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