1 biology sylvia s. mader michael windelspecht chapter 2 basic chemistry copyright © the...

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BiologySylvia S. Mader

Michael Windelspecht

Chapter 2 Basic Chemistry

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

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Mills Biology 2001

Mader Chapter 2 ~ Basic Chemistry• This chapter should be a review.

We will go over this material very quickly.

• Read second ½ of Ch 2 for tomorrow.

• You should also read appropriate pages of CliffsAP

• Take the Sample test on page 27, grade it and turn in by Sept 2.

• Topics2.1 Chemical Elements2.2 Compounds and Molecules2.3 Chemistry of Water2.4 Acids and Bases

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2.1 Chemical Elements

• Matter is defined as anything that has mass and occupies space.

• Matter exists in three states: solid, liquid, and gas.

• All matter (both living and non-living) is composed of elements.

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4

Elements

• An element is a substance that cannot be broken down into substances with different properties; composed of one type of atom.

• Six elements make up 95% of the body weight of organisms: (acronym CHNOPS)

Carbon

Hydrogen

Nitrogen

Oxygen

Phosphorus

Sulfur

4

5

60

40

20

0Fe Ca K S P Si Al Mg Na O N C H

Earth’s crustorganisms

Element

Per

cen

t b

y W

eig

ht

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© Gunter Ziesler/Peter Arnold, Inc.

Composition of Earth’s Crust and Its Organisms

6

Atoms

• An atom is the smallest part of an element that displays the property of the element.

• An element and its atom share the same name.

Composed of subatomic particles: protons, neutrons, electrons

Central nucleus

• Protons- positively charged

• Neutrons- no charge

Orbiting clouds around nucleus (electron shells)

• Electrons- negatively charged, very low mass-negligible in calculations

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7c.

Subatomic Particles

= proton

= neutron

= electron

b.a.

Particle

Proton

Neutron

Electron

Nucleus

Nucleus

Electron shell

+1

0

–1

1

1

0

Atomic Mass Unit(AMU) Location

ElectricCharge

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8

Atomic Number and Mass Number

• Each element is represented by one or two letters to give it a unique atomic symbol. H = hydrogen, Na = sodium, C = carbon

• The atomic number is equal to the number of protons in each atom of an element.

• The mass number of an atom is equal to the sum of the number of protons and neutrons in atom’s nucleus. The atomic mass is approximately equal to the mass number.

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9

mass number

atomic numberatomic symbol

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Atomic number?

Atomic mass?

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Periodic Table

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• Atoms of an element are arranged horizontally by increasing atomic number in rows called periods.

• Atoms of an element arranged in vertical columns are called groups. Atoms within the same group share the same binding

characteristics.

• Atoms shown in the periodic table are electrically neutral. Therefore, the atomic number tells you the number of electrons

as well as the number of protons.

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Per

iod

s

1

2

3

4

atomic number

atomic symbol atomic mass

VIII

Groups

20.1819.0016.0014.0112.0110.819.0126.941

22.99 24.31 39.9535.4532.0730.9728.0926.98

83.6079.9078.9674.9272.5969.7240.0839.10

KrBrSeAsGeGaCaK

3619 20 31 32 33 34 35

11 12 13 14 15 16 17 18

Na Mg Al Si P S Cl Ar

NeFONCBBeLi

109876543

4.003

He

2

VIIVIVIVIIIII1.008

I

1

H

A Portion of the Periodic Table

Mills Biology 2001

2.1 Chemical Elements

Know highlighted elements

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Isotopes

• Isotopes are atoms of the same element that differ in the number of neutrons (and therefore different atomic masses). Some isotopes spontaneously decay

• Radioactive isotopes give off energy in the form of rays and subatomic particles

• Can be helpful or harmful

126

Carbon 12

C 136

Carbon 13

C 146

Carbon 14

C

13

14b.

a.

larynx

thyroid gland

trachea

a: © Biomed Commun./Custom Medical Stock Photo; b (left) : Courtesy National Institutes of Health;b: (right) © Mazzlota et al./Photo Researchers, Inc

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.Uses of Low Levels of Radiation

Low levels of radioactive Iodine are used to “see” the thyroid gland.

In a PET scan an isotope of glucose is used to detect active tissues.

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Uses of High Levels of Radiation

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a: (Peaches): © Tony Freeman/PhotoEdit; b: © Geoff Tompkinson/SPL/Photo Researchers, Inc.

a. b.

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Electrons and Energy

• Electrons are attracted to the positively charged nucleus, thus it takes energy to hold electrons in place.

• It takes energy to push them away and keep them in their own shell. The more distant the shell, the more energy it takes to hold in place.

• Electrons have energy due to their relative position (potential energy).

• Electrons determine chemical behavior of atoms.

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The Distribution of Electrons

• The Bohr model is a useful way to visualize electron location. Electrons revolve around the nucleus in energy shells (energy

levels). For atoms with atomic numbers of 20 or less, the following rules

apply:• the first energy shell can hold up to 2 electrons

• each additional shell can hold up to 8 electrons

• each lower shell is filled first before electrons are placed in the next shell

These rules cover most of the biologically significant elements.

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Valence Electrons

• The outermost energy shell is called the valence shell.

• The valence shell is important because it determines many of an atom’s chemical properties.

• The octet rule states that the outermost shell is most stable when it has eight electrons. Exception: If an atom has only one shell, the outermost valence shell is

complete when it has two electrons. • The number of electrons in an atom’s valence shell determines whether the

atom gives up, accepts, or shares electrons to acquire eight electrons in the outer shell.

– Atoms that have their valence shells filled with electrons tend to be chemically stable.

– Atoms that do not have their valence shells filled with electrons are chemically reactive.

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H

P S

C

O

N

electron valence shell

nitrogencarbonhydrogen

sulfurphosphorus

321615

318

16

1476

1211H NC

SPO

oxygen

electron shell

nucleus

Bohr Models of Atoms

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2.2 Compounds and Molecules

• A molecule is two or more elements bonded together. • A compound is a molecule containing at least two different elements

bonded together.

CO2, H2O, C6H12O6, etc.

In Biology – usually used interchangeably (molecule and compound)

• A formula tells you the number of each kind of atom in a molecule.

one molecule

indicates 6 atomsof carbon

indicates 6 atomsof oxygen

indicates 12 atomsof hydrogen

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Chemical Bonding

• Bonds that exist between atoms in molecules contain energy.

• Bonds between atoms are caused by the interactions between electrons in outermost energy shells.

• The process of bond formation is called a chemical reaction.

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Types of Bonds

• Covalent bonds• Ionic bonds• Hydrogen bonds

• An ion is an atom that has lost or gained an electron.

• An ionic bond forms when electrons are transferred from one atom to another atom and the oppositely charged ions are attracted to one.

Example: formation of sodium chloride

• Salts are solid substances that usually separate and exist as individual ions in water.

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Na Cl

sodium atom (Na) chlorine atom (Cl)

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Formation of Sodium Chloride

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Na Cl

sodium atom (Na) chlorine atom (Cl)

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+ –

Na Cl

Na Cl

sodium ion (Na+) chloride ion (Cl–)

sodium chloride (NaCl)

sodium atom (Na) chlorine atom (Cl)

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+ –

Na

sodium atom (Na) chlorine atom (Cl)

sodium ion (Na+)

sodium chloride (NaCl)a. b.

chloride ion (Cl–)

Na Cl

Cl–Na+

Cl

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

b (middle): © Evelyn Jo Johnson; b (right): © Evelyn Jo Johnson

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Types of Bonds: Covalent Bonds• Covalent bonds result when two atoms share electrons so each atom has an octet of electrons in the outer shell.

Note: In the case of hydrogen, the outer energy shell is complete when it contains 2 electrons.

• In a nonpolar covalent bond electrons are shared equally between atoms.

Examples: hydrogen gas, oxygen gas, methane

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a. Hydrogen gas

b. Oxygen gas

c. Methane

StructuralFormulaElectron Model

H C H

H H

H

H

O O

C

O O

H

H

H H

H H

CH4

O2

H2

MolecularFormula

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Covalently Bonded

Molecules

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Types of Bonds: Covalent Bonds

• In a polar covalent bond electrons are shared unequally.

Example: water

• Electronegativity is the ability of an atom to attract electrons towards itself in a chemical bond. In water, the oxygen atom is more electronegative than the hydrogen

atoms and the bonds are polar.

OH H

Oxygen is partially negative

Hydrogens are partially positive

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2.3 Chemistry of Water• Water is a polar molecule.

The shape of a water molecule and its polarity make hydrogen bonding possible.

• A hydrogen bond is a weak attraction between a slightly positive hydrogen atom and a slightly negative atom.

Can occur between atoms of different molecules or within the same molecule A single hydrogen bond is easily broken while multiple hydrogen bonds are

collectively quite strong. Help to maintain the proper structure and function of complex molecules such as

proteins and DNA

32

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Fig. 2.9

H

H H

H

HH

H H

O

O

O

O

Electron Model

Ball-and-stick Model

Space-filling Model

Oxygen attracts the sharedelectrons and is partially negative.

b. Hydrogen bonding between water molecules

hydrogenbond

Hydrogens are partially positive.

a. Water (H2O)

104.5˚

+

+

-

++

-

2.3 Chemistry of Water

Mills Biology 2012

2.3 Chemistry of Water

• Properties of water Makes up 60-80% of most living

cells Most abundant compound in living

tissue Makes up about 66% of weight of

an adult human• About 75% of your brain is water!

• Why do we need it? Cohesion, adhesion, surface

tension, heat transfer, solvent, transport, properties of freezing.

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Properties of Water

• Water molecules cling together because of hydrogen bonding.

This association gives water many of its unique chemical properties.

• Water has a high heat capacity.

The presence of many hydrogen bonds allow water to absorb a large amount of thermal heat without a great change in temperature.

The temperature of water rises and falls slowly.

• Allows organisms to maintain internal temperatures

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Cal

ori

es

of

He

at

En

erg

y /

g

0

800

600

400

200

Solid

evaporation occurs

Liquid

540calories

Gas

80calories

a. Calories lost when 1 g of liquid water freezes and calories required when 1 g of liquid water evaporates.

b. Bodies of organisms cool when their heat is used to evaporate water.

freezing occurs

b: © Grant Taylor/Stone/Getty Images

Temperature (°C)120100800 20 40 60

Temperature and Water

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Properties of Water• Water has a high heat of vaporization.

Hydrogen bonds must be broken to evaporate water.

Bodies of organisms cool when their heat is used to evaporate water.

• Water is a good solvent. Water is a good solvent because of its polarity.

Polar substances dissolve readily in water.

Hydrophilic molecules dissolve in water.

Hydrophobic molecules do not dissolve in water.

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H

H

H H HH H

H H H

H

An ionic saltdissolves in water.

H H

Cl–Na+

O

O

O OO O

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Water as a Solvent

Cohesion and Adhesion

• Cohesion Sticks to itself Polarity

• Caused by H bonds• Without these bonds water would

boil at -80C (instead of +100) and freeze at –100C (instead of 0C) this would not be compatible with life

• Adhesion Sticks to other substances polarity “add” hesion Capillary action

High surface tension due to hydrogen bonding of water.

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Water as a Transport Medium

Water evaporates, pulling the watercolumn from the roots to the leaves.

Water molecules cling together andadhere to sides of vessels in stems.

Water enters a plant at root cells.

H2O

H2O

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40

Properties of Water• Ice is less dense than liquid water.

At temperatures below 4°C, hydrogen bonds between water molecules become more rigid but also more open.

Water expands as it reaches 0°C and freezes. Ice floats on liquid water.

• Acts as an insulator on top of a frozen body of water

Ice floats, I’m glad!

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Density of Water at Various Temperatures

0 4 100

1.0

0.9

De

nsi

ty (

g/c

m3 )

Temperature (ºC)

liquid water

ice lattice

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42

A Pond in Winter

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ice layer

Protists providefood for fish.

River otters visitice-covered ponds.

Aquatic insects survivein air pockets.

Freshwaterfish takeoxygenfrom water.

Common frogs and pond turtles hibernate.

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2.4 Acids and Bases

• pH is a measure of hydrogen ion concentration in a solution.

• When water ionizes or dissociates, it releases an equal number of hydrogen (H+) ions and hydroxide (OH-) ions.

• Acids are substances that dissociate in water, releasing hydrogen ions.

• Bases are substances that either take up hydrogen ions (H+) or release hydroxide ions (OH−).

Mills Biology 2012

Soren Sorenson

1909 Beer Brewer

Developed pH scale

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The pH Scale

• The pH scale is used to indicate the acidity or basicity (alkalinity) of a solution. Values range from 0-14

• 0 to <7 = Acidic

• 7 = Neutral

• >7 to 14 = Basic (or alkaline)

• Actually a measure of H ion concentration (negative log of the H ion concentration) (log is the power to which 10 must be raised to get a certain number)

measures grams of ion/liter of solution pH is a shorthand measurement scale wide range 10 fold change for each change in pH

• concentration of 0.1gm H ion/L = pH 1 move decimal to left for each increase of 1 pH

pH of 1 = 10-1

pH of 6 = 10-6

46

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10

23

45 6 7 8 9

13

101112

14

hydrochloric

acid (HCl)

stomachacid

lemon juice

sodabeer, vinegar

tomatoes

bread, black coffeen

orm

al rainw

aterro

ot b

eer, urin

em

ilk

pu

re w

ater, tears

hu

man

blo

od

egg

wh

ites

, sea

wat

erba

king

sod

a,

stom

ach

anta

cids

Great S

alt Lake

household

amm

onia

bicarbonate

of soda

oven

cleaner

sodiumhydroxide(NaOH)

Acidic BasicOH–

Neu

tral

pH

H+

47

Buffers and pH• A buffer is a chemical or a combination of chemicals that keeps pH

within normal limits.

• Health of organisms requires maintaining the pH of body fluids within narrow limits. Human blood is normally pH 7.4 (slightly basic)

• If blood pH drops below 7.0, acidosis results

• If blood pH rises above 7.8, alkalosis results

• Both are life-threatening situations.

Body has built-in mechanisms to prevent pH changes.

Read Connecting the Concepts with the Big Ideas pg 34

Mills Biology 2012

THE END