1. Schedule and Announcements
Chapter 3
Chapter notes and reviews on website
Lab Quiz Thursday over metric and Sci Method
Exam 1- Tuesday September 8 over chapters 1-4
40 Multiple choice + 2 discussion questions
Bring pencil for scantron

2. Chapter 3 Learning Objectives
Describe what a cell is and the two general types of cells.
Describe the structure and functions of cell membranes.
Describe several ways in which molecules move across membranes.
Describe how cells are connected and how they communicate with each other.
Describe nine important landmarks in eukaryotic cells.

3. 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.

4. 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.

5. 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.

6. 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.

7. 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). 

8. Figure 3-6 (Structures found in animal and plant cells
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.

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.

10. 3-4. Every cell is bordered by a plasma membrane.
Just as skin covers our bodies, every cell of every living thing on earth, whether a prokaryote or a eukaryote, is enclosed by a plasma membrane, a two-layered membrane that holds the contents of a cell in place and regulates what enters and leaves the cell. Plasma membranes are thin (a stack of a thousand would be only as thick as a single hair) and flexible, and in photos or diagrams it often appears that the membranes resemble simple plastic bags, holding the cell contents in place.
This image is a gross oversimplification, however. Membranes are indeed thin and flexible, but they are far from simple: A close look at a plasma membrane will reveal that its surface is filled with pores, outcroppings, channels, and complex molecules floating around within the two layers of the membrane itself (Figure 3-8 More than just an outer layer). 10

11. 3.5 Molecules embedded within the plasma membrane help it perform its functions.
While the plasma membrane’s phospholipid bilayer construction gives the cell its basic boundary with its environment, there is much more to a plasma membrane. Embedded within or attached to the phospholipid bilayer are different types of protein, carbohydrate, and lipid molecules (Figure Protein and carbohydrate molecules are embedded in the plasma membrane). 
The proteins found in the plasma membrane enable it to carry out most of its gatekeeping functions. For every 50 to 100 phospholipids, there is a protein in the membrane. Some of these proteins, called transmembrane proteins, penetrate right through the lipid bilayer, from one side to the other. Others, called surface proteins, reside primarily on the outside of the membrane. 11

12. There are four primary types of membrane proteins, each of which performs a different function.
Receptor proteins bind to chemicals in the cell’s external environment and, by doing so, regulate certain processes within the cell.
Recognition proteins give each cell a “fingerprint” that makes it possible for the body’s immune system (which fights off infections) to distinguish the cells that belong inside you from those that are invaders and need to be attacked. (Note that carbohydrates also play a role in recognition.) Recognition proteins also can help cells to bind to adhere to other cells or molecules.
Transport proteins are transmembrane proteins that help large and/or strongly charged molecules to pass through the plasma membrane. Transport proteins come in a variety of shapes and sizes, making it possible for a wide variety of molecules to be transported.
Enzymatic proteins accelerate chemical reactions on the cell membrane’s surface (a variety of different enzymatic proteins exist, with some accelerating reactions on the inside of the plasma membrane and other accelerating reactions on the outside of the plasma membrane). 12

13. The Plasma Membrane “Fluid Mosaic”
In addition to proteins, two other molecules are found in the plasma membrane:
Short, branched carbohydrate chains
Cholesterol
Short, branched carbohydrate chains that are attached to proteins and phospholipid heads on the outside of the cell membrane serve as part of a membrane’s fingerprint along with recognition proteins. This fingerprint allows the cell to be recognized by other cells, such as those of the immune system.
The plasma membrane also can contain cholesterol, a lipid that helps the membrane maintain its flexibility. It prevents the membrane from becoming too fluid or floppy at moderate temperatures and acts like a sort of anti-freeze, preventing the membrane from becoming too rigid at freezing temperatures. The membranes of some cells are about 25% cholesterol; other cell membranes, such as those of most bacteria and plants, have no cholesterol at all.
As we’ve seen, the plasma membrane is made up from several different types of molecules, like a mosaic, and many of those molecules float around, held in proper orientation by hydrophobic and hydrophilic forces, but not always anchored in place. For these reasons, the plasma membrane is often described as a fluid mosaic. 13

14. 3-6. Faulty membranes can cause disease.
With all the complexity of plasma membranes, it’s not surprising that there are many ways in which they can malfunction. One disease that results from an improperly functioning membrane is cystic fibrosis, the single most common fatal genetic disease in the United States. At any given time, about 30,000 people have cystic fibrosis.
Cystic fibrosis occurs when an individual inherits from both parents incorrect genetic instructions for producing one type of transmembrane protein. This protein occurs primarily in the membranes of cells in the lungs and digestive tract. When functioning normally, the protein serves as a passageway that allows one type of molecule—chloride ions—to get into and out of cells.
There are more than a thousand different ways in which these genetic instructions can be defective, but in every case the result is the same: the lack of properly working chloride passageways in a cell’s membrane. This defect leads to gradual accumulation of chloride ions within cells. Although it is not clear exactly how the chloride ion accumulation leads to the symptoms of cystic fibrosis, in nearly all cases two primary effects occur: an improper salt balance in the cells and a buildup of thick, sticky mucus—particularly in the lungs. Normal mucus helps to protect the lungs by trapping dust and bacteria. This mucus is then moved out of the lungs (helped along by coughing). The mucus produced by someone with cystic fibrosis, however, is too thick and sticky to be moved out of the lungs, so it collects there where it impairs lung function and increases the risk of bacterial infection. Because of the improper cellular salt balance, one way to test for cystic fibrosis is to measure the concentration of salt in the sweat—abnormally high concentrations indicate that the person has the disease.
One of the most common treatments is decidedly low-tech. Parents help their children with cystic fibrosis clear the mucus out of their lungs by holding them on a steep slant, almost upside down, and vigorously patting or thumping their chest and back to shake loose the mucus in their lungs and move it to a place where they can cough it up. With careful treatment, the life expectancy of someone with cystic fibrosis can be 35 to 40 years or longer (Figure Moving mucus manually, or through an inhalation vest).  14

15. 3.7 Membrane surfaces have a “fingerprint” that identifies the cell.
Cells with an improper fingerprint are recognized as foreign and are attacked by your body’s defenses.
As mentioned earlier, every cell in your body has a “fingerprint” made from a variety of molecules on the outside-facing surface of the cell membrane.
Some of the membrane molecules are based on the specific function of the cell.
Others are common to all cells within an individual and convey to your immune system: “I belong here.”
Cells with an improper fingerprint are recognized as foreign and are attacked by your body’s defenses. 15

16. Throughout our evolutionary history, this system has been tremendously valuable in helping our bodies to fight infection. In some cases, however, this vigilance is a problem, like a car alarm that goes off even when we don’t want it to.
Suppose you receive a liver (or any other organ) transplant. Even if the donor is a close relative, the molecular fingerprint on the cells of the donated liver is not identical to your own. Consequently, your body fights the new organ because it is a foreign object (Figure Mismatched molecular fingerprints can cause difficulty in organ transplantation).  
Because your body will naturally try to reject the new organ, doctors must administer drugs that suppress your immune system. Immune suppression helps you tolerate the new liver but, as you can imagine, it leaves you without some of the defenses to fight off other foreign invaders, such as bacteria that may cause infection.
The presence or absence of certain plasma membrane molecular markers is also responsible for a person’s blood type and can lead to problems with simple blood transfusions. 16

17. Why is it extremely unlikely that a person will catch HIV from casual contact—such as shaking hands—with an infected individual?
The AIDS-causing HIV virus uses the molecular markers on a cell’s plasma membranes to infect an individual’s cells. These same molecular markers are also the reason why it is extremely unlikely that a person can catch AIDS from casual contact—such as shaking hands—with an infected individual.
The specific molecular markers involved in infection by the HIV virus belong to a group of identifying markers called “clusters of differentiation.” Abbreviated as “CD markers” and having names such as CD1, CD2, and CD3, these marker molecules are proteins embedded within the plasma membrane that enable a cell to bind to outside molecules and, sometimes, transport them into the cell. 17

18. One CD marker is called the CD4 marker
One CD marker is called the CD4 marker. It is found only on cells deep within the body and in the bloodstream, such as immune system cells and some nerve cells.
It is the CD4 marker, in conjunction with another receptor, that is targeted by the HIV virus. If the HIV virus can find a cell with a CD4 marker, it can infect you, and because the CD4 markers never occur on the surface of your skin cells, casual contact such as touching is very unlikely to transmit the virus (Figure HIV is not transmitted through casual contact).  
Even if millions of HIV particles are present on one person’s hands, they just can’t gain access to any of the other person’s surface cells. 18

19. There are two types of passive transport:
3.8 Passive transport is the spontaneous diffusion of molecules across a membrane.
There are two types of passive transport:
Diffusion
Osmosis 19

20. Diffusion and Concentration Gradients
Solutes
Solvents
Diffusion is passive transport in which a particle, called a solute, is dissolved in a gas or liquid (called a solvent) and moves from an area of high solute concentration to an area of lower concentration (Figure Diffusion: a form of passive transport that results in an even distribution of molecules). (When talking about cells, diffusion usually refers to the situation in which the solutes move across a membrane.)
In the absence of other forces, molecules of a substance will always tend to move from where they are more concentrated to where they are less concentrated. This movement occurs because molecules move randomly and are equally likely to move in any direction.
When certain molecules are highly concentrated, they keep bumping into each other and eventually end up evenly distributed. For this reason, we say that molecules tend to move down their concentration gradient. For a simple illustration, drop a tiny bit of food coloring into a bowl of water and wait for a few minutes. The molecules of color are initially clustered together in a very high concentration. Gradually, they disperse down their concentration gradient until the color is equally spread throughout the bowl. 20

21. Simple Diffusion
Molecules such as oxygen and carbon dioxide, that are small and carry no charge, can pass directly through the lipid bilayer of the membrane without the assistance of any other molecules in a process called simple diffusion.
Each time you take a breath, for example, there is a high concentration of oxygen molecules in the air you pull into your lungs. That oxygen diffuses across membranes of the lung cells and into your bloodstream where red blood cells pick it up and deliver it to parts of your body where it is needed. Similarly, because carbon dioxide in your bloodstream is at a higher concentration than in the air in your lungs, it diffuses from your blood into your lungs and is released to the atmosphere when you exhale (Figure Simple and facilitated diffusion).  21

22. Facilitated Diffusion
Most molecules can’t get through plasma membranes on their own.
Carrier molecules
Transport proteins
Most molecules, however, can’t get through plasma membranes on their own.
They may be electrically charged and, hence, repelled by the hydrophobic middle region of the phospholipid bilayer. Or the molecules may be too big to squeeze through the membrane.
Nonetheless, when there is a concentration gradient from one side of the membrane to the other, these molecules may still be able to diffuse across the membrane with the help of a carrier molecule, one of the transport proteins we discussed in section 3-5, earlier in this chapter. Often, this transport protein spans the membrane and functions like a revolving door.
When spontaneous diffusion across a plasma membrane requires a transport protein, it is called facilitated diffusion. 22

23. Defects in Transport Proteins
Can reduce or even bring facilitated diffusion to a complete stop
Serious health consequences
Many genetic diseases
Cystinuria and kidney stones
Defects in transport proteins can reduce or even bring facilitated diffusion to a complete stop, with serious health consequences. Many genetic diseases are the result of inheriting incorrect genetic instruction for building transport proteins.
In the disease cystinuria, for example, incorrect genetic instructions result in a malformed transport protein in the plasma membrane. When structured and functioning properly, this transport protein facilitates the diffusion of some amino acids (including cystine, from which the disease gets its name) out of the kidneys. When the proteins are malformed, they cannot facilitate this diffusion and these amino acids build up in the kidneys, forming painful and dangerous kidney stones. 23

24. 3.9 Osmosis is the passive diffusion of water across a membrane.
Just as solutes will passively diffuse down their concentration gradients, water molecules will also move from areas of high concentration to low concentration to equalize the concentration of water inside and outside of the cell.
The diffusion of water across a membrane is a special type of passive transport called osmosis (Figure Osmosis overview).  
As molecules diffuse across a plasma membrane, molecules of water also move across the membrane, equalizing the concentration of water inside and outside of the cell. 24

25. Cells in Solution Tonicity Hypertonic Hypotonic Isotonic
The relative concentration of solutes outside of the cell relative to inside the cell
Hypertonic
Hypotonic
Isotonic
When a cell is in a solution, we describe the concentration of solutes outside of the cell relative to inside the cell as the tonicity of the solution.
A hypertonic solution has a greater concentration of solutes than the solution inside the cell. As a consequence, if the cell membrane is not permeable to the solutes, water will move out of the cell into the surrounding solution, equalizing the solute concentration inside and out (and the cell shrivels).
A hypotonic solution has lower solute concentration than the solution inside the cell. If the cell membrane is not permeable to the solutes, water will move into the cell and it will swell.
In an isotonic solution, the concentration of solutes is the same inside and outside of the cell. 25

26. Two distinct types of active transport:
Primary
Secondary
(Differ only in the source of the fuel)
In all active transport, proteins embedded within the membrane act like motorized revolving doors, pushing molecules into the cell regardless of the concentration of those molecules on either side of the membrane.
There are two distinct types of active transport, primary and secondary, which differ only in the source of the fuel that keeps the revolving doors spinning  next slides.
[Query – Are the arrow and the words “next slides” supposed to be at the end of the last line of notes above? Or should they be deleted?] 26

27. Primary Active Transport: Uses Energy Directly from ATP
Every time you eat a meal you start the motors that spin the revolving door to transport proteins in your stomach (Figure Active transport).  
To help break down the food into more digestible bits, the cells lining your stomach create an acidic environment by pumping large numbers of H+ ions (also called protons) into the stomach contents, against their concentration gradient. (That is, there are more H+ ions in the stomach contents than there are inside the stomach lining cells.)
All of this H+ pumping increases your ability to digest the food but comes at a great energetic cost—in the form of usage of a high-energy molecule called ATP—because the protons would not normally flow into a region against their concentration gradient.
When active transport uses energy directly from ATP to fuel the revolving door, the process is called primary active transport. (We explore ATP in more detail in Chapter 4.) 27

28. Secondary Active Transport
An indirect method many transporter proteins use for fueling their activities
The transport protein simultaneously moves one molecule against its concentration gradient while letting another flow down its concentration gradient.
Many transporter proteins use an indirect method of fueling their activities rather than using energy released directly from ATP.
In the process called secondary active transport, the transport protein simultaneously moves one molecule against its concentration gradient while letting another flow down its concentration gradient. 28

29. Secondary Active Transport
No ATP is used directly.
At some other point and in some other location, energy from ATP was used to pump one of the types of molecules involved against their concentration gradient.
Although no ATP is used directly in this process, at some other point and in some other location, energy from ATP was used to pump one of the types of molecules involved against their concentration gradient. The process is a bit like using energy to pump water up to the top of a high water tower.
Later, the water can be allowed to run out of the tower over a water wheel that can, in turn, power some process like grinding wheat into flour. Our bodies will frequently use the energy from one reaction that occurs spontaneously to fuel another reaction that requires energy to occur. 29

30. 3.11 Endocytosis and exocytosis are used for bulk transport of particles.
Many molecules are just too big to get
into a cell by passive or active transport.
Many molecules are just too big to get into a cell by passive or active transport. After all, a protein embedded in a thin plasma membrane can only be so big and some cells in the immune system, for example, must ingest (and destroy) entire bacterial cells that are invading your body. To absorb such large molecules, cells engulf them with their plasma membrane in a process called endocytosis.
Cells also have another method besides passive and active transport for moving molecules out of them. Cells that manufacture molecules (such as digestive enzymes) for use elsewhere in the body must get those molecules out of the cell and often use the process of exocytosis to do so. 30

31. Three types of endocytosis:
Phagocytosis
Pinocytosis
Receptor-mediated endocytosis
There are three types of endocytosis: phagocytosis, pinocytosis, and receptor-mediated endocytosis. All three involve the basic process of the plasma membrane oozing around an object that is outside of the cell, surrounding it, forming a little pocket called a vesicle, and then pinching off the vesicle so it is separated from the rest of the contents inside the cell. 31

32. Phagocytosis and Pinocytosis
Phagocytosis is the process by which relatively large particles are engulfed by cells (Figure Through phagocytosis, amoebas and other unicellular protists, as well as white blood cells, consume other organisms for food or for defense).  Amoebas and other unicellular protists as well as white blood cells use phagocytosis to entirely consume other organisms either as food or as their way of defending the body against pathogens (disease-causing organisms or substances). 32

33. Pinocytosis: the process of cells taking in dissolved particles and liquid
Whereas phagocytosis comes for the Greek words for cellular “eating,” pinocytosis comes from the Greek words describing cellular “drinking,” and describes the process of cells taking in dissolved particles and liquid.
The process is largely the same, except that the vesicles formed during pinocytosis are generally much smaller than those formed during phagocytosis.

34. Receptor-mediated Endocytosis
The third type of endocytosis, receptor-mediated endocytosis, is much more specific than either phagocytosis or pinocytosis. In this process, receptor molecules on the surface of a cell sit waiting until the one molecule for which they are waiting bumps into them. For one receptor it might be insulin, for another it might be cholesterol. Many receptors of the same type are often clustered together in a cell’s plasma membrane. When the appropriate molecule binds to each of the receptor proteins, the membrane begins to fold inward, first forming a little pit and then completely engulfing the molecules, which are still attached to their receptors.
One of the most important examples of receptor-mediated endocytosis involves cholesterol (Figure Receptor proteins aid in endocytosis).  Most cholesterol that circulates in the bloodstream is in the form of particles called low-density lipoproteins, or LDL.
Each molecule of LDL is a cholesterol globule coated by phospholipids.
Proteins embedded within the LDL’s phospholipid coat are recognized by receptor proteins built into the plasma membranes of liver cells. Once bound to the receptors, the LDL molecule is then consumed by the cell via endocytosis. Once inside the cell, the cholesterol is broken down and used to make a variety of other useful molecules, such as the hormones estrogen and testosterone. 34

35. Cells in the pancreas produce a chemical called insulin that moves throughout the circulatory system, informing body cells that there is glucose in the bloodstream that ought to be taken in and utilized for energy. The insulin molecule is much too large to pass through the cell membranes of the cells in which it is manufactured. As a result, after molecules of insulin are produced, they are coated with a phospholipid membrane forming a vesicle. The insulin-carrying vesicle then moves through the cytoplasm to the inner surface of the cell’s plasma membrane. Once there, the phospholipid membranes surrounding the insulin and the phospholipid membrane of the cell fuse together, dumping the contents of the vesicle into the bloodstream outside of the cell (Figure Exocytosis moves molecules out of the cell).  
Exocytosis, the movement of molecules out of a cell, occurs throughout the body and is not restricted to large molecules. In the brain and other parts of the nervous system, for example, communication between cells occurs as one cell releases large numbers of very small molecules, called neurotransmitters, via exocytosis. 35

36. Receptor-mediated endocytosis Exocytosis
When a woman nurses her baby, proteins are released from the mammary cells, accumulate in the ducts of the breast, and flow out of the nipple. Which process listed below is involved?
Phagocytosis
Pinocytosis
Receptor-mediated endocytosis
Exocytosis
Answer: 4 36

37. We examine three primary types of connections between animal cells: 1) tight junctions, 2) desmosomes, and 3) gap junctions (Figure Cell connections: tight junctions, desmosomes, and gap junctions) and one type of connection between plant cells: plasmodesmata. 37

38. Tight Junctions
form continuous, water-tight seals around cells and also anchor cells in place
particularly important in the small intestine where digestion occurs
Tight junctions form continuous, water-tight seals around cells and also anchor cells in place. Much like the caulking around a tub or sink that keeps water from leaking into the walls surrounding it, tight junctions prevent fluid flow between cells. Tight junctions are particularly important in the small intestine where digestion occurs.
Cells lining the small intestine absorb nutrients from the watery fluid moving through your gut. If the fluid and bacteria inside the intestine were to leak out to your body cavity, you would not be able to extract sufficient energy and nutrients from it, and the bacteria would make you sick. The tight junctions instead force fluid to pass into the cells that line the intestine where the nutrients can be utilized. 38

39. Desmosomes
are like spot welds or rivets that fasten cells together into strong sheets
function like Velcro: they hold cells together but are not water-tight
found in much of the tissue-lining cavities of animal bodies
Desmosomes are like spot welds or rivets that fasten cells together into strong sheets. They occur at irregular intervals and function like Velcro: they hold cells together but are not water-tight, allowing fluid to pass around them.
Desmosomes are found in much of the tissue lining cavities of animal bodies. They also are found in muscle tissue, holding fibers together. Genetic disorders that reduce cells’ ability to form desmosome proteins or lead to desmosome destruction by the immune system result in the formation of blisters where layers of the skin separate from each other. 39

40. Gap Junctions pores surrounded by special proteins that form open channels between two cells
Finally, gap junctions are pores surrounded by special proteins that form open channels between two cells (Figure 3-25). Functioning like secret passageways, these junctions are large enough for salts, sugars, amino acids, and electrical signals to pass through, but are too small for the passage of organelles or larger molecules such as proteins and nucleic acids.
Gap junctions are an important mechanism for cell-to-cell communication.
In the heart, for example, the electrical signal telling the muscle cells to contract is passed from cell to cell through gap junctions. Gap junctions are also important in allowing a cell to recognize that it has bumped up against another cell; chemicals flowing from one cell to the next can signal to the body to stop producing cells of a particular type.
Gap junctions are an important mechanism
for cell-to-cell communication. 40

41. Your skin cells form a waterproof barrier, therefore they are held together by…
Tight junctions
Desmosomes
Gap junctions
Glue
Answer: 1

42. Plasmodesmata
Tube-like channels connecting the cells to each other and enabling communication and transport between them
Consider a plant as one big cell?
In most plants, the cells have anywhere from 1,000 to 100,000 microscopic tube-like channels, called plasmodesmata, connecting the cells to each other and enabling communication and transport between them. In fact, because so many of the cells are connected to each other, sharing cytoplasm and other molecules, some biologists have wondered whether we should just consider a plant as one big cell. How would you respond to that idea? 42

43. 3.13 The nucleus is the cell’s genetic control center.
The nucleus―the largest and most prominent organelle in most eukaryotic cells.
The nucleus has two primary functions:
genetic control center
storehouse for hereditary information
Insert new fig 3-26 to right
As we have seen, all cells are surrounded by a complex plasma membrane that actively regulates what materials get into and out of a cell. Now it’s time to look at the cellular contents surrounded by the plasma membrane in eukaryotic cells.
The nucleus is the largest and most prominent organelle in most eukaryotic cells. In fact, the nucleus is generally larger than any prokaryotic cell. If a cell were the size of a large lecture hall or movie theater, the nucleus would be the size of a big-rig 18-wheeler truck parked in the front rows.
The nucleus has two primary functions, both related to the fact that most of the cell’s DNA resides in the nucleus. First, the nucleus is the genetic control center, directing most cellular activities by controlling which molecules are produced and in what quantity they are produced. Second, the nucleus is the storehouse for hereditary information. 43

44. 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. 44

45. Chromatin
a mass of long, thin fibers consisting of DNA with some proteins attached
The second prominent structure in the nucleus is called chromatin, a mass of long, thin fibers consisting of DNA with some proteins attached to it that keep it from getting impossibly tangled. Most of the time as the DNA directs cellular activities, the chromatin resembles a plate of spaghetti.
When it comes time for cell division (a process described in detail in Chapter 6), the chromatin coils up and the threads become shorter and thicker until they become visible as chromosomes―the compacted, linear DNA molecules on which all of the hereditary information is carried. 45

46. Nucleolus
an area near the center of the nucleus where subunits of the ribosomes are assembled
Ribosomes are like little factories.
A third structure in the nucleus is the nucleolus, an area near the center of the nucleus where subunits of the ribosomes, a critical part of the cellular machinery, are assembled.
Ribosomes are like little factories that copy bits of the information stored in the DNA and use them to construct proteins, such as enzymes and the proteins that make up tissues such as bark in trees or bone in vertebrates. The ribosomes are built in the nucleolus but pass through the nuclear pores and into the cytoplasm before starting their protein production work. 46

47. 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. 47

48. 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. 48

49. 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. 49

50. 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. 50

51. Endosymbiosis
Mitochondria may have existed as separate single-celled, bacteria―like organisms billions of years ago.
Mitochondria have their own DNA!
As we learned in our earlier discussion of endosymbiosis, mitochondria may very well have existed as separate single-celled, bacteria-like organisms one day billions of years ago. They are similar to bacteria in size and shape and may have originated when symbiotic bacteria took up permanent residence within other cells. Perhaps the strongest evidence for this is that mitochondria have their own DNA.
Mixed in among the approximately 3,000 proteins in each mitochondrion, there are anywhere from two to ten copies of its own little ring-shaped DNA. This DNA carries the instructions for making 13 important mitochondrial proteins necessary for metabolism and energy production. 51

52. We all have more DNA from one parent than the other.
Who is the bigger contributor:
mom or dad?
Why?
We’re always taught that our mothers and fathers contribute equally to our genetic composition, but this isn’t quite true because the mitochondria in every one of your cells (and the DNA that comes with them) come from the mitochondria that are initially present in your mother’s egg, which, when fertilized by your father’s sperm, developed into you. In other words: all of your mitochondria came from your mother.
The tiny sperm contributes DNA but no cytoplasm, and hence, no mitochondria. Consequently, mitochondrial DNA is something that we inherit exclusively from our mothers.
This is true not only in humans, but in most multicellular eukaryotes. As the fertilized egg develops into a two-cell, then four-cell embryo, the mitochondria split themselves by a process called fission, the same process of cell division and DNA duplication used by bacteria—so that there are always enough mitochondria for the newly produced cells. This similarity between mitochondria and bacteria is another characteristic that supports the theory that mitochondria were originally symbiotic bacteria. 52

53. Which statement about mitochondria is false?
Mitochondria are surrounded by two membranes.
Mitochondria make energy of the cell (ATP).
You inherited half of your mitochondria from your mother.
The characteristics of mitochondria can be explained by endosymbiosis.
Answer: 3

54. Which cell type contains the most mitochondria per cell?
Liver
Muscle
White blood cell
Dermal cell
White adipose cell
Red blood cell
Please insert Figure 3-31
PROVIDE ANSWER

55. Which cell type in the graph might require the most energy?
Liver
Muscle
White blood cell
Dermal cell
White adipose cell
Red blood cell
Use to start a discussion. This subject is covered at the end of this chapter (p. 44) where students are asked to explore whether the number of mitochondria per cell is the best measure of the energy capacity of the cell. If you want you can use this to have students postulate on why a muscle cell has fewer mitochondria per cell than a liver cell.

56. 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).  56

57. 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. 57

58. Why is Tay-Sachs disease like a strike by trash collectors?
50 different enzymes necessary
Malfunctions sometimes occur
Genetic disorder
With 50 different enzymes necessary for lysosomes to carry out their metabolic salvaging act, malfunctions sometimes occur. A common genetic disorder called Tay-Sachs disease is the result of just such a genetic mishap.
In Tay-Sachs disease, an individual inherits an inability to produce a critical lipid-digesting enzyme. Because the lysosomes cannot digest certain lipids, they [the lipids?] continue to be sent to the lysosome where they accumulate, undigested. This leads to a sort of lysosome constipation. The lysosome swells until it bursts and digests the whole cell [it digests the cell after it bursts?] or until it chokes the cell to death. Within the first few years of life, this process occurs in large numbers of cells and eventually leads to death. 58

59. 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. 59

60. 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. 60

61. 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. 61

62. Which organ below is likely composed of cells with the greatest amount of SER?
Heart
Lungs
Kidney
Liver
Brain
Answer: 4

63. 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. 63

64. 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. 64

65. Rough endoplasmic reticulum Smooth endoplasmic reticulum
You can think of a cell as a car factory. The control center holds the directions for making the car. There are assembly lines for constructing the engine and frame of the car. After the main structure of the car is built, the finishing touches are added (paint, leather seats, chrome bumpers). Lastly, the car is shipped to different car dealers. Which organelle would be responsible for putting the finishing touches on the car (protein)?
Nucleus
Ribosome
Rough endoplasmic reticulum
Smooth endoplasmic reticulum
Golgi apparatus
Answer: 5 65

66. 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. 66

67. 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.) 67

68. 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).  68

69. Figure 3-41 (Review of the structures and functions of cellular organelles) summarizes all of the parts of a cell and their functions. 69