Lecture 2: Atoms, Molecules & Life

Covers Chapter 2

• Yesterday we talked about the fact that all matter (and life as well, because life is made of matter) is composed of elements, atoms and molecules.

• Today we will talk more about elements, atoms & molecules, and organic molecules specifically. We will also discuss water, perhaps one of the most important molecules on the planet.

Element

• A substance that can neither be separated into simpler substances nor converted into other substances by ordinary chemical means. All matter is composed of elements.

• There are 92 types of elements that occur naturally in this world.

• Units of elements are called atoms.

Atoms• Fundamental structural units of matter• Composed of three types of particles*– Protons: positively charged particles located in central

atomic nucleus– Neutrons: neutrally charged particles located in

central atomic nucleus– Electrons: negatively charged particles in orbit around

atomic nucleus. They orbit the nucleus at fixed distances. (We will get back to this shortly.)

Atoms are electrically neutral because they contain the same number of protons and electrons.

Copyright © 2011 Pearson Education, Inc.

(a) Hydrogen (H)

electronshell

atomicnucleus

e

p

(b) Helium (He)

nn

e

p

p

e

Atomic Number/Mass of an element

• Each element has an atomic number that corresponds to the number of protons– Ex: Hydrogen’s Atomic number is 1– Ex: Helium’s Atomic number is 2

• Atomic Mass (Atomic weight): total mass of an atom’s protons, neutrons and electrons

• Mass Number: count of total number of protons and neutrons in an atom’s nucleus.

• Isotope: elements of the same element with different numbers of neutrons

Periodic Table

Table 2-1

Electron Shells

• The orbits around the nucleus in which electrons revolve are called electron shells

• These are 3-DIMENSIONAL spaces

• The first shell (closest to nucleus) of every element can hold TWO electrons

• The second shell and third shells can hold up to eight electrons

• The third shell can hold 18 electrons• The fourth shell can hold 32 electrons

Electron Shells in Atoms of various elements

Fig. 2-2

Carbon (C) Oxygen (O) Phosphorus (P) Calcium (Ca)

CaOC P

4e 6e5e

2e

8e8e

8e

2e 2e

2e

2e

6p 8p 15p20p

6n 8n 16n 20n

Reactive/Inert elements*

• If an atom’s electron shell(s) are full, the atom (and the element) is considered inert and will not react with other atoms.

• If an atom has partially empty electron shells, it can form bonds with other atoms. (An atom with space in its outer electron shell will “take” or “share” electrons from other atoms, thus forming a chemical bond between the two atoms.) This atom and the element is considered reactive.

Example of a bond

• Hydrogen: Atomic number is 1– (1 electron in innermost shell)

• Oxygen: Atomic number is 6– (2 electrons in innermost shell, 4 in outer shell)

• Because oxygen has room for FOUR more electrons in it’s outermost shell, it will react with TWO hydrogen atoms, creating water

Types of chemical bonds*

• There are three major types of chemical bonds that can occur between 2 atoms:– Ionic: One atom donates an electron to the other

in the bond, creating positive and negative charges between the atoms

– Covalent: Electrons are shared by the two atoms– Hydrogen: not a bond really, more like an

interaction resulting from the +/- charges of molecules

Ionic Bond Example

• Sodium atom (11 E, 11P) has one lone electron in it’s outer shell (2 innermost, 8 outer, 1 in far outer shell)

• Chloride (17 E, 17P) has 7 electrons in outer shell (2 innermost, 8 outer, 7 in far outer shell-which has space for one more electron)

• Sodium wants to give up one electron to be more stable and chloride wants to take one to be more stable

• Result is chloride “takes” a sodium electron into it’s outer shell and now chloride is negatively charged (has 1 excess electron), while sodium is positively charged (short 1 electron)

The Formation of Ions and Ionic Bonds

Fig. 2-5

Electron transferred

Na

Cl

Cl

Na

Cl

Cl

Na

Na

Cl

(b) Ions

(c) An ionic compound: NaCl

Attraction betweenopposite charges

– –

–– –

–

–––

–

11p

11n

–

––

– –

––

– ––

––

––

––

––

17p

18n

Sodium ion () Chloride ion (–)

(a) Neutral atoms

Sodium atom (neutral) Chlorine atom (neutral)

– –

–– –

–

––

–

––

11p

11n

– –

––

– –

––

– ––

––

––

––

17p

18n

Example of Covalent Bond• H20: Each H atom has 1 electron in shell. Each O atom

has 2 electrons in inner shell and 6 electrons in outer shell (room for 2 more!)

• Each H atom “shares” it’s electron so that oxygen atom is now stable with 8 electrons in outer shell.

• Result is oxygen is slightly negative charged and H atoms are slightly positively charged (because electrons from H spend more time circling oxygen atom!)

• This is a polar molecule.• There are also non-polar covalent bonds, where the

shared atoms spend equal “time” circling each atom in the molecule.

Covalent Bonds Involve Shared Electrons

Fig. 2-6

(b) Polar covalent bonding in water (H2O)

+

(+) (+)

(oxygen: slightly negative)(–)

(hydrogens:slightly positive)

8p

8n

+

__ _

__

_

_ ___

__

(a) Nonpolar covalent bonding in hydrogengas (H2)

(hydrogens: uncharged)

+ +

Electrons spendequal time neareach nucleus

Same charge onboth nuclei

Larger positivecharge

Electrons spendmore time nearthe larger nucleus

Smaller positivecharge

Example of Hydrogen Bond

• Can only happen between 2 polar molecules(not atoms, this bond occurs between 2

MOLECULES)• Ex: bonds between multiple H20 molecules• H bonds can be easily broken and then re-

form.• This fluidity of bonding results in the surface

tension of water: molecules like to stick together and resist breakage.

Hydrogen Bonds in Water

Fig. 2-7

Water’s Importance in Life

• Water is important for life for many reasons:– A wide range of substances dissolve in water (ex: salt)– Water interacts with many other molecules: hydrophilic vs

hydrophobic– Water-based solutions have wide ranging pH levels– Water forms an unusual solid: ice. It is less dense than

liquid water (ice cubes float) and ponds and lakes freeze from the top down (sparing the living fish at the bottom)

Hydrophilic vs Hydrophobic*

• Hydrophilic: a molecule that will dissolve in water (water-loving.) The water molecules surround the hydrophilic molecule Ex: sugars

• Hydrophobic: a molecule that will not dissolve in water. These molecules will “clump” together if placed in water (water-hating). Ex: oil

Solids, Gases

• Elements may be in different states, depending on intermolecular forces (beyond scope)…– Ex: Gases-hydrogen, oxygen, helium– Ex: Solids-gold, silver, lead

Molecules/Compounds*

• Two or more atoms bonded together are called molecules.

• A compound is a substance whose molecules are formed by different types of atoms.

• Can you think of an example for each?