As the smallest living units, cells carry out the chemical transactions of life. Collectively termed metabolism, this set of chemical reactions uses energy to maintain life (a condition that requires the constant input of chemical energy to continue). In Biology 100, we will be concerned with molecules assembled mostly from the elements carbon, oxygen, hydrogen, nitrogen, and phosphorus. In most of the compounds we will encounter, atoms of these elements are strongly bound together with covalent bonds. Think of covalently bonded atoms like metal parts welded together. It takes a great deal of energy to make or break these strong bonds. In contrast, weak bonds are more like parts held together by velcro- they are quite sticky, but can be taken apart without a great deal of effort.

A water molecule is a good way to think about the two types of bonds. As shown in figure 2.9, the two hydrogen atoms of a water molecule are held together by strong covalent bonds. Recall that these covalent bonds are actually a shared pair of electrons. This sharing can be equal (where the electrons spend the same amount of time with the atoms on each end of the bond) or unequal (where the electrons spend more time with one atom than with the other). In figure 2.9, the partial negative charge on the oxygen atom and the partial positive charges on the hydrogen atoms result from the negatively charged electrons spending more time near the oxygen atom. The presence of such partial charges makes a molecule polar. Remember that covalently bonded carbon and hydrogen atoms share electrons equally and that covalently bonded oxygen or nitrogen atoms share electrons unequally with hydrogen, resulting in polar molecules, like water. As you can see in figure 2.9 (b) the polar water molecules arrange themselves in an orderly way. The weak bonds that hold this grid pattern together are called hydrogen bonds.

The network of hydrogen bonds gives water special properties - high boiling point, resistance to temperature change, and the ability to dissolve other polar molecules, which can fit into the grid of partially charged water molecules. Non-polar molecules cannot form the hydrogen bonds required by the grid, and are excluded (pushed out). To visualize this, mix a little cooking oil with water. No matter how you shake, the oil is always pushed out of the water because of the very strong tendency of water molecules to form grids like the one shown in figure 2.9. Substances that dissolve in water are called hydrophilic, those that are excluded like the oil are called hydrophobic

Water is one biological molecule. Some others are carbohydrates, lipids, proteins, and nucleic acids. Carbohydrates are used for two main purposes in biological systems - energy storage and structural support. Table sugar and chitin (the hard covering on insects) are examples of each of these types of carbohydrates. Lipids are non-polar (hydrophobic) molecules. Although they are often used for high-density energy storage (think about the number of calories (energy) in a stick of butter) we will also encounter lipids in the membranes of cells (Chapter 3). A glance at the lipids in figure 2.21 should convince you that these are very hydrophobic molecules.

Proteins are the all-purpose molecules of biology. For any biological function, it is possible to specify a protein that will carry out that function. From the lock-and key recognition of a virus and its host cell to machines that assemble molecules to order, proteins do the work of biology. This diversity of function is possible because an almost infinite number of proteins (polymers) can be assembled from the twenty amino acid monomers (see Figure 2.25). Ultimately, the three-dimensional structure of a protein gives rise to its special properties.

How does the cell know when, where, and how to make a particular protein? Protein sequence is specified by nucleic acids (think DNA - the molecule that carries genetic information.) Remember that the information contained in DNA is only useful if it can be used to build proteins. Like letters forming words and ideas, the sequence of DNA bases is read by the cell and used to assemble proteins. Note that the double-stranded DNA molecule in Figure 2.29 is arranged so that the strands spiral around each other - a double helix.

As the smallest units that retain the characteristics of living things, cells must be able to carry out metabolism and reproduction. Minimally, each cell has an interior (the cytoplasm), an exterior, and a membrane. The cell membrane is composed of phospholipids and proteins (See Figures 2.23 and 3.2 in your text.) Unlike many lipids, phospholipids are amphipathic molecules, that is they have both hydrophobic and hydrophilic portions. These molecules spontaneously form bilayer structures where the hydrophilic heads face either the cytoplasm or the exterior of the cell and the hydrophobic tails are inside the bilayer. Proteins in the cell membrane carry out transport, adhesion, structural, and signal transduction roles.

Section 3.3 in your text is a good introduction to the sizes of the various structures that you will be seeing under the light microscope in the lab. Keep in mind that the x-axis scale in figure 3.3 is logarithmic rather than linear.

Much like complex animals, eukaryotic cells segregate functions into compartments. These compartments, called organelles, are membrane-bounded structures, each of which carries out a specific function in the cell. The table on page 46 of your text is a good summary of the roles of several organelles. We will concentrate on the organelles that we are most likely to see when using the light microscope - the nucleus, mitochondrion, and the chloroplast. The Nucleus is bounded by two phospholipid bilayers, and houses the cell's DNA. We will discuss DNA at length later in the course, but for now, think of DNA as a cookbook containing recipes (genes) needed to carry out cellular metabolism and reproduction. Mitochondria and chloroplasts are organelles that that originated as cellular endosymbionts (See section 17.5). These organelles carry out energy transformations in eukaryotic cells, and unusually for subcellular organelles, each has its own complement of DNA.The cell's cytomembrane system serves to transport proteins and other molecules to the correct location in (or outside of; Figure 3.13) the cell. The cytoskeletal system provides structure to the cell and is involved whenever movement occurs.

Recall that energy, the ability to do work, is separate from matter - objects that have mass. Cells use energy to change matter from one form to another or move matter from place to place. If these processes stop, the cell dies. Depending of the type of cell, energy may be obtained from sunlight, or high-energy molecules present outside the cell. Whatever form the energy takes, it is important to remember that maintaining the condition called "alive" requires a constant supply of nutrients (matter) and the wherewithal to rearrange that matter into the desired form (energy).

Your text reminds you of the obvious fact that no pile of stones will ever rearrange itself onto the Egyptian pyramids. Quite the reverse, the pyramids are destined to continue to crumble until they are nothing but a pile of stones. This illustrates the fact that entropy (disorder; the state of the pile of stones) tends to increase and order tends to decrease in all systems. This is not to say that the input of energy could not temporarily reverse the increase in disorder. This reversal, though, must always be temporary and localized. (Humans might expend energy to maintain the pyramids, but as soon as they stop, the crumbling begins again.)

The principles of diffusion and osmosis are good examples of the interrelationship of energy and entropy. Diffusion is simply the tendency of dissolved molecules to spread out over the space available (to move down their concentration gradient). Osmosis refers to the same tendency on the part of water molecules. When the molecules are evenly distributed, energy must be expended to get them into any other state. A gradient is the condition that exists whenever anything (molecules in the case of diffusion) is distributed unevenly, and in the absence of energy input, gradients tend to decrease over time. Another way to say this is that it takes energy to create or maintain a gradient, and that energy can be harvested as the gradient decays. Living things must maintain concentration gradients of many molecules - one of the main energy-requiring parts of being alive. Since many of these gradients occur across cell membranes, it makes sense that the transport of dissolved molecules by proteins in the membranes of cells and organelles either requires energy (when it goes against the gradient) or does not require energy (when it goes with the gradient).

For the purposes of Biology 100, useful energy can take the form of ATP (everyone's favorite high-energy molecule; see section 4.7) reducing equivalents (like NADH; see section 6.3), other high-energy molecules like fats and sugars, or gradients of dissolved molecules. These four forms of biological energy have differing roles. ATP, for example is the most useful form of energy inside the cell, while fats and sugars are often used of the exchange of energy between cells. When cells use energy, in any of the four forms above, they are carrying out the process shown in figure 4.13 (b): making a process occur through energy input. Cells carry out thousands of such reactions, collectively termed metabolism. The steps of metabolism (use of energy in the conversion of matter from one form to another) are carried out by enzymes - the machines of biology. Enzymes are large protein molecules that accelerate one specific type of chemical reaction. Like most useful machines, they are not destroyed in the process.

A group of sequential metabolic steps, each carried out by a different enzyme, ending in a product useful to the cell is called a metabolic pathway. Most pathways have one or more enzymes whose activity is controlled by the presence or absence of the end-product of the pathway (see Figure 4.18). Another set of metabolic pathways is the subject of chapter six. This pathway converts high energy sugars to reducing equivalents, proton gradients, and ATP. We will cover this pathway at greater length later in the course. For now, you should think about how the concepts of metabolism (enzymes, substrates, intermediates, products, energy in all of its forms) apply to the pathways illustrated in Figures 6.2 and 6.7.