2 Chemical Principles

The Structure of Atoms Learning Objective 2-1 Describe the structure of an atom and its relation to the physical properties of elements.

The Structure of Atoms Chemistry is the study of interactions between atoms and molecules The atom is the smallest unit of matter and cannot be subdivided into smaller substances Atoms interact to form molecules

The Structure of Atoms Atoms are composed of Electrons: negatively charged particles Protons: positively charged particles Neutrons: uncharged particles

The Structure of Atoms Protons and neutrons make up the nucleus Electrons move around the nucleus

Figure 2.1 The structure of an atom. Electron shells Proton (p+) Neutron (n0) Nucleus Electron (e–)

Chemical Elements Atoms with the same number of protons are classified as the same chemical element Each different chemical element has a different number of protons Atomic number: number of protons in the nucleus

Chemical Elements Atomic weight is the total number of protons and neutrons in an atom Isotopes of an element are atoms with different numbers of neutrons Isotopes of oxygen:

Table 2.1 The Elements of Life*

Electronic Configurations Electrons are arranged in electron shells corresponding to different energy levels

Check Your Understanding  How does differ from Check Your Understanding  How does differ from ? What is the atomic number of each carbon atom? The atomic weight? 2-1

How Atoms Form Molecules: Chemical Bonds Learning Objective 2-2 Define ionic bond, covalent bond, hydrogen bond, molecular weight, and mole.

How Atoms Form Molecules: Chemical Bonds Atoms form molecules by combining to fill their outermost shells The number of missing or extra electrons in the outermost shell is known as the valence Molecules hold together because the valence electrons of the combining atoms form attractive forces, called chemical bonds, between the atomic nuclei

How Atoms Form Molecules: Chemical Bonds A compound is a molecule that contains two or more kinds of atoms Water: two atoms of hydrogen, one atom of oxygen H2O

Ionic Bonds The number of protons and electrons are equal in an atom Ions are charged atoms that have gained or lost electrons

Figure 2.2a Ionic bond formation. Loss of electron Gain of electron Sodium atom (electron donor) Sodium ion (Na+) Chlorine atom (electron acceptor) Chloride ion (Cl–) A sodium atom (Na) loses one electron to an electron acceptor and forms a sodium ion (Na+). A chlorine atom (Cl) accepts one electron from an electron donor to become a chloride ion (Cl–).

Ionic Bonds Cations are atoms that lose electrons and become positively charged ions Anions are atoms that gain electrons and become negatively charged ions

Ionic Bonds Ionic bonds are attractions between ions of opposite charge One atom loses electrons, and another gains electrons

Figure 2.2b Ionic bond formation. Sodium ion (Na+) Chloride ion (Cl–) Sodium chloride molecule Na+ Cl– NaCl The sodium and chloride ions are attracted because of their opposite charges and are held together by an ionic bond to form a molecule of sodium chloride.

Covalent Bonds Covalent bonds form when two atoms share one or more pairs of electrons Covalent bonds are stronger and more common in organisms than ionic bonds

Figure 2.3a Covalent bond formation.

Figure 2.3b Covalent bond formation.

Hydrogen Bonds Hydrogen bonds form when a hydrogen atom that is covalently bonded to an O or N atom is attracted to another N or O atom in another molecule

Figure 2.4b Hydrogen bond formation in water.

Molecular Weight and Moles The sum of the atomic weights in a molecule is the molecular weight One mole of a substance is its molecular weight in grams H2O 2H = 2  1 = 2 O = 16 MW = 18 1 mole weighs 18 g

Check Your Understanding  Differentiate an ionic bond from a covalent bond. 2-2

Chemical Reactions Learning Objective 2-3 Diagram three basic types of chemical reactions.

Chemical Reactions Chemical reactions involve the making or breaking of bonds between atoms A change in chemical energy occurs during a chemical reaction Endergonic reactions absorb energy Exergonic reactions release energy

Synthesis Reactions Occur when atoms, ions, or molecules combine to form new, larger molecules Anabolism is the synthesis of molecules in a cell

Decomposition Reactions Occur when a molecule is split into smaller molecules, ions, or atoms Catabolism are decomposition reactions in a cell

Exchange Reactions Are part synthesis and part decomposition

The Reversibility of Chemical Reactions Can readily go in either direction Each direction may need special conditions

Check Your Understanding  This chemical reaction below is used to remove chlorine from water. What type of reaction is it? 2-3 HClO + Na2SO3 Na2SO4 + HCl

Important Biological Molecules Organic compounds always contain carbon and hydrogen; typically structurally complex Inorganic compounds typically lack carbon; usually small and structurally simple

Inorganic Compounds Learning Objectives 2-4 List several properties of water that are important to living systems. 2-5 Define acid, base, salt, and pH.

Water Inorganic Polar molecule Solvent Hydrogen bonds absorb heat Unequal distribution of charges Solvent Polar substances undergo dissociation in water, forming solutes Hydrogen bonds absorb heat Temperature buffer

Figure 2.4a Hydrogen bond formation in water.

Figure 2.4b Hydrogen bond formation in water.

Figure 2.5 How water acts as a solvent for sodium chloride (NaCl).

Acids, Bases, and Salts Substances that dissociate into one or more H+ (protons) and one or more negative ions HCl  H+ + Cl−

Figure 2.6a Acids, bases, and salts.

Acids, Bases, and Salts Substances that dissociate into one or more OH− (hydroxide) ions NaOH  Na+ + OH−

Figure 2.6b Acids, bases, and salts.

Acids, Bases, and Salts Substances that dissociate into cations and anions, neither of which is H+ or OH− NaCl  Na+ + Cl−

Figure 2.6c Acids, bases, and salts.

Acid-Base Balance: The Concept of pH The concentration of H+ in a solution is expressed as pH pH = –log10[H+] Increasing [H+] increases acidity Increasing [OH−] increases alkalinity Most organisms grow best between pH 6.5 and 8.5

Figure 2.7 The pH scale. pH scale 1 Stomach acid H+ 2 Lemon juice OH– 1 Stomach acid H+ 2 Lemon juice OH– 3 Grapefruit juice Increasingly ACIDIC Wine Tomato juice Acidic solution 4 5 6 Urine Milk NEUTRAL [H+] = [OH–] 7 Pure water Human blood 8 Seawater Neutral solution 9 10 Increasingly BASIC Milk of magnesia 11 Household ammonia 12 Household bleach 13 Oven cleaner Basic solution 14 Limewater

Check Your Understanding  Why is the polarity of a water molecule important? 2-4  Antacids neutralize acid by the following reaction. Mg(OH)2 + 2HCl  MgCl2 + H2O Identify the acid, base, and salt. 2-5

Organic Compounds Learning Objectives 2-6 Distinguish organic and inorganic compounds. 2-7 Define functional group.

Structure and Chemistry Organic compounds commonly contain hydrogen, oxygen, and/or nitrogen in addition to carbon The chain of carbon atoms in an organic molecule is the carbon skeleton

Structure and Chemistry Functional groups bond to carbon skeletons and are responsible for most of the chemical properties of a particular organic compound

Unnumbered Figure pg. 34

Table 2.4 Representative Functional Groups and the Compounds in Which They Are Found (1 of 2)

Table 2.4 Representative Functional Groups and the Compounds in Which They Are Found (2 of 2)

Structure and Chemistry Identify the functional groups in an amino acid Amino group Carboxyl group

Structure and Chemistry Small organic molecules can combine into large macromolecules Macromolecules are polymers consisting of many small repeating molecules called monomers

Structure and Chemistry Monomers join by dehydration synthesis or condensation reactions

Unnumbered Figure 2 pg. 35

Check Your Understanding  Define organic Check Your Understanding  Define organic. 2-6  Add the appropriate functional group(s) to the ethyl group below to produce each of the following compounds: ethanol, acetic acid, acetaldehyde, ethanolamine, diethyl ether. 2-7

Organic Compounds Learning Objectives 2-8 Identify the building blocks of carbohydrates. 2-9 Differentiate simple lipids, complex lipids, and steroids. 2-10 Identify the building blocks and structure of proteins. 2-11 Identify the building blocks of nucleic acids. 2-12 Describe the role of ATP in cellular activities.

Carbohydrates Serve as cell structures and cellular energy sources Include sugars and starches Consist of C, H, and O with the formula (CH2O)n Many carbohydrates are isomers Molecules with same chemical formula, but different structures

Monosaccharides Monosaccharides are simple sugars with three to seven carbon atoms Glucose and deoxyribose are examples of common monosaccharides

Disaccharides Disaccharides are formed when two monosaccharides are joined in a dehydration synthesis Disaccharides can be broken down by hydrolysis

Figure 2.8 Dehydration synthesis and hydrolysis.

Polysaccharides Polysaccharides consist of tens or hundreds of monosaccharides joined through dehydration synthesis Starch, glycogen, dextran, and cellulose are polymers of glucose that differ in their bonding and function

Check Your Understanding Give an example of a monosaccharide, a disaccharide, and a polysaccharide. 2-8

Lipids Primary components of cell membranes Consist of C, H, and O Are nonpolar and insoluble in water

Simple Lipids Fats or triglycerides Contain glycerol and fatty acids; formed by dehydration synthesis

Figure 2.9a-b Structural formulas of simple lipids. Glycerol Carboxyl group Fatty acid (palmitic acid, saturated) (C15H31COOH) Hydrocarbon chain

Simple Lipids Saturated fat: no double bonds in the fatty acids Unsaturated fat: one or more double bonds in the fatty acids Cis: H atoms on the same side of the double bond Trans: H atoms on opposite sides of the double bond

Figure 2.9c Structural formulas of simple lipids. Glycerol Ester linkage Palmitic acid (saturated) (C15H31COOH) + H2O Oleic acid (unsaturated) (C17H33COOH) + H2O Stearic acid (saturated) (C17H35COOH) + H2O cis configuration Molecule of fat (triglyceride)

Complex Lipids Contain C, H, and O + P, N, and/or S Cell membranes are made of complex lipids called phospholipids Glycerol, two fatty acids, and a phosphate group Phospholipids have polar as well as nonpolar regions

Figure 2.10 Phospholipid and orientation, showing saturated and unsaturated fatty acids and the molecules' polarity. Organic group Phosphate group Saturated fatty acids (closely packed) Glycerol Polar heads (hydrophilic) Nonpolar tails (hydrophobic) Unsaturated fatty acids (loosely packed) This structure (greatly reduced) is used to represent phospholipids throughout the text. Sterol molecules separate fatty acid chains Orientation of phospholipids in a plasma membrane Saturated fatty acid Unsaturated fatty acid Phospholipid structure 74

Steroids Four carbon rings with an –OH group attached to one ring Part of membranes that keep the membranes fluid

Figure 2.11 Cholesterol, a steroid.

Check Your Understanding  How do simple lipids differ from complex lipids? 2-9

Proteins Made of C, H, O, N, and sometimes S Essential in cell structure and function Enzymes that speed chemical reactions Transporter proteins that move chemicals across membranes Flagella that aid in movement Some bacterial toxins and cell structures

Amino Acids Proteins consist of subunits called amino acids Amino acids contain an alpha-carbon that has an attached: Carboxyl group (–COOH) Amino group (–NH2) Side group

Figure 2.12 Amino acid structure.

Table 2.5 The 20 Amino Acids Found in Proteins* (1 of 2) 81

Table 2.5 The 20 Amino Acids Found in Proteins* (2 of 2) 82

Amino Acids Exist in either of two stereoisomers: D or L L-forms are most often found in nature

Figure 2.13 The L- and D-isomers of an amino acid, shown with ball-and-stick models.

Peptide Bonds Peptide bonds between amino acids are formed by dehydration synthesis

Figure 2.14 Peptide bond formation by dehydration synthesis.

Levels of Protein Structure The primary structure is a polypeptide chain

Figure 2.15 Protein structure (1 of 4).

Levels of Protein Structure The secondary structure occurs when the amino acid chain folds and coils in a helix or pleated sheet

Figure 2.15 Protein structure (2 of 4). Hydrogen bond Hydrogen bond Secondary structure: helix and pleated sheet (with three polypeptide strands) Helix Pleated sheet

Levels of Protein Structure The tertiary structure occurs when the helix or sheet folds irregularly, forming disulfide bridges, hydrogen bonds, and ionic bonds between amino acids in the chain

Figure 2.15 Protein structure (3 of 4). Tertiary structure: helix and pleated sheets fold into a 3D shape Disulfide bridge

Levels of Protein Structure The quaternary structure consists of two or more polypeptides

Figure 2.15 Protein structure (4 of 4).

Figure 2.15 Protein structure. Peptide bonds Primary structure: polypeptide strand (amino acid sequence) Hydrogen bond Hydrogen bond Secondary structure: helix and pleated sheet (with three polypeptide strands) Helix Pleated sheet Tertiary structure: helix and pleated sheets fold into a 3D shape Disulfide bridge Quaternary structure: the relationship of several folded polypeptide chains, forming a protein

Levels of Protein Structure Proteins can undergo denaturation Denaturation occurs when proteins encounter hostile environments such as temperature and pH, and therefore lose their shapes and functions

Levels of Protein Structure Conjugated proteins consist of amino acids and other organic molecules Glycoproteins Nucleoproteins Lipoproteins

Check Your Understanding What two functional groups are in all amino acids? 2-10

Nucleic Acids Consist of nucleotides Nucleotides consist of A five-carbon (pentose) sugar Phosphate group Nitrogen-containing (purine or pyrimidine) base Nucleosides consist of Pentose Nitrogen-containing base

DNA Deoxyribonucleic acid Contains deoxyribose Exists as a double helix Adenine hydrogen bonds with Thymine Cytosine hydrogen bonds with Guanine Order of the nitrogen-containing bases forms the genetic instructions of the organism

Figure 2.16 The Structure of DNA.

RNA Ribonucleic acid Contains ribose Is single-stranded Adenine hydrogen bonds with Uracil Cytosine hydrogen bonds with Guanine Several kinds of RNA play a specific role in protein synthesis

Figure 2.17 A uracil nucleotide of RNA. Uracil (U) Phosphate Ribose

Check Your Understanding How do DNA and RNA differ? 2-11

Adenosine Triphosphate (ATP) Made of ribose, adenine, and three phosphate groups

Figure 2.18 The structure of ATP.

Adenosine Triphosphate (ATP) Stores the chemical energy released by some chemical reactions Releases phosphate groups by hydrolysis to liberate useful energy for the cell

Unnumbered Figure pg. 46

Check Your Understanding Which can provide more energy for a cell and why: ATP or ADP? 2-12