Chapter 2: Basic Chemistry (Outline)

Chemical elements Atoms Isotopes Molecules and compounds

Covalent and ionic bonding/reactions Ionic and Covalent Hydrogen

Properties of Water Define/describe acids and bases

pH scale and buffers

Chemical Elements

Matter refers to anything that has mass and occupies space Only 92 naturally occurring fundamental types of

matter – 92 Elements

Organisms composed primarily (98%) of only six elements Carbon, Hydrogen, Nitrogen, Oxygen,

Phosphorus and Sulfur

CHNOPS

Elements Composition of Earth’s Crust vs. Organisms

Atomic Structure

Atoms - smallest particles of elements Atoms composed of 3 types of subatomic

particles Protons: positively charged particles

within the nucleus Neutrons: electrically neutral charged

particles also found in nucleus Electrons: negatively charged particles

orbiting the nucleus

Atomic Symbol

Each element represented by unique atomic symbol

One or two letters

First letter capitalized

Superscripted number before: Represents mass number

Number of protons & neutrons in nucleus

Subscripted number before: Represents atomic number

Number of protons in nucleus

MassMassNumberNumber

AtomicAtomicNumberNumber

AtomicAtomicSymbolSymbol

126

Carbon

C

Periodic table Elements grouped in periodic table based on

characteristics Vertical columns = groups; chemically similar Horizontal rows = periods; larger and larger

1

H1.008

3

Li6.941

11

Na22.99

19

K39.10

4

Be9.012

12

Mg24.31

20

Ca40.08

5

B10.81

13

Al26.98

21

Ga69.72

6

C12.01

14

Si28.09

22

Ge72.59

7

N14.01

15

P30.97

23

As74.92

8

O16.00

16

S32.07

24

Se78.96

9

F19.00

17

Cl35.45

25

Br79.90

10

Ne20.18

18

Ar39.95

26

Kr83.60

2

He4.003

II

IIII IIIIII IVIV VV VIVI VIIVII

VIIIVIII

11

22

33

44

Groups

Periods

Isotopes

Isotopes: Atoms of the same element that differ in the number of neutrons. Isotopes of an element have the same chemical properties but different weights

Example:

126

Carbon 12C 13

6

Carbon 13C 14

6

Carbon 14C

Electron Shells, Orbitalsand Energy Levels Atoms normally have as many electrons as

protons Opposite charges balance leaving atom neutral Electrons are attracted to the positive nucleus

Revolve around nucleus in orbitals

Can be pushed into higher orbitals with energy

Release that energy when they fall back to lower orbital

Different energy levels referred to as electron shells

The Octet Rule forDistribution of Electrons

Bohr models show electron shells as concentric circles around nucleus Each shell has two or more electron orbitals

Innermost shell has 2 orbitals

Others have 8 or multiples thereof

Atoms with fewer than 8 electrons in outermost shell are chemically reactive If 3 or less – Tendency is to donate electrons

If 5 or more – Tendency is to receive electrons

Periodic Table

Elements and Compounds

Molecule - two or more atoms react or bond together If all atoms in molecule are of the same element

Material is still an element

O2, H2, N2, etc.

If at least one atom is from a different element

Material formed is a compound

CO2, H2O, C6H12O6, etc.

Characteristics of compounds dramatically different from constituent elements

Chemical Bonding

Bonds between atoms are caused by electrons in outermost shells

The process of bond formation is called a reaction

The intensity of simple reactions can be predicted by the periodic table If two elements are horizontally close in the

table, they usually react mildly

If they are horizontally far apart, they usually react vigorously

Types of Bonds:Ionic Bonding

Octet rule Atoms need 8 electrons in outer shell

If have < 4 outers, desire to donate them If have > 4 outers, desire to receive more

Consider two elements from opposite ends of periodic table Element from right side:

Has 7 electrons in outer shell “Desperately needs” one more (7+1=8)

Element from left side: Has only 1 electron in outer shell “Desperately needs” to donate it (1-1=0=8)

Formation of Sodium Chloride

Types of Bonds:Covalent Bonds

When atoms are horizontally closer together in the periodic table

The electrons are not permanently transferred from one atom to the other like in NaCl

A pair of electrons from the outer shell will “time share” with one atom and then the other

This also causes the atoms to remain together

Known as covalent bonding

Covalently Bonded Molecules

Sometimes two pairs of electrons are shared between atoms – a double covalent bond (e.g. O2 )

Three pairs of electrons – a triple bond (e.g. N2)

Covalently Bonded Molecules

Nonpolar Covalent Bonds

Consider two elements that are equidistant from the edges of the periodic table Atoms will have about equal affinity for electrons

One will “want” to donate electron(s)

The other will “want” to receive electron(s)

When bonded covalently:

The bond electrons will spend about equal time with both atoms

Such covalent bonds are said to be nonpolar

Polar Covalent Bonds

Some atoms attract electrons more strongly than others - electronegativity

Atoms will have unequal affinity for electrons When bonded covalently:

The bond electrons will spend more time with one atom than the other The atom that gets the most time with the

electrons will be slightly negative

The other will be slightly positive

Such covalent bonds are said to be polar

Types of Bonds:Hydrogen Bonds

Water (H2O or H–O–H) is a polar molecule Electrons spend more time with the larger oxygen

atom than the smaller hydrogen atom

H becomes slightly positive and O slightly negative

When polar molecules are dissolved in water The H of water molecules are attracted to the

negative parts of the solute molecules

Results in a weak bond – the hydrogen bond

Easily broken, but many together can be quite strong

One of the most important interactions in biological molecules (e.g. proteins, DNA, etc.)

Water Molecule and Hydrogen Bonding

The Chemistry of Water:Heat Capacity Water has a high heat capacity

Temperature = rate of vibration of molecules When water is heated

Hydrogen bonds restrain bouncing Temperature rises more slowly per unit heat

Thermal inertia – resistance to temperature change Because of hydrogen bonding – takes a large heat

loss or gain for each 1C change in temperature. Hydrogen bonds must absorb heat to break, and

they release heat when they form Keeps temperature fluctuations within a range

suitable for life

Properties of Water:Heat of Vaporization

Water has a high heat of vaporization - the energy required to convert 1g of liquid water to a gas To raise water from 99 to 100 ºC; ~1 calorie

To raise water from 100 to 101 ºC; ~540 calories!

Large numbers of hydrogen bonds must be broken to evaporate water

This is why sweating (and panting) cools Evaporative cooling is best when humidity is low

because evaporation occurs rapidly

Great example is when you get out of the shower!

Properties of Water:Heat of Fusion

Heat of fusion (melting) To raise water from -1 to 0 ºC; ~1 calorie To raise water from 0 to 1 ºC; ~80 calories!

This is why ice at 0 ºC keeps stuff cold MUCH longer than water at 1 ºC

This is why ice is used for cooling NOT because ice is cold But because it absorbs so much heat before it

will warm by one degree

Heat Content of Waterat Various Temperatures

Properties of Water:Water as a Solvent

Solution - liquid that is a completely homogenous mixture of two or more substances Solvent - dissolving agent of a solution Solute - substance dissolved in a solution Hydrophilic

Water loving, property of having an affinity for H2O

Ionic and polar compounds

Hydrophobic Water fearing, not water-soluble

Nonpolar compounds

Ionic compounds dissociate in water

Properties of Water:Cohesion & Adhesion

Cohesion – Hydrogen bonds hold water molecules tightly together

Adhesion – Hydrogen bonds for between water and other polar materials

High Surface Tension A measure of how difficult it is

to stretch or break the surface of a liquid

Allows small nonpolar objects (like water strider) to sit on top of water

Cohesion & adhesion are both important because combined together they form an event called capillary action

Capillary action defies gravity and helps move water up the plant to its leaves

Water as a Transport Medium

Properties of Water:Uniqueness of Ice Frozen water is less dense than

liquid water The density of water:

Prevents water from freezing from the bottom up

Ice forms on the surface first – the freezing of the water releases heat to the water below creating insulation

Makes transition between season less abrupt

pH of Water: Acids

Acids Dissociate in water and release hydrogen ions

[H+] Sour to taste DO NOT TASTE ACIDS IN THE LAB!! Turn litmus red Hydrochloric acid (stomach acid) is an inorganic

acid with symbol HCl In water, it dissociates into H+ and Cl-

Dissociation of HCl is almost total, therefore it is a strong acid

pH of Water: Bases

Bases: Either take up hydrogen ions [H+] or release

hydroxide ions [OH-] Feel soapy or slippery Turn litmus blue Bitter to taste DO NOT TASTE BASES IN THE LAB! Sodium hydroxide is a solid with symbol NaOH

In water, it dissociates into Na+ and OH-

Dissociation of NaOH is almost total, therefore it is a strong base

pH Scale

pH scale used to indicate acidity and alkalinity of a solution Values range from 0-14

Acidic: if pH is less than 7 Basic: if pH is greater than 7 Nuetral: is pH is equal to 7

Logarithmic Scale Each unit change in pH represents a change of 10

times pH of 4 is 10 times as acidic as pH of 5 pH of 10 is 100 times more basic than pH of 8

The pH Scale

Increasing pH means the H+ ions are decreasing Decreasing pH means H+ ions are increasing

Buffers and pH

When H+ is added to pure water at pH 7, pH goes down and water becomes acidic

When OH- is added to pure water at pH 7, pH goes up and water becomes alkaline

Buffers are solutes in water that resist change in pH

When H+ is added, buffer may absorb, or counter by adding OH-

When OH- is added, buffer may absorb, or counter by adding H+

Buffers in Nature

Biological buffer system Human blood normally 7.4 (slightly alkaline) Many foods and metabolic processes add or

subtract [H+] or [OH-] Reducing blood pH to 7.0 results in acidosis

Increasing blood pH to 7.8 results in alkalosis

Both life threatening situations

Bicarbonate ion [-HCO3] in blood buffers pH to 7.4