondrial matrix. In addition to many proteins, the matrix contains some ribosomes and DNA that are used to make some of the proteins needed for cellular respiration.

Plastids photosynthesize or store materials

One class of organelles—the plastids—is produced only in plants and certain protists. There are several types of plastids, with different functions.

Chloroplasts

Chloroplasts contain the green pigment chlorophylland are the sites of photosynthesis. In photosynthesis, light energy is converted into the chemical energy of bonds between atoms. The molecules formed in photosynthesis provide food for the photosynthetic organisms, as well as for other organisms that eat them. Directly or indirectly, photosynthesis is the energy source for most of the living world. Like a mitochondrion, a chloroplast is surrounded by two membranes. In addition, there is a series of internal membranes whose structure and arrangement vary from one group of photosynthetic organisms to another. Here we concentrate on the chloroplasts of the flowering plants. Even these chloroplasts show some variation but the pattern shown in Figure is typical. The internal membranes of chloroplasts look like stacks of flat, hollow pita bread. These stacks, called grana(singular, granum), consist of a series of flat, closely packed, circular compartments called thylakoids. In addition to phospholipids and proteins, the membranes of the thylakoids contain chlorophyll and other pigments that harvest light for photosynthesis. The thylakoids of one granum may be connected to those of other grana, making the interior of the chloroplast a highly developed network of membranes, much like the ER. The fluid in which the grana are suspended is the stroma. Like the mitochondrial matrix, the chloroplast stroma contains ribosomes and DNA, which are used to synthesize some, but not all, of the proteins that make up the chloroplast. Animal cells do not produce chloroplasts, but some do contain functional chloroplasts. These are either taken up as free chloroplasts derived from the partial digestion of green plants or contained within unicellular algae that live within the animal’s tissues. The green color of some corals and sea anemones results from the chloroplasts in algae that live within those animals. The animals derive some of their nutrition from the photosynthesis that their chloroplast-containing “guests” carry out. Such an intimate relationship between two different organisms is called symbiosis.

Other types of plastids also store pigments or polysaccharides:

Chromoplastscontain red, orange, and/or yellow pigments and give color to plant organs such as flowers. The chromoplasts have no known chemical function in the cell but the colors they give to some petals and fruits probably encourage animals to visit flowers and thus aid in pollination or to eat fruits and thus aid in seed dispersal. On the other hand, carrot roots gain no apparent advantage from being orange.

Leucoplastsare storage depots for starch and fats.

Endosymbiosis may explain the origin of mitochondria and chloroplasts

Although chloroplasts and mitochondria are about the size of prokaryotic cells and have the genetic material and protein synthesis machinery needed to make some of their own components, they are not independent of control by the nucleus. The vast majority of their proteins are encoded by nuclear DNA, made in the cytoplasm, and imported into the organelle.

Observations of these organelles have led to the proposal that they originated by endosymbiosis—that is, that they were once independent prokaryotic organisms. About 2 billion years ago, only prokaryotes inhabited Earth. Some of them absorbed their food directly from the environment. Others were photosynthetic. Still others fed on smaller prokaryotes by engulfing them. Suppose that a small, photosynthetic prokaryote was ingested by a larger one, but was not digested. Instead, it somehow survived, trapped within a vesicle in the cytoplasm of the larger cell. The smaller, ingested prokaryote divided at about the same rate as the larger one, so successive generations of the larger cell also contained the offspring of the smaller one. This phenomenon, called endosymbiosis (endo-, “within”; symbiosis, “living together”), exists today, as in the case of the algae that live within sea anemones (see Figure ). According to this scenario, endosymbiosis provided benefits for both partners: The larger cell obtained the photosynthetic products from the smaller cell, and the smaller cell was protected by the larger one. Over evolutionary time, the smaller cell gradually lost much of its DNA to the nucleus of the larger cell, resulting in the modern chloroplast. Much circumstantial evidence favors the endosymbiosistheory:

On an evolutionary time scale of millions of years, there is evidence for DNA moving between organelles in the cell.

There are many biochemical similarities between chloroplasts and modern photosynthetic bacteria.

DNA sequencing shows strong similarities between modern chloroplast DNA and that of a photosynthetic prokaryote.

The double membrane that encloses mitochondria and chloroplasts could have arisen through endosymbiosis.

The outer membrane may have come from the engulfing cell’s plasma membrane and the inner membrane from the engulfed cell’s plasma membrane. Similar evidence and arguments also support the proposition that mitochondria are the descendants of respiring prokaryotes prokaryotes engulfed by larger prokaryotes. The benefit of this endosymbiotic relationship might have been the capacity of the engulfed prokaryote to detoxify molecular oxygen (O₂), which was increasing in Earth’s atmosphere as a result of photosynthesis.

Other Organelles

Eukaryotic cells have several other organelles that are surroundedby a single membrane.

Peroxisomes house specialized chemical reactions

Peroxisomesare organelles that collect the toxic peroxides (such as hydrogen peroxide, H₂O₂) that are the unavoidable by-products of chemical reactions. These peroxides can be safely broken down inside the peroxisomes without mixing with other parts of the cell. Peroxisomes are small organelles, about 0.2 to 1.7 µm in diameter. They have a single membrane and a granular interior containing specialized enzymes. Peroxisomes are found at one time or another in at least some of the cells of almost every eukaryotic species. Astructurally similar organelle, the glyoxysome, is found only in plants. Glyoxysomes, which are most prominent in young plants, are the sites where stored lipids are converted into carbohydrates for transport to growing cells.

Vacuoles are filled with water and soluble substances

Many eukaryotic cells, but particularly those of plants and protists, contain membrane-enclosed vacuolesfilled with aqueous solutions containing many dissolved substances. Plant vacuoles have several functions:

Storage: Plant cells produce a number of toxic by-products and waste materials, many of which are simply stored within vacuoles. And since they are poisonous or distasteful, these stored materials deter some animals from eating the plants. Thus these stored wastes may contribute to plant survival.

Structure: In many plant cells, enormous vacuoles take up more than 90 percent of the cell volume and grow as the cell grows. The dissolved substances in the vacuole, working together with the vacuolar membrane, provide the turgor or stiffness of the cell which, in turn, provides support for the structure of nonwoody plants. The presence of the dissolved substances causes water to enter the vacuole, making it swell like a balloon. Plant cells have a rigid cell wall which resists the swelling of the vacuole, providing strength in the process.

Reproduction: Some pigments (especially blue and pink ones) in petals and fruits are contained in vacuoles. These pigments—the anthocyanins—are visual cues that help attract the animals that assist in pollination or seed dispersal.

Digestion: In some plants, the vacuoles contain enzymes that hydrolyze seed proteins into monomers that a developing plant embryo can use as food.

Food vacuolesare found in some simple and evolutionarily ancient groups of organisms—single-celled protists and simple multicellular organisms such as sponges, for example. In these organisms, the cells engulf food particles by phagocytosis, generating a food vacuole. Fusion of this vacuole with a lysosome results in digestion and small molecules leave the vacuole and enter the cytoplasm for use or distribution to other organelles.

Contractile vacuolesare found in many freshwater protists. Their function is to get rid of the excess water that rushes into the cell because of the imbalance in salt concentration between the relatively salty interior of the cell and its freshwater environment. The contractile vacuole enlarges as water enters, then abruptly contracts, forcing the water out of the cell through a special pore structure.

Cytoskeleton

In addition to its many membrane-enclosed organelles, the eukaryotic cytoplasm contains a set of long, thin fibers called the cytoskeleton. The cytoskeleton fills at least three important roles:

It maintains cell shape and support.

It provides for various types of cellular movement.

Some of its fibers act as tracks or supports for motor proteins which help move things within the cell.

Microfilaments function in support and movement

Microfilamentscan exist as single filaments in bundles or in networks. They are about 7 nm in diameter and several micrometers long. They are assembled from actin, a protein that exists in several forms and has many functions among members of the animal phyla. The actin found in microfilaments (which are also known as actin filaments) is extensively folded and has distinct “head” and “tail” sites. These sites interact with other actin molecules to form long, double helical chains. The polymerization of actin into microfilaments is reversible and they can disappear from cells, breaking down into units of free actin. Microfilaments have two major roles: a)they help the entire cell or parts of the cell to move; b)they stabilize cell shape.

In muscle cells, actin fibers are associated with another protein, myosin, and the interactions of these two proteins account for the contraction of muscles. In non-muscle cells, actin fibers are associated with localized changes of shape in the cell. For example, microfilaments are involved in a flowing movement of the cytoplasm called cytoplasmic streamingand in the “pinching” contractions that divide an animal cell into two daughter cells. Microfilaments are also involved in the formation of cellular extensions called pseudopodia(pseudo-, “false;” podia, “feet”) that enable some cells to move. In some cell types, microfilaments form a meshwork just inside the plasma membrane. Actin-binding proteins then cross-link the microtubules to form a rigid structure that supports the cell. Microfilaments support the tiny microvilli that line the intestine, giving it a larger surface area through which to absorb nutrients.

Intermediate filaments are tough supporting elements

Intermediate filamentsare found only in multicellular organisms. In contrast to the other components of the cytoskeleton, there are at least 50 different kinds of intermediate filaments, often specific to a few cell types. They generally fall into six molecular classes, based on amino acid sequence, and share the same general structure being composed of fibrous proteins of the keratin family, similar to the protein that makes up hair and fingernails. In cells, these proteins are organized into tough, ropelike assemblages 8 to 12 nm in diameter. Intermediate filaments have two major structural functions:

They stabilize cell structure.

They resist tension.

In some cells, intermediate filaments radiate from the nuclear envelope and may maintain the positions of the nucleus and other organelles in the cell. The lamins of the nuclear lamina are intermediate filaments. Other kinds of intermediate filaments help hold a complex apparatus of microfilaments in place in muscle cells. Still other kinds stabilize and help maintain rigidity in surface tissues by connecting “spot welds” called desmosomes between adjacent cells.

Microtubules are long and hollow

Microtubulesare long, hollow, unbranched cylinders about 25 nm in diameter and up to several micrometers long. Microtubules have two roles in the cell:

They form a rigid internal skeleton for some cells.

They act as a framework along which motor proteins can move structures in the cell.

Microtubules are assembled from molecules of the protein tubulin. Tubulin is a dimer—a molecule made up of two monomers. The polypeptide monomers that make up this protein are known as a-tubulin and b-tubulin. Thirteen chains of tubulin dimers surround the central cavity of the microtubule. The two ends of a microtubule are different. One end is designated the plus (+) end, the other the minus (–) end. Tubulin dimers can be added or subtracted, mainly at the plus end, lengthening or shortening the microtubule. This capacity to change length rapidly makes microtubules dynamic structures. This dynamic property of microtubules is seen in animal cells, where they are often found in parts of the cell that are changing shape. Many microtubules radiate from a region of the cell called the microtubule organizing center. Tubule polymerization results in rigidity and tubule depolymerization leads to a collapse of this rigid structure. In plants, microtubules help control the arrangement of the cellulose fibers of the cell wall. Electron micrographs of plants frequently show microtubules lying just inside the plasma membrane of cells that are forming or extending their cell walls. Experimental alteration of the orientation of these microtubules leads to a similar change in the cell wall and a new shape for the cell. In many cells, microtubules serve as tracks for motor proteins, specialized molecules that use energy to change their shape and move. Motor proteins bond to and move along the microtubules, carrying materials from one part of the cell to another. Microtubules are also essential in distributing chromosomes to daughter cells during cell division. And they are intimately associated with movable cell appendages: the flagella and cilia.

Microtubules power cilia and flagella

Many eukaryotic cells possess flagella or cilia or both. These whiplike organelles may push or pull the cell through its aqueous environment, or they may move surrounding liquid over the surface of the cell. Cilia and eukaryotic (but not prokaryotic) flagella are both assembled from specialized microtubules and have identical internal structures but they differ in their relative lengths and their patterns of beating:

Flagellaare longer than cilia and are usually found singly or in pairs. Waves of bending propagate from one end of a flagellum to the other in snakelike undulation.

Ciliaare shorter than flagella and are usually present in great numbers. They beat stiffly in one direction and recover flexibly in the other direction (like a swimmer’s arm), so that the recovery stroke does not undo the work of the power stroke.

In cross section, a typical cilium or eukaryotic flagellum is surrounded by the plasma membrane and contains a “9 + 2” array of microtubules. Nine fused pairs of microtubules—called doublets—form an outer cylinder and one pair of unfused microtubules runs up the center. A spoke radiates from one microtubule of each doublet and connects the doublet to the center of the structure. In the cytoplasm at the base of every eukaryotic flagellum or cilium is an organelle called a basal body. The nine microtubule doublets extend into the basal body. In the basal body, each doublet is accompanied by another microtubule, making nine sets of three microtubules. The central, unfused microtubules do not extend into the basal body.

Centriolesare almost identical to the basal bodies of cilia and flagella. Centrioles are found in all eukaryotes except the flowering plants, pine trees and their relatives and some protists. It is made up of a precise bundle of microtubules arranged as nine sets of three fused microtubules each. Centrioles lie in the microtubule organizing center in cells that are about to divide.

Motor proteins move along microtubules

The nine microtubule doublets of cilia and flagella are linkedby proteins. The motion of cilia and flagella results from the sliding of the microtubules past each other. This sliding is driven by a motor protein called dynein, which can undergo changes in its shape. All motor proteins work by undergoing reversible shape changes powered by energy from ATP. Dynein molecules attached to one microtubule doublet bind to a neighboring doublet. As the dynein molecules change shape, they move the microtubule past its neighbor. Dynein and another motor protein, kinesin, are responsible for carrying protein-laden vesicles from one part of the cell to another. These motor proteins bind to a vesicle or other organelle, then “walk” it along a microtubule by changing their shape. Recall that microtubules have a plus end and a minus end. Dynein moves attached organelles toward the minus end, while kinesin moves them toward the plus end.

Extracellular Structures

Although the plasma membrane is the functional barrier between the inside and the outside of a cell, many structures are produced by cells and secreted to the outside of the plasma membrane, where they play essential roles in protecting, supporting or attaching cells. Because they are outside the plasma membrane, these structures are said to be extracellular. The peptidoglycan cell wall of bacteria is such an extracellular structure. In eukaryotes, other extracellular structures—the cell walls of plants and the extracellular matrices found between the cells of multicellular animals—play similar roles. Both of these structures are made up of a prominent fibrous macromolecule embedded in a jellylike medium.

The plant cell wall consists largely of cellulose

The cell wall of plant cells is a semirigid structure outside the plasma membrane (Figure). It consists of cellulose fibers embedded in other complex polysaccharides and proteins. The cell wall has three major roles in plants:

It provides support for the cell and limits its volume by remaining rigid.

It acts as a barrier to infections by fungi and other organisms that can cause plant diseases.

It contributes to plant form by growing as plant cells expand.

Because of their thick cell walls, plant cells viewed under a light microscope appear to be entirely isolated from each other. But electron microscopy reveals that this is not the case. The cytoplasm of adjacent plant cells is connected by numerous plasma membrane-lined channels, called plasmodesmata, that are about 20 to 40 nm in diameter and extend through the walls of adjoining cells. Plasmodesmata permit the diffusion of water, ions, small molecules, and RNA and proteins between connected cells. Such diffusion ensures that the cells of a plant have uniform concentrations of these substances.

Animal cells have elaborate extracellular matrices

The cells of multicellular animals lack the semirigid cell wall that is characteristic of plant cells, but many animal cells are surrounded by, or are in contact with, an extracellular matrix. This matrix is composed of fibrous proteins such as collagen (the most abundant protein in mammals) and glycoproteins. These proteins, along with other substances that are specific to certain body tissues, are secreted by cells that are present in or near the matrix. The functions of the extracellular matrix are many:

It holds cells together in tissues.

It contributes to the physical properties of cartilage, skin, and other tissues.

It helps filter materials passing between different tissues.

It helps orient cell movements during embryonic development and during tissue repair.

It plays a role in chemical signaling from one cell to another.

In the human body, some tissues, such as those in the brain, have very little extracellular matrix; other tissues, such as bone and cartilage, have large amounts. Bone cells are embedded in an extracellular matrix that consists primarily of collagen and calcium phosphate. This matrix gives bone its familiar rigidity. Epithelial cells, which line body cavities, lie together as a sheet spread over a basal lamina, or basement membrane,a form of extracellular matrix.

Some extracellular matrices are made up, in part, of an enormous proteoglycan. A single molecule of this proteoglycan consists of many hundreds of polysaccharides covalently attached to about a hundred proteins, all of which are attached to one enormous polysaccharide. The molecular weight of this proteoglycan can exceed 100 million; the molecule takes up as much space as an entire prokaryotic cell.

How Things Get Into & Out Of Cells

Cells are able to regulate the passage of materials across cell membranes. This is an important capacity. One of the criteria by which we identify living systems is that living matter, although surrounded on all sides by nonliving matter, is different from it in the kinds & amounts of chemical substances it contains. Without this difference, of course, living matter would be unable to maintain the organization & structure on which its existence depends. The cell membrane is not simply an impenetrable barrier, however. Living matter constantly exchanges substances with the nonliving world around it. Control of these exchanges is essential in order to protect the cell’s integrity & to maintain those very narrow conditions of pH and salt concentrations, common to all cells, at which enzyme activity can take place. The cell membrane, thus, has a complex double function of keeping things out & letting things in. Moreover, cell membranes not only control the passage of material from outside the cell, but internal membranes, such as those surrounding mitochondria, chloroplast and the nucleus, regulate the passage of materials between intracellular compartment & so regulate their internal environment.

The regulation of substances moving across membranes depends on interactions between the physical & chemical properties of the membrane & those of the molecules that penetrate through them. Of the many kinds of molecules moving in & out of cells, the most important is water. Let us therefore look again at water, focusing our attention this time on how water moves.

Moving processes (passive transport)

Three principles govern the movement of substances: bulk flow, diffusion, and osmosis.

Bulk flowis the overall movement of water (or some other liquid). It occurs in response to differences in the potential energy of water, usually referred to as water potential.

A simple example of water that has potential energy is water at the top of a hill. As this water runs downhill, its potential energy can be converted to mechanical energy by a watermill or to electrical energy by a hydroelectric turbine.

Water moves from an area where water potential is greater to an area where water potential is less regardless of the reason for the water potential. Your heart pumps blood to your brain against gravity by creating a greater water (blood) potential.

Molecules constantly move. They constantly bumper into and bounce off one another. Life scientists call the movement of molecules from a crowded area to less crowded area diffusion.In other words diffusion is the movement of suspended or dissolved particles from a more concentrated to a less concentrated region as a result of the random movement of individual particles; the process tends to distribute them uniformly throughout a medium.

When drops of red ink are added to a glass of water, the ink molecules are very close together. Diffusion takes place as the ink molecules move through the water. In time, the ink molecules spread out evenly until all of the water is of a light red color.

Apermeablemembrane of the cell has small holes through which molecules can move. Diffusion will take place if ink molecules are more crowded on one side of a permeable membrane, than on the other. The ink molecules will diffuse through the permeable membrane until they are evenly spaced on both sides of the membrane.

The holes in a cell membrane allow only some molecules to diffuse through, but not all. For this reason, life scientists describe a cell membrane as semipermeable. Water and other small molecules can easily pass through a cell membrane. Proteins and other large molecules must be broken down into smaller parts to get through a cell membrane. Once inside a cell, the larger molecules can be rebuilt.

Every cell continually uses sugar and blood must bring new supplies of sugar to cells. Sugar molecules diffuse in through the cell membrane, because there are fewer sugar molecules on the inside of the cell than on the outside. The cells also continually produce wastes. These wastes diffuse out of the cell through the semipermeable cell membrane because there are fewer waste molecules outside the cell than inside (Fig. 2.1). As the blood carries the wastes away, more wastes can diffuse out of the cells.

The diffusion of water into and out of the cell is known as osmosis.The process can cause a cell to swell or to shrink depending on the amount of water around the cell. The effects of osmosis can be easily seen in large cells, such as yolks of chicken eggs.

Osmosis can cause shrinking and swelling in plants too. When plant cells swell because of extra water in their environment, they push against their cell walls. This keeps the stems and leaves upright. When plant cells lack water in their environment, they shrink away from their cell walls, this makes a plant wilt.