The Internal Organization of Cells

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Question 1

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The Internal Organization of Cells In addition to the plasma membrane, many cells have membrane-bound regions inside the cell where specific functions are carried out. These cells can be compared to a large factory with many rooms and different departments. Each department has a specific function and internal organization that contribute to the overall “life” of the factory. In this section, we give an overview of two broad classes of cells that can be distinguished by the presence or absence of these membrane-enclosed compartments.

Eukaryotes and prokaryotes differ in internal organization. All cells have a plasma membrane and contain genetic material. In some cells, the genetic material is housed in a membrane-bound space called the nucleus. Cells can be divided into two classes based on the presence or absence of a nucleus. Prokaryotes, such as bacteria, lack a nucleus, and eukaryotes, such as plants, animals, fungi, and protists, have a nucleus (Fig. 1).

Fig. 1 Prokaryotic and eukaryotic cells. Prokaryotic cells lack a nucleus and extensive internal compartmentalization. Eukaryotic cells have a nucleus and extensive internal compartmentalization.

While the two groups are defined by the presence or absence of a nucleus, they differ in many other aspects as well. For example, we learned in lecture 16 that promoter recognition during transcription is different in prokaryotes and eukaryotes. In addition, there are differences in the specific types of lipids that make up their cell membranes. In mammals, as we have seen, cholesterol is present in membranes. Cholesterol belongs to a group of chemical compounds known as sterols, which are molecules containing a hydroxyl group attached to a four-ringed structure. In eukaryotes other than mammals, diverse sterols are synthesized and present in cell membranes. Most prokaryotes do not synthesize sterol molecules, but some synthesize compounds called hopanoids instead. These five-ringed structures are thought to serve a similar function as cholesterol does in mammalian cell membranes. Additional differences between prokaryotes and eukaryotes are discussed below.

Question: Eukaryotic cells have a __________ and ____________, which prokaryotes do not.

nucleus; hopanoids Correct!

nucleus; cholesterol genome; hopanoids genome; hopanoids

Question 2

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Prokaryotic cells lack a nucleus and extensive internal compartmentalization. Prokaryotes do not have a nucleus. That is, there is no physical barrier separating the genetic material from the rest of the cell. Instead, the DNA is concentrated in a discrete region of the cell interior known as the nucleoid. Bacteria often contain additional small circular molecules of DNA known as plasmids that carry a small number of genes. Plasmids are commonly transferred between bacteria through threadlike, hollow structures known as pili (singular pilus), which extend from one cell to another. Genes for antibiotic resistance are commonly transferred in this way, which accounts for the quick spread of antibiotic resistance among bacterial populations. While the absence of a nucleus is a defining feature of prokaryotes, other features also stand out. For example, prokaryotes are small, just 1-2 micrometers (1/1,000th of a meter) in diameter or smaller. By contrast, eukaryotic cells are commonly much larger, on the order of 10 times larger in diameter and 1,000 times larger in volume. Being small means that cells have a relatively high ratio of surface area to volume, which makes sense for an organism that absorbs nutrients from the environment. In other words, there is a large amount of membrane surface area for absorption relative to the volume of the cell that it serves. In addition, most prokaryotes lack the extensive internal organization characteristic of eukaryotes.

Question: Prokaryotic DNA is concentrated in a discrete region called the _______.

You Answered

nucleus

Correct Answer

nucleoid plasmid pili

Question 3

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Eukaryotic cells have a nucleus and specialized internal structures. Eukaryotes are defined by the presence of a nucleus, which houses the vast majority of the cell’s DNA. The nuclear membrane allows for more complex regulation of gene expression than is possible in prokaryotic cells. In eukaryotes, DNA is transcribed to RNA inside the nucleus, but the RNA molecules carrying the genetic message travel from inside to outside the nucleus and there they instruct the synthesis of proteins. In addition, eukaryotes have a remarkable internal array of membranes. These membranes define compartments, called organelles, that divide the cell contents into smaller spaces specialized for different functions. Fig. 2a shows a typical animal cell (a macrophage) with various organelles. The endoplasmic reticulum (ER) is involved in the synthesis of proteins and lipids. The Golgi apparatus modifies proteins and lipids produced by the ER, and acts as a sorting station as they move to their final destinations. Lysosomes contain enzymes that break down macromolecules such as proteins, nucleic acids, lipids, and complex carbohydrates. Finally, mitochondria are specialized to harness energy for the cell. In addition to defining these organelles, many membranes are associated with a protein scaffold called the cytoskeleton that helps cells to maintain their shape and serves as a network of tracks for the movement of substances within cells. Some cells even move with the help of the cytoskeleton.

Fig. 2 An animal cell and a plant cell. Animal and plant cells share many cell components.

Fig. 2b shows a typical plant cell. In addition to the organelles described above, plant cells have a cell wall outside of the plasma membrane, vacuoles specialized for water uptake, and chloroplasts that convert energy of sunlight into chemical energy. The entire contents of a cell other than the nucleus make up the cytoplasm. The region of the cell inside the plasma membrane but outside the organelles is referred to as the cytosol. This is the jelly-like internal environment surrounding the organelles. In the next two sections, we consider these organelles in more detail, focusing on the role of membranes in forming distinct compartments within the cell.

1) True or false: A nuclear envelope allows enables more complex gene regulation. 2) True or false: Cytoplasm is the jelly-like substance that bathes the organelles within a cell.

You Answered

1) True, 2) True A nuclear envelope allows DOES enable more complex gene regulation, but the CYTOSOL is the jelly-like substance that bathes the organelles within a cell.

Correct Answer

1) True, 2) False 1) False, 2) True 1) False, 2) False

Question 4

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The Endomembrane System In eukaryotes, the total surface area of intracellular membranes is about 10-fold greater than that of the plasma membrane. This high ratio of internal membrane area to plasma membrane area underscores the significant degree to which a eukaryotic cell is divided into internal compartments. Many of the organelles inside cells are not distinct, isolated entities, but instead communicate with each other. In fact, the membranes of these organelles are either physically connected by membrane “bridges” or communicate by the budding off and fusing of vesicles, small membrane-enclosed sacs that transport substances. In total, these membranes make up the endomembrane system. The endomembrane system includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, the plasma membrane, and the vesicles that move between them (Fig. 3)

Fig. 3 The endomembrane system. The endomembrane system is a series of membrane-bound internal compartments in eukaryotic cells.

Endomembranes are not common in prokaryotic cells, which in general lack extensive internal membranes. However, photosynthetic bacteria do have internal membranes that are specialized for harnessing light energy.

Question: Which of the following are members of the endomembrane system? A) nuclear envelope B) ribosomes C) endoplasmic reticulum D) Golgi apparatus E) lysosomes F) the cytoskeleton G) plasma membrane H) the cytosol I) vesicles

A, B, C, D, E, F, G, H, and I B, C, D, and G Correct!

A, C, D, E, G, and I B, F, and H

Question 5

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The endomembrane system compartmentalizes the cell. Due to the selective permeability of cell membranes, the endomembrane essentially divides the interior of a cell into two distinct “worlds,”

one inside the spaces defined by these membranes and one outside these spaces. Note that a molecule within the interior space of the ER can stay in the ER or end up within the Golgi or even outside of the cell by the budding off and fusing of a vesicle between these organelles. Similarly, a molecule associated with the ER membrane can move to the Golgi membrane or the plasma membrane by vesicle transport. However, molecules in the cytosol are in a different physical space, separated by membranes of the endomembrane system. This physical separation allows specific functions to take place within the spaces defined by the membranes and also within the membrane itself. In spite of forming a continuous and interconnected system, the various compartments nevertheless have unique properties and maintain distinct identities determined by which lipids and proteins are present in their membranes. Recall that membranes are not fixed, but instead are dynamic with the ability to change their lipid and protein composition over time. As we have seen, vesicles can bud off and fuse with components of the endomembrane system, creating a set of interconnected spaces. They can even fuse with the plasma membrane. This process, called exocytosis, provides a way for a vesicle to empty its contents to the extracellular space or to deliver proteins embedded in the vesicle membrane to the plasma membrane (see Fig. 3). The process also works in reverse, in which a vesicle can bud off from the plasma membrane, bringing material from outside of the cell into a vesicle, which can then fuse with other organelles. This process is called endocytosis. Together, exocytosis and endocytosis provide a way to move material into and out of cells without passing through the cell membrane.

1) True or False: A molecule in the cytosol can end up in the Golgi apparatus. 2) True or False: A molecule in the ER can end up in the cytosol. 3) True or False: A molecule outside the cell can end up in the Golgi apparatus.

You Answered

1) True, 2) False, 3) True Consider endocytosis, and the concept that the endomembrane system separates molecules that are within it and those that are outside of it into two "distinct worlds."

1) False, 2) False, 3) False 1) True, 2) False, 3) False Correct Answer

1) False, 2) False, 3) True

Question 6

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The nucleus houses the genome and is the site of RNA synthesis. The nucleus stores DNA, the genetic material that encodes the information necessary for all the activities and structures of the cell. The nuclear envelope defines the boundary of the nucleus (Fig. 4). It consists of two membranes, called the inner and outer membranes, and each is a lipid bilayer with associated proteins.

Fig. 4 A surface v iew of the nuclear env elope. The nucleus is surrounded by a double membrane and houses the cell’s DNA.

These two membranes are continuous with each other at protein openings called nuclear pores. These pores act as gateways that allow molecules to move into and out of the nucleus, and thus are essential for the nucleus to communicate with the rest of the cell. In fact, the transfer of information encoded by DNA depends on the movement of RNA molecules out of the nucleus, while the control of how and when this information is expressed depends on the movement of proteins into the nucleus. The nuclear envelope with its associated proteins regulates which molecules can move into and out of the nucleus.

Question: Nuclear pores a) connect the two membrane of the nuclear envelope b) regulate access in and out of the nucleus

(a) You Answered

Correct Answer

(b)

(a) and (b) neither (a) nor (b)

Question 7

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The endoplasmic reticulum is involved in protein and lipid synthesis. The outer membrane of the nuclear envelope is physically continuous with the endoplasmic reticulum (ER), an organelle bounded by a single membrane (Fig. 5). The ER is a conspicuous feature of many eukaryotic cells, accounting in some cases for as much as half of the total amount of membrane. The ER is responsible for the production and transporting of many of the lipids and proteins used inside and outside of the cell. For example, it is the site of production of most of the lipids that make up the various cell membranes. In addition, many proteins are synthesized in the ER: these are transmembrane proteins and proteins destined for the Golgi apparatus, lysosomes, or export out of the cell. Unlike the nucleus, which exists as a single rounded structure in the cell, the ER consists of a complex network of tubules and flattened sacs all interconnected with each other. The interior of the tubules and flattened sacs is continuous throughout the ER and is called the lumen. As shown in Fig. 5, the ER has an almost maze-like appearance when sliced and viewed in cross-section. The ER membrane is extensively convoluted, allowing a large amount of membrane surface area to fit within the cell. The amount of ER membrane in a cell varies among cells of different functions. For example, mucous producing cells of the gut synthesize a large amount of protein for export and thus have an extensive ER, as do the cells of the pancreas that produce the protein insulin. In cells that do not secrete large quantities of protein,

the ER can be quite small. When viewed using an electron microscope, ER membranes have two different appearances (Fig. 5). In most cells, the majority of ER membranes have small rounded particles associated with them that are exposed to the cytosol. This portion of the ER is referred to as rough endoplasmic reticulum (RER). The particles bound to the cytosolic face of the RER are ribosomes. Ribosomes are the sites of protein production, where amino acids are assembled into polypeptides guided by the information stored in mRNA. Ribosomes can be free in the cytosol or associated with the ER membrane.

Fig. 5 The endoplasmic reticulum (ER). The ER is a major site for lipid and protein synthesis. Proteins are also synthesized in the cytoplasm

In most cells, there is a small amount of ER membrane that lacks ribosomes and is called smooth endoplasmic reticulum (SER) (Fig. 5). Portions of the smooth ER membrane actively bud off to produce small vesicles that are free to move in the cytosol. Since each vesicle is formed from a patch of ER membrane and encloses a portion of the ER lumen, vesicles are an effective means of moving proteins that are either embedded in the ER membrane or free floating inside. SER is also the site of fatty acid and phospholipid biosynthesis. Thus, this type of ER predominates in cells specialized in the production of lipids. For example, cells that synthesize steroid hormones have a well-developed SER that produces large quantities of cholesterol and contains enzymes that convert cholesterol into steroid hormones.

Question: The RER serves as the site for the synthesis of _______ (among other things), and the SER serves as the site for the synthesis of __________ (among other things).

fatty acids; transmembrane proteins phospholipids; proteins destined for the Golig apparatus transmembrane proteins; proteins destined for the Golgi aparatus Correct!

proteins destined for export out of the cell; phospholipids The RER is responsible for synthesizing proteins that are destined for the endomembrane system or to be secreted. The SER is the site of fatty acid and phospholipid synthesis.

Question 8

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The Golgi apparatus modifies and sorts proteins and lipids. While not physically continuous with the ER, the Golgi apparatus is often the next stop for vesicles that bud off the ER. These vesicles carry lipids and proteins either free floating in the vesicle interior or embedded in their membranes. The movement of these vesicles from the ER to the Golgi and then to the rest of the cell or plasma membrane is part of a biosynthetic pathway in which lipids and proteins are successively modified and delivered to their final destinations. The Golgi apparatus has three primary roles: (1) it further modifies proteins and lipids produced by the ER, (2) it acts as a sorting station as they move to their final destinations, and (3) it is the site where most of cell’s carbohydrates are synthesized.

Under the microscope, the Golgi apparatus looks like a series of flattened membrane sacs, called cisternae (Fig. 6). The cisternae are stacked and they are surrounded by many small vesicles. These vesicles transport proteins from the ER to the Golgi, between the various cisternae of the Golgi apparatus, and between the Golgi apparatus and the plasma membrane or other organelles. Vesicles are therefore the primary means by which proteins and lipids move through the Golgi apparatus to their final destinations.

Fig. 6 The Golgi apparatus. The Golgi apparatus sorts proteins and lipids to other organelles or to the plasma membrane or to the cell exterior.

Enzymes within the Golgi apparatus chemically modify proteins and lipids as they pass through it. These modifications are sequential since each region of the Golgi apparatus contains a different set of enzymes that catalyze specific reactions. As a result, there is a general movement of vesicles from the ER, through the Golgi apparatus, and then to their final destinations. An example of a chemical modification that occurs predominantly in the Golgi apparatus is glycosylation, in which sugars are covalently linked to lipids or specific amino acids of proteins. As these lipids and proteins move through the Golgi apparatus, sugars are added and trimmed in a sequential fashion. Glycoproteins are important components of the eukaryotic cell surface since their attached sugars can protect the protein from enzyme digestion by blocking access to the peptide chain. As a result, glycoproteins form a relatively flexible and protective coating over the plasma membrane. The distinctive shapes that sugars contribute to glycoproteins and glycolipids also allow cell surface components to be recognized specifically by other cells and molecules in the external environment. For example, human blood groups (A, B, AB, or O) are distinguished based on the particular sugars that are linked to proteins and lipids on the surface of red blood cells. Traffic from the ER to the Golgi apparatus and through the Golgi apparatus itself is not one way. While the usual pathway is from ER to Golgi, in which molecules are synthesized and modified as they move to their final destinations, there is also a small amount of reverse traffic moving from Golgi to ER. This reverse pathway is important to retrieve ER or Golgi resident proteins that are accidentally moved forward, and to recycle membrane components. Question: Which is NOT a function of the Golgi apparatus?

Synthesizes carbohydrates Modifies proteins You Answered

Correct Answer

Sorts proteins and lipids

Degrades proteins

Question 9

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Lysosomes degrade macromolecules The Golgi’s ability to specifically sort and dispatch proteins to particular destinations is dramatically illustrated by the formation of lysosomes. Lysosomes are specialized vesicles derived from the Golgi apparatus that contain a variety of enzymes that break down macromolecules such as proteins, nucleic acids, lipids, and complex carbohydrates (Fig. 7). The various macromolecules destined for degradation are delivered to lysosomes by vesicles that fuse with lysosomes. The specialized membranes of lysosomes contain proton

pumps that keep the internal environment at an acidic pH of around 5, the optimum pH for the activity of the large collection of enzymes within it. In addition, the membrane contains proteins that transport the breakdown products of macromolecules, such as amino acids and simple sugars, across the lysosomal membrane to the cytosol for use by the cell.

Fig. 7 Lysosomes. Lysosomes are vesicles that degrade macromolecules.

The activity of lysosomes illustrates the importance of having separate compartments within the cell bounded by selectively permeable membranes. Many of a cell’s enzymes and proteins would unfold and degrade if the entire cell were at a pH of 5, and lysosomal enzymes in turn cannot function in the normal cellular environment, which has a pH of about 7. By restricting the activity of these enzymes to the lysosome, proteins and organelles in the cytosol are protected from degradation. Question: The function of the lysosome is to

store macromolecules Correct!

degrade macromolecules sort macromolecules throughout the cell chemically modify macromolecules

Question 10

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Mitochondria and Chloroplasts The membranes of two organelles, mitochondria and chloroplasts, are not part of the endomembrane system. Both of these organelles are specialized to harness energy for the cell. Interestingly, they are both semi-autonomous organelles that grow and multiply independently of the other membrane-bound compartments. In addition, they contain their own genomes. In fact, the similarities between mitochondrial and chloroplast DNA and the DNA of certain bacteria have led scientists to conclude that these organelles originated as bacteria that were captured by a eukaryotic cell and, over time, evolved to their current function. Mitochondria provide the eukaryotic cell with most of its useable energy. Mitochondria (the singular form is mitochondrion) are specialized organelles that harness energy from chemical compounds like sugars and

convert it into ATP, which serves as the universal energy currency of the cell. ATP is able to drive the many chemical reactions in the cell. Mitochondria are present in nearly all eukaryotic cells. Mitochondria are rod-shaped organelles (Fig. 8) with an outer membrane and a highly convoluted inner membrane that projects into the interior. The inner mitochondrial membrane is the site where a proton electrochemical gradient is generated, and the energy stored in the gradient is used to synthesize ATP for use by the cell. In the process of breaking down sugar and ATP synthesis, oxygen is consumed and carbon dioxide is released. If this sounds familiar, it is, because it describes your own breathing, or respiration. Mitochondria undergo cellular respiration, and the oxygen that you take in with each breath is used by mitochondria to produce ATP. This is the reason why you breathe.

Fig. 8 Mitochondria. Mitochondria produce most of the ATP required to meet the cell’s energy needs.

True or False: Mitochondria are found in plant cells.

Correct Answer

You Answered

True False

Question 11

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Chloroplasts capture energy from sunlight. While both animal and plant cells have mitochondria to provide them with life-sustaining ATP, plant cells and green algae have additional organelles called chloroplasts that are able to capture the energy of sunlight to synthesize simple sugars (Fig. 5.28). This process is called photosynthesis and results in the release of oxygen as a waste product. Like the nucleus and mitochondria, chloroplasts are surrounded by a double membrane. In addition, they have a separate internal membrane-bound compartment called the thylakoid. The thylakoid membrane contains specialized light-collecting molecules called pigments, of which chlorophyll is the most common.

Fig. 9 Chloroplasts. Chloroplasts capture energy from sunlight and use it to synthesize sugars.

Chlorophyll plays a key role in the organelle’s ability to capture energy from sunlight. The green color of chlorophyll explains why so many

plants have green leaves. The light energy collected by pigments plus the actions of enzymes present in the cytoplasm use carbon dioxide as a carbon source to produce carbohydrates. Question: Which of the following is a semi-autonomous organelle?

choloroplast, but not a mitochondrion mitochondrion, but not a chloroplast Correct!

both mitochondria and chloroplasts neither mitochondria nor chloroplasts

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