2 Atoms: The Constituents of Matter All matter is composed of atoms. Each atom consists of at least one proton and one electron. Atoms have mass. The mass comes mostly from the proton and a neutrally charged body called a neutron.

2 Atoms: The Constituents of Matter Each element contains only one type of atom. Information on elements is arranged in logical order in a table called the periodic table. The periodic table arranges elements left to right based on their atomic number, and in columns based on similarities in their properties.

2 Atoms: The Constituents of Matter Each element has a unique atomic number which is the number of protons found in an atom of the element. The mass number is the number of protons plus the number of neutrons. The mass number is used as the weight of the atom, in units called daltons. Each element has a unique symbol: H is hydrogen, C is carbon, Na is sodium, and Fe is iron.

2 Atoms: The Constituents of Matter All atoms of an element have the same number of protons, but not necessarily the same number of neutrons. Atoms of the same element that have different atomic weights are called isotopes.

2 Chemical Bonds: Linking Atoms Together Covalent bonds are very strong. Each covalent bond has a predictable length, angle, and direction, which makes it possible to predict the three-dimensional structures of molecules. A double covalent bond occurs when atoms share two pairs of electrons; in triple covalent bonds atoms share three electron pairs.

Figure 2.10 Covalent Bonding With Carbon Properties of Molecules

2 Chemical Bonds: Linking Atoms Together Electrons are not always shared equally between covalently bonded atoms. The attractive force that an atom exerts on electrons is called electronegativity. When a molecule has nuclei with different electronegativities, an electron spends most of its time around the nucleus with the greater electronegativity.

2 Chemical Bonds: Linking Atoms Together Unequal sharing of electrons causes a partial negative charge around the more electronegative atom, and a partial positive charge around the less electronegative atom, resulting in a polar covalent bond. Molecules that have polar covalent bonds are called polar molecules.

Figure 2.11 The Polar Covalent Bond in the Water Molecule Properties of Molecules

2 Chemical Bonds: Linking Atoms Together Hydrogen bonds may form within or between atoms with polar covalent bonds. The  – portion of one molecule has a weak attraction to the  + portion of another molecule. Each of these attractions is called a hydrogen bond. Hydrogen bonds do not share electrons. Although hydrogen bonds are weak, they tend to be additive, and they are of profound biological importance.

Figure 2.12 Hydrogen Bonds Can Form between or within Molecules Properties of Molecules

2 Chemical Bonds: Linking Atoms Together Ionic bonds involve a complete transfer of one or more electrons. Ions are formed when an atom loses or gains electrons. Positively charged ions are called cations. Negatively charged ions are called anions.

Figure 2.13 Formation of Sodium and Chloride Ions Properties of Molecules

2 Chemical Bonds: Linking Atoms Together Ionic bonds are formed by the electrical attraction between ions with opposite charges. Table salt has chloride and sodium ions, held together by ionic bonds. When salt is introduced into water, the partial charges of the water molecules can easily interfere with the ionic bonds.

Figure 2.14 Water Molecules Surround Ions Properties of Molecules

2 Chemical Bonds: Linking Atoms Together Polar molecules tend to be hydrophilic. Substances that are ionic or polar often dissolve in water due to hydrogen bonds. Nonpolar molecules are called hydrophobic because they tend to aggregate with other nonpolar molecules. Nonpolar molecules are also attracted to each other via relatively weak attractions called van der Waals forces.

2 Chemical Reactions: Atoms Change Partners Chemical reactions occur when atoms combine or change partners. In a chemical reaction, reactants are converted to products. A chemical reaction can be written as an equation. The equation must balance because matter is neither created nor destroyed.

2 Chemical Reactions: Atoms Change Partners Changes in energy usually accompany chemical reactions. Stored energy, such as that in chemical bonds, is called potential energy and is available for future use.

2 Water: Structure and Properties Due to its shape, polarity, and ability to form hydrogen bonds, water has some unusual properties.

2 Water: Structure and Properties Ice is held in a crystalline structure by the orientation of water molecules’ hydrogen bonds. Each molecule forms hydrogen bonds with four other molecules. These four hydrogen bonds increase the space the water molecules take up, so water expands as it freezes, and ice is less dense than liquid water. For these reasons, ice floats in liquid water.

2 Water: Structure and Properties A great deal of heat energy is required to change the temperature of liquid water because the hydrogen bonds must be broken. Specific heat is the number of calories needed to raise one gram of a substance 1 o C. The specific heat of liquid water is 1. Liquid water has a higher specific heat than most other small molecules in liquid form.

2 Water: Structure and Properties The heat of vaporization is the amount of heat needed to change a substance from its liquid state to its gaseous state. A lot of heat is required to change water to a gaseous state because the hydrogen bonds of the liquid water must be broken. Evaporation has a cooling effect by absorbing calories. Condensing has the opposite effect, releasing heat.

2 Water: Structure and Properties Water has a cohesive strength because of hydrogen bonds. The cohesive strength of water molecules allows the transport of water from the roots to the tops of trees. Water has high surface tension, which means that the surface of liquid water is relatively difficult to puncture.

2 Water: Structure and Properties Water is the solvent of life. Living organisms are over 70 percent water by weight and many reactions take place in this watery environment.

2 Water: Structure and Properties The mole concept is fundamental to quantitative analysis. A mole is the amount of a substance in grams whose weight is equal to its molecular weight. One mole of any given compound contains approximately 6.03 x molecules of that compound (Avogadro’s number).

2 Acids, Bases, and the pH Scale Some substances dissolve in water and release hydrogen ions (H + ); these are called acids. Their release is called ionization. Other substances dissolve in water and release hydroxide ions (OH – ); these are called bases. Acids donate H + ; bases accept H +.

2 Acids, Bases, and the pH Scale Acids release H + ions in solution. If the reaction is complete, it is a strong acid, such as HCl. The carboxyl group (—COOH) is common in biological compounds. It functions as an acid because  —COOH  —COO– + H +

2 Acids, Bases, and the pH Scale Bases accept H + in solution. NaOH ionizes completely to Na + and OH –. The OH – absorbs H + to form water.It is a strong base. The amino group (—NH 2 ) is an important part of many biological compounds; it functions as a weak base by accepting H + :  —NH 2 + H +  —(NH3) +

2 Acids, Bases, and the pH Scale Ionization of strong acids is virtually irreversible. Ionization of weak acids and bases is somewhat reversible. Many large molecules in biological systems contain weak acid or base groups.

2 Acids, Bases, and the pH Scale Water is really a weak acid and has a slight tendency to ionize into H + and OH –. This ionization is very important for living creatures and the chemical reactions they must perform because the H + ion is so reactive.

2 Acids, Bases, and the pH Scale pH is the measure of hydrogen ion concentration. It is defined as the negative logarithm of the hydrogen ion concentration in moles per liter. The pH scale indicates the strength of a solution of an acid or base. The scale values range from 1 through 14. A pH 7 means the concentration of hydrogen ions is 1 x 10 –7 moles per liter of water.

2 Acids, Bases, and the pH Scale A buffer is a mixture of a weak acid and its corresponding base. Because buffers can react with both added bases and acids, they make the overall solution resistant to pH change.

2 Properties of Molecules Functional groups give specific properties to molecules. Functional groups are covalently bonded to organic molecules. Amino acids are biological molecules that contain both a carboxyl group and an amino group.

Figure 2.20 Some Functional Groups Important to Living Systems (Part 1) Properties of Molecules

Figure 2.20 Some Functional Groups Important to Living Systems (Part 2) Properties of Molecules

Figure 2.20 Some Functional Groups Important to Living Systems (Part 3) Properties of Molecules

2 Isomers are molecules that have the same chemical formula but different arrangements of the atoms. Structural isomers differ in terms of how atoms are joined together. Optical isomers are mirror images of each other. Optical isomers can occur whenever a carbon has four different atoms or groups attached to it.

Figure 2.21 Optical Isomers Properties of Molecules