Bioenergetics & Metabolism

Mitochondria: Cellular Power Plants

Blink. Breathe. Wiggle your toes. These subtle movements—as well as the many chemical reactions that take place inside organelles—require vast amounts of cellular energy. The main energy source in your body is a small molecule called ATP, for adenosine triphosphate.
Mitochondria
Mitochondria

ATP is made in organelles called mitochondria. Let's see if we can find some. They look like blimps about as long as pickup trucks but somewhat narrower. Oh, a few of them are over there. As we get nearer, you may hear a low whirring or humming sound, similar to that made by a power station. It's no coincidence. Just as power plants convert energy from fossil fuels or hydroelectric dams into electricity, mitochondria convert energy from your food into ATP.

Like all other organelles, mitochondria are encased in an outer membrane. But they also have an inner membrane. Remarkably, this inner membrane is four or five times larger than the outer membrane. So, to fit inside the organelle, it doubles over in many places, extending long, fingerlike folds into the center of the organelle. These folds serve an important function: They dramatically increase the surface area available to the cell machinery that makes ATP. In other words, they vastly increase the ATP-production capacity of mitochondria.

The mazelike space inside mitochondria is filled with a strong brew of hundreds of enzymes, DNA (mitochondria are the only organelles to have their own genetic material), special mitochondrial ribosomes, and other molecules necessary to turn on mitochondrial genes.


ACTUAL SIZE (AVERAGE) PERCEIVED SIZE WHEN MAGNIFIED 3 MILLION TIMES
Cell diameter 30 micrometers* 300 feet
Nucleus diameter 5 micrometers 50 feet
Mitochondrion length Typically 1–2 micrometers, but can be up to 7 micrometers long 18 feet
Lysosome diameter 50–3,000 nanometers* 5 inches to 30 feet
Ribosome diameter 20–30 nanometers 2–3 inches
Microtubule width 25 nanometers 3 inches
Intermediate filament width 10 nanometers 1.2 inches
Actin filament width 5–9 nanometers 0.5–1 inch
*A micrometer is one millionth (10-6) of a meter. A nanometer is one billionth (10-9) of a meter.

Got Energy?

Energy from the food you eat is converted into ATP.
Energy from the food you eat is converted in mitochondria into ATP. Cells use ATP to power their chemical reactions. For example, muscle cells convert ATP energy into physical work, allowing you to lift weights, jog, or simply move your eyeballs from side to side.

The largest human cell (by volume) is the egg. Human eggs are 150 micrometers in diameter and you can just barely see one with a naked eye. In comparison, consider the eggs of chickens...or ostriches!

When you think about food, protein, and energy, what may come to mind is the quick meal you squeeze in before racing off to your next activity. But while you move on, your cells are transforming the food into fuel (ATP in this case) for energy and growth.

As your digestive system works on an apple or a turkey sandwich, it breaks the food down into different parts, including molecules of a sugar called glucose. Through a series of chemical reactions, mitochondria transfer energy in conveniently sized packets from glucose into ATP. All that's left are carbon dioxide and water, which are discarded as wastes.

This process is extremely efficient. Cells convert nearly 50 percent of the energy stored in glucose into ATP. The remaining energy is released and used to keep our bodies warm. In contrast, a typical car converts no more than 20 percent of its fuel energy into useful work.

Your body uses ATP by breaking it apart. ATP stores energy in its chemical bonds. When one of these bonds is broken, loosing a chemical group called a phosphate, energy is released.

ATP is plentifully produced and used in virtually every type of cell. A typical cell contains about 1 billion molecules of ATP at any given time. In many cells, all of this ATP is used up and replaced every 1 to 2 minutes!

Peter Mitchell, a British scientist, proposed the theory of chemiosmosis in 1961 to describe the way in which ATP is actually synthesized; he received the Nobel Prize for his work in 1978. In prokaryotes, it occurs at the cell membrane. In eukaryotic animal cells, chemiosmosis takes place in the cristae of the mitochondria, and in autotrophic cells, it occurs across the thylakoid membranes in the chloroplasts. Since chemiosmosis is the same for all three membranes, in the following discussion we will not need to differentiate between the membranes. Chemiosmosis

On one side of the membrane (we will call this side the "inside") is a supply of hydrogen atoms. Special carrier molecules use the energy released in the electron transport chain to bring hydrogen atoms close to the membrane and separate the hydrogen into an H+ ions and electrons. The electrons are brought back to the inside of the membrane while the H+ ions are forced to the other side (the "outside"). As more and more H+ ions accumulate on the outside of the membrane, two gradients are formed. First, a pH gradient is formed. This means that the outside is more acidic (because it has H+ ions) than the inside of the membrane. Also, an electrical gradient forms, since H+ ions have a positive charge.

When these gradients become sufficiently intense, they force the H+ ions through a channel (sometimes called the F0 channel) in the membrane in a tremendous gush. The ions end up in a large structure called the F1 unit where an enzyme called ATP synthetase is located. Also present in the F1 are ADP molecules and phosphate molecules. As the H+ ions rush by, they provide the energy which brings the ATP synthetase, ADP, and phosphates together. The ATP synthetase bonds the ADP and phosphate molecules, forming ATP. The H+ ions, now on the inside of the membrane, can be transported by the carrier molecules across the membrane so that the process may be repeated when enough energy is released from the electron transport chain.


Plastids

Plastids are organelles which are found only in autotrophic cells. In many respects, plastids are similar to entire prokaryotic organisms; they contain their own DNA and can replicate themselves. Like the mitochondria, plastids have an outer membrane which separates them from the cytoplasm and a highly folded inner membrane. Plastids come in three different types: leucoplasts, chloroplasts, and chromoplasts.
Leucoplasts are colorless plastids which store starch (a carbohydrate), proteins, and lipids. These materials are released from the leucoplast when the cell requires them.
Chloroplasts are the organelles in which photosynthesis takes place. Photosynthesis is an important process by which autotrophic cells manufacture their own food. Chloroplasts contain the green pigment chlorophyll (this is why plant leaves are green) which absorbs light to provide the energy necessary to complete photosynthesis.





A chloroplast





A chloroplast
(image courtesy of Nanoworld)
Chloroplasts have two membranes: an outer membrane and an inner membrane. A solution called the stroma fills the part of the chloroplast inside of the inner membrane. In this area, there are stacks of flattened vesicles. The stacks themselves are known as grana, and the vesicles are called thylakoids. The thylakoids are where photosynthesis actually occurs.
Chromoplasts are very similar to chloroplasts, but they do not contain the green pigment chlorophyll. Instead, they contain other pigments which give color to flowers and to leaves during the fall. These other pigments absorb colors of light than chlorophyll.


Organelles

Overview
 
Welcome! I hope the transformation wasn't too alarming. You have shrunk down to about 3 millionths of your normal size. You are now about 0.5 micrometers tall (a micrometer is 1/1000 of a millimeter). But don't worry, you'll return to your normal size before you finish this chapter.

At this scale, a medium-sized human cell looks as long, high, and wide as a football field. But from where we are, you can't see nearly that far. Clogging your view is a rich stew of molecules, fibers, and various cell structures called organelles. Like the internal organs in your body, organelles in the cell each have a unique biological role to play.
Now that your eyes have adjusted to the darkness, let's explore, first-hand and up close, the amazing world inside a cell.

A typical animal cell, sliced open to reveal cross-sections of organelles.
A typical animal cell, sliced open to reveal cross-sections of organelles.

Nucleus: The Cell's Brain

Look down. Notice the slight curve? You're standing on a somewhat spherical structure about 50 feet in diameter. It's the nucleus—basically the cell's brain.

Nucleus
Nuclear Pores

The nucleus is the most prominent organelle and can occupy up to 10 percent of the space inside a cell. It contains the equivalent of the cell's gray matter—its genetic material, or DNA. In the form of genes, each with a host of helper molecules, DNA determines the cell's identity, masterminds its activities, and is the official cookbook for the body's proteins.

Go ahead—jump. It's a bit springy, isn't it? That's because the nucleus is surrounded by two pliable membranes, together known as the nuclear envelope. Normally, the nuclear envelope is pockmarked with octagonal pits about an inch across (at this scale) and hemmed in by raised sides. These nuclear pores allow chemical messages to exit and enter the nucleus. But we've cleared the nuclear pores off this area of the nucleus so you don't sprain an ankle on one.

If you exclude the nucleus, the rest of the cell's innards are known as the cytoplasm. Virtually all forms of life fall into one of two categories: eukaryotes or prokaryotes.

Eukaryotic Cells Prokaryotic Cells
The cells of “complex” organisms, including all plants and animals “Simple” organisms, including bacteria and blue-green algae
Contain a nucleus and many other organelles, each surrounded by a membrane (the nucleus and mitochondrion have two membranes) Lack a nucleus and other membrane-encased organelles
Can specialize for certain functions, such as absorbing nutrients from food or transmitting nerve impulses; groups cells can form large, multicellular organs and organisms Usually exist as single, virtually identical cells
Most animal cells are 10–30 micrometers across, and most plant cells are 10–100 micrometers across Most are 1–10 micrometers across


Endoplasmic Reticulum: Protein Clothier and Lipid Factory

If you peer over the side of the nucleus, you'll notice groups of enormous, interconnected sacs snuggling close by. Each sac is only a few inches across but can extend to lengths of 100 feet or more. This network of sacs, the endoplasmic reticulum (ER), often makes up more than 10 percent of a cell's total volume.
The endoplasmic reticulum comes in two types: Rough ER is covered with ribosomes and prepares newly made proteins; smooth ER specializes in making lipids and breaking down toxic molecules.Smooth ER
 
The endoplasmic reticulum comes in two types: Rough ER is covered with ribosomes and prepares newly made proteins; smooth ER specializes in making lipids and breaking down toxic molecules.

Take a closer look, and you'll see that the sacs are covered with bumps about 2 inches wide. Those bumps, called ribosomes, are sophisticated molecular machines made up of more than 70 proteins and 4 strands of RNA, a chemical relative of DNA. Ribosomes have a critical job: assembling all the cell's proteins. Without ribosomes, life as we know it would cease to exist.

To make a protein, ribosomes weld together chemical building blocks one by one. As naked, infant protein chains begin to curl out of ribosomes, they thread directly into the ER. There, hard-working enzymes clothe them with specialized strands of sugars.

Rough ER

Now, climb off the nucleus and out onto the ER. As you venture farther from the nucleus, you'll notice the ribosomes start to thin out. Be careful! Those ribosomes serve as nice hand- and footholds now. But as they become scarce or disappear, you could slide into the smooth ER, unable to climb out.

In addition to having few or no ribosomes, the smooth ER has a different shape and function than the ribosome-studded rough ER. A labyrinth of branched tubules, the smooth ER specializes in synthesizing lipids and also contains enzymes that break down harmful substances. Most cell types have very little smooth ER, but some cells—like those in the liver, which are responsible for neutralizing toxins—contain lots of it.

Next, look out into the cytosol. Do you see some free-floating ribosomes? The proteins made on those ribosomes stay in the cytosol. In contrast, proteins made on the rough ER's ribosomes end up in other organelles or are sent out of the cell to function elsewhere in the body. A few examples of proteins that leave the cell (called secreted proteins) are antibodies, insulin, digestive enzymes, and many hormones.

Golgi: Finishing, Packaging, and Mailing Centers

Golgi
Golgi

Now, let's slog through the cytosol a bit. Notice that stack of a half dozen flattened balloons, each a few inches across and about 2 feet long? That's the Golgi complex, also called the Golgi apparatus or, simply, the Golgi. Like an upscale gift shop that monograms, wraps, and mails its merchandise, the Golgi receives newly made proteins and lipids from the ER, puts the finishing touches on them, addresses them, and sends them to their final destinations. One of the places these molecules can end up is in lysosomes.

Lysosomes: Recycling Centers and Garbage Trucks

Lysosomes

See that bubble about 10 feet across? That's a lysosome. Let's go—I think you'll like this. Perhaps even more than other organelles, lysosomes can vary widely in size—from 5 inches to 30 feet across.

Go ahead, put your ear next to it. Hear the sizzling and gurgling? That's the sound of powerful enzymes and acids chewing to bits anything that ends up inside.

But materials aren't just melted into oblivion in the lysosome. Instead, they are precisely chipped into their component parts, almost all of which the cell recycles as nutrients or building blocks. Lysosomes also act as cellular garbage trucks, hauling away unusable waste and dumping it outside the cell. From there, the body has various ways of getting rid of it.

Cool Tools for Studying Cells

Cell biologists would love to do what you just did—shrink down and actually see, touch, and hear the inner workings of cells. Because that's impossible, they've developed an ever-growing collection of approaches to study cellular innards from the outside. Among them are biochemistry, physical analysis, microscopy, computer analysis, and molecular genetics. Using these techniques, researchers can exhaustively inventory the individual molecular bits and pieces that make up cells, eavesdrop on cellular communication, and spy on cells as they adapt to changing environments. Together, the approaches provide vivid details about how cells work together in the body's organs and tissues. We'll start by discussing the traditional tools of the trade—microscopes—then touch on the new frontiers of quantum dots and computational biology.

Light Microscopes: The First Windows Into Cells

Robert Hooke, the British scientist who coined the word "cell," probably used this microscope when he prepared Micrographia. Published in 1665, Micrographia was the first book describing observations made through a microscope. It was a best-seller.
Robert Hooke, the British scientist who coined the word "cell," probably used this microscope when he prepared Micrographia. Published in 1665, Micrographia was the first book describing observations made through a microscope. It was a best-seller.

This fireworks explosion of color is a dividing newt lung cell seen under a light microscope and colored using fluorescent dyes: chromosomes in blue, intermediate filaments in red, and spindle fibers (bundled microtubules assembled for cell division) in green.
This fireworks explosion of color is a dividing newt lung cell seen under a light microscope and colored using fluorescent dyes: chromosomes in blue, intermediate filaments in red, and spindle fibers (bundled microtubules assembled for cell division) in green.

Scientists first saw cells by using traditional light microscopes. In fact, it was Robert Hooke (1635–1703), looking through a microscope at a thin slice of cork, who coined the word "cell." He chose the word to describe the boxlike holes in the plant cells because they reminded him of the cells of a monastery.

Scientists gradually got better at grinding glass into lenses and at whipping up chemicals to selectively stain cellular parts so they could see them better. By the late 1800s, biologists already had identified some of the largest organelles (the nucleus, mitochondria, and Golgi).
Researchers using high-tech light microscopes and glowing molecular labels can now watch biological processes in real time. The scientists start by chemically attaching a fluorescent dye or protein to a molecule that interests them. The colored glow then allows the scientists to locate the molecules in living cells and to track processes—such as cell movement, division, or infection—that involve the molecules.

Fluorescent labels come in many colors, including brilliant red, magenta, yellow, green, and blue. By using a collection of them at the same time, researchers can label multiple structures inside a cell and can track several processes at once. The technicolor result provides great insight into living cells—and is stunning cellular art.

Electron Microscopes: The Most Powerful of All

In the 1930s, scientists developed a new type of microscope, an electron microscope that allowed them to see beyond what some ever dreamed possible. The revolutionary concept behind the machine grew out of physicists' insights into the nature of electrons.

As its name implies, the electron microscope depends not on light, but on electrons. The microscopes accelerate electrons in a vacuum, shoot them out of an electron gun, and focus them with doughnut-shaped magnets. As the electrons bombard the sample, they are absorbed or scattered by different cell parts, forming an image on a detection plate.

Scanning electron microscopes allow scientists to see the three-dimensional surface of their samples.
Scanning electron microscopes allow scientists to see the three-dimensional surface of their samples.

Although electron microscopes enable scientists to see things hundreds of times smaller than anything visible through light microscopes, they have a serious drawback: They can't be used to study living cells. Biological tissues don't survive the technique's harsh chemicals, deadly vacuum, and powerful blast of electrons.

Electron microscopes come in two main flavors: transmission and scanning. Some transmission electron microscopes can magnify objects up to 1 million times, enabling scientists to see viruses and even some large molecules. To obtain this level of detail, however, the samples usually must be sliced so thin that they yield only flat, two-dimensional images. Photos from transmission electron microscopes are typically viewed in black and white.

Scanning electron microscopes cannot magnify samples as powerfully as transmission scopes, but they allow scientists to study the often intricate surface features of larger samples. This provides a window to see up close the three-dimensional terrain of intact cells, material surfaces, microscopic organisms, and insects. Scientists sometimes use computer drawing programs to highlight parts of these images with color.

Studying Single Molecules: Connecting the Quantum Dots

Dyes called quantum dots can simultaneously reveal the fine details of many cell structures. Here, the nucleus is blue, a specific protein within the nucleus is pink, mitochondria look yellow, microtubules are green, and actin filaments are red. Someday, the technique may be used for speedy disease diagnosis, DNA testing, or analysis of biological samples.
Dyes called quantum dots can simultaneously reveal the fine details of many cell structures. Here, the nucleus is blue, a specific protein within the nucleus is pink, mitochondria look yellow, microtubules are green, and actin filaments are red. Someday, the technique may be used for speedy disease diagnosis, DNA testing, or analysis of biological samples.

Whether they use microscopes, genetic methods, or any other technique to observe specific molecules, scientists typically flag every molecule of a certain type, then study these molecules as a group. It's rather like trying to understand a profession—say, teaching, architecture, or medicine—by tagging and observing all the workers in that profession simultaneously. Although these global approaches have taught us a lot, many scientists long to examine individual molecules in real time—the equivalent of following individual teachers as they go about their daily routines.

Now, new techniques are beginning to allow scientists to do just that. One technology, called quantum dots, uses microscopic semiconductor crystals to label specific proteins and genes. The crystals, each far less than a millionth of an inch in diameter, radiate brilliant colors when exposed to ultraviolet light. Dots of slightly different sizes glow in different fluorescent colors—larger dots shine red, while smaller dots shine blue, with a rainbow of colors in between. Researchers can create up to 40,000 different labels by mixing quantum dots of different colors and intensities as an artist would mix paint. In addition to coming in a vast array of colors, the dots also are brighter and more versatile than more traditional fluorescent dyes: They can be used to visualize individual molecules or, like the older labeling techniques, to visualize every molecule of a given type.

Quantum dots promise to advance not only cell biology but also a host of other areas. Someday, the technology may allow doctors to rapidly analyze thousands of genes and proteins from cancer patients and tailor treatments to each person's molecular profile. These bright dots also could help improve the speed, accuracy, and affordability of diagnostic tests for everything from HIV infection to allergies. And, when hitched to medicines, quantum dots might deliver a specific dose of a drug directly to a certain type of cell.

Computers Clarify Complexity

Say you're hungry and stranded in a blizzard: If you eat before you seek shelter, you might freeze to death, but if you don't eat first, you might not have the strength to get yourself out of the storm. That's analogous to the decisions cells have to make every day to survive.

For years, scientists have examined cell behaviors—like the response to cold or hunger—one at a time. And even that they did bit by bit, laboriously hammering out the specific roles of certain molecules. This approach made it difficult or impossible to study the relative contributions of—and the interplay between—genes that share responsibility for cell behaviors, such as the 100 or so genes involved in the control of blood pressure.

Now, computers are allowing scientists to examine many factors involved in cellular behaviors and decisions all at the same time. The field of computational biology blossomed with the advent of high-end computers. For example, sequencing the 3.2 billion base pairs of the human genome, which was completed in 2003, depended on computers advanced enough to tackle the challenge. Now, state-of-the-art equipment and a wealth of biological data from genome projects and other technologies are opening up many new research opportunities in computer analysis and modeling. So, much as microscopes and biochemical techniques revolutionized cell biology centuries ago, computers promise to advance the field just as dramatically in this new century.



Transport across the Plasma Membrane

Overview: Just passin' thru....

There are many ways in which a material can pass through the membrane. One such method is simple diffusion, which only occurs for small, nonpolar molecules (for example CO2 or O2). These molecules are small enough to squeeze between the phosphate heads of the phospholipids. Small polar molecules can also pass through, but usually the nonpolar fatty acids in the membrane repel them. The rate at which the small nonpolar molecules pass through is based upon the difference in concentration of that molecule on either side of the membrane. 

Facilitated Diffusion The second method by which molecules can move through the cell membrane is by passive transport. Passive transport allows highly polar molecules to move through the fatty acid layer which would normally not permit them to. One form of passive transport utilizes protein channels, whereby protein molecules in the membrane form a tunnel through which polar molecules may diffuse without ever coming in contact with the fatty acids. A second type of passive transport is known as facilitated diffusion. In this process, proteins called carrier proteins bond with the molecule on one side of the membrane, move through the membrane, and then release it on the other side. Like enzymes, carrier proteins usually bond with a specific molecule, but little else is known about them. 
Protein channel

In simple diffusion and passive transport, the cell did not expend any energy since the processes occurred naturally by diffusion and the free movement of proteins in the cell membrane. Another type of transport, called active transport, requires an input of energy by the cell








 Membrane proteins

Integral membrane proteins

Also referred to as transmembrane proteins. Commonly, integral membrane proteins have membrane spanning domains which are alpha helical. May be 1 , 2, 7 or more membrane spanning alpha helical domains. The alpha helix neutralizes the polar character of the peptide bonds. The hydrophobic side chains assoc. with these amino acids interact with the fatty acid chains of membrane lipids. Most transmembrane proteins are also glycosylated [have carbohydrate groups attached].

Peripheral membrane proteins
Not embedded in the bilayer but indirectly associated with the membrane through interactions with integral membrane proteins or by weak electrostatic interactions with the hydrophilic head groups of membrane lipids. Located extracellular or associated with the cytoplasmic surface of the bilayer.
  
Lipid-anchored proteins
Located outside the lipid bilayer, but covalently linked to a lipid molecule that is situated within the bilayer. An increasingly large number of proteins have been found to be linked by a short oligosaccharide to a molecule of glycophosphatidylinositol (GPI) that is embedded in the outer leaflet of the lipid bilayer. These proteins are released when membrane is treated with enzymes that (Phospholipases) that specifically recognized and cleaved inositol-containing phospholipids. Another group of proteins are actually present on the cytoplasmic side of the membrane and are anchored by long hydrocarbon chains embedded in the inner leaflet of the lipid bilayer.


THE GLYCOCALYX

The extracellular portion of the plasma membrane proteins are generally glycosylated. Likewise, the carbohydrate portions of glycolipids are exposed on the outer face of the plasma membrane. Consequently, the glycocalyx, is formed by the oligosaccharides of glycolipids and transmembrane glycoproteins.

Role:
Protection of cell surface
Markers for cell-cell interactions


TRANSPORT ACROSS CELL MEMBRANES
Membranes are selectively permeable --- small, uncharged molecules can diffuse freely through the phospholipid bilayer. O2, CO2. Also some small polar molecules H2O, ethanol and some small relatively hydrophobic molecules such as benzene.

Passive diffusion
Molecule simply dissolves in the phospholipid bilayer, diffuses across it, and then dissolves in the aqueous solution at the other side of the membrane. No membrane proteins involved in process. The net movement of molecules is simply according to the concentration gradient, with molecules moving from an area of higher concentration to an area of lower concentration.

Water is actually a rather special case - readily diffusable according to concentration gradient. Process is known as osmosis.

Larger polar molecules such as glucose cannot cross by passive diffusion. Charged ions also cannot [Na+, Ca++, K+, Cl-], even H+ cannot.
  
Facilitated Diffusion
Like passive diffusion, involves the movement of molecules in a net direction determined by concentration gradient---but with the assistance of specialized proteins.

Channel Proteins: Proteins which form open pores allowing for free passage of any molecule of appropriate size and charge by free diffusion. Form a passage through the lipid bilayer, allowing polar or charged molecules to cross without interacting with the hydrophobic fatty acid chains of the phospholipids.
ION CHANNELS-specific example of a channel protein. They are not permanently open [GATED]. There is a very wide variety of ion channels. All are integral membrane proteins that surround an aqueous pore. Bidirectional flow of ions based upon the electrochemical concentration gradient. Most channel proteins are said to be gated meaning that they can exist in open or closed conformation.

Carrier Proteins [Transporter Proteins]: Selectively bind and transport specific small molecules such as glucose. The molecules bind and the protein undergoes a conformational change that allows specific molecules to pass through. Involved in facilitated diffusion of sugars, amino acids, and nucleosides.

Active transport
Carrier proteins also provide a mechanism through which the energy changes associated with transporting molecules can be coupled to the use or production of other forms of metabolic energy.  Molecules can be transported against a concentration gradient if the transport is coupled to ATP hydrolysis, the absorption of light, the transport of electrons, or the flow of other substances down a gradient - as a source of energy.

Typically the K+ concentration inside a mammalian cell is about 100 mM, while that outside the cell is only 5mM. Diffusion of potassium out of the cell is favored. Sodium ions and Calcium ions have the opposite concentration gradient. Such gradients are maintained by active transport [ION PUMPS].

Depends on integral membrane proteins that are capable of selectively binding a particular solute and moving that substance across the membrane- driven by changes in the protein's conformation.

Vesicular Transport across the Plasma Membrane
   
The Endocytic Pathway

Uptake of macromolecules and particles is done by ENDOCYTOSIS.

Pinocytosis effectively internalizes portions of the cell membrane, any proteins or receptors on the membrane, and any ligands attached to those receptors. Fate of these receptors and their ligands varies after endocytosis. When soluble Ig binds to antigen, both receptor and ligand are directed to the lysosmes. The other possible route is that vesicles may be transported to another region of the membrane where the ligand is released.

One form of pinocytosis involves the use of coated pits [receptor-mediated endocytosis]. Ligand binds to receptor. Complex travels laterally through the membrane to a coated pit region. Complexes are retained and concentrated in these pits. Clathrin is a protein whose subunits form the surface of the pit. Pit then invaginates and eventually forms a vesicle known as a clathrin coated vesicle. The clathrin coated vesicle first fused with vesicles known as early endosomes. Fusion with the early endosome brings the pH of the clathrin coated vesicle down to between pH 6 and 6.2. This shift to an acidic pH allows the clathrin and the receptor to be transported back to the surface. Late endosomes then fuse with the vesicle, further lowering the pH to between 5.5-6.0. Finally, lysosomes fuse bringing the pH down to about 5.0. Lysosomes also release a battery of hydrolytic enzymes that digest the material remaining in the vesicle.

The other major form of endocytosis is termed: Phagocytosis. Phagocytosis can only be carried out by phagocytic cells such as macrophages and neutrophils. Phagocytosis involves the internalization of particles such as bacteria, protozoa, etc. In the process of phagocytosis, the particle first binds to the phagocytic cell, then the cell sends out extensions of the cyotplasm known as pseudopodia which surround the particle. The formation of psuedopodia is dependent upon the polymerization of the cytoskeletal protein, actin. The internalized particle is now enclosed in a membrane-bound structure known as a phagosome. Lysosmes subsequently fuse with the phagosome forming a phagoslysosome. The hydrolytic enzymes released by the lysosome function in the digestion of the internalized particle.
  
Exocytosis
Material enclosed in a cell vacuole is passed to the extracellular fluid by fusion of the vacuole with the plasma membrane. Secretory process and a mechanisim of replenishing lipids and proteins of plasma membrane.

The Plasma Membrane

What is the plasma membrane?

Fig. 1 Membrane Permeability and Function




Surrounding every cell is some sort of covering that keeps what's inside the cell inside and prevents harmful particles in the external environment from diffusing into the cell. There are two types of organelles which serve as a covering for the cell: the cell membrane and the cell wall. All cells have a cell membrane, and certain cells also have a cell wall. We'll discuss each of these separately, because they perform very different functions.
Cell membrane
The cell membrane's main purpose is to regulate the movement of materials into and out of the cell. By doing so, the internal environment of the cell can be different than the external environment, since only certain materials can pass through. Scientists say that the cell membrane is selectively permeable, which means that only certain substances can permeate (go through) the membrane. The next section discusses how the cell membrane accomplishes this very important function, but for now, let's discuss what the cell membrane is made of.

Phospholipid
Cell membranes consist mainly of phospholipids. Phospholipids have two parts: a polar phosphate "head" and two nonpolar fatty acid "tails." These molecules are arranged in what is called a bilayer (a double layer) so that the polar heads face the external and the internal environments of the cell and the fatty acids form the inside of the membrane. The phospholipids are free to move around, often switching places with their neighbors. This allows for the membrane to stretch and change shape.

Also contained within the membrane are large protein molecules. Some of them jut out on either side of the membrane, while others are only on one side.

Unlike the cell membrane which is found in all cells, not all cells have a cell wall, another structure which surrounds the cell membrane. In particular, prokaryotes usually have a cell wall of some sort, and a type of eukaryotes called algae may also have a cell well. The cell walls in each of these two types of organisms is different.

For prokaryotes, the cell wall usually contains large polymers called peptidoglycans. These molecules provide for the strength of the bacterial cell wall. Some prokaryotic cell walls have two layers: an inner layer made of peptidoglycans and an outer layer composed of lipoproteins and lipopolysaccharides.

You will learn later that in eukaryotes, the cell wall has three main parts: the primary cell wall, the middle lamella, and the secondary cell wall. The primary cell wall is located closest to the inside of the cell. It is made mostly of cellulose which allows the wall to stretch as the cell grows. The middle lamella is composed of polysaccharides called pectins. Outside of the middle lamella is the secondary cell wall, which contains both cellulose and a strong material called lignin. Lignin strengthens the wall and gives the cell a somewhat rectangular shape.

STRUCTURAL PROPERTIES OF CELL MEMBRANES

Formation of cell membranes is based upon the properties of lipids. All are bi-layers of phospholipids with associated proteins. As previously mentioned, phospholipids are amphipathic meaning that they possess both a hydrophobic and hydrophilic end.

Polar head groups are in contact with water while fatty acid tails aggregate in the interior of the membrane. The four major phospholipids found in cell membranes:
  • phosphatidyl choline
  • phosphatidyl ethanolamine
  • phosphatidyl serine
  • sphingomyelin - a non-glycerol phospholipid 
Various glycolipids are also found in the outer leaflet of the cell membrane. Cholesterol is another important constituent of the animal cell membrane. Lipid composition differs in the different types of cells and in different types of organisms. The average eukaryotic plasma membrane - ~50% of mass is lipid and 50% protein.
The lipid bilayer behaves as a fluid.   
 
 
FLUID MOSAIC MODEL 
 
The fluid mosaic model was first proposed by Singer and Nicolson . Lipids and proteins can readily move laterally and can also undergo rotation. The degree of membrane fluidity is determined by temperature and lipid composition. Lipids with shorter fatty acid chains are less rigid and remain fluid at lower temperatures. This is because interactions between shorter chains is weaker than for longer chains. Lipids containing unsaturated fatty acids increase membrane fluidity The = bonds introduce kinks, preventing tight packing of the fatty acids.
 
Cholesterol with its hydrocarbon ring structure plays a distinct role in determining membrane fluidity.  Polar hydroxyl group positions close to the phosphate head group. Rigid rings interact with regions of fatty acid chain adjacent to phospholipid head groups. This interaction decreases the mobility of the outer portions of the fatty acid chains, making this region of the membrane more rigid, even at higher temperatures.
 
On the other hand... 
 
Insertion of cholesterol interferes with interactions between fatty acids, thereby maintaining fluidity at lower temperatures. Cholesterol is not present in bacteria or plant cells. Plant cell membranes do contain sterols which function in a manner similar to cholesterol. In the fluid mosaic model of the membrane ----there are membrane proteins inserted into the lipid bilayer. The lipids provide the basic structure, but proteins carry out the specific functions of the different types of membranes.