Chapter 2Basic Chemistry

Matter and Energy Matter—anything that occupies space and has mass Matter may exist as one of three states

o Solid: definite shape and volumeo Liquid: definite volume; shape of containero Gaseous: neither a definite shape nor volume

Matter and Energy Matter may be changed

o Physically Changes do not alter the basic nature of a substance Examples include changes in the state of matter (solid, liquid, or gas)

o Chemically Changes alter the chemical composition of a substance

Matter and Energy Energy—the ability to do work

o Has no mass and does not take up spaceo Kinetic energy: energy is doing worko Potential energy: energy is inactive or stored

Matter and Energy Forms of energy

o Chemical energy is stored in chemical bonds of substanceso Electrical energy results from movement of charged particleso Mechanical energy is energy directly involved in moving mattero Radiant energy travels in waves; energy of the electromagnetic spectrum

Matter and Energy Energy form conversions

o ATP (adenosine triphosphate) traps the chemical energy of food in its bonds

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Composition of Matter Elements—fundamental units of matter

o 96 percent of the body is made from four elements:1. Oxygen (O)—most common; 65% of the body’s mass2. Carbon (C)3. Hydrogen (H)4. Nitrogen (N)

Periodic table contains a complete listing of elements

Composition of Matter Atoms

o Building blocks of elementso Atoms of elements differ from one anothero Atomic symbol is chemical shorthand for each element

The Basic Atomic Subparticles Protons (p+) are positively charged Neutrons (n0) are uncharged or neutral Electrons (e–) are negatively charged

The Basic Atomic Subparticles All atoms are electrically neutral

o Number of protons equals numbers of electrons in an atom o Positive and negative charges cancel each other out

Ions are atoms that have lost or gained electrons

Planetary and Orbital Models of an Atom Planetary model

o Portrays the atom as a miniature solar systemo Protons and neutrons are in the atomic nucleuso Electrons are in orbitals around the nucleus

Planetary and Orbital Models of an Atom Orbital model

o Electrons are depicted by an electron cloud, a haze of negative charge, outside the nucleus

Planetary and Orbital Models of an Atom

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Electrons determine an atom’s chemical behavior and bonding properties Although outdated, the planetary model is simple and easy to understand and use

Identifying Elements To identify an element, we need to know the:

o Atomic numbero Atomic mass numbero Atomic weight

Identifying Elements Atomic number—equal to the number of protons that the atom contains

o Unique to atoms of a particular elemento Indirectly tells the number of electrons in an atom

Atomic mass number—sum of the protons and neutrons contained in an atom’s nucleus Atomic weight—approximately equal to the mass number of the element’s most abundant isotope (to be discussed in a moment)

Atomic Weight and Isotopes Isotopes

o Atoms that have the same number of protons and electrons but vary in the number of neutrons

o Isotopes have the same atomic number but different atomic masses

Atomic Weights and Isotopes Radioisotope

o Heavy isotope of certain atomso Tends to be unstableo Decomposes to more stable isotope

Radioactivity—process of spontaneous atomic decayo Used to tag and trace biological molecules through the body

Molecules and Compounds Molecule—two or more atoms of the same elements combined chemically Example of a chemical reaction, shown as a chemical equation, resulting in a molecule:

H (atom) + H (atom) → H2 (molecule)o The reactants are the atoms on the lefto The product is the molecule on the right, represented by a molecular formula

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Molecules and Compounds Compound—two or more atoms of different elements combined chemically to form a molecule of a compound Example of a chemical reaction resulting in a compound:

4H + C → CH4 (methane)

Chemical Bonds and Chemical Reactions Chemical reactions occur when atoms combine with or dissociate from other atoms Chemical bonds are energy relationships involving interactions among the electrons of reacting atoms

Role of Electrons Electrons occupy energy levels called electron shells (or energy levels) Electrons closest to the nucleus are most strongly attracted to its positive charge Distant electrons further from the nucleus are likely to interact with other atoms

Role of Electrons Each electron shell has distinct properties How to fill the atom’s electrons shells

o Shell 1 can hold a maximum of 2 electronso Shell 2 can hold a maximum of 8 electronso Shell 3 can hold a maximum of 18 electronso Subsequent shells can hold more electrons

Bonding involves interactions only between electrons in the outermost (valence) shell Atoms with full valence shells do not form bonds

Role of Electrons Rule of eights

o The key to chemical reactivityo Atoms are considered stable when their outermost (valence) shell has 8

electronso Atoms with 8 electrons in the valence shell are considered stable and

chemically inactive (inert)o The exception to this rule of eights is shell 1, which can hold only 2 electrons

Role of Electrons Reactive elements

o Atoms will gain, lose, or share electrons to complete their outermost orbitals when fewer than 8 electrons are in the valence shell

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o Chemical bonding helps atoms achieve a stable valence shell

Types of Chemical Bonds Ionic bonds

o Form when electrons are completely transferred from one atom to anothero Allow atoms to achieve stability through the transfer of electrons

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Types of Chemical Bonds Ions

o Result from the loss or gain of electrons Anions have negative charge due to gain of electron(s) Cations have positive charge due to loss of electron(s)

o Tend to stay close together because opposite charges attract

Types of Chemical Bonds Covalent bonds

o Atoms become stable through shared electronso Electrons are shared in pairso Single covalent bonds share one pair of electronso Double covalent bonds share two pairs of electrons

Types of Chemical Bonds Covalent bonds can be described as either nonpolar or polar

o Nonpolar covalent bonds Electrons are shared equally between the atoms of the molecule Electrically neutral as a molecule Example: carbon dioxide

Types of Chemical Bonds Covalent bonds can be described as either nonpolar or polar (continued)

o Polar covalent bonds Electrons are not shared equally between the atoms of the molecule Molecule has a positive and negative side, or pole Example: water

Types of Chemical Bonds Hydrogen bonds

o Extremely weak chemical bondso Formed when a hydrogen atom is attracted to the negative portion, such as

an oxygen or nitrogen atom, of a polar moleculeo Responsible for the surface tension of watero Important for forming intramolecular bonds, as in protein structure

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Patterns of Chemical Reactions Synthesis reaction (A + B → AB)

o Atoms or molecules combine to form a larger, more complex moleculeo Energy is absorbed for bond formationo Underlies all anabolic (building) activities in the body

Decomposition reaction (AB → A + B)o Molecule is broken down into smaller moleculeso Chemical energy is releasedo Underlies all catabolic (destructive) activities in the body

Patterns of Chemical Reactions Exchange reaction

AB + C → AC + Band

AB + CD → AD + CBo Involves simultaneous synthesis and decomposition reactions as bonds are

both made and brokeno Switch is made between molecule parts, and different molecules are made

Patterns of Chemical Reactions Most chemical reactions are reversible Reversibility is indicated by a double arrow

o When arrows differ in length, the longer arrow indicates the more rapid reaction or major direction of progress

Factors influencing the rate of chemical reactions are shown in Table 2.4

Biochemistry: The Chemical Composition of Living Matter Inorganic compounds

o Lack carbono Tend to be small, simple moleculeso Include water, salts, and many (not all) acids and bases

Organic compoundso Contain carbono All are large, covalent moleculeso Include carbohydrates, lipids, proteins, and nucleic acids

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Inorganic Compounds Water

o Most abundant inorganic compound in the bodyo Accounts for two-thirds of the body’s weighto Vital properties include:

High heat capacity Polarity/solvent properties Chemical reactivity Cushioning

Inorganic Compounds High heat capacity

o Water absorbs and releases a large amount of heat before it changes temperature

o Prevents sudden changes in body temperature

Inorganic Compounds Polarity/solvent properties

o Water is often called the “universal solvent” o Solvents are liquids or gases that dissolve smaller amounts of soluteso Solutes are solids, liquids, or gases that are dissolved or suspended by

solventso Solution forms when solutes are very tinyo Colloid forms when solutes of intermediate size form a translucent mixture

Inorganic Compounds Chemical reactivity

o Water is an important reactant in some chemical reactionso Reactions that require water are known as hydrolysis reactionso Example: water helps digest food or break down biological molecules

Inorganic Compounds Cushioning

o Water serves a protective functiono Examples: cerebrospinal fluid protects the brain from physical trauma, and

amniotic fluid protects a developing fetus

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Inorganic Compounds Salts

o Ionic compoundo Contain cations other than H+ and anions other than OH–

o Easily dissociate (break apart) into ions in the presence of watero Vital to many body functions

Example: sodium and potassium ions are essential for nerve impulses

Inorganic Compounds Salts (continued)

o All salts are electrolytes o Electrolytes are ions that conduct electrical currents

Inorganic Compounds Acids

o Electrolytes that dissociate (ionize) in water and release hydrogen ions (H+) o Proton (H+) donorso Example: HCl → H+ + Cl–

o Strong acids ionize completely and liberate all their protonso Weak acids ionize incompletely

Inorganic Compounds Bases

o Electrolytes that dissociate (ionize) in water and release hydroxyl ions (OH–)o Proton (H+) acceptors o Example: NaOH → Na+ + OH–

Inorganic Compounds Neutralization reaction

o Type of exchange reaction in which acids and bases react to form water and a salt

o Example: NaOH + HCl → H2O + NaCl

Inorganic Compounds pH

o pH measures relative concentration of hydrogen (and hydroxide) ions in body fluids

o pH scale is based on the number of protons in a solutiono pH scale runs from 0 to 14

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o Each successive change of 1 pH unit represents a tenfold change in H+ concentration

Inorganic Compounds pH (continued)

o Neutral 7 is neutral Neutral means that the number of hydrogen ions exactly equals the number of hydroxyl ions

o Acidic solutions have a pH below 7 More H+ than OH–

o Basic solutions have a pH above 7 Fewer H+ than OH–

o Buffers—chemicals that can regulate pH change

Organic Compounds Polymer: chainlike molecules made of many similar or repeating units (monomers) Many biological molecules are polymers, such as carbohydrates and proteins

Organic Compounds Dehydration synthesis—monomers are joined to form polymers through the removal of water molecules

o A hydrogen ion is removed from one monomer while a hydroxyl group is removed from the monomer it is to be joined with

o Water is removed at the site where monomers join (dehydration)

Organic Compounds Hydrolysis—polymers are broken down into monomers through the addition of water molecules

o As a water molecule is added to each bond, the bond is broken, and the monomers are released

Organic Compounds Carbohydrates

o Contain carbon, hydrogen, and oxygeno Include sugars and starcheso Classified according to size and solubility in water

Monosaccharides—simple sugars and the structural units of the carbohydrate group Disaccharides—two simple sugars joined by dehydration synthesis

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Polysaccharides—long-branching chains of linked simple sugars

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Organic Compounds Monosaccharides—simple sugars

o Single-chain or single-ring structureso Contain three to seven carbon atomso Examples: glucose (blood sugar), fructose, galactose, ribose, deoxyribose

Organic Compounds Disaccharides—two simple sugars joined by dehydration synthesis

o Examples include sucrose, lactose, and maltoseo Too large to pass through cell membranes

Organic Compounds Polysaccharides: long, branching chains of linked simple sugars

o Large, insoluble molecules o Function as storage productso Examples include starch and glycogen

Organic Compounds Lipids

o Most abundant are the triglycerides, phospholipids, and steroidso Contain carbon, hydrogen, and oxygen

Carbon and hydrogen outnumber oxygeno Insoluble in water, but soluble in other lipids

Organic Compounds Triglycerides, or neutral fats

o Found in fat depositso Source of stored energyo Composed of two types of building blocks—fatty acids and one glycerol

molecule Saturated fatty acids Unsaturated fatty acids

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Organic Compounds Fatty acid chains of triglycerides

o Saturated fats Contain only single covalent bonds Chains are straight Exist as solids at room temperature since molecules pack closely together

o Unsaturated fats Contain one or more double covalent bonds, causing chains to kink Exist as liquid oils at room temperature “Heart healthy”

Organic Compounds Trans fats

o Oils that have been solidified by the addition of hydrogen atoms at double bond sites

o Increase risk of heart disease Omega-3 fatty acids

o Found in cold-water fish and plant sources, including flax, pumpkin, and chia seeds; walnuts and soy foods

o Appear to decrease risk of heart disease

Organic Compounds Phospholipids

o Contain two fatty acids chains rather than three; they are hydrophobic (“water fearing”)

o Phosphorus-containing polar “head” carries an electrical charge and is hydrophilic (“water loving”)

o Charged “head” region interacts with water and ions while the fatty acid chains (“tails”) do not

o Form cell membranes

Organic Compounds Steroids

o Formed of four interlocking ringso Include cholesterol, bile salts, vitamin D, and some hormoneso Some cholesterol is ingested from animal products; the liver also makes

cholesterolo Cholesterol is the basis for all steroids made in the body

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Organic Compounds Proteins

o Account for over half of the body’s organic matter Provide for construction materials for body tissues Play a vital role in cell function Act as enzymes, hormones, and antibodies

o Contain carbon, oxygen, hydrogen, nitrogen, and sometimes sulfuro Built from building blocks called amino acids

Organic Compounds Amino acid structure

o Contain an amine group (NH2)o Contain an acid group (COOH)o Vary only by R-groups

Organic Compounds Protein structure

o Polypeptides contain fewer than 50 amino acidso Proteins contain more than 50 amino acidso Large, complex proteins contain 50 to thousands of amino acidso Sequence of amino acids produces a variety of proteins

Organic Compounds Structural levels of proteins

o Primary structure—strand of amino acid “beads”o Secondary structure—chains of amino acids twist or bend

Alpha helix—resembles a metal spring Beta-pleated sheet—resembles pleats of a skirt or sheet of paper folded into a fan

o Tertiary structure—compact, ball-like (globular) structureo Quaternary structure—result of a combination of two or more polypeptide

chains

Organic Compounds Fibrous (structural) proteins

o Appear in body structureso Exhibit secondary, tertiary, or even quaternary structureo Bind structures together and exist in body tissueso Stable proteins

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o Examples include collagen and keratin

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Organic Compounds Globular (functional) proteins

o Function as antibodies, hormones, or enzymeso Exhibit at least tertiary structureo Hydrogen bonds are critical to the maintenance of structureo Can be denatured and no longer perform physiological roleso Active sites “fit” and interact chemically with other molecules

Organic Compounds Enzymes

o Act as biological catalystso Increase the rate of chemical reactionso Bind to substrates at an active site to catalyze reactionso Can be recognized by their –ase suffix

Hydrolase Oxidase

Organic Compounds Nucleic acids

o Form geneso Composed of carbon, oxygen, hydrogen, nitrogen, and phosphorus atomso Largest biological molecules in the bodyo Two major kinds:

DNA RNA

Organic Compounds Nucleic acids are built from building blocks called nucleotides Nucleotides contain three parts

1. A nitrogenous base A = Adenine G = Guanine C = Cytosine T = Thymine U = Uracil

2. Pentose (five-carbon) sugar3. A phosphate group

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Organic Compounds Deoxyribonucleic acid (DNA)

o The genetic material found within the cell’s nucleuso Provides instructions for every protein in the bodyo Organized by complementary bases to form a double-stranded helixo Contains the sugar deoxyribose and the bases adenine, thymine, cytosine,

and guanineo Replicates before cell division

Organic Compounds Ribonucleic acid (RNA)

o Carries out DNA’s instructions for protein synthesiso Created from a template of DNAo Organized by complementary bases to form a single-stranded helixo Contains the sugar ribose and the bases adenine, uracil, cytosine, and

guanineo Three varieties are messenger, transfer, and ribosomal RNA

Organic Compounds Adenosine triphosphate (ATP)

o Composed of a nucleotide built from ribose sugar, adenine base, and three phosphate groups

o Chemical energy used by all cellso Energy is released by breaking high-energy phosphate bond

Organic Compounds ADP (adenosine diphosphate) accumulates as ATP is used for energy ATP is replenished by oxidation of food fuels Three examples of how ATP drives cellular work are shown next

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