Ch 2 PowerPoint Biology 201

Chapter 02

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1

The Nature of Molecules andthe Properties of Water

Chapter 2

2

3

Nature 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

4

Atomic 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

5


neutron(no charge)

1 Proton1 Electron

8 Protons8 Neutrons8 Electrons

Hydrogen Oxygen

proton(positive charge)

electron(negative charge)

a.

b.

6

Atomic 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 protons• Element

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

7

Atomic 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

Electrons

• 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 charge8

Isotopes

• 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

9

10


Carbon-12 Carbon-13 Carbon-14

6 Protons 6 Neutrons 6 Electrons



11

Electron arrangement

• Key to the chemical behavior of an atom lies in the number and arrangement of its electrons in their orbitals

• Bohr model – electrons in discrete orbits• Modern physics defines orbital as area

around a nucleus where an electron is most likely to be found

• No orbital can contain more than two electrons

12


One spherical orbital (1s)

Electron Shell Diagram Corresponding Electron Orbital

EnergyLevel K

x

zy

Neon

Electron Shell Diagram Electron Orbitals

x

y z

One spherical orbital (2s)

Corresponding Electron OrbitalsElectron Shell Diagram

Three dumbbell-shaped orbitals (2kk)

Energylevel L

Energy levels

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

energy• Be careful not to confuse energy levels,

which are drawn as rings to indicate an electron’s energy, with orbitals, which have a variety of three-dimensional shapes and indicate an electron’s most likely location 13

14


NM

LK

Energyabsorbed

Nucleus

Energyreleased Nucleus

KLMN

15

Redox

• 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


++

Oxidation Reduction

+

16

Elements

• 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

17

Periodic Table of the Elements

1H

3Li

4Be

19K

12Mg

93Np

94Pu

95Am

96Cm

97Bk

98Cf

99Es

100Fm

101Md

102No

103Lr

37Rb

38Sr

39Y

42Mo

45Rh

46Pd

47Ag

48Cd

49In

50Sn

51Sb

52Te

53I

54Xe

21Sc

40Zr

22Ti

23V

24Cr

25Mn

27Co

28Ni

29Cu

30Zn

36Kr

5B

6 C

8O 2

He

55Cs

56Ba

72Hf

73Ta

74W

75Re

76Os

77Ir

78Pt

79Au

80Hg

81Tl

82Pb

83Bi

84Po

85At

86Rn

87Fr

88Ra

57La89Ac

104 105 106 107 108 109

58Ce

59Pr

60Nd

61Pm

62Sm

63Eu

64Gd

65Tb

66Dy

67Ho

68Er

69Tm

70Yb

71Lu

90Th

91Pa

92U(Actinide series)

11Na

20Ca

41Nb

43Tc

44Ru

26Fe

13Al

31Ga

32Ge

14Si

7N15P33As

16S

35Br

34Se

9F

18Ar

10Ne

17Cl

110

Rf Ob Sg Bh Hs Mt Ds111 112 113 114 115 116 117

Rg Cn Uut Fl Uup Lv Uus Uuo118

Key

1H

atomic numberchemical symbol

Mg

Fe

S

P

Ca

Cl

Na

N

H

C

a. b.

O

(Lanthanide series)

Carbon (C)

Oxygen (O)

Hydrogen (H)

Nitrogen (N)

Sodium (Na)

Chlorine (Cl)

Calcium (Ca)

Phosphorus (P)

Potassium (K)K

Sulfur (S)

Iron (Fe)

Magnesium (Mg)


• 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

important18

Mg

Fe

S

P

Ca

Cl

Na

N

H

C

b.

O

Carbon (C)

Oxygen (O)

Hydrogen (H)

Nitrogen (N)

Sodium (Na)

Chlorine (Cl)

Calcium (Ca)

Phosphorus (P)

Potassium (K)K

Sulfur (S)

Iron (Fe)

Magnesium (Mg)


19

Chemical 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

20

Ionic 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

21

Sodium atom

Cl

Chlorine atom

a.

Sodium ion (+)

Cl–

Chloride ion (–)

b. NaCl crystal

Cl– Cl–

Cl– Cl–

Cl–


NaNa++

NaNa++

NaNa++

NaNa++

Na Na+

22

Covalent 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

23


NNN2N N

H H

O2O O

H2

O O

Single covalent bondHydrogen gas

covalent bond

Double covalent bondoxygen gas

Triple covalent bondNitrogen gas

H H

24

Electronegativity

• 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

25

Chemical 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

26

• Extent of chemical reaction influenced by1. Temperature2. Concentration of reactants and products3. Catalysts

• Many reactions are reversible

27

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Water

• 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 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

a. Solid b. Liquid c. Gasa: © Glen Allison/Getty Images RF; b: © PhotoLink/Getty Images RF; c: © Jeff Vanuga/Corbis

29

Polarity of water

• Within a water molecule, the bonds between oxygen and hydrogen are highly polar– Oxygen is much more electronegative than

Hydrogen• Partial electrical charges develop

– Oxygen is partially negative δ+

– Hydrogen is partially positive δ–


+

–

+

+

a. b.

c.

Bohr Model

Space-Filling Model

8p

Ball-and-Stick Model

8n

–

+

+

–

–

+

+

–

104.5

+

31

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

32


+

a.

b.

Water moleculeHydrogen atom

–Hydrogen bond

Oxygen atom

Hydrogen atom

Hydrogen bond+

–

An organic molecule

Oxygen atom

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

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

33

34

Properties of water

1. 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

35


Hydration shells

Water molecules

Salt crystal

Cl–

Na+

Cl–

+

+

+

++

–

–

–

–

–

Na+

36

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 shapes6. Water can form ions

H2O OH– + H+

hydroxide ion hydrogen ion

37

Acids 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

Acids and Bases - pH

• 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+]

38

39


Hydrogen IonConcentration [H+] Examples of Solutions

Stomach acid, lemon juice

pH Value

Hydrochloric acidAcidic

Basic

10–2

10–3 Vinegar, cola, beer10–4 Tomatoes10–5 Black coffee10–6 Urine10–7 Pure water10–8 Seawater10–9 Baking soda10–10 Great Salt Lake10–11 Household ammonia10–12

Household bleach10–13

10–14 Sodium hydroxide

0123456

891011121314

100

10–1

Buffers

• 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

40

41


1X0 3X 4X 5X2X

pH

9876543210

Amount of base added

Buffering range

42

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


+Bicarbonate

ion(HCO3

–)+

++

–

+

Water(H2O)

Carbondioxide(CO2)

Carbonicacid

(H2CO3)

Hydrogenion(H+)

Education

Ch 2 PowerPoint Biology 201