Chapter 2: Chemical Basis of Life PDF

**Chapter 2: Chemical Basis of Life** **2.1** Everything, including you, is made of matter, which occupies space and has mass. Matter exists in three states: solid, liquid, and gas. All types of matter, like water, rocks, air, and biology students, are made of chemical elements. An element is a s...

**Chapter 2: Chemical Basis of Life** **2.1** Everything, including you, is made of matter, which occupies space and has mass. Matter exists in three states: solid, liquid, and gas. All types of matter, like water, rocks, air, and biology students, are made of chemical elements. An element is a substance that cannot be broken down by ordinary chemical means. There are 92 naturally occurring elements, such as gold, copper, carbon, and oxygen. Chemists have also created synthetic elements. Each element has a symbol derived from its English, Latin, or German name, like \"O\" for oxygen and \"Na\" for sodium (from the Latin word \"natrium\"). A compound is a substance made of two or more different elements combined in a fixed ratio. For example, table salt (NaCl) is made of sodium (Na) and chlorine (Cl). Pure sodium is a metal, and pure chlorine is a poisonous gas, but together they form an edible compound. Similarly, hydrogen (H) and oxygen (O) combine in a 2:1 ratio to form water (H₂O). Water and table salt are examples of organized matter having emergent properties: A compound has characteristics different from those of its elements. Most compounds in living organisms contain at least three or four elements. For example, sugar is made of carbon, hydrogen, and oxygen. Proteins, which make up about 20% of your body, contain carbon, hydrogen, oxygen, nitrogen, and a small amount of sulfur. Humans need 25 essential elements for life, while plants require 17. Six elements---oxygen, carbon, hydrogen, nitrogen, calcium, and phosphorus---make up about 99% of the human body. The first four are key components of proteins, carbohydrates, and lipids, while calcium and phosphorus are major components of bones and teeth. The remaining 1% includes elements like potassium, sulfur, sodium, chlorine, and magnesium, which are involved in functions such as nerve signaling and chemical reactions. Trace elements make up less than 0.01% of human body weight and include elements like boron, chromium, cobalt, copper, fluorine, iodine, iron, manganese, molybdenum, selenium, silicon, tin, vanadium, and zinc. Iron, which is only about 0.004% of body weight, is crucial for energy processing and oxygen transport in the blood. While iron is needed by all life forms, some trace elements, like iodine, are essential only for certain species, such as vertebrates. **Terms to know** **Matter**-defined as anything that occupies space and has mass. Matter is found on Earth in three physical states: solid, liquid, and gas. **Chemical**-a substance with a distinct molecular composition that is produced by or used in a chemical process. Chemicals can be elements, compounds, or mixtures, and they are involved in various reactions and processes in both natural and industrial settings. **element**-a substance that cannot be broken down to other substances by ordinary chemical means. **Compound**-a substance consisting of two or more different elements combined in a fixed ratio. **2.3 Atoms consist of protons, neutrons, and electrons** Each element has its own unique type of atom, which is different from the atoms of other elements. An atom is the smallest unit of matter that retains the properties of an element. Atoms are incredibly small, with about a million of them fitting across the period at the end of a sentence. Physicists have identified over a hundred types of subatomic particles, but only three are relevant here: protons (positive charge), electrons (negative charge), and neutrons (no charge). Figure 2.3 shows two simple models of a helium atom. The nucleus contains two protons and two neutrons, while two electrons form a cloud of negative charge around it. The left model shows electrons on a circle around the nucleus, and the right model shows a spherical cloud. Neither model is to scale; in reality, electrons are much smaller than protons and neutrons, and the electron cloud is much larger than the nucleus. If the atom were the size of a baseball stadium, the nucleus would be the size of a pea, and the electrons would be like tiny gnats buzzing around. Atoms of different elements are distinguished by their unique number of protons, known as the atomic number. For example, a helium atom with 2 protons has an atomic number of 2. Typically, an atom has an equal number of protons and electrons, resulting in a net electrical charge of zero. An atom\'s mass number is the sum of its protons and neutrons. For helium, this number is 4. Protons and neutrons have nearly identical masses, close to 1 dalton each. Electrons are much lighter, contributing very little to an atom\'s mass. Therefore, an atom\'s atomic mass is approximately equal to its mass number in daltons. All atoms of an element have the same atomic number but may differ in mass number due to different numbers of neutrons. These variations are called isotopes. For example, carbon has three isotopes: carbon-12 (6 neutrons), carbon-13 (7 neutrons), and carbon-14 (8 neutrons). Carbon-12 makes up about 99% of naturally occurring carbon, while carbon-13 and carbon-14 are less common. All isotopes of carbon have 6 protons. Carbon-12 and carbon-13 are stable isotopes with nuclei that remain intact indefinitely. In contrast, carbon-14 is an unstable, radioactive isotope that decays spontaneously, emitting particles and energy. This radiation can damage cellular molecules and pose risks to living organisms. However, radioactive isotopes are useful in dating fossils and are also employed in biological research and medicine. **Terms to know** **Atom**-named from a Greek word meaning \"indivisible,\" is the smallest unit of matter that still retains the properties of an element. **Nucleus**-protons (+) and neutrons are tightly packed in the atom\'s central core **proton**-a subatomic particle with a single positive electrical charge (+). **Electron**-An electron is a subatomic particle with a single negative charge (-). **Neutron**-is electrically neutral (has no charge). **2.5 The distribution of electrons determines an atom\'s chemical properties** To understand how atoms interact, we need to explore atomic structure further. Of the three subatomic particles---protons, neutrons, and electrons---only electrons are directly involved in the chemical activity of an atom. In a helium atom, the 2 electrons are shown on a circle around the nucleus. For atoms with more than 2 electrons, like carbon, 2 electrons are on an inner circle, and the remaining 4 are on a larger outside circle. Electrons can be in different electron shells, each with a characteristic distance from the nucleus. Depending on the atomic number, an atom may have one, two, or more electron shells. Figure 2.58 is an abbreviated periodic table showing the distribution of electrons for the first 18 elements. These elements are arranged in rows based on the number of electron shells (one, two, or three). Within each shell, electrons occupy different orbitals, which are volumes of space where electrons are most likely found. Each orbital can hold up to 2 electrons. The first shell has one orbital (holding 2 electrons), so hydrogen and helium are the only elements in the first row. The second and third shells have four orbitals, holding up to 8 electrons (four pairs). The number of electrons in the outermost shell, called the valence shell, primarily determines an atom\'s chemical properties. Atoms with incomplete outer shells tend to interact with other atoms to fill their valence shells. Hydrogen, carbon, nitrogen, and oxygen have incomplete outer shells, making them reactive with other atoms. In contrast, elements like helium, neon, and argon have full outer shells and do not readily interact with other atoms, making them inert. When two atoms with incomplete outer shells interact, they may give up, accept, or share electrons to complete their outer shells. This interaction usually results in the atoms staying close together, held by attractions known as chemical bonds. The transfer of an electron between atoms creates an attraction called an ionic bond. For example, the sodium and chlorine atoms in salt (NaCl) are held together by ionic bonds. In a covalent bond, atoms share electrons instead of transferring them. Sharing electrons allows atoms to complete their outer shells. The number of covalent bonds an atom can form depends on the number of electrons needed to fill its valence shell, known as the atom\'s valence or bonding capacity. **2.6** Covalent bonds join atoms into molecules through electron sharing A molecule consists of two or more atoms held together by covalent bonds. In a hydrogen molecule, two hydrogen atoms share a pair of electrons. However, the sharing of electrons in covalent bonds is not always equal. An atom\'s electronegativity measures its attraction for shared electrons. In a covalent bond between two atoms of the same element, electrons are shared equally due to identical electronegativity, forming nonpolar covalent bonds. Atoms with similar electronegativity, like carbon and hydrogen, also share electrons fairly equally. When two atoms differ in electronegativity, they form a polar covalent bond. The more electronegative atom attracts the shared electrons more closely, resulting in a partial negative charge, while the other atom becomes partially positive. Oxygen, being highly electronegative, is often involved in polar covalent bonds. Fluorine and nitrogen are also highly electronegative in biological terms. A diagram of a molecule Description automatically generated **Terms to know** **Bonds**-refers to the force that holds atoms together in a molecule or compound **ionic bond**-Formed when one atom transfers electrons to another atom, resulting in the attraction between positively and negatively charged ions. **covalent bond**-Formed when atoms share pairs of electrons to achieve a full outer shell. **molecule**- consists of two or more atoms held together by covalent bonds **2.7** Ionic bonds are attractions between ions of opposite charge When two atoms have significantly different attractions for electrons, the more electronegative atom can strip an electron completely from its partner. This transfer of electrons creates an ionic bond, as seen in table salt (NaCl). Sodium, with 1 electron in its outer shell, transfers this electron to chlorine, which has 7 electrons in its outer shell. This transfer results in both atoms achieving full outer shells, forming sodium ions (Na⁺) and chloride ions (Cl⁻). The transfer of an electron between sodium (Na) and chlorine (Cl) results in an ionic bond. In table salt (NaCl), sodium (Na) has 11 protons and 11 electrons, with only 1 electron in its outer shell. Chlorine (Cl) has 17 protons and 17 electrons, with 7 electrons in its outer shell. When these atoms interact, sodium transfers its outer electron to chlorine. As a result, sodium becomes a positively charged ion (Na⁺) with 11 protons and 10 electrons, and chlorine becomes a negatively charged ion (Cl⁻) with 17 protons and 18 electrons (Note that the names of negatively charged ions often end in -ide, such as chloride). This transfer of electrons results in both atoms achieving full outer shells. The attraction between the positively charged sodium ion and the negatively charged chloride ion forms an ionic bond, creating the compound NaCl, which is electrically neutral. Sodium chloride, commonly known as salt, is an ionic compound. Salts often form crystals in nature. In a sodium chloride crystal, sodium (Na⁺) and chloride (Cl⁻) ions are always present in a 1:1 ratio, although the crystal can be of any size. The ratio of ions can vary in different types of salts. The environment affects the strength of ionic bonds. In a dry salt crystal, the bonds are very strong and require significant force to break. However, when the salt crystal is placed in water, the ionic bonds break as the ions interact with water molecules, causing the salt to dissolve. Most drugs are manufactured as salts because they are stable when dry but can dissolve easily in water. **2.8** **Hydrogen bonds are weak bonds important in the chemistry of life** In living organisms, most strong chemical bonds are covalent, linking atoms to form a cell\'s molecules. However, weaker bonds, such as ionic bonds, are crucial for cell function. One of the most important types of weak bonds is the hydrogen bond, best illustrated with water molecules. The hydrogen atoms in a water molecule are attached to oxygen by polar covalent bonds, making water a polar molecule with an unequal distribution of charges. The oxygen end is slightly negative, while the hydrogen ends are slightly positive. This partial positive charge allows each hydrogen to be attracted to nearby atoms with a partial negative charge, such as oxygen or nitrogen. Hydrogen bonds occur when one atom in the attraction is always a hydrogen atom. In water molecules, each hydrogen atom can form a hydrogen bond with a nearby partially negative oxygen atom of another water molecule. The negative oxygen pole of a water molecule can form hydrogen bonds with two hydrogen atoms, allowing each water molecule to bond with up to four partners. Hydrogen bonds play a crucial role in creating a protein\'s shape and function. They hold the two strands of a DNA molecule together and are essential for translating hereditary information into proteins. Later, we will explore how water\'s polarity and hydrogen bonds give it unique, life-supporting properties. **Terms to know** **Hydrogen Bond**-a weak bond that occurs when a hydrogen atom, which is covalently bonded to a more electronegative atom (like oxygen or nitrogen), is attracted to another electronegative atom in a different molecule or a different part of the same molecule. This type of bond is crucial in many biological processes, such as the structure of DNA and the properties of water. **polar molecule**-A polar molecule is a molecule that has an uneven distribution of charges, resulting in regions with partial positive and partial negative charges. This occurs because the atoms in the molecule have different electronegativities, causing the shared electrons to be pulled more towards one atom than the other. A common example of a polar molecule is water (H₂O), where the oxygen atom is more electronegative than the hydrogen atoms, creating a partial negative charge at the oxygen end and partial positive charges at the hydrogen ends. **2.9 Chemical reactions make and break chemical bonds** Your cells are continuously involved in chemical reactions, where molecules are rearranged by breaking existing chemical bonds and forming new ones. A simple example of such a reaction is the combination of hydrogen gas and oxygen gas to form water. This reaction is explosive, but fortunately, it does not occur within your cells. The chemical equation for this reaction is: 2 H~2~ + O~2~ --\> 2 H~2~O In this example, two molecules of hydrogen (2H₂) react with one molecule of oxygen (O₂) to produce two molecules of water (2H₂O). The arrow in the equation indicates the conversion of the starting materials, called reactants, to the product, which is the material resulting from the chemical reaction. The same number of hydrogen and oxygen atoms appear on both sides of the arrow, although they are grouped differently. Chemical reactions do not create or destroy matter; they only rearrange it in various ways. The covalent bonds holding hydrogen atoms together in H₂ and oxygen atoms together in O₂ are broken, and new bonds are formed to yield the H₂O product molecules. Organisms can\'t create water from hydrogen (H₂) and oxygen (O₂), but they perform numerous chemical reactions that significantly rearrange matter. One crucial reaction for life on Earth is photosynthesis. In this process, plants take in carbon dioxide (CO₂) from the air and water (H₂O) from the soil. Sunlight powers the conversion of these reactants into glucose (C₆H₁₂O₆) and oxygen (O₂), which is released into the air. The chemical equation for photosynthesis is: 6 CO~2~ + 6 H~2~O -\> C~6~H~12~O~6~ + 6 O~2~ Photosynthesis involves a series of chemical reactions, but the number and types of atoms remain unchanged. This process demonstrates the theme of energy and matter, as matter is rearranged with the input of energy from sunlight. Similarly, your body performs thousands of chemical reactions in the watery environment of your cells. **Terms to know** **Product**-the material resulting from the chemical reaction. They are on the right side of the equation. **Reactants**-the starting materials for a chemical reaction. They are on the left side of the equation. **2.10 Hydrogen bonds make liquid water cohesive** Water\'s life-supporting properties stem from the structure and interactions of its molecules. The polarity of water molecules and the resulting hydrogen bonding between them are key factors. Hydrogen bonds between water molecules last only a few trillionths of a second, but many molecules are hydrogen-bonded at any given moment. This tendency of molecules to stick together, called cohesion, is much stronger for water than for most other liquids. Cohesion is crucial in the living world, such as in trees, where it helps transport water and nutrients from roots to leaves. The evaporation of water from a leaf creates a pulling force that is relayed down to the roots due to cohesion. Adhesion, the clinging of one substance to another, also plays a role. The thinness of a plant\'s veins enhances the adhesion of water to its cell walls, helping to counter the downward pull of gravity. This demonstrates the theme of structure and function, where the structure of the plant\'s veins supports its function in water transport. Surface tension, related to cohesion, measures how difficult it is to stretch or break the surface of a liquid. Hydrogen bonds give water an unusually high surface tension, making it behave as if coated with an invisible film. This can be observed by slightly overfilling a glass, where the water stands above the rim. The water strider takes advantage of this high surface tension to \"stride\" across ponds without breaking the surface. **Terms to Know** **Cohesion**-tendency of molecules of the same kind to stick together. It is especially high for water. **Adhesion**-the clinging of one substance to another. Organisms structure and function tends to enhance waters adhesion to biological structures. **Solute**-a substance that is dissolved. **Solvent**-The dissolving agent. **Solution**-a liquid consisting of a uniform mixture of two or more substances. **2.11 Water\'s hydrogen bonds moderate temperature** Thermal energy is the energy associated with the random movement of atoms and molecules. When thermal energy transfers from a warmer to a cooler body, it is defined as heat. Temperature measures the intensity of heat, which is the average speed of molecules in a body of matter. Water heats up more slowly than metal due to hydrogen bonding, giving it a stronger resistance to temperature change compared to most other substances. Heat must be absorbed to break hydrogen bonds, and heat is released when hydrogen bonds form. To raise the temperature of water, hydrogen bonds between water molecules must be broken before the molecules can move faster. As a result, water absorbs a large amount of heat while warming up only slightly. Conversely, when water cools, water molecules slow down and more hydrogen bonds form, releasing a significant amount of heat. Earth\'s vast water supply helps moderate temperatures, keeping them within life-permitting limits. Oceans, lakes, and rivers absorb a large amount of heat from the sun during warm periods and release it gradually, warming the air. This is why coastal areas generally have milder climates than inland regions. Water\'s resistance to temperature change also stabilizes ocean temperatures, creating a favorable environment for marine life. Additionally, since water makes up about 66% of your body weight, it helps regulate your body temperature. When a substance evaporates (changes from a liquid to a gas), the surface of the remaining liquid cools down. This evaporative cooling happens because the molecules with the highest energy (the \"hottest\" ones) leave. It\'s like the fastest runners leaving a track team, lowering the average speed of the remaining team. Evaporative cooling helps prevent land-dwelling organisms from overheating. For example, evaporation from a plant\'s leaves keeps them cool in the sun, and sweating helps dissipate excess body heat in humans. On a larger scale, the evaporation of surface waters cools tropical seas. **2.12 Ice floats because it is less dense than liquid water** Water exists on Earth in three forms: gas (water vapor), liquid, and solid. Unlike most substances, water is less dense as a solid than as a liquid due to hydrogen bonds. When water freezes, each molecule forms stable hydrogen bonds with its neighbors, creating a three-dimensional crystal. The ice crystal has fewer molecules than an equal volume of liquid water, making ice less dense and allowing it to float on liquid water. If ice sank, ponds, lakes, and oceans would eventually freeze solid. Instead, when water cools, floating ice insulates the water below from the colder air above. This \"blanket\" of ice prevents the water from freezing completely, allowing fish and other aquatic life to survive under the frozen surface. In the Arctic, the frozen surface serves as the winter hunting ground for polar bears. However, the shrinking ice cover due to climate change threatens their survival. **2.13 Water is the solvent of life** When you add a teaspoon of salt to a glass of water, the salt dissolves, forming a solution. A solution is a liquid mixture of two or more substances. The dissolving agent (water) is called the solvent, and the substance that is dissolved (salt) is called the solute. An aqueous solution is one where water is the solvent. Water\'s versatility as a solvent comes from the polarity of its molecules. The positively charged hydrogen ends of water molecules are attracted to negative chloride ions, while the oxygen ends, with their partial negative charge, cling to positive sodium ions. This process allows water molecules to surround and separate all the ions in a salt crystal. Water also dissolves other ionic compounds, such as those found in seawater and within your cells. A compound doesn\'t need to be ionic to dissolve in water. For example, a spoonful of sugar will dissolve in a glass of water. Polar molecules like sugar dissolve as water molecules surround them and form hydrogen bonds with their polar regions. Even large molecules, such as proteins, can dissolve if they have ionic or polar regions on their surface. As the solvent inside all cells, in blood, and in plant sap, water dissolves a wide variety of solutes necessary for life. **2.14 The chemistry of life is sensitive to acidic and basic conditions** In liquid water, a tiny fraction of water molecules dissociates into hydrogen ions (H+) and hydroxide ions (OH-). These ions are highly reactive, and fluctuations in their concentrations can significantly impact a cell\'s proteins and other complex molecules. Some chemical compounds add H+ to an aqueous solution, while others remove H+. A substance that donates hydrogen ions to solutions is called an *acid.* For example, hydrochloric acid (HCl) in stomach gastric juice is a strong acid. An acidic solution has a higher concentration of H+ than OH-. A base reduces the hydrogen ion concentration in a solution. Some bases, like sodium hydroxide (NaOH), donate OH- ions, which combine with H+ to form water (H2O), thus lowering the H+ concentration. Sodium hydroxide is commonly found in oven cleaners. Other bases increase the OH- concentration by accepting H+ ions from the solution. The pH scale measures how acidic or basic a solution is, ranging from 0 (most acidic) to 14 (most basic). Each pH unit represents a 10*^x^* change in H+ concentration. For example, lemon juice at pH 2 has 10 times more H+ than cola at pH 3 and 100 times more H+ than tomato juice at pH 4. Pure water and neutral aqueous solutions have a pH of 7, with equal concentrations of H+ and OH- ions. The pH inside most cells is close to 7, while human blood has a pH of about 7.4. Blood pH must remain within a narrow range (7.0 to 7.8) for survival. Biological fluids contain buffers that help maintain a constant pH by accepting or donating H+ ions as needed. **Key terms** **Acid**-A substance that donates hydrogen ions to solutions **Base**-a substance that reduces the hydrogen ion concentration of a solution **pH**-a measure of how acidic or basic a solution is. It stands for \"potential of hydrogen\" and is calculated based on the concentration of hydrogen ions (H+) in the solution. The pH scale ranges from 0 to 14, with 7 being neutral. Values below 7 indicate acidity, while values above 7 indicate basicity. Each unit change on the pH scale represents a tenfold difference in H+ concentration.