The Nature of Molecules andThe Nature of Molecules andthe Properties of Waterthe Properties of Water

Chapter 2

Nature of AtomsNature of Atoms

• Matter has mass and occupies space• All matter is composed of atoms

• Understanding the structure of atoms is critical to understanding the nature of biological molecules

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Atomic StructureAtomic Structure• Atoms are composed of

– Protons• Positively charged particles• Located in the nucleus

– Neutrons• Neutral particles• Located in the nucleus

– Electrons • Negatively charged particles• Found in orbitals surrounding the nucleus

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Atomic numberAtomic number

Number of protons equals number of electrons◦Atoms are electrically neutral

Atomic number = number of protons◦Every atom of a particular element has the same

number of protonsElement

◦Any substance that cannot be broken down to any other substance by ordinary chemical means

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Atomic massAtomic mass

• Mass or weight?– Mass – refers to amount of substance– Weight – refers to force gravity exerts

on substance• Sum of protons and neutrons is the

atom’s atomic mass• Each proton and neutron has a mass

of approximately 1 dalton

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ElectronsElectrons

• Negatively charged particles located in orbitals

• Neutral atoms have same number of electrons and protons

• Ions are charged particles – unbalanced– Cation – more protons than electrons = net

positive charge– Anion – fewer protons than electrons = net

negative charge

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IsotopesIsotopes

• Atoms of a single element that possess different numbers of neutrons

• Radioactive isotopes are unstable and emit radiation as the nucleus breaks up– Half-life – time it takes for one-half of

the atoms in a sample to decay

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Energy levelsEnergy levels

• Electrons have potential energy related to their position– Electrons farther from nucleus have

more energy

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RedoxRedox

• During some chemical reactions, electrons can be transferred from one atom to another– Still retain the energy of their position in the

atom– Oxidation = loss of an electron– Reduction = gain of an electron

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ElementsElements

• Periodic table displays elements according to valence electrons

• Valence electrons – number of electrons in outermost energy level

• Inert (nonreactive) elements have all eight electrons

• Octet rule – atoms tend to establish completely full outer energy levels

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• 90 naturally occurring elements• Only 12 elements are found in

living organisms in substantial amounts

• Four elements make up 96.3% of human body weight– Carbon, hydrogen, oxygen,

nitrogen

• Organic molecules contain primarily CHON

• Some trace elements are very important

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Chemical BondsChemical Bonds

• Molecules are groups of atoms held together in a stable association

• Compounds are molecules containing more than one type of element

• Atoms are held together in molecules or compounds by chemical bonds

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Ionic bondsIonic bonds• Formed by the attraction

of oppositely charged ions• Gain or loss of electrons

forms ions– Na atom loses an electron

to become Na+

– Cl atom gains an electron to become Cl–

– Opposite charges attract so that Na+ and Cl– remain associated as an ionic compound

• Electrical attraction of water molecules can disrupt forces holding ions together 13

Covalent bondsCovalent bonds• Form when atoms share 2 or

more valence electrons• Results in no net charge,

satisfies octet rule, no unpaired electrons

• Strength of covalent bond depends on the number of shared electrons

• Many biological compounds are composed of more than 2 atoms – may share electrons with 2 or more atoms

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ElectronegativityElectronegativity

• Atom’s affinity for electrons

• Differences in electronegativity dictate how electrons are distributed in covalent bonds– Nonpolar covalent bonds = equal sharing

of electrons– Polar covalent bonds = unequal sharing

of electrons

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Chemical reactionsChemical reactions

• Chemical reactions involve the formation or breaking of chemical bonds

• Atoms shift from one molecule to another without any change in number or identity of atoms

• Reactants = original molecules• Products = molecules resulting from

reaction

6H2O + 6CO2 → C6H12O6 + 6O2

reactants products 16

• Extent of chemical reaction influenced by

1. Temperature2. Concentration of reactants and

products3. Catalysts

• Many reactions are reversible

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WaterWater• Life is inextricably tied to water• Single most outstanding chemical

property of water is its ability to form hydrogen bonds– Weak chemical associations that

form between the partially negative O atoms and the partially positive H atoms of two water molecules

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Polarity of waterPolarity of water• Within a water molecule,

the bonds between oxygen and hydrogen are highly polar– O is much more

electronegative than H

• Partial electrical charges develop– Oxygen is partially negative

δ+

– Hydrogen is partially positive δ–

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Hydrogen bonds• Cohesion – polarity of

water allows water molecules to be attracted to one another

• Attraction produces hydrogen bonds

• Each individual bond is weak and transitory

• Cumulative effects are enormous

• Responsible for many of water’s important physical properties

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• Cohesion – water molecules stick to other water molecules by hydrogen bonding

• Adhesion – water molecules stick to other polar molecules by hydrogen bonding

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Properties of waterProperties of water1. Water has a high specific heat

– A large amount of energy is required to change the temperature of water

2. Water has a high heat of vaporization– The evaporation of water from a surface

causes cooling of that surface

3. Solid water is less dense than liquid water

– Bodies of water freeze from the top down

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4. Water is a good solvent– Water dissolves polar molecules and ions

5. Water organizes nonpolar molecules– Hydrophilic “water-loving”– Hydrophobic “water-fearing”– Water causes hydrophobic molecules to

aggregate or assume specific shapes

6. Water can form ions H2O OH– + H+

hydroxide ion hydrogen ion

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Acids and basesAcids and bases

• Pure water– [H+] of 10–7 mol/L– Considered to be neutral– Neither acidic nor basic

• pH is the negative logarithm of hydrogen ion concentration of solution

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• Acid– Any substance that dissociates in water to

increase the [H+] (and lower the pH)– The stronger an acid is, the more

hydrogen ions it produces and the lower its pH

• Base– Substance that combines with H+

dissolved in water, and thus lowers the [H+]

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BuffersBuffers• Substance that resists changes in pH• Act by

– Releasing hydrogen ions when a base is added

– Absorbing hydrogen ions when acid is added

• Overall effect of keeping [H+] relatively constant

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• Most biological buffers consist of a pair of molecules, one an acid and one a base

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Question 1

Which subatomic particle has a positive charge?

a. Electron

b. Neutron

c. Proton

d. Neutrino

e. Photon

Question 2

Isotopes are atoms of the same element but differ in the number of

a. Electrons

b. Protons

c. Neutrons

d. Orbitals

e. Bonds

Question 3

Radioactive isotopes –

a. Are unstable

b. Decay over time

c. Emit radiation

d. May occur naturally

e. All of the above

Question 4

Typically an increase in temperature causes the rate of a chemical reaction to –

a. Decrease

b. Increase

c. Remain the same

Question 5

Which of the following has the lowest concentration of H+ ions?

a. pH = 2

b. pH = 6

c. pH = 8

d. pH = 12

e. pH = 14

Question 6

Which of the following properties of water is not a consequence of its ability to form H bonds?

a. Cohesion

b. High specific heat

c. Adhesion

d. Ability to function as a solvent

e. Neutral pH

Question 7

An atom with more protons than electrons is –

a. An element

b. An isotope

c. A cation

d. An anion

Question 8

What kind of chemical bond is formed when atoms share one or more pairs of electrons?

a. Covalent bondb. Ionic bondc. Hydrogen bondd. Polar bond

Question 9

If a molecule gains an electron, it has been –

a. Oxidized

b. Reduced

c. Electrified

d. Deprotonated

Question 10

Which of the following types of chemical bonds is the strongest?

a. Hydrogen bondb. Ionic bondc. Covalent bondd. All are equal strength

Question 11

In the formation of salt, the sodium atom –

a. Loses an electron to chlorine

b. Becomes a positive ion

c. Has one more proton than electron

d. A and B are correct

e. A, B and C are correct

Question 12

Magnesium chloride is a salt formed from ionic bonds between one magnesium ion and two chloride ions. Magnesium atoms has two electrons in their outer (third) shell and chlorine atoms have seven electrons in their outer shell. How many electrons would be in the outer shell of magnesium once it becomes a ion?

• 1• 2• 4• 6• 8

Question 13

18O has an atomic number of 8. How many neutrons does 18O have?

a. 8

b. 10

c. 12

d. 18

Question 14

Carbon’s atomic number is 6. How many electrons

are in carbon’s outer shell?

a. 2

b. 4

c. 6

d. 8

Question 15

Paleontologists distinguish rocks from dinosaur bones by touching their tongues to the object. If their tongue sticks, it is considered bone. This occurs because the water from the tongue moves up the porous spaces of bone. What property of water is allowing this to occur?

a. Cohesion

b. Capillary action

c. Water ionization

d. Heat of vaporization

Question 16

A water strider is an insect that can walk on water. How is this possible?

a. Capillary actionb. Hydration shellsc. Hydrophobic exclusiond. Surface tension

Question 17

Hydrogen bonding between water molecules makes them tend to stick together. How does this affect the specific heat (SH) and heat of vaporization (HOV) of water?

a. The SH and HOV of water are highb. The SH and HOV of water are lowc. SH is high but HOV is lowd. HOV is high but SH is lowe. None of these answers are correct

Question 18

What property of an atom determines how it forms bonds?

a. Atomic Massb. Atomic numberc. Valance electronsd. Orbitse. Neutrons