Taking a close look at cell structure

Containing the cell: cell membrane

A cell is bound by a membrane, the cell membrane, also called the plasma membrane or the plasmalemma. The cell membrane of all eukaryotes is made of phospholipid molecules. The molecules are made by cells, a process that requires energy. The molecules assemble spontaneously (without input of energy) into the membrane, obeying the forces of polarity. Turn to Chapter 16 for a discussion of polarity and how the membrane takes its distinctive form, often called the phospholipid bilayer.

Don’t confuse cell membranes with cell walls. Every cell has a membrane, and a cell membrane is a fundamental characteristic of a cell. Some cells also have cell walls outside and separate from the cell membrane. No animal cells have cell walls, but some plant cells and fungal cells have them. They’re dissimilar to cell membranes in structure and function.

 

Permeating the membrane: the fluid-mosaic model

The phospholipid bilayer is embedded with structures of many different kinds. Though the bilayer itself is essentially similar in all cells, the embedded structures are as various and specialized as the cells themselves. Some identify the cell to other cells (very important in immune system functioning); some control the movement of certain substances in or out of the cell across the membrane. Figure 3-2 is a diagrammatic representation of the phospholipid bilayer and embedded structures. This model of the cell membrane is called the fluid-mosaic model. "Fluid" describes the ability of molecules in the bilayer to move; "mosaic" pertains to the embedded structures.

The chemical properties of the phospholipid bilayer and the embedded structures contribute to a very important feature of the membrane: It’s able to control which substances pass through it and which do not. This means the membrane is semipermeable.

 

Crossing the membrane passively

Some substances, mainly small molecules and ions, cross the membrane by a passive transport mechanism, meaning they more or less flow unimpeded across the bilayer, driven by the forces of "ordinary" chemistry, such as concentration gradients, random molecular movement, and polarity. Here are some ways that substances cross a membrane passively:

• Diffusion: A substance moves spontaneously down a concentration gradient (from an area where it’s highly concentrated to an area where it’s less concentrated). If you drop a teaspoon of salt into a jar of water, the dissolved sodium and chloride ions will, in time, diffuse (spread themselves evenly through the water). You can measure the time in seconds if you stir the solution or in days if you keep the solution perfectly still at room temperature. (To find out why, see Chapter 16.) Cellular and extracellular fluids are constantly being "stirred" and are at temperatures between 95 and 100 degrees Fahrenheit. Molecules to which the cell membrane is permeable (such as oxygen and carbon dioxide) may diffuse into or out of the cell, constantly attempting to reach equilibrium.
  The cell membrane is generally not permeable to ions and larger molecules like glucose. They must enter (or leave) the cell through a transport protein via facilitated diffusion. This still doesn’t require energy because the molecules are moving down their concentration gradient — they just need a door to open for them.
• Osmosis: The diffusion of water molecules across a selectively permeable membrane gets a special name: osmosis. As with diffusion, a concentration gradient drives the mechanism. The pressure at which the movement of water across a membrane stops (that is, when the concentration of the solutions on either side of the membrane is equal) is termed the osmotic pressure of the system.
• Filtration: This form of passive transport occurs during capillary exchange. (Capillaries are the smallest blood vessels — they bridge arterioles and venules; see Chapter 9). Capillaries are only one cell layer thick, and the capillary wall acts as a filter, controlling the entrance and exit of small molecules. Small molecules dissolved in tissue fluid, such as carbon dioxide and water, are pushed through the capillary wall, sliding between the cells and into the blood, while substances dissolved in the blood, such as glucose and oxygen, do the same in the opposite direction. The pulsating force of blood flow provides a steady force to drive this movement.

The blood pressure in the capillaries is highest at the arterial end and lowest at the venous end. At the arterial end, blood pressure pushes substances through the capillary wall and into the tissue fluid. At the venous end, lower blood pressure (thus higher net osmotic pressure) pulls water from the extracellular fluid (and anything dissolved in it) into the capillary.

Does passive transport contradict the idea that the cell controls what comes in and out through the membrane? No. The substances that move by passive mechanisms are "ordinary" small molecules and ions that are always present in abundance within and between every cell and kept within a physiologically healthy concentration range by the forces of homeostasis, the first line of defense against physiological abnormality. If at any time the physiological levels get too high or too low, the cell has pumps that can counteract the passive transport.

 

Crossing the membrane actively

Active transport allows a cell to control which big, active, biological molecules move in and out of the cytoplasm. Active transport is a fundamental characteristic of living cells (whereas you can set up a system for diffusion, as we note earlier, in a jar of water).

Like many matters in cell biology, active transport mechanisms are numerous and widely varied. When there is a molecule outside the cell that it needs, a simple active transport mechanism is used. Cell membranes have embedded proteins for the active transport of a single, specific molecule. They must be activated, or opened, for the molecule to be pumped in or out. This is generally done by a binding site on the same protein, but it can also be triggered by another protein with the membrane.

With very large molecules, another energy-requiring transport method is used. For example, a large protein made within the cell could require far too much space to exit — effectively rupturing the cell. Instead, the protein is packaged in a vesicle whose outer membrane is the same phospholipid bilayer as the cell membrane. During this transport process, called exocytosis, the lipids realign, letting the protein out of the cell without ever breaching the seal. This same process can occur in reverse, called endocytosis, to bring large molecules in.

 

Controlling the cell: nucleus

As we mention previously, the defining characteristic of a eukaryotic cell is the presence of a nucleus (plural, nuclei) that directs the cell’s activity. The largest organelle, the nucleus is oval or round and is plainly visible under a microscope. Refer to Figure 3-1, earlier in the chapter, to see the relationship of the nucleus to the cell; Figure 3-7, later in the chapter, shows a closer view of the nucleus’s structure.

All cells have one nucleus, at least at the beginning of their life cycle. As a cell develops, it may lose its nucleus, as do red blood cells and the keratinocytes of the integument; or the cell may merge with other cells, with the merged cell retaining the nuclei of all the cells, such as the fibers of skeletal muscle. This type of cell is called a syncytium.

The nucleus contains one complete (diploid) copy of the organism’s genome — the DNA that embodies the organism’s unique genetic material. Every nucleus of every cell in an organism has its own complete and exact copy of the entire genome. It’s bound by a semipermeable membrane called the nuclear envelope.

The cells produced from this identical DNA are unimaginably varied in structure, in function, and in the substances they produce (proteins, hormones, and so on). The differentiation of the cell (the structure it takes on) and everything about its products are directed by the nucleus, which controls gene expression, the selective activation of individual genes.

 

Cytoplasm

Within the cell membrane, between and around the organelles, is a fluid matrix called cytoplasm or cytosol and an internal scaffolding made up of microfilaments and microtubules that support the cell, give processes the space they need, and protect the organelles. The organelles are suspended in the cytoplasm.

The cytoplasm is gelatinous in texture because of dissolved proteins. These are the enzymes that break glucose down into pyruvate molecules in the first steps of cellular respiration (see Chapter 2). Other dissolved substances are fatty acids and amino acids. Waste products of respiration and protein construction are first ejected into the cytoplasm and then enclosed by vacuoles and expelled from the cell.

Organelles — including the nucleus, the mitochondria, the endoplasmic reticulum, and the Golgi body — contain a fluid with a particular composition, similar to the cytosol and to one another but each suited to the particular organelle’s needs.

 

Internal membranes

The plasma membrane isn’t the only membrane in a cell. Phospholipid bilayer membranes (without the "mosaic" of embedded structures) are present all through the cell, encapsulating each organelle and floating around, waiting to be useful. The network of membranes is sometimes called the endomembrane system. When an organelle makes a substance that must be expelled from the cell, a piece of bilayer moves in and encapsulates (surrounds) the material for exocytosis.

 

Powering the cell: mitochondria

A mitochondrion (plural, mitochondria) is an organelle that transforms energy into a form that can be used to fuel the cell’s metabolism and functions. It’s often called the cell’s "powerhouse". We discuss the role of the mitochondrion in cellular respiration in Chapter 2.

The number of mitochondria in a cell depends on the cell’s function. Cells whose function requires only a little energy, like nervous cells, have relatively few mitochondria; muscle cells may contain several thousand individual mitochondria because of their function in using energy to do "work". A mitochondrion can divide, like a cell, to produce more mitochondria, and it can grow, move, and combine with other mitochondria, all to support the cell’s need for energy.

Mitochondria are very small, usually rod-shaped organelles (see Figure 3-3). A mitochondrion has an outer membrane that covers and contains it. The fluid inside the mitochondrion, called the mitchondrial matrix, is filled with water and enzymes that catalyze the oxidation of glucose to ATP. A highly convoluted (folded) inner membrane sits within the matrix, increasing the surface area for the chemical reactions.

Unique among organelles, the mitochondrion contains a small amount of DNA in a separate chromosome. This DNA behaves separately and independently from the chromosomes in the nucleus. It duplicates and divides to give birth to new mitochondria within the cell, a separate event from mitosis.

The mitochondrion’s two membranes aren’t the same as the bilayer membrane of the nucleus.

 

The protein factory

The process of protein construction is a truly elegant system, as you see in the "Synthesizing protein" section later in the chapter. Here we look at the structures of the protein-construction system: the organelles and other intracellular structures and their relationships with one another.

The process of protein construction begins in the nucleus. In response to many different kinds of signals, certain genes become active, setting off the production of a specific protein molecule (gene expression). Think of the nucleus as a factory’s administrative department.

The endoplasmic reticulum (or ER; literally, "within-cell network") is a chain of membrane-bound canals and cavities that run in a convoluted path, connecting the cell membrane with the nuclear envelope. The ER brings all the components required for protein synthesis together. The ribosomes, another organelle involved in protein synthesis, adhere to the outer surface of some parts of the membrane, sticking out into the cytoplasm. These areas are called rough ER in contrast to smooth ER, where no ribosomes adhere. Think of the ER as the factory’s logistics function.

The ribosome is the site of protein synthesis, where the binding reactions that build a chain of amino acids are performed. Ribosomes may float in the cytoplasm or attach to the ER. Ribosomes are tiny, even by the standard of organelles, but they’re highly energetic, and a typical cell contains thousands of them. Think of the ribosomes as the production machinery.

The Golgi body forms a part of the cellular endomembrane system. It functions in the storage, modification, and secretion of proteins and lipids. Think of it as the shipping department. The boxes used to ship the product are the vesicles.

 

Lysosomes

Old, worn-out cell parts need to be removed from the cells; if they aren’t, they can become sources of toxins or severe energy drains. Lysosomes are organelles that do the dirty work of autodigestion. Lysosomal enzymes destroy another part of the cell, say an old mitochondrion, through a digestive process. Molecules that can be recovered from the mitochondrion are recycled in that cell or in another cell. Waste products are excreted from the cell in a membrane-bound vacuole.

 

Building blocks that build you

Though the processes of life may appear to be miraculous, biology always follows the laws of chemistry and physics. Biochemical processes are much more varied and more complex than other types of chemistry, and they happen among molecules that exist only in living cells. Molecules many thousands of times larger than water or carbon dioxide are constructed in cells and react together in seemingly miraculous ways. This section talks about these large molecules, called macromolecules, and their complex interactions.

 

Joining together: the structure of macromolecules

The four categories of these macromolecules, often called the biomolecules of life, include polysaccharides (carbohydrates), lipids, proteins, and nucleic acids. All are made mainly of carbon, with varying proportions of oxygen, hydrogen, nitrogen, and phosphorus. Many incorporate other elements, such as magnesium, sulfur, or copper.

Macromolecules, as the term suggests, are huge. Like a lot of huge things, they’re made up of smaller things, as a class is made up of students. A student is a subunit of the class, almost identical in many important ways to the other students but unique in other important ways. Macromolecules are made up of molecular subunits called, generically, monomers ("one piece"). Each type of macromolecule has its own kind of monomer. Macromolecules are, therefore, polymers ("many pieces").

In popular usage, polymer suggests plastics. Well, plastics are polymers, but not all polymers are plastics. The term refers to molecules that are made up of repeating subunits — its monomers. The chemical behavior of polymers is different from that of their constituent monomers.

The chemistry of macromolecules is like an infinite Lego set. Any block (monomer) can connect to another block if the shape of their connectors match. With enough blocks, some special connectors, and the energy to do so, you can eventually create a complex structure with bells, whistles, and wheels that turn. Then, you can do that 1,000 times more, and then connect all the complex structures together into one very large, very complex, highly functioning structure. (What’s that? You don’t have the materials or the energy to do that, and anyway, you wouldn’t know how to make a structure fit for the Lego museum? That’s okay. Your cells build much more complex things all day every day. All you need to do is keep supplying them with fuel.)

 

Polysaccharides

The simple carbohydrate molecule glucose is the main energy molecule in physiology. A common polysaccharide (polymer of carbohydrate monomers) is glycogen, which is made by linking numerous glucose molecule together to function as fuel storage.

Polysaccharides are also used for cell structures. Carbohydrate chains can be found attached to proteins embedded in the cell membrane for both recognition by and attachment to other cells.

 

Lipids

Lipids are polymers of glycerol and fatty acids (three chains of them) and are insoluble in water. The most common lipids are fats, which are an incredibly efficient energy source (which is unfortunate for us but explains the body’s propensity for storing it!). Cholesterol is also an important lipid that is used to manufacture steroid hormones (see Chapter 8) and can be found in cell membranes providing stabilization.

The phospholipids I discuss earlier also belong in this category. They replace one of the fatty acid chains with a phosphate group — giving them a hydrophilic head that interacts with water (see Figure 3-2).

 

Proteins

Proteins are polymers of amino acids. The amino acid monomers are arranged in a linear chain, called a polypeptide, and may be folded and refolded into a globular form. Structural proteins comprise about 75 percent of your body’s material. The integument, the muscles, the joints, and the other kinds of connective tissue are made mostly of structural proteins like collagen, keratin, actin, and myosin. In addition, the enzymes that catalyze all the complex chemical reactions of life are also proteins.

 

Amino acids

Twenty different amino acids exist in nature. Amino acids themselves are, by the standards of nonliving chemistry, huge and complex. A typical protein comprises hundreds of amino acid monomers that must be attached in exactly the right order for the protein to function properly.

The binding proclivities among all the amino acids result in the structural precision that makes proteins functional for the exacting processes of biology. That is, the order of amino acids determines how the protein twists and folds. Every protein depends on its unique, three-dimensional structure to perform its function. A misfolded protein won’t work and in some cases can result in disease.

 

Enzymes

Enzymes are protein molecules that catalyze the chemical reactions of life. Enzymes can only speed up a reaction that is otherwise chemically possible. How effective are enzymes in speeding up reactions? Well, a reaction that may take a century or more to happen spontaneously happens in a fraction of a second with the right enzyme. And better yet, they are not "used up" in the process. Enzymes are involved in every physiological process, and each enzyme is extremely specific to one or a very few individual reactions. Your body has tens of thousands of different enzymes.

Any time an enzyme is discovered, it is named, usually with some physiology shorthand for its function, frequently with the suffix –ase. An enzyme named pyruvate dehydrogenase removes hydrogen atoms from pyruvate molecules in the processes of cellular respiration (see Chapter 2).

The malfunctioning of a single enzyme, which can be caused by a single nucleotide being out of order, is responsible for some very nasty, sometimes fatal diseases. Phenylketonuria (PKU) is an inherited metabolic disease caused by faulty phenylalanine hydroxylase. The inability to properly metabolize the amino acid phenylalanine, found in many foods, results in mental retardation, organ damage, unusual posture, and even death, unless the afflicted person can limit the ingestion of foods containing phenylalanine, which is a very difficult thing to do.

 

Nucleic acids

The nucleic acids deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are polymers made of monomers called nucleotides and arranged in a chain, one after another... and another, and another. DNA molecules are thousands of nucleotides long (see Figure 3-4). The functioning of genes is inseparable from the chemical structure of the nucleic acid monomers.

A nucleotide is made up of a sugar molecule and a phosphate group attached to a nitrogenous base. The sugar molecule is either deoxyribose (in DNA) or ribose (in RNA). The nitrogenous base is one of four:

• Cytosine (C), guanine (G), thymine (T), or adenine (A) in DNA
• Cytosine (C), guanine (G), uracil (U), or adenine (A) in RNA

The bases connect with each other in specific pairs. (Refer to the section "Gene structure" later in the chapter for a discussion of the biological significance of this complementary pairing.) The complementary pairs are:

• C with G
• A with T in DNA
• A with U in RNA

The structural similarities and differences between DNA and RNA allow them to work together to produce proteins within cells. The DNA molecule remains stable in the nucleus during normal cell functioning, protected from damage by the nuclear envelope. An RNA molecule is built on demand to transmit a gene’s coded instructions for building proteins, and then it disintegrates. Some of its nucleotide subunits remain intact and are recycled into new RNA molecules.