CHEMISTRY PART 2

Chemical Bonds Electron shells, or energy levels, surround the nucleus of an atom Bonds are formed using the electrons in the outermost energy level Valence shell – outermost energy level containing chemically active electrons Octet rule – atoms usually react in a manner to have 8 electrons in their valence shell. (2 in first, 8 in second and third)

Chemically Inert and Reactive Elements Inert elements have their outermost energy level fully occupied by electrons Figure 2.4a

Chemically Inert and Reactive Elements Reactive elements do not have their outermost energy level fully occupied by electrons Figure 2.4b

Types of Chemical Bonds Ionic Covalent Hydrogen

Ionic Bonds Ions are charged atoms resulting from the gain or loss of electrons Anions have gained one or more electrons Cations have lost one or more electrons Opposite charges on anions and cations hold them close together, forming ionic bonds

Formation of an Ionic Bond Ionic compounds form crystals instead of individual molecules Example: NaCl (sodium chloride)

Formation of an Ionic Bond Figure 2.5

Covalent Bonds Electrons are shared by two atoms Electron sharing produces molecules

Covalent Bonds Figure 2.6a

Covalent Bonds Figure 2.6b

Covalent Bonds Figure 2.6c

Polar and Nonpolar Molecules Electrons shared equally between atoms produce nonpolar molecules Unequal sharing of electrons produces polar molecules Atoms with 6 or 7 valence shell electrons are electronegative Atoms with 1 or 2 valence shell electrons are electropositive

Comparison of Ionic, Polar Covalent, and Nonpolar Covalent Bonds Figure 2.8

Hydrogen Bonds Too weak to bind atoms together Common in dipoles such as water Responsible for surface tension in water Important as intramolecular bonds, giving the molecule a three-dimensional shape Figure 2.9

Chemical Reactions Occur when chemical bonds are formed, rearranged, or broken Are written in symbolic form using chemical equations Chemical equations contain: Number and type of reacting substances, and products produced Relative amounts of reactants and products H + H  H2 (reactants) (product)

Patterns of Chemical Reactions Combination reactions: Synthesis reactions which always involve bond formation A + B  AB Decomposition reactions: Molecules are broken down into smaller molecules AB  A + B Exchange reactions: Bonds are both made and broken AB + C  AC + B

Oxidation-Reduction (Redox) Reactions Reactants losing electrons are electron donors and are oxidized Reactants taking up electrons are electron acceptors and become reduced

Energy Flow in Chemical Reactions Exergonic reactions – reactions that release energy Endergonic reactions – reactions whose products contain more potential energy than did its reactants

Reversibility of Chemical Reactions All chemical reactions are theoretically reversible A + B  AB AB  A + B If neither a forward nor reverse reaction is dominant, chemical equilibrium is reached

Factors Influencing Rate of Chemical Reactions Temperature – chemical reactions proceed quicker at higher temperatures Particle size – the smaller the particle the faster the chemical reaction Concentration – higher reacting particle concentrations produce faster reactions Catalysts – increase the rate of a reaction without being chemically changed Enzymes – biological catalysts

Biochemistry Organic compounds Inorganic compounds Contain carbon, are covalently bonded, and are often large Inorganic compounds Do not contain carbon Water, salts, and many acids and bases

Water High heat capacity – absorbs and releases large amounts of heat before changing temperature High heat of vaporization – changing from a liquid to a gas requires large amounts of heat Polar solvent properties – dissolves ionic substances, forms hydration layers around large charged molecules, and serves as the body’s major transport medium Reactivity – is an important part of hydrolysis and dehydration synthesis reactions Cushioning – resilient cushion around certain body organs

Salts Inorganic compounds Contain cations other than H+ and anions other than OH– Are electrolytes; they conduct electrical currents

Acids and Bases Acids release H+ and are therefore proton donors HCl  H+ + Cl – Bases release OH– and are proton receptors NaOH  Na+ + OH–

Acid-Base Concentration (pH) Acidic solutions have higher H+ concentration and therefore a lower pH Alkaline solutions have lower H+ concentration and therefore a higher pH Neutral solutions have equal H+ and OH– concentrations

Acid-Base Concentration (pH) Acidic: pH 0–6.99 Basic: pH 7.01–14 Neutral: pH 7.00 Figure 2.12

Buffers Systems that resist abrupt and large swings in the pH of body fluids Carbonic acid–bicarbonate system Carbonic acid dissociates reversibly releasing bicarbonate ions and protons The chemical equilibrium between carbonic acid and bicarbonate resists pH changes in the blood

Break

Organic Compounds Carbohydrates Lipids Proteins Nucleic Acids

Carbohydrates Contain carbon, hydrogen, and oxygen Their major function is to supply a source of cellular food Examples: Monosaccharides or simple sugars Figure 2.13a

Carbohydrates Disaccharides or double sugars Figure 2.13b

Carbohydrates Polysaccharides or polymers of simple sugars Figure 2.13c

Lipids Contain C, H, and O, but the proportion of oxygen in lipids is less than in carbohydrates Examples: Neutral fats or triglycerides Phospholipids Steroids Eicosanoids

Neutral Fats (Triglycerides) Composed of three fatty acids bonded to a glycerol molecule Figure 2.14a

Other Lipids Phospholipids – modified triglycerides with two fatty acid groups and a phosphorus group Figure 2.14b

Other Lipids Steroids – flat molecules with four interlocking hydrocarbon rings Eicosanoids – 20-carbon fatty acids found in cell membranes Figure 2.14c

Representative Lipids Found in the Body Neutral fats – found in subcutaneous tissue and around organs Phospholipids – chief component of cell membranes Steroids – cholesterol, bile salts, vitamin D, sex hormones, and adrenal cortical hormones Fat-soluble vitamins – vitamins A, E, and K Eicosanoids – prostaglandins, leukotriens, and thromboxanes Lipoproteins – transport fatty acids and cholesterol in the bloodstream

Amino Acids Building blocks of protein, containing an amino group and a carboxyl group Amino acid structure Figure 2.15

Protein Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Figure 2.16

Structural Levels of Proteins Primary – amino acid sequence Secondary – alpha helices or beta pleated sheets Tertiary – superimposed folding of secondary structures Quaternary – polypeptide chains linked together in a specific manner

Structural Levels of Proteins Figure 2.17

Fibrous and Globular Proteins Fibrous proteins Extended and strandlike proteins Examples: keratin, elastin, collagen, and certain contractile fibers Globular proteins Compact, spherical proteins with tertiary and quaternary structures Examples: antibodies, hormones, and enzymes

Protein Denaturation Reversible unfolding of proteins due to drops in pH and/or increased temperature Figure 2.19a

Protein Denaturation Irreversibly denatured proteins cannot refold and are formed by extreme pH or temperature changes Figure 2.19b

Molecular Chaperones (Chaperonins) Help other proteins to achieve their functional three-dimensional shape Maintain folding integrity Assist in translocation of proteins across membranes Promote the breakdown of damaged or denatured proteins

Characteristics of Enzymes Most are globular proteins that act as biological catalysts Holoenzymes consist of an apoenzyme (protein) and a cofactor (usually an ion) Enzymes are chemically specific Frequently named for the type of reaction they catalyze Enzyme names usually end in -ase Lower activation energy

Characteristics of Enzymes Figure 2.20

Mechanism of Enzyme Action Enzyme binds with substrate Product is formed at a lower activation energy Product is released Figure 2.21

Nucleic Acids Composed of carbon, oxygen, hydrogen, nitrogen, and phosphorus Their structural unit, the nucleotide, is composed of N-containing base, a pentose sugar, and a phosphate group Five nitrogen bases contribute to nucleotide structure – adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U) Two major classes – DNA and RNA

Deoxyribonucleic Acid (DNA) Double-stranded helical molecule found in the nucleus of the cell Replicates itself before the cell divides, ensuring genetic continuity Provides instructions for protein synthesis

Structure of DNA Figure 2.22a

Structure of DNA Figure 2.22b

Ribonucleic Acid (RNA) Single-stranded molecule found in both the nucleus and the cytoplasm of a cell Uses the nitrogenous base uracil instead of thymine Three varieties of RNA: messenger RNA, transfer RNA, and ribosomal RNA

Adenosine Triphosphate (ATP) Source of immediately usable energy for the cell Adenine-containing RNA nucleotide with three phosphate groups Figure 2.23