Chapter 2

Chemistry

Matter

• The “stuff” of the universe

• Anything that has mass and takes up space

• States of matter

• Solid – has definite shape and volume

• Liquid – has definite volume, changeable shape

• Gas – has changeable shape and volume

Energy

• The capacity to do work (put matter into motion)

• Types of energy

• Kinetic – energy in action

• Potential – energy of position; stored (inactive) energy

Forms of Energy

• Chemical – stored in the bonds of chemical substances

• Electrical – results from the movement of charged particles

• Mechanical – directly involved in moving matter

• Radiant or electromagnetic – energy traveling in waves (i.e., visible light, ultraviolet light, and X rays)

Composition of Matter

• Elements – unique substances that cannot be broken down by ordinary chemical means

• Atoms – more-or-less identical building blocks for each element

• Atomic symbol – one- or two-letter chemical shorthand for each element

Major Elements of the Human Body

• Oxygen (O)

• Carbon (C)

• Hydrogen (H)

• Nitrogen (N)

Lesser and Trace Elements of the Human Body

• Lesser elements make up 3.9% of the body and include:

• Calcium (Ca), phosphorus (P), potassium (K), sulfur (S), sodium (Na), chlorine (Cl), magnesium (Mg), iodine (I), and iron (Fe)

• Trace elements make up less than 0.01% of the body

• They are required in minute amounts, and are found as part of enzymes

Atomic Structure

• The nucleus consists of neutrons and protons

• Neutrons – have no charge and a mass of one atomic mass unit (amu)

• Protons – have a positive charge and a mass of 1 amu

• Electrons are found orbiting the nucleus

• Electrons – have a negative charge and 1/2000 the mass of a proton (0 amu)

Models of the Atom

• Planetary Model –
electrons move around the nucleus in fixed, circular orbits

• Orbital Model –
regions around the nucleus in which electrons are most likely to be found

Identification of Elements

• Atomic number – equal to the number of protons

• Mass number – equal to the mass of the protons and neutrons

• Atomic weight – average of the mass numbers of all isotopes

• Isotope – atoms with same number of protons but a different number of neutrons

• Radioisotopes – atoms that undergo spontaneous decay called radioactivity

Molecules and Compounds

• Molecule – two or more atoms held together by chemical bonds

• Compound – two or more different kinds of atoms chemically bonded together

• Mixtures – two or more components physically intermixed (not chemically bonded)

• Solutions – homogeneous mixtures of components

• Solvent– substance present in greatest amount

• Solute– substance(s) present in smaller amounts

Concentration of Solutions

• Percent, or parts per 100 parts

• Molarity, or moles per liter (M)

• A mole of an element or compound is equal to its atomic or molecular weight (sum of atomic weights) in grams

Colloids and Suspensions

• Colloids, or emulsions, are heterogeneous mixtures whose solutes do not settle out

• Suspensions are heterogeneous mixtures with visible solutes that tend to settle out

Mixtures Compared with Compounds

• No chemical bonding takes place in mixtures

• Most mixtures can be separated by physical means

• Mixtures can be heterogeneous or homogeneous

• Compounds cannot be separated by physical means

• All compounds are homogeneous

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 react in a manner to have 8 electrons in their valence shell

Chemically Inert and Reactive Elements

• Inert elements have their outermost energy level fully occupied by electrons

Chemically Inert and Reactive Elements

• Reactive elements do not have their outermost energy level fully occupied by electrons

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

Covalent Bonds

• Electrons are shared by two atoms

• Electron sharing produces molecules

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

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

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

• 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

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

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

• Disaccharides or double sugars

• Polysaccharides or polymers of simple sugars

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

Other Lipids

• Phospholipids – modified triglycerides with two fatty acid groups and a phosphorus group

• Steroids –
flat molecules with four interlocking hydrocarbon rings

• Eicosanoids –
20-carbon fatty acids found in cell membranes

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

Protein

• Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds

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

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

• Irreversibly denatured proteins cannot refold and are formed by extreme pH or temperature changes

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

Mechanism of Enzyme Action

• Enzyme binds with substrate

• Product is formed at a lower activation energy

• Product is released

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

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