1. The cell: The smallest unit of life that can function independently and perform all the necessary functions of life, including reproducing itself.
Where do we begin if we want to understand how organisms work?
In the case of organisms, whether we are studying a creature as small as a flea or as large as an elephant or giant sequoia, they can be broken down into smaller units that are more easily studied and understood (Figure 3-1 What do these diverse organisms have in common? Cells).
The most basic unit of any organism is the cell, the smallest unit of life that can function independently and perform all the necessary functions of life, including reproducing itself. Understanding cell structure and function is the basis for our understanding of how complex organisms are organized.

2. Cell Theory All living organisms are made up of one or more cells.
All cells arise from other pre-existing cells.
The facts that 1) all living organisms are made up of one or more cells, and 2) all cells arise from other pre-existing cells, are the foundations of cell theory, one of the unifying theories in biology, and one that is universally accepted by all biologists.
As we will see in Chapter 10, the origin of life on earth was a one-time deviation from cell theory: The first cells on earth likely originated from free-floating molecules in the oceans early in earth’s history (about three-and-a-half billion years ago). Since that time, however, all cells and thus all life have been produced as a continuous line of cells, originating from these initial cells.
In this chapter, we investigate the two different kinds of cells that make up all of the organisms on earth, the processes by which cells control how materials move into and out of the cell, and how cells communicate with each other. We also explore some of the important landmarks found in many cells. We also look at the specialized roles these structures play in a variety of cellular functions and learn about some of the health consequences that occur when they malfunction.

3. 3.2 Prokaryotic cells are structurally simple, but there are many types of them. Every cell on earth falls into one of two basic categories:
A eukaryotic cell
has a central control structure called a nucleus, which contains the cell’s DNA.
eukaryotes
A prokaryotic cell
does not have a nucleus; its DNA simply resides in the middle of the cell.
prokaryotes
Although there are millions of diverse species on earth, billions of unique organisms alive at any time, and trillions of different cells in many of those organisms, every cell on earth falls into one of two basic categories:
A eukaryotic cell (from the Greek for “true nucleus”) has a central control structure called a nucleus, which contains the cell’s DNA. Organisms composed of eukaryotic cells are called eukaryotes.

4. All prokaryotes are one-celled organisms and are thus invisible to the naked eye. Prokaryotes have four basic structural features (Figure 3-3 Structural features of a prokaryote).  
A plasma membrane encompasses the cell. For this reason, anything inside the plasma membrane is referred to as intracellular, while everything outside of the plasma membrane is extracellular.
The cytoplasm is the jelly-like fluid that fills the inside of cell.  
Ribosomes are little granular bodies where proteins are made; thousands of them are scattered throughout the cytoplasm. 
Each prokaryote has one or more circular loops or linear strands of DNA.
In addition to the characteristics common to all prokaryotes, some prokaryotes have additional unique features. Many have a rigid cell wall, for example, that protects and gives shape to the cell. Some have a slimy, sugary capsule as their outermost layer. This sticky outer coat provides protection and enhances the prokaryotes’ ability to anchor themselves in place when necessary.
Many prokaryotes have a flagellum, a long, thin, whip-like projection that rotates like a propeller and moves the cell through the medium in which it lives. Other appendages include pili, much thinner, hair-like projections that help prokaryotes attach to surfaces.

5. 3.3 Eukaryotic cells have compartments with specialized functions.
Eukaryotes showed up about 1.5 billion years after prokaryotes, and in the 2 billion years that they have been on earth, they have evolved into some of the most dramatic and interesting creatures, such as platypuses, dolphins, giant sequoias, and the Venus fly trap.
Because all prokaryotes are single-celled and thus invisible to the naked eye, every organism that we see around us is a eukaryotic organism (Figure 3-4 Diversity of the eukaryotes).  All fungi, plants, and animals are eukaryotes, for instance. Not all eukaryotes are multicellular, however. There is a huge group of eukaryotes called the Protista, nearly all of which are single-celled organisms visible only with a microscope.

6. Eukaryotic cells have organelles.
The chief distinguishing feature of eukaryotic cells is the presence of a nucleus, a membrane-bound structure that contains linear strands of DNA. In addition to a nucleus, eukaryotic cells usually contain in their cytoplasm several other specialized structures, called organelles, many of which are enclosed separately within their own lipid membranes. Eukaryotic cells are also about 10 times larger than prokaryotes. All of these physical differences make it easy to distinguish eukaryotes from prokaryotes under a microscope (Figure 3-5 Comparison of eukaryotic and prokaryotic cells). 

7. Figure 3-6 (Structures found in animal and plant cells) illustrates a generalized animal cell and a generalized plant cell.
Because they share a common, eukaryotic ancestor, they have much in common.
Both can have a plasma membrane, nucleus, cytoskeleton, ribosomes, and a host of membrane-bound organelles including rough and smooth endoplasmic membranes, Golgi apparatus, and mitochondria.
Animal cells have centrioles, which are not present in most plant cells.
Plant cells have a rigid cell wall (as do fungi and many protists) and chloroplasts (also found in some protists).
Plants also have a vacuole, a large central chamber (occasionally found in animal cells).
We explore each of these plant and animal organelles in detail later in this chapter.

8. Endosymbiosis Theory
Developed to explain the presence of two organelles in eukaryotes, chloroplasts in plants and algae, and mitochondria in plants and animals.
When you compare a complex eukaryotic cell to the structurally simple prokaryotic cell, it’s hard not to wonder how eukaryotic cells came about. How did they get filled up with so many organelles?
We can’t go back two billion years to watch the initial evolution of eukaryotic cells, but we can speculate about how it might have occurred.
One very appealing idea, called the endosymbiosis theory, has been developed to explain the presence of two organelles in eukaryotes, chloroplasts in plants and algae, and mitochondria in plants and animals. Chloroplasts help plants and algae convert sunlight into a more usable form of energy. Mitochondria help plants and animals to harness the energy stored in food molecules.

9. After a long while, the two cells may have become more and more dependent on each other until neither cell could live without the other, and they became a single, more complex organism.
Eventually, the photosynthetic prokaryote evolved into a chloroplast, the organelle in plant cells in which photosynthesis occurs.
A similar scenario might explain how a prokaryote unusually efficient at converting food and oxygen into easily usable energy might take up residence in another prokaryote and evolve into a mitochondrion, the organelle in plant and animal cells that converts the energy stored in food into a form usable by the cell (Figure 3-7 How did eukaryotic cells become so structurally complex?). 
The idea of endosymbiosis is supported by several observations.
Chloroplasts and mitochondria are similar in size to prokaryotic cells.
Chloroplasts and mitochondria have small amounts of circular DNA, similar to the organization of DNA in prokaryotes and in contrast to the linear DNA strands found in the eukaryote’s nucleus.
Chloroplasts and mitochondria divide by splitting, just like prokaryotes.
Chloroplasts and mitochondria have internal structures called ribosomes, which are similar to those found in bacteria.
In addition to the theory of endosymbiosis as an explanation for the existence of chloroplasts and mitochondria, another theory about the origin of organelles in eukaryotes is the idea that the plasma membrane around the cell may have just folded in on itself (a process called invagination) to create the inner compartments, which subsequently became modified and specialized (see Fig. 3-7). It may turn out that organelles arose from both processes. Perhaps mitochondria and chloroplasts originated from endosymbiosis, while all of the other organelles arose from plasma membrane invagination. We just don’t know.

11. Three important structural components stand out in the nucleus.
First is the nuclear membrane, a membrane sometimes called the nuclear envelope that surrounds the nucleus and separates it from the cytoplasm. Unlike most plasma membranes, however, the nuclear membrane consists of two bilayers on top of each other, much like if you have your groceries double-bagged at the market.
The nuclear membrane is not a sack, though. It is covered with tiny pores, made from multiple proteins embedded within the phospholipid membranes and spanning both of the bilayers. These pores enable large molecules to pass from the nucleus to the cytoplasm and from the cytoplasm to the nucleus. 11

12. 3.14 Cytoplasm and cytoskeleton: the cell’s internal environment, physical support, and movement
If we again imagine ourselves inside a cell the size of a big lecture hall, it might come as a surprise that we can barely even see that big-rig of a nucleus parked down in front. Visibility is almost zero not only because the room is filled with jelly-like cytoplasm, but also because there is a dense web of thick and thin, straight and branched ropes, strings, and scaffolding running every which way throughout the room. 12

13. Cytoskeleton: Three Chief Purposes
This inner scaffolding of the cell, which is made from proteins, is the cytoskeleton. It has three chief purposes:
It gives animal cells shape and support—making red blood cells look like round little doughnuts (without the hole in the middle) while giving neurons a very long and threadlike appearance. Plant cells are shaped primarily by their cell wall (a structure we discuss later in the chapter) but they also have a cytoskeleton.
The cytoskeleton controls the intracellular traffic flow, serving as a series of tracks on which a variety of organelles and molecules are guided across and around the inside of the cell.
Because the elaborate scaffolding of the cytoskeleton is dynamic and can generate force, it gives all cells some ability to control their movement. 13

14. Cilia and Flagellum
The cytoskeleton also plays a more direct and obvious role in helping some cells to move.
Cilia are short projections that often occur in large numbers on a single cell (Figure Cilia and flagella assist the cell with movement). Cilia beat swiftly, often in unison and in ways that resemble blades of grass in a field blowing in the wind. Cilia can move fluid along and past a cell. This movement can accomplish many important tasks, including sweeping the airways to our lungs clean of debris (such as dust) from the air that we breathe.
Flagella (singular: flagellum) are much longer than cilia. Flagella occur in many prokaryotes and single-celled eukaryotes, and many algae and plants have cells with one or more flagella. In animals, however, only one type of cell has a flagellum. But this one type of cell has a critical role in every single animal species. By forming the tail of a sperm cell, a flagellum makes possible the rapid movement of the most mobile of animal cells. Some spermicidal birth control methods prevent conception by disabling the flagellum and immobilizing the sperm cells. 14

15. 3.15 Mitochondria: the cell’s energy converters
Cars have it easy: we put only a single type of fuel in them and it is exactly the same fuel every time. With human bodies it’s a different story.
During some meals we put in meat and potatoes. Other times it’s juice and fruits. Still others involve bread or vegetables, popcorn and gummi bears, pizza and ice cream. Yet no matter what we eat, we expect our body to utilize the energy in all this food to power all the reactions in our bodies that make it possible for us to breathe, move, and think.
The mitochondria are the organelles that make this possible (Figure Mitochondria: the cell’s all-purpose energy converters).  15

16. Mitochondria (singular: mitochondrion) are the cell’s all-purpose energy converters and they are present in virtually all plant cells, animal cells, and every other eukaryotic cells.
Although we consume a variety of foods, our mitochondria allow us to convert the energy contained within the chemical bonds of the carbohydrates, fats, and proteins in food into carbon dioxide, water, and ATP―the molecule that is the energy source all cells use to fuel all their functions and activities. (ATP and how it works are described in detail in Chapter 4.)
Because this energy conversion requires a significant amount of oxygen, organisms’ mitochondria consume most of the oxygen used by each cell. In humans, for example, our mitochondria consume as much as 80% of the oxygen we breathe. They give a significant return on this investment by producing about 90% of the energy our cells use to function. 16

17. Bag-within-a-Bag Structure: the intermembrane space and the matrix
To visualize the structure of a mitochondrion, imagine a plastic sandwich bag.
Now take another bigger plastic bag and stuff it inside the sandwich bag. That’s the structure of mitochondria: there is a smooth outer membrane and a scrunched up inner membrane.
This construction creates two separate compartments within the mitochondrion: a region outside of the inner plastic bag (called the intermembrane space) and another region, called the matrix, that is inside the inner plastic bag.
This bag-within-a-bag structure has important implications for energy conversion.
And having a heavily folded inner membrane that is much larger than the outer membrane provides a huge amount of surface area on which to conduct chemical reactions. (We discuss the details of mitochondrial energy conversion and the role of mitochondrial structure in Chapter 4.) 17

18. 3.16 Lysosomes are the cell’s garbage disposals.
Garbage. What does a cell do with all the garbage it generates? Mitochondria wear out after about ten days of intensive activity, for starters. And white blood cells constantly track down and consume bacterial invaders, which they then have to dispose of. Similarly, the thousands of ongoing reactions of cellular metabolism produce many waste macromolecules that cells must digest and recycle. Many eukaryotic cells deal with this garbage by maintaining hundreds of versatile floating “garbage disposals” called lysosomes (Figure Lysosomes: digestion and recycling of the cell’s waste products).  18

19. Lysosomes
round, membrane-enclosed, acid-filled vesicles that function as garbage disposals
Lysosomes are round, membrane-enclosed, acid-filled vesicles that function as garbage disposals. Lysosomes are filled with about 50 different digestive enzymes and a super-acidic fluid, a corrosive broth so powerful that if a lysosome were to burst, it would almost immediately kill the cell by rapidly digesting all of its component parts.
The selection of enzymes represents a broad spectrum of chemicals designed for dismantling macromolecules no longer needed by cells or generated as by-products of cellular metabolism.
Some of the enzymes break down lipids, others carbohydrates, others proteins, and still others nucleic acids.
Consequently, lysosomes are frequently also a first step when, via phagocytosis, a cell consumes and begins digesting a particle of food or even an invading bacterium. And, ever the efficient system, most of the component parts of molecules that are digested, such as amino acids, are released back into the cell where they can be re-used by the cell as raw materials. 19

20. The Endomembrane System
The information for how to construct the molecules essential to a cell’s smooth functioning and survival is stored on the DNA found in the cell’s nucleus. The energy used to construct these molecules and to run cellular functions comes primarily from the mitochondria. The actual production and modification of biological molecules, however, occurs in a system of organelles called the endomembrane system (Figure
3-33 The endomembrane system: the smooth endoplasmic reticulum, rough endoplasmic reticulum, and Golgi apparatus).
This mass of interrelated membranes spreads out from and surrounds the nucleus, forming chambers within the cell that contain their own mixture of chemicals. The endomembrane system takes up as much as one-fifth of the cell’s volume and is responsible for many of the fundamental functions of the cell. Lipids are produced within these membranes, products for export to other parts of the body are modified and packaged here, polypeptide chains are assembled into functional proteins here, and many of the toxic chemicals that find their way into our bodies—from recreational drugs to antibiotics—are broken down and neutralized in the endomembrane system. 20

21. Rough Endoplasmic Reticulum
Perhaps the organelle with the most cumbersome name, the rough endoplasmic reticulum or rough ER (from the Greek words for a “within-cell network”), is a large series of interconnected, flattened sacs (they look like a stack of pancakes) that are connected directly to the nuclear envelope. In most eukaryotic cells, the rough ER almost completely surrounds the nucleus (Figure The rough endoplasmic reticulum is studded with ribosomes).  It is called “rough” because its surface is studded with little bumps. These bumps are protein-making machines called ribosomes, and generally cells with high rates of protein production have large numbers of ribosomes. We cover the details of ribosome structure and protein production in Chapter 5.
The primary function of the rough ER is to fold and package proteins that will be shipped elsewhere in the organism. Poisonous frogs, for example, package their poison in rough ER of the cells in which it is produced before transporting it to the poison glands on their skin. Proteins that are used within the cell itself are generally produced on free-floating ribosomes in the cytoplasm. 21

22. The Smooth Endoplasmic Reticulum
As its name advertises, the smooth endoplasmic reticulum is part of the endomembrane network that is smooth because there are no ribosomes bound to it (Figure In the smooth endoplasmic reticulum, lipids are synthesized and alcohol, antibiotics, and other drugs are detoxified).  Although it is connected to the rough ER, it is farther from the nucleus and differs slightly in appearance. Whereas the rough ER looks like stacks of pancakes, the smooth ER sometimes looks like a collection of branched tubes.
The smooth surface gives us the first hint that smooth ER has a different job than rough ER. Since ribosomes are absolutely essential for protein production, we can be certain that without them the smooth ER is not involved in folding or packaging proteins. It isn’t. Instead, it synthesizes lipids such as fatty acids, phospholipids, and steroids. Exactly which lipids are produced varies throughout the organism and across plant and animal species. Inside the smooth ER of mammalian ovaries and testes, for example, the hormones estrogen and testosterone are produced. Inside the smooth ER of liver and fat cells, lipids are produced. As in the rough ER, following their production these lipids are packaged in transport vesicles and are then sent to either other parts of the cell or to the plasma membrane for export. 22

23. 3.18 Golgi apparatus: Where the cell processes products for delivery throughout the body
Moving further outward from the nucleus, we encounter another organelle within the endomembrane system: the Golgi (GOHL-jee) apparatus.  
The Golgi apparatus processes molecules synthesized within a cell—primarily proteins and lipids—and packages those that are destined for use elsewhere in the body. The Golgi apparatus is also a site of carbohydrate synthesis, including the complex polysaccharides found in many plasma membranes. 23

24. The Golgi apparatus, which is not connected to the endoplasmic reticulum, is a flattened stack of membranes (each of which is called a Golgi body) that are not interconnected (Figure Golgi apparatus: processing of molecules synthesized in the cell and packaging of those molecules destined for use elsewhere in the body).
After transport vesicles bud from the endoplasmic reticulum, they move through the cytoplasm until they reach the Golgi apparatus. There, the vesicles fuse with the Golgi apparatus and dump their contents into a Golgi body.
There are about four successive Golgi body chambers to be visited and the molecules get passed from one to the next.
In each Golgi body, enzymes make slight modifications to the molecule (such as the addition or removal of phosphate groups or sugars). The processing that occurs in the Golgi apparatus often involves tagging molecules (much like adding a postal address or tracking number) to direct them to some other part of the organism. After they are processed, the molecules then bud off from the Golgi apparatus in a vesicle which then moves into the cytoplasm. If the molecule is destined for delivery and used elsewhere in the body, the transport vesicle eventually fuses with the cell’s plasma membrane and dumps the molecule into the bloodstream via exocytosis. 24

26. Figure 3-37 (The endomembrane system: producing, packaging, and transporting molecules) shows how the various parts of the endomembrane system work to produce, modify, and package molecules within a cell. 26

27. 3.19 The cell wall provides additional protection and support for plant cells.
Up until now, we’ve discussed organelles and structures that are common to both plants and animals.
Now we’re going to look at a couple of structures that are not found in all eukaryotic cells.
Because plants are stuck in the ground, unable to move, they have several special needs beyond those of animals. In particular, they can’t outrun or outmaneuver their competitors to get more food. Nor can they outrun organisms that want to eat them. If they want more sunshine, they have few options beyond simply growing larger or taller. And if they want to resist plant-eating animals, they must simply grow tougher outer layers.
One organelle that helps plants achieve both of these goals is the cell wall, a structure that surrounds the plasma membrane. The cell wall is made from polysaccharides, in which another carbohydrate called cellulose is embedded.
Note that although animal cells do not have cell walls, some non-plants such as archaea, bacteria, protists, and fungi also have cell walls, but the chemical composition of their cell walls differs from those found in plants.
The cell wall is nearly 100 times thicker than the plasma membrane, and the tremendous structural strength it confers on plant cells makes it possible for some plants to grow several hundred feet tall (Figure The plant cell wall: providing strength).  Cell walls also help to increase plants’ water resistance—an important feature in organisms that cannot reduce water loss to evaporation by moving out of the hot sun—and provide some protection from insects and other animals that might eat them.
Surprisingly, despite its great strength, the cell wall does not completely seal off plant cells from one another. Rather, it is porous, allowing water and solutes to reach the plasma membrane. It also has plasmodesmata, the channels connecting adjacent cells, allowing the passage of some molecules between them. 27

28. 3.20 Vacuoles: multipurpose storage sacs for cells
If you look at a mature plant cell through a microscope, one organelle, the central vacuole, usually stands out more than all the others because it is so huge and appears empty (Figure The vacuole: multipurpose storage).  
Although it appears to just be an empty sac, the central vacuole is anything but.
Surrounded by a membrane, filled with fluid, and occupying from 50 to 90% of a plant cell’s interior space, the central vacuole can play an important role in five different areas of plant life. (Although vacuoles are found in some other eukaryotic cells― including some protists, fungi, and animals―they tend to be particularly prominent in plant cells.) 28

29. 3.21 Chloroplasts: the plant cell’s power plant
It would be hard to choose the “most important organelle” in a cell, but if we had to, the chloroplast would be a top contender.
The chloroplast, an organelle found in all plants and eukaryotic algae, is the site of photosynthesis, the conversion of light energy into the chemical energy of food molecules, with oxygen as a by-product. Because all photosynthesis in plants and algae takes place in chloroplasts, they are directly or indirectly responsible for everything we eat and for the oxygen we breathe.
Life on earth would be vastly different without the chloroplast (Figure The chloroplast: location of photosynthesis).  29

30. The stroma and interconnected little flattened sacs called thylakoids
In a green leaf, each cell has about 40–50 chloroplasts. This means there are about 500,000 chloroplasts per square millimeter of leaf surface (that’s more than 200 million chloroplasts in the area the size of a small postage stamp). Chloroplasts are oval, somewhat flattened objects. On the outside, the chloroplast is encircled by two distinct layers of membranes (similar to the structure of mitochondria). The fluid-filled inside compartment is called the stroma, and it contains some DNA and much protein-making machinery.
With a simple light microscope, it is possible to see little spots of green within the chloroplasts. Up close, these spots look like stacks of pancakes. Each stack consists of numerous, interconnected little flattened sacs called thylakoids, and it is on the membranes of the thylakoids that the light collecting for photosynthesis occurs. (In Chapter 4, we discuss the details of how chloroplasts convert the energy in sunlight into the chemical energy stored in sugar molecules.) 30

31. Figure 3-41 (Review of the structures and functions of cellular organelles) summarizes all of the parts of a cell and their functions. 31

32. Take-home message 3.21
The chloroplast is an organelle in plants and algae in which photosynthesis occurs.
Chloroplasts may have originally been bacteria that were engulfed by a predatory cell by endosymbiosis.