The Membranes of Cells

Preface

Philip L. Yeagle

The reception of the first two editions of The Membranes of Cells was gratifying. Both editions have been useful to students and postdocs who needed to become conversant in membranes since this subject underlies so much of cell biology, biochemistry, microbiology, and biophysics. These editions have also aided senior researchers embarking on research requiring a familiarity with the fundamentals of membrane structure and function.

This third edition of The Membranes of Cells is written in response to a revolution in the study of cell membrane structure and function. At the time of the second edition, virtually no high-resolution structure information was available for membrane proteins. Now over 1000 high-resolution structures of membrane proteins are available from X-ray crystallography, electron crystallography, and nuclear magnetic resonance (http://blanco.biomol.uci.edu/mpstruc/). While this represents only about 1% of the Protein Data Bank (http://www.rcsb.org/pdb/home/home.do) and only a small fraction of all known membrane proteins, nevertheless it provides a critical window through which we can see much more clearly the amazing functions catalyzed by membrane proteins. That universe of new information is well represented in this third edition. It is the new foundation of our understanding of membrane function. And it both inspires and informs the writing of the third edition of The Membranes of Cells.

As this book is intended primarily as a resource for learning about the membranes of cells, the referencing is representative, not exhaustive. The second edition introduced in-text referencing as requested by users of the book. That feature is continued in this edition. The references are often to review articles to help introduce students of membranes to the field. Therefore sincere apologies to those many scientists who contributed to the understandings described herein, but whose primary papers may not have been included in the reference lists.

References included date from the 18th century to the 21st century. It is important to acknowledge the roots of many of our understandings of membrane structure and it is intellectually satisfying to trace some of those understandings as far back as Mr Franklin! At the same time, enormous progress has been made in the 21st century so naturally many of the references are very recent publications.

The figures of membrane protein structure in this edition were created from multiple resources. PDB files were obtained from the Protein Data Bank and membrane structures were initially explored through Membrane Proteins of Known Structure (links for both these databases are listed above). The figures were drawn using PyMol (http://pymol.org) or VMD (Humphrey W, Dalke A, Schulten K. VMD—Visual Molecular Dynamics. J Mol Graphics 1996;14:33–8). I thank Professor Victoria Robinson for help in creating those figures. Many of the molecular dynamics images were obtained from files available at MemProtMD (http://sbcb.bioch.ox.ac.uk/memprotmd/beta/). I thank Professor Mark Sansom, University of Oxford, and his colleagues for introducing me to molecular dynamics of membranes over a number of years. I also thank Virge Kask for drawing several of the more artistic membrane figures in the book.

In addition to the many scientists who were acknowledged in previous editions, I would like to highlight for this edition the professional opportunities and intellectual insights provided by Professor Tony Watts at the University of Oxford, during my sabbatical when this book project was begun. I thank both him and Valerie Watts for their generous hospitality. Appreciation is due to Rutgers University and President Emeritus Richard McCormick for that sabbatical following service as Dean of Arts and Sciences and Interim Chancellor.

I thank Professor Michael Lynes, Head of the Department of Molecular & Cell Biology at the University of Connecticut, for inviting me back to UConn, where I had been Head, to reestablish my academic residence after completing my work at Rutgers University.

I thank the members of my research group for over more than three decades of exploration of the amazing properties of membranes, both at UConn and previously at the University at Buffalo School of Medicine and Biomedical Sciences, who are acknowledged in the many papers to which they contributed. And I thank my longtime colleagues at both institutions. This book is also the result of innumerable conversations over many years with talented researchers in the field from whom I learned so much of what constitutes my understanding of membranes.

Professor Arlene Albert has been priceless in her support of building my understanding of cell membranes and her critical analysis has transformed my science and my writing into something much better over many years.

I thank Janice Audet and Fenton Coulthurst from the Publisher for the invitation to do this book and their patience as I completed it.

Chapter 1

Introduction

Abstract

This chapter begins the exploration of the structure and function of biological membranes. Membranes are amazing structures. They are not a covalent whole like an individual protein, yet they exhibit stable structures. Membranes are not gene products and their most ubiquitous component, lipids, are not gene products. Yet they play roles in gene expression and may have been essential for the first genetic operations promoted by DNA. Biological membranes surround prokaryotes, both bacteria and archaebacteria, and constitute some of their internal structure. Membranes surround, define the outer limits of, and constitute much of the internal structure of, eukaryotes. Membranes surround and define the outer limits of enveloped viruses. As such, the most fundamental property of the biological membrane is to separate the inside from the outside of the biological entity. The hydrophobic effect determines the interaction between hydrocarbons and water (or lack thereof). The hydrophobic effect drives the lipids, based on their amphipathic chemical structure, to form lipid bilayers, the fundamental architecture of all biological membranes.

Keywords

Hydrophobic effect; lipid bilayer; compartmentalization; cell structure; bacteria; archaebacteria; prokaryotes; viruses

The study of the membranes of cells is the study of the most fundamental structures that enable the function and stabilize the structure of cells (and enveloped viruses). Essential to the development of life forms as we know them is the compartmentalization of functions that we identify as cellular functions, separating them and protecting them from the milieu in which the life form is found. A promembrane (in the early stages of the genesis of life on earth) constricts what became the molecules of life inside a compartment to a region of relatively close contact, enhancing probability of chemical reactions. This compartmentalization opened the opportunity for a different chemistry inside the compartment than outside the compartment. The origins of biology as we know it today arguably began with the formation of such a promembrane. Thus the development of a simple membrane that defines an inside and an outside of a compartment and that protects and concentrates molecules in a space in which self-replication could evolve was essential to life. Membranes must therefore be at the core of basic requirements for the evolution of the first life forms. As will be seen in this book, even the complex cell membranes we know today are built of components that have a remarkable capability of spontaneous self-assembly. The chemical requirements for formation of membranes from individual molecules are relatively simple. Certainly the membrane lipids, which have dominated biology for much of the existence of biological cells, do form suitable promembranes spontaneously in water and achieve the properties described above. Other amphipathic molecules might also form promembranes if they have a suitably strong amphipathic chemical structure. Therefore in the evolution of primitive cells it is not difficult to imagine how the first cell membranes might have formed.

The molecules that spontaneously assemble into biological membranes are not covalently linked. The lipids that form the lipid bilayer common to all biological membranes are not gene products. Therefore the development of genetic material did not have to precede the development of membranes. However the development of membranes could have facilitated the development of self-replicating genes by providing them a protected space in which to evolve and eventually function.

A broad understanding of the membranes of cells requires a synthesis of experimental insights from the whole range of molecular biology, including biophysical chemistry, molecular genetics, physiology, cell biology, microbiology, biochemistry, and computational biology. Such a synthesis is not normally possible in a discipline-delineated approach. The goal of this book is to obtain such a synthesis with biological membranes as the focal point of the study. A multidisciplinary approach is required. In this book, it will not be the purpose to become expert in the many disciplines, but rather to learn to appreciate and understand the structure and function of biological membranes from many points of view.

The pursuit of this goal will begin with an overview of the incredible diversity of biological membranes and the roles they play in cells and enveloped viruses. Gaining an understanding of how membrane structure leads to the functions of biological membranes will then be the province of the remainder of this book.

The membranes found in cells and enveloped viruses will be introduced below. The reader is referred to standard textbooks on cell biology for further information on the structure and biology of these organisms.

1.1 Prokaryote Cell Membranes

Prokaryotes are divided into two kingdoms: eubacteria (bacteria) and archaea, each identified by their distinctive genetic markers. Both are single-celled organisms. The prokaryotic cell exhibits the simplest organization of cell membranes. They have one or two membranes, both following the margin of the cell. Most have no intracellular organelles. Some have intracellular membranes bounding a compartment with specialized functions. Examples of the latter include thylakoids, magnetosomes, and chlorosomes. An organized nucleus such as is found in eukaryotes is absent from prokaryotes. Commonly a single, circular genome of DNA is found in the cell.

The boundary of the cytoplasm of the eubacterial cell is determined by the plasma membrane. In bacteria with two membranes, the plasma membrane is the inner membrane. The plasma membrane forms a semipermeable boundary allowing differentiation between the components inside the cell from those outside of the cell. This plasma membrane is constructed of membrane proteins and lipids that form a lipid bilayer. The components (proteins and lipids) of the plasma membrane are stabilized in a structure by noncovalent forces. Thus the plasma membrane of prokaryotic cells is not a rigid structure. Although it effectively forms a semipermeable boundary, the plasma membrane is deformable. It gains rigidity from its association with the cell wall.

The plasma membrane is the most basic structural feature that all cells must have. Some distinction is needed between the life processes inside the cell and the soup in which the cell is living. The plasma membrane provides the required distinction for all cells.

The cell wall surrounds the plasma membrane. This extracellular (in some species) matrix is a relatively rigid structure that is connected largely by covalent chemical bonds. It consists of peptidoglycan that is formed from oligosaccharides and cell wall proteins. The cell wall is not a membrane. It does not contain membrane lipids. The peptidoglycan is extensively cross-linked through covalent bonds, providing the rigidity that gives the cell its shape. Many bacteria have this simple structure. As such their cell wall is exposed to the medium and tends to be relatively thick. This cell wall takes up the Gram stain. Bacteria with this structure are therefore referred to as Gram-positive bacteria.

Other bacteria have a second membrane. This outer membrane completely surrounds the cell wall and also the plasma membrane. The region between the outer membrane and the plasma membrane is the periplasmic space. The outer membrane has a very different molecular composition from the plasma membrane. Both the outer membrane proteins and the outer membrane lipid composition are different from the inner (plasma) membrane of these bacteria. Among the unique lipids of the outer membrane are large glycolipids. An example is lipopolysaccharide. Among the proteins of the outer membrane are the porins. These are large, transmembrane β-barrels, quite distinct from other membrane proteins. Some can form channels through the interior of the β-barrel. These channels can permit passive transport of solutes across the outer membrane. Because the cell wall is completely covered by the outer membrane, these bacteria do not take up the Gram stain and are referred to as Gram negative. An example of a Gram-negative bacterium (widely studied in laboratories) is Escherichia coli.

Archaea membranes are fundamentally built on a lipid bilayer as in bacteria. However, the lipids of the archaea plasma membranes are distinct from the lipids in bacteria and in eukaryotes. Both the headgroups of the lipids and the hydrocarbon tails are largely different from the lipids in other cells. The hydrocarbon chains are largely built of isoprenoid units and without carbon–carbon double bonds. The lack of double bonds (that are chemically labile) may contribute to the ability of various archaea to live in extreme environmental conditions. By making their membrane lipids resistant to oxidation through the lack of carbon–carbon double bonds, the lipids can survive chemically in more harsh conditions. Through the inclusion of branched chain lipids, the membranes stabilize a liquid crystal state of the membrane over a wide range of temperature. These hydrocarbon chains are bonded to the lipid headgroups by ether bonds. The connections of these ether bonds to the glycerol backbone of the lipid are to the 2′ and 3′ positions of the glycerol, different from common lipids of bacteria and eukaryotes. These are the archaeols (see chapter: The Lipids of Biological Membranes). Each of these lipids fits into lipid bilayers in a manner analogous to lipids of bacteria and eukaryotes. One interesting variant is a lipid that chemically resembles a covalent dimer of archaeols, two archaeols bonded tail to tail. This creates a lipid with two polar headgroups separated by hydrocarbon chains double the length of other membrane lipids. Thus this lipid can span a lipid bilayer as a unit. These lipids are called caldarchaeols. Many Archaea have a cell wall, but unlike bacteria, the cell wall does not contain peptidoglycan like bacterial cell walls. Instead they are made largely of protein. Halobacterium salinarum is a member of the Archaea. An example of an H. salinarum membrane protein is bacteriorhodopsin discussed further in chapter Membrane Proteins.

1.2 Eukaryote Cell Membranes

The structure of eukaryotes is much more complex than the structure of prokaryotes. The similarity to prokaryotes is the plasma membrane that delineates the boundary of the cell in both eukaryotes and prokaryotes, and controls communication and nutrient flow into and out of the cell. These plasma membranes also have in common the expression of carbohydrate on their extracellular surface, from both glycolipids and glycoproteins. Plasma membranes of prokaryotes often carry some functions closely analogous to mitochondrial membranes in eukaryotes.

Once inside the eukaryote, however, the differences from prokaryotes are dramatic and complex. Eukaryotes have a variety of membrane-bound compartments called organelles. These intracellular membranes subdivide cellular activities and compartmentalize functions. They permit more diverse and specialized functions than are possible in prokaryotes. Among the intracellular membrane-bounded intracellular organelles are the nucleus, the mitochondria, the endoplasmic reticulum, the Golgi, and the lysosome. These will be described below. Each of these organelle membranes exhibits a unique lipid and protein composition crucial to their individual functions. In each organelle, the surrounding membrane is built on the fundamental structure of the lipid bilayer.

Communication among these organelles and between intracellular organelles and the plasma membrane is by vesicular transport. Vesicles bud from one organelle and transit to another and fuse with that target membrane. This moves material from the lumen of one organelle to another (or to, or from, the exterior of the cell). Vesicular transport also moves membrane components, membrane proteins and lipids, from one organelle to another.

Structure within the eukaryote is created by the cell cytoskeleton. Intracellular membranes interact with the cell cytoskeleton through protein–protein recognition and binding. Plasma membranes also interact with the cell cytoskeleton.

The membranes of plant eukaryotes follow much the same structural and functional motifs exhibited by the more widely studied nonplant cell membranes. To mention a few, plant cell membranes are built on a lipid bilayer just as are all other biological membranes. Membrane proteins of plant cell membranes endow these membranes with a variety of critical functions. The semipermeable property of biological membranes and the ability to create and utilize transmembrane chemical and electrical potentials by the membrane proteins leads to ATP synthesis in both mammalian and plant cells by analogous pathways.

The significant difference seen in plant cells compared to most other eukaryotes is the cell wall. The plant cell wall surrounds the plasma membrane. Although the composition and thickness of plant cell walls varies, the roles of all plant cell walls include imparting structural rigidity to the cell and playing roles in cell–cell communication and interaction in the organism. Cell walls are constructed of cellulose and matrix polysaccharides, as well as a variety of proteins.

1.3 Plasma Membranes

The plasma membrane of the cell defines the cell boundary. This membrane by mass is about half lipid and half protein. The plasma membrane of a cell exemplifies the basic compartmental function of membranes: it separates and delineates the intracellular space from the extracellular space.

It is the role of the plasma membrane to maintain the difference between the inside and the outside of the cell by controlling the entrance and exit of materials across the plasma membrane. All chemical species entering and exiting the cell must do so in a manner mediated by the plasma membrane. Specific cellular nutrients (and products) enter (and leave) the cell through the transport (and membrane fusion) functions of the plasma membrane. Consequently, the plasma membrane plays an important regulatory role in the metabolism of the cell.

Consider the plasma membrane of the human erythrocyte membrane as an example of a plasma membrane. The mammalian erythrocyte has a simple structure compared to other eukaryote cells because it has no intracellular organelles (interestingly avian erythrocytes do have nuclei—mammalian erythrocytes become enucleated during maturation). The simple structure and the relative ease with which erythrocytes can be isolated from mammalian blood made the erythrocyte plasma membrane accessible for early studies of plasma membrane structure and function.

As all plasma membranes, the mammalian erythrocyte plasma membrane facilitates transport of nutrients. The plasma membrane of the human erythrocyte contains a membrane protein specific for the transmembrane movement of the cellular nutrient glucose. If this transport system is blocked, glucose transport into the cell is effectively blocked (and since the erythrocyte is too simple a cell to make ATP it is dependent upon obtaining glucose from the blood plasma). The protein responsible for glucose transport is a (transmembrane) protein embedded in the plasma membrane. Membrane proteins responsible for transport of molecules into or out of a cell are usually embedded in the membrane. Another example of transport is provided by one of the most abundant membrane proteins of the human erythrocyte membrane, the anion transport protein. This protein functions as a channel that specifically allows anions to move rapidly across the membrane. In erythrocytes, rapid chloride–bicarbonate exchange across the plasma membrane is functionally integrated with the binding and absorption of oxygen by hemoglobin inside the erythrocyte and in CO2 transport.

The inside and outside of the mammalian erythrocyte, as in the case in most cells, is distinctly different in ion composition. Sodium ion concentration is relatively low inside the cell and potassium ion concentration is relatively high inside the cell. Correspondingly outside the cell, sodium ion concentration is relatively high and potassium ion concentration is relatively low. How can these transmembrane ion gradients be created and maintained?

The Na+ K+ ATPase, an enzyme (and transmembrane protein) of the erythrocyte plasma membrane, simultaneously pumps sodium ion out of the cell and potassium ion into the cell. The ion-pumping function of the Na+ K+ ATPase maintains the distinct difference in Na+ and K+ concentrations between the inside and the outside of the cell. The pump (the Na+ K+ ATPase) hydrolyzes ATP to provide the necessary energy for the transport process, to transport these ions against their respective concentration gradients.

The Na+ gradient across the plasma membrane generated by the Na+ K+ ATPase is itself used for a variety of other functions. One of the ways the Na+ can respond to the difference in chemical potential across the plasma membrane is to re-enter the cell through a co-transport system. In a co-transport system, a nutrient the cell requires can be transported (against its own concentration gradient) across the plasma membrane along with a sodium ion. Sodium is moving with its concentration gradient, from high concentration to low concentration. Therefore the energy stored in the sodium gradient can be used to drive a nutrient against its concentration gradient and into the cell. One example of this type of transport across a plasma membrane is found in intestinal epithelial cells. How these transport systems work and their structure is the subject of chapter Membrane Transport.

Communication between the outside of a cell or organism and the environment in which the cell or organism functions is critical. Extracellular signals can alter intracellular behavior. The inside of a cell can send signals to the outside that can also lead to alterations in behavior. Communication from the outside to the inside is often mediated by receptors. A number of receptors in the plasma membrane are responsible for signal transduction. For example, the β-adrenergic receptor will respond to a hormone outside the cell. When the hormone binds to the extracellular surface of the receptor on the plasma membrane, the receptor changes the conformation of its cytoplasmic surface. This allows the cytoplasmic surface of the receptor to interact with G proteins inside the cell. Those G proteins can subsequently activate adenylate cyclase, also a membrane protein and located with its active site on the cytoplasmic face of the plasma membrane. Receptor-stimulated adenylate cyclase generates a signal or second messenger in the cytoplasm, increasing cAMP levels in the cell cytoplasm. An increase in intracellular cAMP levels can cause a number of changes in the metabolic activity of the cell. The function and structure of this class of receptors is examined in chapter Membrane Receptors.

Another function of the plasma membrane of the cell is to modulate cell–cell interactions. During development, cells differentiate and organize into organs or organisms. This process depends on cells recognizing the right matrix and building the structure of the organism or organ according to the pattern dictated by its genome. This cell–cell recognition and cell–matrix recognition are mediated by the plasma membrane through transmembrane proteins that function as receptors. The opposite of well-regulated cell–cell interaction, when cells do not properly recognize extracellular matrix or other cells, is a characteristic of tumor cells. These processes are explored in chapter Membrane Receptors.

A pathway of cell–cell communication provided by the plasma membrane is found in the gap junction. This pathway of communication is particularly important in cell layers that function in a concerted manner, as in involuntary muscle contractions. The gap junction connects two plasma membranes with a relatively close approach of about 2 nm. Oligomers of the protein, connexion, form a channel that can connect one cell cytoplasm with the cytoplasm of another cell. Ions can pass through this channel from one cell to another. This movement of ions constitutes a primitive cell–cell communication system that can function quite rapidly.

Cell plasma membranes also form tight junctions. This is a region between cells in which the electron microscope does not reveal any significant intercellular space between the two cell plasma membranes. They are a characteristic feature of cell layers, forming just below the apical surface of the cell layer. Tight junctions allow epithelial tissue, such as the lining of the intestine, to form sealed cell layers. As a consequence, solutes cannot diffuse between the cells to pass the cell layer. Instead solutes must be transported across one side of the cell, through the cell cytoplasm, and across the plasma membrane on the opposite side of the cell to cross the cell layer (however some regulation of tight junction permeability is possible). Thereby the plasma membrane controls the passage of solutes from one side of the cell layer to the other. Tight junctions are formed from integral membrane proteins in the plasma membrane including claudin and occludin. These proteins bind each other across the intercellular space in rows and hold the two plasma membranes closely opposed.

Tight junctions divide the plasma membrane. The lipid and protein composition in the plasma membrane on one side of the cell (ie, basolateral) is therefore different from the lipid and protein composition in the plasma membrane on the other side of the cell (ie, apical). In intestinal epithelial cell layers, the basal lateral membrane of the cells faces one side of the cell layer and the brush border faces the other side of the cell layer. The name, brush border, derives from the microvilli that decorate that surface of the cell. These numerous projections of the plasma membrane greatly increase the surface area, which facilitates the active transport carried out by the brush border membrane.

The Schwann cell provides another example of a specialized plasma membrane function. During development, the Schwann cell wraps itself around a nerve axon in a concentric and multilayered structure. The Schwann cell creates a rather simple membrane for this purpose. The membrane has a higher lipid content than most other membranes and a lower protein content and more simple protein composition (mostly P0 and myelin basic protein) than most other biological membranes. The P0 extramembraneous domains from each of the membraneous layers of the sheath bind to each other stabilize the myelin structure. Multiple Schwann cells are required to sheath an axon. The myelin sheath serves as an electrical insulator for the nerve. When the myelin sheath breaks down, the axon is no longer properly insulated and its ability to carry an electrical signal is compromised. Nerve conduction therefore becomes faulty in demyelinating diseases.

Extending outward from the plasma membranes of some cells, particularly in unicellular organisms and in specialized epithelia, are flagella and cilia. Flagella and cilia are long projections of the plasma membrane surrounding a core of cytoskeletal elements. These structures are built of microtubules in the axoneme covalently cross-linked. They are responsible for locomotion of microorganisms and for sperm, and for the movement of fluids across the cell surfaces.

From this discussion, the multitude of functions of the cell plasma membrane can (just) begin to be imagined. Among other functions, the plasma membrane defines the inside and outside of the cell. The plasma membrane controls the passage of materials into and out of the cell through its transport functions. The plasma membrane is the starting point for much of the regulation of cellular metabolism. The plasma membrane provides means for cell–cell communication. The plasma membrane provides the basis for organization of cells into specialized tissues during development.

1.4 Intracellular Membranes

Organelles within eukaryotes are bounded by either single or double membranes. These internal membranes not only enclose specialized spaces within the cell but also are involved in important cellular processes such as biosynthesis, transport, energy metabolism, and catabolic degradation.

1.4.1 Nuclear Membranes

A double membrane surrounds the nucleus. There is therefore an inner and an outer nuclear membrane that together form the nuclear envelope. The outer part of the nuclear envelope is continuous with the endoplasmic reticulum. The inner and outer membranes are in continuity with each other through the nuclear pores. The nuclear envelope is important to gene expression, protein synthesis, and nuclear shape, among other issues. The nuclear envelope is punctured by a number of nuclear pores. The nuclear pores are complicated and extraordinarily large structures formed from a protein complex called the nuclear pore complex (an order of magnitude larger than a ribosome). The lipid bilayer of the nuclear envelope is largely made up of phospholipids and cholesterol. Among the phospholipids, phosphatidylcholine is predominant with lesser amounts of phosphatidylethanolamine and phosphatidylinositol. Small amounts of other lipids can also be found.

The nuclear pores confer the major functions of the nuclear envelope. Proteins called nucleoporins create the nuclear pores. These include structural nucleoporins, membrane nucleoporins, and FG-nucleoporins. The structural nucleoporins form a structural scaffold around which the pore can be formed. The membrane nucleoporins interact with the inner and outer nuclear membranes (and connect those membranes) and induce those membranes to open in a disk shape into a pore inside the scaffold of the structural porins. Many more protein components participate to create the physical structure that is capable of the functions listed above.

1.4.2 Endoplasmic Reticulum Membranes

The endoplasmic reticulum is an internal membrane system of the eukaryote. The endoplasmic reticulum encloses a specialized region, the lumen of the endoplasmic reticulum. Because the lumen of the endoplasmic reticulum is separate from the cytoplasm of the cell, the endoplasmic reticulum creates a physical separation of function and of molecular contents. The lumen of the endoplasmic reticulum has some connectivity to the lumen or space between the nuclear membranes.

The endoplasmic reticulum is the site of biosynthesis of many cellular components. Many membrane components are synthesized on the endoplasmic reticulum, including membrane proteins and membrane lipids. The endoplasmic reticulum is subdivided into rough and smooth endoplasmic reticulum. The designation arises from the morphology observed in the electron microscope images of the endoplasmic reticulum. Some parts of the endoplasmic reticulum have bumps, giving it a rough appearance. The bumps are ribosomes. One class of ribosomes is membrane bound and they bind to the endoplasmic reticulum. Membrane-bound ribosomes synthesize membrane proteins and secreted proteins. The smooth endoplasmic reticulum refers to regions on the endoplasmic reticulum where ribosomes are not attached. These two regions of the endoplasmic reticulum are distinct from each other.

The lumen of the endoplasmic reticulum contains the newly synthesized soluble proteins that are to be secreted. The luminal contents of the endoplasmic reticulum can be transported to the lumen of the Golgi by membrane-bound transport vesicles. From the Golgi, the proteins to be secreted advance again by membrane-bound transport vesicles to the plasma membrane. These transport vesicles fuse with the plasma membrane and the inside of the vesicle becomes continuous with the outside of the cell. The lumen of the endoplasmic reticulum is thus morphologically related to the exterior of the cell. The proteins to be secreted are synthesized in the lumen of the endoplasmic reticulum and subsequently transferred to the cell exterior.

To carry out the biosynthetic roles assigned to the endoplasmic reticulum, the endoplasmic reticulum membrane contains a set of specialized proteins. Some of these are integral membrane proteins that provide passage across the membrane of protein as it is being synthesized. This is co-translational protein synthesis. Others are integral membrane proteins that bind cytoplasmic factors that enhance the binding of those particular ribosomes that are beginning synthesis of either membrane proteins or proteins to be secreted. Some enzymes in the lumen of the endoplasmic reticulum are required for processing of newly synthesized proteins. Membrane protein synthesis will be examined in chapter Membrane Biogenesis.

The endoplasmic reticulum contains a variety of membrane lipids. Phosphatidylcholine is a major lipid as is phosphatidylethanolamine. Cholesterol and other lipids are found in minor amounts. Synthesis of these membrane lipids is described in chapter Membrane Biogenesis.

The lumen of the endoplasmic reticulum is much higher in calcium concentration than the cell cytoplasm. Cytoplasmic calcium levels in some cells can be increased by release of Ca²+ from the lumen of the endoplasmic reticulum. This is achieved by a calcium pore activated by a second messenger system. To maintain the Ca²+ gradient requires a calcium pump protein that pumps the calcium ions into the lumen of the endoplasmic reticulum utilizing ATP as an energy source.

1.4.3 Golgi Membranes

The Golgi complex, named for the Italian physician who first identified the structure, is a stack of closed membranes roughly located between the endoplasmic reticulum and the plasma membrane. The Golgi is a waypoint for newly synthesized proteins from the endoplasmic reticulum on their way to the plasma membrane or to be secreted by the cell. Newly synthesized lipids from the endoplasmic reticulum destined for the plasma membrane also pass through the Golgi.

Communication from the endoplasmic reticulum to the Golgi is by vesicular transport (membranes closed around an interior aqueous space). Transport vesicles bud from the endoplasmic reticulum and are targeted to move to the Golgi membranes and fuse with the Golgi membranes. Therefore the lumen of the endoplasmic reticulum is functionally connected to the lumen of the Golgi. The luminal face of the endoplasmic reticulum membrane is morphologically connected to the luminal face of the Golgi membranes. Likewise the lumen of the Golgi is functionally connected to the exterior of the cell because transport vesicles bud from the Golgi and some are targeted to the plasma membrane where they fuse and expose their interior to the exterior of the cell. The luminal domains of the membrane proteins that are transported to the plasma membrane get exposed to the exterior of the cell after this transport process to the plasma membrane.

The flattened disks of the Golgi stack are called the cisternae. The cisternae of the Golgi can be subdivided into the cis-, medial- and trans-Golgi cisternae. The cis-Golgi receive transport vesicles from the endoplasmic reticulum that fuse with the cis-Golgi. Posttranslational modifications of newly synthesized proteins (including glycosylation and acylation) and lipids (glycosylation) occur in the Golgi and begin in the cis-Golgi. These proteins (and in some cases lipids) are passed from the cis-Golgi to the medial-Golgi and on to the trans-Golgi. Further biochemistry occurs as the posttranslational modifications mature to those characteristic of the final protein or lipid products.

The Golgi support a complex pattern of trafficking. In addition to the directional movement of newly synthesized proteins and lipids toward the plasma membrane, retrograde movement also occurs. Proteins in the transport vesicles from the endoplasmic reticulum that are part of the transport vesicles but not destined for further transport or export are recycled back to the donor membranes. Transport vesicles that bud from the trans-Golgi can go to the plasma membrane or to other organelles such as lysosomes. Therefore another important function of Golgi is sorting of components into the appropriate and specific transport pathways.

The transport vesicles that facilitate transport from the endoplasmic reticulum to the cis-Golgi are coated with proteins. These are called COPII vesicles. COPI vesicles have similar protein coats, but with different protein composition, and mediate transport from the cis-Golgi to the endoplasmic reticulum, and between cisternae of the Golgi. The transport vesicles that enable movement of proteins and lipids from the trans-Golgi to the plasma membrane and other organelles are clathrin-coated vesicles. These transport vesicles have a protein coat, analogous to the COPII and COPI vesicles, but of different proteins. Vesicle transport is discussed in chapter Membrane Fusion.

One of the challenges in the study of cell membranes is to understand the mechanisms of movement of newly synthesized membrane proteins, secreted proteins, and membrane lipids, through the cell and to the appropriate organelles. These organelles are all morphologically and functionally different from each other. The protein composition of the membranes of the various organelles is distinctly different from each of the other organelles. The distribution of proteins in the endoplasmic reticulum membrane is not the same as the distribution of proteins in the plasma membrane, which is not the same as the distribution of proteins in the lysosomal membrane. What governs the movement of materials among these membranes? How are these differences in membrane composition maintained in the face of extensive interorganelle communication? These questions will be discussed in chapter Membrane Biogenesis.

1.4.4 Mitochondrial Membranes

Mitochondria are bounded by two membranes, reminiscent of Gram-negative bacteria. Mitochondria have the inner mitochondrial membrane and the outer mitochondrial membrane, separated by the intermembrane space (analogous to the periplasmic space in Gram-negative bacteria—however, mitochondria have no equivalent to the cell wall). Inside the inner mitochondrial membrane is the matrix, which, among other constituents, contains a small (relative to nuclear) DNA that codes for a minority of the proteins found in the mitochondria (the majority of mitochondrial proteins, including membrane proteins, are transcribed from nuclear mRNA).

The outer membrane, like that of many bacteria, contains a class of membrane proteins distinct in structure from most other membrane proteins in other cell membranes. The mitochondrial outer membrane contains porins. The porins in both bacteria and in mitochondria are β-barrels. In some of these proteins, the center of the β-barrel forms a pore enabling passive transport across the membrane. The outer membrane also contains a protein apparatus for the import of proteins used in the mitochondria but synthesized from cytoplasmic mRNA. The β-barrel proteins will be explored in chapter Membrane Proteins.

The inner mitochondrial membrane has a much higher membrane protein content than most membranes. The inner mitochondrial membrane thus has the lowest lipid–protein ratio of eukaryotic cell membranes. The inner membrane also contains the lipid, cardiolipin, or diphosphatidylglycerol, which is found almost uniquely in that membrane (and not in the outer mitochondrial membrane, for example). The inner membrane is highly invaginated to form cristae that fold back and forth across the interior of the mitochondrion. This structure provides a large membrane surface area to support the major work of the mitochondrion, ATP synthesis, which occurs on the inner membrane.

Multiple mitochondria are found within a single eukaryotic cell, sometimes hundreds or more. Mitochondria are about the size of an E. coli bacterium. In fact it has been hypothesized that bacteria are the precursor to mitochondria. The endosymbiot hypothesis asserts that endocytosis of a bacterium by a eukaryote early in evolution led to the formation of the mitochondrion. This process would explain the two membranes of the mitochondria, the primary role of mitochondria in synthesizing ATP (by the same overall mechanism as in E. coli, for example), and the presence of a separate DNA in the mitochondria. Mitochondrial DNA is inherited separately from nuclear DNA (and plays unique roles in DNA identification of organisms, including humans). A similar process is hypothesized for the development of chloroplasts, after endocytosis of a prokaryote capable of photosynthesis.

ATP synthesis is perhaps the most important function of mitochondria (and chloroplasts). The amazing path of ATP synthesis flows through an intricate set of enzymes, many transmembrane proteins, located in the inner membrane. Some of these proteins will be examined in depth later in chapter Membrane Transport. This pathway is an excellent example of the motif that some cellular functions are crucially dependent on the structure of a membrane, in addition to utilizing membrane-bound enzyme complexes. The inner membrane supports the enzymes of the electron transport and oxidative phosphorylation pathways in specified protein complexes. Electron transport by the inner mitochondrial membrane crucially creates a transmembrane electrochemical gradient across the inner mitochondrial membrane. This gradient is then used to phosphorylate ADP and form ATP (and oxygen is reduced to water) through oxidative phosphorylation by a transmembrane protein complex in the inner mitochondrial membrane.

Not only do all these chemical reactions take place in and around the inner mitochondrial membrane, but also oxidative phosphorylation would not take place without a membrane and its structural features. The process leading to ATP synthesis creates, through a mechanism involving the movement of electrons through a series of coupled oxidation and reduction reactions, a proton gradient across the inner mitochondrial membrane. Embedded in that membrane is an enzyme that synthesizes ATP from ADP and Pi, the ATP synthase. The ATP synthase obtains the energy for that energetically highly unfavorable reaction from the transmembrane proton gradient. The process consequently first drives protons across the inner mitochondrial membrane using the energy from the electron transport process. Then the protons are allowed to flow back across the membrane (and down a concentration gradient) through the ATP synthase in the process that produces ATP. The ATP synthase will be discussed in more detail in chapter Membrane Transport. The unequal proton concentrations (on either side of the inner mitochondrial membrane) and the pathway whereby that gradient is dissipated driven by thermodynamics are what provide the energy for ATP production. A membrane that is otherwise impermeable to protons is a required component of the major pathway of ATP synthesis in bacteria and in eukaryotes. Therefore ATP synthesis, upon which our life depends, is possible only because of a biological membrane and its unique properties that are the subject of this book.

1.4.5 Lysosome

The lysosome is an intracellular organelle of eukaryotes that is bounded by a single membrane. The lysosome is a degradative organelle. In the lysosome, where the pH is lower than in most of the rest of the cell, there are found enzymes (in the lumen of the lysosome) responsible for degradation of biochemical components. These include enzymes for cleaving proteins, and others for hydrolyzing phospholipids, cholesterol esters, as well as ligands of receptors from the cell surface, and cleaving carbohydrates into its sugar subunits. The lysosomal membrane contains proton pumps, transmembrane proteins that pump protons into the lumen of the lysosome. These pumps utilize ATP hydrolysis for an energy source. As protons enter the lysosome, the pH of the lumen of the lysosome drops, facilitating the chemical degradation processes.

Transport of material to the lysosome is by membrane-bounded structures. Those cell surface membrane proteins destined for lysosomal degradation, for example, are initially endocytosed by clathrin-coated vesicles. After loss of the clathrin coat and formation of the early endosome, the latter fuses with a late endosome. Vesicles then bud from the membrane of the endosome, by initial invagination of the late endosomal membrane. This forms new vesicles within the lumen of the late endosome and the product is called the multivesicular endosome. The multivesicular endosome then fuses with the lysosomal membrane, introducing the vesicles containing the plasma membrane proteins to be degraded (that budded from the endosomal membrane into the lumen of the late endosome) into the interior of the lysosome. Once there, hydrolysis of the plasma membrane proteins can take place by the enzymes of the lysosome.

Cytosolic material can be delivered to the lysosome by a different pathway. A membraneous structure in the form of a deflated ball (one membrane folded upon itself to form a cup-shaped structure) surrounds the target material and fuses to become an autophagic vesicle containing molecules to be degraded and surrounded by two membranes. The outer membrane of the autophagic vesicle fuses with the lysosomal membrane, introducing into the lumen of the lysosome a vesicle with a single membrane and containing the material to be degraded.

1.4.6 Peroxisome

One further example of an intracellular organelle of eukaryotic cells is the peroxisome. A functional cousin to the lysosome, the peroxisome is a degradative organelle. The chemistry in a peroxisome is different than in a lysosome. The peroxisome contains oxidases that engage in chemical oxidation of target materials such as toxins, amino acids, fatty acids, and in other oxidation–reduction reactions. Like lysosomes but unlike mitochondria and chloroplasts, peroxisomes contain no DNA. The interior of the peroxisome is called the peroxisomal matrix. The oxidases (and other peroxisomal matrix proteins) are imported into the peroxisome after synthesis on cytosolic ribosomes. A specialized import pathway, supported by membrane proteins in the peroxisomal membrane, enables the stocking of the interior of the peroxisome with the appropriate oxidases and other enzymes for the catabolic processes.

1.5 Viral Membranes

A virus is fundamentally a protected piece of genetic material coding for its own structural and functional proteins. When that genetic material gains access to the interior of living cells, it can hijack the biosynthetic machinery of the cell to synthesize the virus-coded proteins. This supports viral replication (often to the detriment of the host cell). The protection is provided in the case of one major class of viruses by an envelope membrane and for the other major class of viruses by a protein coat. The membranes of viral envelopes will be examined in this book and in more detail in chapter "Membrane