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AP Biology, Second Edition comes complete with a targeted review of biology, two full-length practice tests, plus Kaplan's renowned test-taking strategies. You'll get what you need to help you score higher on this challenging exam.
* In-depth review of all the material on the exam from the test prep experts
* Exclusive strategies to help you manage your time more effectively and successfully answer every question type
* Intensive practice for the exam with hundreds of practice questions and detailed explanations for every answer
* A special glossary of biology terms to help you understand the key biological concepts that you'll see on the exam
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Chapter One: The Chemistry of Life
Living organisms display amazing diversity, ranging from the simplest bacteria to blue whales, but all living organisms share basic unifying principles starting with the chemistry of life. For example, water is essential to all forms of life, no matter how simple or complex. A second principle is that all living organisms, and the molecules and reactions they are composed of, must obey the same physical laws of chemistry and energy that rule the rest of the universe.
All life shares common biological molecules including carbohydrates, lipids, proteins, and nucleic acids. Organisms from fungi to man even share many reactions and metabolic pathways. These basic features of all life will play a role in the more complex life activities of cells, organs, organisms, and ecosystems presented later.
At a molecular level the human cell shares a great deal in common with the single-cell yeasts that make bread, a fact that may not be immediately evident to the baker. Simple organisms like yeasts, worms, and fruit flies have proven invaluable to biologists in discerning the complexities of human biology since there are so many features that they share despite their differences. These common traits contribute to the interdependence of all living organisms on earth, another important trait common to all life, including man.
1.1 The Properties of Water
Water is essential to all life on Earth. Water covers a majority of the surface of the earth and is the site of some of the key ecosystems of the earth. Each cell contains water that bathes the reactions of life and is indispensable to all life. The presence of liquid water on Earth is one of the features of the planet that probably allowed life to originate and persist. It is the physical properties of water that allow it to play this key role for life. The properties of water that make it ideally suited to play this unique role are:
1. Water molecules are polar.
2. Water expands when it freezes.
3. Water absorbs a great deal of heat when it evaporates.
4. Water absorbs a large amount of heat when it is heated.
5. Water is cohesive and has a high surface tension.
6. Water is an excellent solvent for a large variety of molecules.
7. Water dissociates to form protons and hydroxyls in solution.
Water molecules are polar.
Water molecules have one atom of oxygen with two atoms of hydrogen at an angle from each other. Each water molecule as a whole lacks a net charge, but within each molecule the oxygen atom pulls electrons toward itself more than the hydrogens, causing the oxygen to have a partial negative charge and the hydrogens to have a partial positive charge (see figure). This unequal distribution of charges is what makes water a polar substance.
The polarity of water allows water molecules to readily form hydrogen bonds with each other. A hydrogen bond is formed when a hydrogen atom with a partial positive charge interacts with a negatively charged atom such as oxygen in another molecule. The polarity of a water molecule allows it to form hydrogen bonds with other polar molecules as well, such as sugars or proteins, allowing water to dissolve these substances. The polar nature of water molecules is involved in most of the exceptional properties of water.
Water expands when it freezes.
One of the consequences of the polarity of water is that water molecules interact with each other in a network of hydrogen bonds. In liquid water, these bonds form and break very rapidly as the individual water molecules move. When water freezes, the individual water molecules stop moving and the hydrogen bonds between molecules are frozen in place in a rigid crystalline structure. The positions of the water molecules are further apart in frozen water than in liquid water, leading to one of the unusual properties of water. In most substances, the solid occupies less space than the liquid as molecules fall into the crystalline lattice. Since solid water occupies more space than liquid water, water expands as it freezes and ice is less dense than liquid water. This property of water affects life on earth. When the temperature of the environment falls below the freezing point for water, a lake or ocean will freeze on the surface, with ice floating on top of the denser liquid water beneath. The ice on top insulates the water beneath it, and slows further freezing, allowing life to continue beneath the surface ice. If, like most substances, water became denser as it froze, then a lake or ocean would freeze from the bottom up and would freeze solid, fish, plankton and all. Freezing of lakes and oceans would be far more extensive and destructive to life in this scenario and it is possible that if ice were denser than liquid water, a past period of glaciation would have frozen the oceans solid, perhaps forever.
Water absorbs a great deal of heat when it evaporates.
Water molecules in liquid water interact with each other through a large number of hydrogen bonds. When water molecules are converted into a gas in the process called evaporation, the water molecules are separated from each other in space and no longer have these hydrogen bonds. When water is heated on a stove, the molecules have more kinetic energy and are able to break the hydrogen bonds more readily. Breaking the hydrogen bonds to cause evaporation takes a large amount of energy called the molar heat of evaporation.
The heat of evaporation is used by terrestrial organisms as a cooling mechanism. Since heat energy is required for evaporation, evaporating water will absorb heat (see figure). Water on the skin when it evaporates on a hot day will draw heat from the skin. The sweating or panting of mammals on a hot day uses the absorption of heat by evaporating water to draw heat out of the body and make it possible to maintain a cooler interior temperature than the external environment. In the absence of this, the body temperature would equilibrate with the exterior temperature on a hot day, causing harm or even death.
Water absorbs a large amount of heat when it is heated.
The temperature of a liquid is a measure of the kinetic energy of its molecules. The quicker molecules move, the greater the temperature. When heat energy is added to water, a great deal of the heat goes to breaking hydrogen bonds between molecules and not directly to making the molecules move faster. As a result, water can absorb a large amount of heat energy while its temperature changes little. If this were not the case, it would be much more difficult for the body to maintain a constant internal temperature. It also means that the temperature of aquatic environments does not fluctuate dramatically or rapidly. Fish do not need to adapt to sudden temperature changes the same way that a terrestrial mammal does. In fact, the oceans of the earth have a strong moderating influence on the climate of the planet, absorbing and redistributing heat around the globe and moderating the larger changes in temperature found on land. The role of the oceans in absorbing heat is likely to play an important role in the effects of global warming on the world's weather.
Water is cohesive and has a high surface tension.
In solution, water molecules have many hydrogen bonds with each other, and therefore stick readily to each other. The hydrogen bonds make water molecules near the surface stick to each other, pulling inward causing a force called surface tension. Surface tension causes water to pull together into round droplets on wax paper rather than spreading out flat and allows insects like water striders to float on the surface of water instead of sinking. Surface tension plays a role at any interface between air and liquid, such as in the lungs. Detergents tend to break up surface tension. Detergents play an essential role in the human lungs where they are secreted, and a harmful role in the environment when dumped as pollutants in the environment. The cohesiveness between water molecules is also what draws water up from roots into trees in an unbroken column.
Water is an excellent solvent for a large variety of molecules.
The polar nature of water makes it an excellent solvent for a wide variety of polar and charged substances, including salts, sugars, amino acids, and other molecules essential to life. Water hydrogen bonds with these substances in the same manner it does to itself, drawing these substances into the water, surrounded by a shell of interacting water molecules. Polar substances that water interacts with are called hydrophilic (water loving). The ability of water to dissolve substances is essential to life.
Water does not dissolve nonpolar molecules well. Hydrocarbons such as benzene or long-chain alkyl groups do not have any polar groups that water can hydrogen bond with and so are repelled from water and will not mix with it. These molecules are called hydrophobic (water hating). The repulsion of hydrophobic groups from water causes hydrophobic groups to draw together to present the smallest possible surface to water. An example of this occurs when oil is stirred with water in salad dressing -- the hydrophobic oil separates, unable to dissolve or mix with the water. This repulsion is what causes membranes to form spontaneously from lipids mixed with water, allowing one region of the cell to be separated from another by the lipid bilayer membrane. Hydrophobic interactions also cause proteins to fold with hydrophobic regions on the inside of the protein, hidden from water.
Water dissociates to form protons and hydroxyls in solution.
The aqueous portion of a cell contains a large variety of solutes, including salt ions, sugars and macromolecules such as nucleic acids. Some of the most important solutes in water are acids and bases. At a small but predictable frequency, water molecules in solution will break down into a hydrogen ion (H+) and a hydroxide (OH-). The hydrogen ion is not really a free proton in solution, as it is often referred to, but complexes with another water molecule to make a hydronium ion: H3O+. For the sake of simplicity though it will be referred to as the H+ ion. The concentration of H+ ions is the acidity of a solution and is given by a term called pH, the negative log of the concentration of H+ ions.
pH = -log[H+]
A concentration of 107M H+ ions translates into a pH of 7, for example. At a pH of 7, the concentration of H+ ions is equal to the concentration of hydroxide ions and the pH is said to be neutral, neither acidic or basic. Pure water has a pH of seven, with equal concentrations of H+ ions and hydroxide ions. The inside of the body and the cytoplasm of the cell have a pH of 7.4, close to neutral pH. At acidic pHs, in which the pH is lower than 7, the concentration of H+ ions is greater than 107M, and the concentration of hydroxide ions is lower.
If a substance donates H+ ions in water, it is called an acid, and if it accepts H+ ions in water, it is called a base. A base will decrease the H+ ion concentration in water, increase the hydroxide ion concentration and increase the pH. Depending on how strongly a molecule donates or accepts H+ ions, it will be called a weak acid or a strong acid. HCl ions completely dissociate in water for example, making HCl a strong acid. If one mole of HCl is placed in water, at equilibrium virtually all of it will dissociate to create one mole of H+ ions, as well as one mole of Cl- ions. A weak acid has more affinity for the H+ ions and dissociates more weakly in water, leaving less than a mole of H+ ions for every mole of acid added to water.
A measure of how strong an acid binds protons (H+ ions) is the pKa of an acid. The pKa is the negative log of the equilibrium constant for the dissociation of an acid. For example, for acetic acid, the dissociation of the acid is given by the equation:
HA <-> H+ + A-
For this equation, the equilibrium constant is Ka, where
Ka = [H+][A-]/[HA]
The smaller the value of pKa, the stronger the acid.
Some materials called buffers have properties that allow them to act as either an acid or a base, minimizing changes in pH. Biological molecules and reactions can be quite sensitive to changes in pH, making buffers important for life. A change in the pH of blood from 7.4 to 7 can be enough of a change to cause a coma in humans. In the absence of a buffer, the addition of a very small amount of acid, 1 X 10-6 micrometer acid, will cause a large change in pH, a whole pH unit, while with sufficient buffer present, the hydrogen ions will be neutralized and the change in pH will be negligible.
A common laboratory procedure is to add acid (or base) to a solution, note the volume of acid added, and measure the change in pH that occurs. The resulting plot from this experiment is termed a titration curve (see figure). When a buffer is present in the solution being titrated, the pH changes very rapidly until the pH nears the pKa of the buffering material. For example, in the figure shown, a base is added to the solution, so that the pH is basic. As acid is added to the base, the pH changes rapidly at first, with most + hydrogen ions remaining in solution. When the concentration of hydrogen ions in solution nears the pKa for the buffer, the hydrogen ions start to bind to the buffer, driving it into the acid form. As the buffer binds the hydrogen ions, the pH changes little. When the buffer is fully protonated, additional acid causes a large change in pH. When the pH equals the pKa for the buffer, half of the buffer is protonated and the other half is not.
There are many different buffers in the body, but the most important buffer in blood in humans is carbonic acid. Carbon dioxide dissolved in water can react with water to form carbonic acid. Carbonic acid can dissociate to release H+ ions and form bicarbonate ions in a reversible reaction. If hydrogen ions are added to blood, some of them will combine with the bicarbonate ion to reform carbonic acid. The body actively controls the pH of the blood to ensure the maintenance of the pH in the range fit for life. One means to control pH is by changing the rate of breathing to alter the rate of carbon dioxide removal from the body.
1.2 Organic Molecules of Life
All living organisms use the same basic molecules to form the structures and perform the activities of life. The primary types of biological molecules are carbohydrates, lipids, proteins, and nucleic acids. All of these molecules are organic, meaning that they are based on carbon skeletons.
Carbon is extremely flexible in its chemistry, with four valence electrons that can form covalent bonds with many other molecules. The simplest organic molecules are hydrocarbons, containing chains or rings of carbons with hydrogens attached. Carbon molecules are reactive enough to be useful, since inert molecules are of little use to perform reactions that will support life, but carbon-based biochemistries are also stable enough that biological molecules do not rapidly degrade. Methane, ethane and butane are examples of hydrocarbons with 1, 2 or 3 carbon a...
Title: Kaplan AP Biology, Second Edition
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