Chapter 2

ChemistryInstructor Jennifer Evens

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Atoms, Ions, and Molecules

• A basic understanding of chemical concepts is necessary to understand physiological processes

• At its simplest level of organization, the human body is composed of chemical structures:– atoms– ions– Molecules

Atoms, Ions, and Molecules: Matter, Atoms, Elements, and the Periodic Table

• Matter is anything that takes up space• Human body is composed of matter

– Three forms:• solid (e.g., bone)• liquid (e.g., blood)• gas (e.g., oxygen)

• Matter is composed of atoms– Atom, smallest particle that exhibits the chemical properties of

an element

Human Body and Chemistry• Chemical Elements

– Element• Simplest form of matter i.e. H2O>Hydrogen and oxygen > (unique)

– Atom smallest piece of an element .– Made up of Protons /Neutrons/Electrons > (Not unique)

• Identified by an atomic number (number of protons in nucleus) arranged in periodic table by atomic number

• Chemical Symbol Based on one or two letters, per Eng name some Latin (Ferrum Fe, Kalium K, natrium NA)

• 91 naturally occurring, 24 pt of nl physiological roles in humans

– Minerals • several elements classified here, extracted by soil (4% wt, ¼ =Ca & P)• P is a major component of nucleic acid , ATP and cell membranes

Atoms, Ions, and Molecules: Matter, Atoms, Elements, and the Periodic Table

The components of an atom• Atoms composed of three subatomic particles:

– protons• mass of one atomic mass unit (amu)• positive charge of one (+1)

– neutrons• mass of one amu• no charge

– electrons• 1/1800th mass of a proton or neutron• negative charge of one (-1)• located at varying distance from the nucleus in regions called orbitals

Periodic Table• Chemical symbol

Based on one or two letters of Chemical name

• Atomic number number of protons in nucleus

• Atomic mass equal to total number of protons and neutrons

http://www.wpclipart.com/education/supplies/periodic_table_of_the_elements.png

Figure 2.1b

Most Common Elements of the Human Body

Major elements(collectively compose more than 98% of body weight)

Lesser elements(collectively compose less than 1% of body weight)

P

Ca

N

H

C

O

Symbol % Body weight

Oxygen

Carbon

Hydrogen

Phosphorus

Calcium

Nitrogen

1.0

1.5

3.0

10.0

18.0

65.0

(b)

Symbol % Body weight

S

K

Fe

Mg

Na

Cl

Sulfur

Potassium

Iron

Magnesium

Chlorine

Sodium

0.25

0.20

0.15

0.15

0.05

0.006

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Atoms, Ions, and Molecules: Matter, Atoms, Elements, and the Periodic Table

Determining the number of subatomic particles• Proton number = atomic number• Neutron number = atomic mass – atomic number

• neutron number = (p + n) – p• neutron number of Na = 23 – 11 = 12

• Electrons number = proton number

Atoms, Ions, and Molecules: Matter, Atoms, Elements, and the Periodic Table

Diagramming Atomic Structures• An atom has shells of electrons

surrounding the nucleus– Each shell with a given energy

level– Each shell holding a limited

number of electrons– Innermost shell two electrons,

second shell up to eight– Shells close to the nucleus: must

be filled first– Valence Electrons-outermost shell

Figure 2.2b

Shell model

(b)

Nucleus: Proton (+)

Neutron (no charge)

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8 electrons

8 protons

8 neutrons

Energyshell

Electron shells: Electron (–)

Atoms, Ions, and Molecules: Matter, Atoms, Elements, and the Periodic Table

Protons and neutrons determine the mass of an atom.

What subatomic particles determine the mass of an atom? The charge of an atom?

Protons and electrons determine the charge of an atom.

Isotopes of HydrogenIsotopes•Same Element• Variety of atoms •Differ from one another in number neutrons•Chemical behavior the same no matter number of neutrons•Reason for variability in atomic weight•Differ in physical behavior•Many decay

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Radioisotopes• Isotopes that

are unstable and decay to more stable forms-Physical Half Life

• Radioactivity is the decaying process

• During high energy radiation electrons are ejected from atoms converting atoms to ions

Carbon–13 Carbon–14

6 protons7 neutrons6 electrons

6 protons8 neutrons6 electrons

Carbon–12

6 electrons

6 protons6 neutrons

Atoms, Ions, and Molecules: Chemical Stability and the Octet Rule

• Elements tend to lose, gain, or share electrons to obtain complete outer shells with eight electrons – Known as the octet rule

Figure 2.4

F

1 2 3 4 5 6 7 8

P

N

H

C O

S

K

B

IA IIA IIIA IVA VA VIA VIIA VIIIA

Li

Na

Ca

ArClSiAl

NeBe

Mg

He

Number of valence electronsCopyright © The McGraw–Hill Companies, Inc. Permission required for reproduction or display.

Atoms, Ions, and Molecules: Chemical Stability and the Octet Rule

A complete outer shell with eight electrons increases chemical stability.

What is the relationship of the octet rule and chemical stability?

Molecules/Bonds

• Molecules – chemical particles composed of 2 or more atoms united by a chemical bond (same or different)– covalent bond - Atoms share electrons – ionic bond- Atoms give up and receive electrons

– Ionically bonded molecules separate to become ions in water. – Ions in solution are electrolytes.

• Compounds - molecules composed of two or more elements

Common Ions in the

Human body and Their

Physiological Significance (Table 2.1a)

Common Ions in the

Human body and Their

Physiological Significance (Table 2.1b)

Ions and Ionic Compounds: Ions

Losing electrons and the formation of cations• Sodium can reach stability by donating an electron

– Now satisfies the octet rule– Now has 11 protons and 10 electrons– Charge is +1

• Ions with positive charge called cations

Ions and Ionic Compounds: Ions

Gaining electrons and the formation of anions• Chlorine can reach stability by gaining an electron

– Now satisfies the octet rule– Now has 17 protons and 18 electrons– Charge is -1

• Ions with negative charge called anions• Polyatomic ions are anions composed of more than

one atom– E.g., bicarbonate ion and phosphate ion

Ions and Ionic Compounds: Ions

General rules for assigning charges• Atoms with one, two, or three electrons in valence

shell become cations– E.g., calcium has two electrons in its outer shell

• reaches stability by donating two electrons• develops a charge of +2

• Atoms with five, six, or seven electrons become anions– E.g., chlorine has seven electrons in its outer shell

• reaches stability by gaining one electron• develops a charge of -1

Ions and Ionic Compounds: Ionic Bonds

• Cations and anions may bind together in ionic bonds– Salts formed– For example, table salt (NaCl)

• Each sodium atom donates one outer shell electron to a chlorine atom• Sodium and chlorine ions are held together by ionic bonds in a lattice

crystal structure• This is an ionic compound

– Another example, magnesium chloride• Each magnesium atom donates one electron to two chlorine atoms

Figure 2.5

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+ =Na11p

Cl17p

Na+

11pCl–

17p

Cl– Na+ Cl–

Cl– Na+Na+

Cl– Na+ Cl–

(d) Lattice salt crystal of NaCl(c) Sodium ion (Na+)(a) Sodium atom (Na) (b) Chlorine atom (Cl) Chloride ion (Cl–)

Ions and Ionic Compounds: Ionic Bonds

No. Positively charged cations and negatively charged anions may form ionic bonds. A cation and another cation cannot form the electrostatic interaction needed. Both want to lose electrons.

Could an ionic bond form between two cations?

Covalent Bonding, Molecules, and Molecular Compounds: Covalent Bonds

• A covalent bond is formed when atoms share electrons– Occurs when both atoms require electrons– Occurs with atoms that have four to seven electrons in their outer shell

• Four elements of the human body form covalent bonds most commonly:– oxygen (O)– carbon (C) – hydrogen (H)– nitrogen (N)

Covalent Bonding, Molecules, and Molecular Compounds: Covalent Bonds

The number of bonds an atom can form• Simplest covalent bond formation occurs between

two hydrogen atoms– Each sharing its single electron

• Oxygen needs two electrons to complete outer shell– Forms two covalent bonds

• Nitrogen forms three bonds• Carbon forms four bonds

Covalent Bonding, Molecules, and Molecular Compounds: Covalent Bonds

Single, double, and triple covalent bonds• Single covalent bond

– One pair of electrons shared• e.g., between two hydrogen atoms

• Double covalent bond– Two pairs of electrons shared

• e.g., between two oxygen atoms

• Triple covalent bond– Three pairs of electrons shared

• e.g., between two nitrogen atoms

Figure 2.7

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N N

H H

O O

H H

O O

N N

Hydrogen gas (H2)Single bond

Double bond

Triple bond

Nitrogen gas (N2)

Oxygen gas (O2)

Single covalent bond

Double covalent bond

Triple covalent bond

(a)

(b)

(c)

Covalent Bonding, Molecules, and Molecular Compounds: Covalent Bonds

Carbon Skeleton Formation• Carbon can bond in straight chains, branched chains,

or rings– Carbon present where lines meet at an angle; additional atoms hydrogen

Figure 2.9

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C CC C C CC C C C CC C CC

C C

C

C C

C

C

CC

C

Straight chain Branched chain Ring

(a) (b) (c)

CH3

CH3

CH3H3C

CH3

H3C

C

Covalent Bonding, Molecules, and Molecular Compounds: Covalent Bonds

Nonpolar and polar covalent bonds (continued)• Atoms in a covalent bond may share electrons equally

or unequally– Atoms with different electronegativity share electrons unequally– This results in a polar covalent bond

Covalent Bonding, Molecules, and Molecular Compounds: Intermolecular Attractions

• Intermolecular attractions– Weak chemical attractions between molecules– Collectively important in maintaining the shape of complex molecules

such as DNA and protein– One type, the hydrogen bond

• forms between polar molecules• attraction between partially positive hydrogen atom and a partially

negative atom• individually weak, collectively strong• influences how water molecules behave

Covalent Bonding, Molecules, and Molecular Compounds: Intermolecular Attractions

• Other intermolecular bonds:– van der Walls forces

• nonpolar molecules• electrons orbiting nucleus briefly, unevenly distributed• induce unequal distribution of adjacent atom of another nonpolar molecule• individually weak

– hydrophobic interactions• nonpolar molecules placed in a polar substance• if occurring between parts of large molecule, termed intramolecular

attractions

Molecular Structure of Water and the Properties of Water: Molecular Structure

• Water– Composes two-thirds of the

human body by weight– Polar molecule composed of

one oxygen atom bonded to two hydrogen atoms

– Oxygen atom with two partial negative charges

– Hydrogen with a single positive charge

– Can form four hydrogen bonds with adjacent molecules

• central to water’s properties

Figure 2.12

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HH

O

Water (H2O)

Hydrogenbonds

+

+

++

–

–

––

(a) (b)

Water is a polar molecule dueto unequal sharing of electrons.

Hydrogen bonds formbetween water molecules.

+

–

+

–

Water• Most chemicals in our body are chemicals that are

dissolved or suspended in water• 50-75% of body = water• Key Functions

– Solvency –ability to dissolve other chemicals separating ionic bonds into electrolytes

• Hydrophilic – substances that dissolve in water• Hydrophobic substances that don’t dissolve in water

– Lubricant- tears, joints…– Transportation– nutrients and waste– Chemical reactivity – waters ability to participate in

chemical reactions, digestion…– Chermal stability – helps stabilize internal temperature

Mixtures of other substances

Solution consists of– Solute Particles of matter that are mixed with (salt)– Solvent a more abundant substance (water)– Solution is Defined by

• Solute and solvent can not be distinguished from one another• Usually transparent• Solute will dissolve through most permeable membranes• Solute does not separate from solvent when allowed to stand• Concentration refers to the amount of solute relative to the amount

of solvent. • In comparing solutions, a hypertonic solution is more concentrated,

an isotonic solution is the same concentration, and a hypotonic solution is less concentrated.

Tonicity

High SoluteLow solute Equal concentration

Refers t o solute/solvent concentrations

Figure 2.14

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NEUTRAL pH

Acidic

Water has a neutral pH.Body fluids are altered inpH with the addition ofeither an acid or a base.

Alkaline

OC

C

C C

C

HH

H

H

H

REGULATES BODY TEMPERATURE

CUSHIONS

TRANSPORTS

LUBRICATES

HIGH SURFACE TENSION

Amphipathic molecules

Hydrophobic molecules

Hydrophilic substance

UNIVERSAL SOLVENT

CH2OH

OH

OH

HO

Na+

Cl–

Cerebrospinalfluid

Water is the fluidmedium to transportsubstances in bloodand other body fluids(e.g., blood, urine).

Fluid cushionsagainst suddenmovements.

Fluid serves as alubricant todecrease friction.

Alveolus

Pericardial sac

Water's high surfacetension causesstructures to adhere.The moist alveoli in thelungs are preventedfrom collapsing andadhering by surfactant.

Pericardial fluid

Surfactant

Amphipathicmolecules formchemical barriers(e.g., plasmamembranes, micelles).

Polar portiondissolves, nonpolarportion excluded.

Water moleculesexclude nonpolarmolecules, thusproteins are requiredfor their transport within the body.

Electrolytesdissolveand dissociate.

Nonelectrolytesdissolve andremain intact.

Heart

Heat

HO

Brain

Skull

Water helpsregulate bodytemperaturedue to its highspecific heatand high heatof vaporization.

Molecular Structure of Water and the Properties of Water: The Universal Solvent

Substances that dissolve in water but remain intact are nonelectrolytes and cannot conduct an electric current (e.g., glucose). Substances that both dissolve and dissociate in water are electrolytes and can conduct an electric current (e.g., NaCl).

How does the interaction of a nonelectrolyte and water differ from the interaction of an electrolyte and water?

Acidity• pH -acidity expession, measure derived from the Molarity

of [H⁺]• Scale 0<7 acid 7neutral 7<14basic (alkaline)

– Lower # the more H⁺ logatithmic of 10– Important to phys function to maintain pH, blood 7.35-7.45– acidosis < 7.35/alkalosis>7.45

• Acid – is a proton donor – molecule that releases a proton in water H⁺

• Base– is a proton acceptor (OH⁻, hydroxide ion; most bases tend to be

substances that accept H⁺, but not necessarily NH₃ ammonium accepts)

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0

1

2

3

4

5

6

8

9

H+

H+

[H+]

H+ <

ExamplespH Value

Sodium hydroxide (NaOH): 14

Household bleach: 12

Household ammonia: 10.5–11

Antacid: 10.5

Seawater: 8

Human blood: 7.4

Pure water: 7

Milk, saliva: 6.3–6.6

Urine: 6

Tomato juice: 4.7

Grapefruit juice: 3

Wine: 2.4–3.5

Lemon juice, stomach acid: 2–3

Hydrochloric acid (HCl): 1

100

10–1

10–2H+

H+

H+

H+

H+

H+H+ H+

H+

H+

H+

H+

H+

H+

H+

H+

H+

Decreasing

Increasing

OH–

pH

H+ Concentration

[H+]

H+ > OH–

pH

Basic

Neutral

Acidic

10–3

10–4

10–5

10–6

10–7

10–8

10–9

10–10

10–11

10–12

10–13

10–14 14

13

12

11

10

7

Decreasing

Increasing

Organic Compounds

• Carbon – Organic chemistry is the study of compounds of carbon– Versatile atom serving foundation for a wide variety of

structures– 4 valence electrons, so binds with other atoms to complete

shell– Readily bonds to each other forming long chains, branched

molecules and rings – 4 primary categories of the organic molecules of life:

• Carbohydrates• lipids• Proteins• nucleic acids

Carbon bonds• Macromolecules – long chains of carbons (starch

/DNA)– Polymers molecules made of repetitive series of similar

subunits called monomers– Polymerization joining of monomers

• DNA - 4 different types (nucleotides)– Purine (Adenine and Guanine)– Pyrimidine (Thymine and Cytosine)

• Proteins - 20 different types (Amino acids)

– Polymerization is achieved through cells by dehydration synthesis/condensation; joining two monomers together by a covalent bond forming a dimer

– hydrolysis is the opposite, where covalent bond is broken, this happens during digestion

Carbohydrates• Hydrophilic• Primary source of body's nutrient energy• General formula = (CH₂0)ⁿ n=number of carbon atoms

-2 H for every O– Monosaccharide – simplest; monomers; C6H12O6

• Glucose/fructose/glactose

– Disaccharides-Sugars composed of 2 monosaccharides• Sucrose/lactose/maltose

– Polysaccharides – long chains of glucose• Glycogen/starch/cellulose

– All listed are sources of energy that can be quickly mobilized and converted to glucose > into ATP

Lipids• Hydrophobic• Not composed of monomers• Consist of carbon, hydrogen, and oxygen atoms

– C atoms form backbone of molecules– Many more H atoms then O atoms– Building blocks are often glycerol and fatty acids Less oxidized then

carbohydrates = higher caloric count• 5 primary types

– Fatty acid– Triglycerides– Phospholipids– Eicosanoids– Steroids

Proteins

• Most versatile molecules in body • Polymer of amino acids

– Amino acids are the building units of proteins.• Composed of carbon, hydrogen, oxygen, and nitrogen• Consist of an amine group, acid group, and R group• 20 different types of amino acids, each different in their

R group

– Long strings of amino acids called polypeptides full to form functional proteins.

Protein structure

Protein structure (concluded)

Protein Functions

• Structure - keratin/collagen• Communication – hormones and cell to cell signals• Membrane transport – carriers of particles, responsible for

turning cell action on and off…• Catalysis – globular proteins (enzymes)are for metabolic

activity• Recognition and protection –immune recognition and

clotting factors• Movement – cell transport to muscle movement • Cell adhesion – keep tissues together, immune response ,

fertilization….

Protein Functions (Table 2.5)

Nucleic Acids

• Two types in cells– Deoxyribonucleic acid (DNA)– Ribonucleic acid (RNA)

• Building blocks are called nucleotides.– Composed of 1 pentose sugar, 1 phosphate, 1

organic base

DNA StructureNucleotide basic unit composed of

– Phosphate– Deoxyribose sugar– Nitrogenous base

• Sugar and Phosphate form backbone (3’5’ bonding order)

• Nitrogenous bases – Two types of nitrogenous bases

• Purine (Adenine and Guanine)• Pyrimidine (Thymine and Cytosine)

– Join back bone by covalent bonds– Form rungs of ladder by paired nitrogenous

bases directed by hydrogen bonding; purine to pyrimidine (not random)

• Adenine to Thyamine • Guanine to Cytosine

– Hydrogen bonding allows for unzipping of genetic material

– Pairing allows for- Law of Complimentary pairing

• Maintains code (semi conservative replication)• Gives variety

ATP(nucleotide)>ADP• Most important energy transfer molecule• Stores energy from exergonic reactions

(glucose oxide)• Releases energy within seconds for

physiological like polymerization reactions

• ATP + H₂O → ADP + Pi + energy Heat

Work

ATPase

Adenosine triphosphatase is an enzyme that hydrolyzes the third phosphate bond to produce adenosine diphosphate

Phosphorylation is the addition of the Pi carried out by enzymes called Kinases; and is sometime the on/off switch

Organic Molecules

Type Elements Building Blocks Examples Where found Function

CARBOHYDRATE C H O Monosaccharides 1. Glucose blood energy

1:2:1 ratio (simple sugars) 2. Glycogen liver & muscle stored energy

LIPIDSC H O(any ratio) Fatty acids & glycerol 1. Fats adipose tissue stored energy, insulation

2. Steroids(sex hormones) blood regulate body

3. Phospholipids cell membrane structure

PROTEINS C H O N amino acids 1. Structural skin strength

(20 different amino acids) 2. Contractile muscle movement

3. Buffers everywhere stabilize pH

4. Antibodies blood attack foreign stuff

5. Transport blood transport stuff

6. Enzymes everywhere catalysts

7.Hormones blood regulate body

NUCLEIC ACIDS C H O N P nucleotides DNA Nucleus contains genetic info

RNAnucleus & cytoplasm processes genetic info