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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