CK-12 Biology I - Honors

by CK-12 Foundation

  Figure 2.20

  This enzyme molecule binds reactant moleculescalled substrateat its active site, forming an enzyme-substrate complex. This brings the reactants together and positions them correctly so the reaction can occur. After the reaction, the products are released from the enzymes active site. This frees up the enzyme so it can catalyze additional reactions.

  The activities of enzymes also depend on the temperature, ionic conditions, and the pH of the surroundings.

  Some enzymes work best at acidic pHs, while others work best in neutral environments.

  Digestive enzymes secreted in the acidic environment (low pH) of the stomach help break down proteins into smaller molecules. The main digestive enzyme in the stomach is pepsin, which works best at a pH of about 1.5 (see the Digestive and Excretory Systems chapter). These enzymes would not work optimally at other pHs. Trypsin is another enzyme in the digestive system which break protein chains in the food into smaller parts. Trypsin works in the small intestine, which is not an acidic environment. Trypsin's optimum pH is about 8.

  Biochemical reactions are optimal at physiological temperatures. For example, most biochemical reactions work best at the normal body temperature of 98.6˚F. Many enzymes lose function at lower and higher temperatures. At higher temperatures, an enzyme’s shape deteriorates and only when the temperature comes back to normal does the enzyme regain its shape and normal activity.

  Importance of Enzymes

  Enzymes are involved in most of the chemical reactions that take place in organisms. About 4,000 such reactions are known to be catalyzed by enzymes, but the number may be even higher. Needed for reactions that regulate cells, enzymes allow movement, transport materials around the body, and move substances in and out of cells.

  In animals, another important function of enzymes is to help digest food. Digestive enzymes speed up reactions that break down large molecules of carbohydrates, proteins, and fats into smaller molecules the body can use (See Chapter: Digestive and Excretory Systems). Without digestive enzymes, animals would not be able to break down food molecules quickly enough to provide the energy and nutrients they need to survive.

  Lesson Summary

  A chemical reaction is a process that changes some chemical substances into others. It involves breaking and forming chemical bonds. Types of chemical reactions include synthesis reactions and decomposition reactions.

  Some chemical reactions are exothermic, which means they release energy. Other chemical reactions are endothermic, which means they consume energy. All chemical reactions require activation energy, which is the energy needed to get a reaction started.

  Rates of chemical reactions depend on factors such as the concentration of reactants and the temperature at which reactions occur. Both factors affect the ability of reactant molecules to react.

  Enzymes are needed to speed up chemical reactions in organisms. They work by lowering the activation energy of reactions.

  Review Questions

  Identify the roles of reactants and products in a chemical reaction.

  What is the general chemical equation for an endothermic reaction?

  State two factors, other than enzymes, that speed up chemical reactions.

  How do enzymes work to speed up chemical reactions?

  What is wrong with the chemical equation below? How could you fix it? CH4 + O2 → CO2 + 2 H2O

  What type of reaction is represented by the following chemical equation? Explain your answer. 2 Na + 2 HCL → 2 NaCl + H2

  Why do all chemical reactions require activation energy?

  Explain why organisms need enzymes to survive.

  Further Reading / Supplemental Links

  Peter Atkins and Julio De Paula, Physical Chemistry for the Life Sciences. Oxford University Press, 2006.

  Rita Elkins, Digestive Enzymes. Woodland Publishing, 2007.

  James Keeler and Peter Wothers, Why Chemical Reactions Happen. Oxford University Press, 2003.

  George W. Roberts, Chemical Reactions and Chemical Reactors. Wiley, 2008.

  http://en.wikipedia.org

  Summary Animations

  http://www.stolaf.edu/people/giannini/flashanimat

  Vocabulary

  activation energy

  Energy needed for a chemical reaction to get started.

  anabolic reaction

  Endothermic reaction that occurs in organisms.

  catabolic reaction

  Exothermic reaction that occurs in organisms.

  chemical reaction

  Process that changes some chemical substances into other chemical substances.

  combustion reaction

  Type of chemical reaction in which a compound or element burns in oxygen.

  decomposition reaction

  Type of chemical reaction in which a compound is broken down into smaller compounds or elements.

  endothermic reaction

  Any chemical reaction that consumes energy.

  enzyme

  Chemical that speeds up chemical reactions in organisms.

  exothermic reaction

  Any chemical reaction that releases energy.

  product

  Substance that forms as a result of a chemical reaction.

  reactant

  Substance involved in a chemical reaction that is present at the beginning of the reaction.

  substitution reaction

  Type of chemical reaction in which one element replaces another element in a compound.

  synthesis reaction

  Type of chemical reaction in which elements or compounds unite to form a more complex product.

  Points to Consider

  Most chemical reactions in organisms take place in an environment that is mostly water.

  What do you know about water?

  Are you aware that water has unique properties?

  Do you know how water behaves differently from most other substances on Earth?

  Do you know why water is necessary for life?

  Water

  Lesson Objectives

  Describe the distribution of Earth’s water, and outline the water cycle.

  Identify the chemical structure of water, and explain how it relates to water’s unique properties.

  Define solution, and describe water’s role as a solvent.

  State how water is used to define acids and bases, and identify the pH ranges of acids and bases.

  Explain why water is essential for life processes.

  Introduction

  Water, like carbon, has a special role in biology because of its importance to organisms. Water is essential to all known forms of life. Water, H2O, such a simple molecule, yet it is this simplicity that gives water its unique properties and explains why water is so vital for life.

  Water, Water Everywhere

  Water is a common chemical substance on Earth. The term water generally refers to its liquid state. Water is a liquid over a wide range of standard temperatures and pressures. However, water can also occur as a solid (ice) or gas (water vapor).

  Where Is All the Water?

  Of all the water on Earth, about two percent is stored underground in spaces between rocks. A fraction of a percent exists in the air as water vapor, clouds, or precipitation. Another fraction of a percent occurs in the bodies of plants and animals. So where is most of Earth’s water? It’s on the surface of the planet. In fact, water covers about 70 percent of Earth’s surface. Of water on Earth’s surface, 97 percent is salt water, mainly in the ocean. Only 3 percent is freshwater. Most of the freshwater is frozen in glaciers and polar ice caps. The remaining freshwater occurs in rivers, lakes, and other freshwater features.

  Although clean freshwater is essential to human life, in many parts of the world it is in short supply. The amount of freshwater is not the issue. There is plenty of freshwater to go around, because water constantly recycles on Earth. However, freshwater is not necessarily located where it is needed, and clean freshwater is not always available.
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br />   How Water Recycles

  Like other matter on Earth, water is continuously recycled. Individual water molecules are always going through the water cycle (see the Principles of Ecology chapter). In fact, water molecules on Earth have been moving through the water cycle for billions of years. In this cycle, water evaporates from Earth’s surface (or escapes from the surface in other ways), forms clouds, and falls back to the surface as precipitation. This cycle keeps repeating. Several processes change water from one state to another during the water cycle. They include:

  Evaporation—Liquid water on Earth’s surface changes into water vapor in the atmosphere.

  Sublimation—Snow or ice on Earth’s surface changes directly into water vapor in the atmosphere.

  Transpiration—Plants give off liquid water, most of which evaporates into the atmosphere.

  Condensation—Water vapor in the atmosphere changes to liquid water droplets, forming clouds or fog.

  Precipitation—Water droplets in clouds are pulled to Earth’s surface by gravity, forming rain, snow, or other type of falling moisture.

  Chemical Structure and Properties of Water

  You are probably already familiar with many of water’s properties. For example, you no doubt know that water is tasteless, odorless, and transparent. In small quantities, it is also colorless. However, when a large amount of water is observed, as in a lake or the ocean, it is actually light blue in color. These and other properties of water depend on its chemical structure.

  The transparency of water is important for organisms that live in water. Because water is transparent, sunlight can pass through it. Sunlight is needed by water plants and other water organisms for photosynthesis (see Biomes, Ecosystems, and Communities chapter).

  Chemical Structure of Water

  Each molecule of water consists of one atom of oxygen and two atoms of hydrogen, so it has the chemical formula H2O. The arrangement of atoms in a water molecule, shown in Figure below, explains many of water’s chemical properties. In each water molecule, the nucleus of the oxygen atom (with 8 positively charged protons) attracts electrons much more strongly than do the hydrogen nuclei (with only one positively charged proton). This results in a negative electrical charge near the oxygen atom (due to the "pull" of the negatively charged electrons toward the oxygen nucleus) and a positive electrical charge near the hydrogen atoms. A difference in electrical charge between different parts of a molecule is called polarity. A polar molecule is a molecule in which part of the molecule is positively charged and part of the molecule is negatively charged.

  Figure 2.21

  This model shows the arrangement of oxygen and hydrogen atoms in a water molecule. The nucleus of the oxygen atom attracts electrons more strongly than do the hydrogen nuclei. As a result, the middle part of the molecule near oxygen has a negative charge, and the other parts of the molecule have a positive charge. In essence, the electrons are "pulled" toward the nucleus of the oxygen atom and away from the hydrogen atom nuclei. Water is a polar molecule, with an unequal distribution of charge throughout the molecule.

  Opposite electrical charges attract one another other. Therefore, the positive part of one water molecule is attracted to the negative parts of other water molecules. Because of this attraction, bonds form between hydrogen and oxygen atoms of adjacent water molecules, as demonstrated in Figure below. This type of bond always involves a hydrogen atom, so it is called a hydrogen bond. Hydrogen bonds are bonds between molecules, and they are not as strong as bonds within molecules. Nonetheless, they help hold water molecules together.

  Figure 2.22

  Hydrogen bonds form between positively and negatively charged parts of water molecules. The bonds hold the water molecules together.

  Hydrogen bonds can also form within a single large organic molecule (see the Organic Compounds lesson). For example, hydrogen bonds that form between different parts of a protein molecule bend the molecule into a distinctive shape, which is important for the protein’s functions. Hydrogen bonds also hold together the two nucleotide chains of a DNA molecule.

  Sticky, Wet Water

  Water has some unusual properties due to its hydrogen bonds. One property is the tendency for water molecules to stick together. For example, if you drop a tiny amount of water onto a very smooth surface, the water molecules will stick together and form a droplet, rather than spread out over the surface. The same thing happens when water slowly drips from a leaky faucet. The water doesn’t fall from the faucet as individual water molecules but as droplets of water. The tendency of water to stick together in droplets is also illustrated by the dew drops in Figure below.

  Figure 2.23

  Droplets of dew cling to a spider web, demonstrating the tendency of water molecules to stick together because of hydrogen bonds.

  Hydrogen bonds also explain why water’s boiling point (100° C) is higher than the boiling points of similar substances without hydrogen bonds. Because of water’s relatively high boiling point, most water exists in a liquid state on Earth. Liquid water is needed by all living organisms. Therefore, the availability of liquid water enables life to survive over much of the planet.

  Density of Ice and Water

  The melting point of water is 0° C. Below this temperature, water is a solid (ice). Unlike most chemical substances, water in a solid state has a lower density than water in a liquid state. This is because water expands when it freezes. Again, hydrogen bonding is the reason. Hydrogen bonds cause water molecules to line up less efficiently in ice than in liquid water. As a result, water molecules are spaced farther apart in ice, giving ice a lower density than liquid water. A substance with lower density floats on a substance with higher density. This explains why ice floats on liquid water, whereas many other solids sink to the bottom of liquid water.

  In a large body of water, such as a lake or the ocean, the water with the greatest density always sinks to the bottom. Water is most dense at about 4° C. As a result, the water at the bottom of a lake or the ocean usually has temperature of about 4° C. In climates with cold winters, this layer of 4° C water insulates the bottom of a lake from freezing temperatures. Lake organisms such as fish can survive the winter by staying in this cold, but unfrozen, water at the bottom of the lake.

  Solutions

  Water is one of the most common ingredients in solutions. A solution is a homogeneous mixture composed of two or more substances. In a solution, one substance is dissolved in another substance, forming a mixture that has the same proportion of substances throughout. The dissolved substance in a solution is called the solute. The substance in which is it dissolved is called the solvent. An example of a solution in which water is the solvent is salt water. In this solution, a solid—sodium chloride—is the solute. In addition to a solid dissolved in a liquid, solutions can also form with solutes and solvents in other states of matter. Examples are given in Table 1.

  Solutions commonly form when a solid solute dissolves in a liquid solvent. However, solutions can form with solutes and solvents in any of the three major states of matter. Solvent Gas Liquid Solid

  Gas Oxygen and other gases in nitrogen (air)

  Liquid Carbon dioxide in water (carbonated water) Ethanol (an alcohol) in water Sodium chloride in water (salt water)

  Solid Hydrogen in metals Mercury in silver and other metals (dental fillings) Iron in carbon (steel)

  (Source: http://en.wikipedia.org/wiki/Solute, License: Creative Commons)

  The ability of a solute to dissolve in a particular solvent is called solubility. Many chemical substances are soluble in water. In fact, so many substances are soluble in water that water is called the universal solvent. Water is a strongly polar solvent, and polar solvents are better at dissolving polar solutes. Many organic compounds and other important biochemicals are polar, so they dissolve well in water. On the other hand, strongly polar solvents like water cannot dissolve strongly nonpolar solutes like oil. Did you ever try to mix oil and water? Even after being well sha
ken, the two substances quickly separate into distinct layers.

  Acids and Bases

  Water is the solvent in solutions called acids and bases. To understand acids and bases, it is important to know more about pure water, in which nothing is dissolved. In pure water (such as distilled water), a tiny fraction of water molecules naturally breaks down, or dissociates, to form ions. An ion is an electrically charged atom or molecule. The dissociation of pure water into ions is represented by the chemical equation:

  2 H2O → H3O+ + OH-.

  The products of this reaction are a hydronium ion (H3O+) and a hydroxide ion (OH-). The hydroxide ion is negatively charged. It forms when a water molecule donates, or gives up, a positively charged hydrogen ion. The hydronium ion, modeled in Figure below, is positively charged. It forms when a water molecule accepts a positively charged hydrogen ion (H+).

  Figure 2.24

  A hydronium ion has the chemical formula HO. The plus sign () indicates that the ion is positively charged. How does this molecule differ from the water molecule in ?