Chapter 2: Chemical Context of Life

Atoms and Molecules

Elements• Organisms are composed of matter,

whichis anything that takes up space and hasmass

• Matter is made up of elements, substancesthat cannot be broken down to other substances by chemical reactions

• 92 unique elements exist in nature• More have been created in the lab

Periodic Table

Essential Elements of Life

Essential elements• Include carbon, hydrogen, oxygen, and

nitrogen

• Make up 96% of living matter

Essential elements• Include carbon, hydrogen, oxygen, and

nitrogen

• Make up 96% of living matter

A few other elements make up the remaining 4% of living matter

• Each element• Consists of a certain kind of atom that is

different from those of other elements• An atom• Is the smallest unit of matter that still

retains the properties of an element

Elements

Subatomic Particles• Atoms of each element are composed of

even smaller parts called subatomic particles

• Relevant subatomic particles include• Neutrons, which have no electrical

charge• Protons, which are positively charged• Electrons, which are negatively charged

• Atoms of each element are composed of even smaller parts called subatomic particles

• Relevant subatomic particles include• Neutrons, which have no electrical

charge• Protons, which are positively charged• Electrons, which are negatively charged

Subatomic Particles• Protons and neutrons• Are found in the atomic nucleus

• Electrons• Surround the nucleus in a “cloud”

• Protons and neutrons• Are found in the atomic nucleus

• Electrons• Surround the nucleus in a “cloud”

Nucleus

(a) (b)In this even more simplifiedmodel, the electrons areshown as two small bluespheres on a circle around thenucleus.

Cloud of negativecharge (2 electrons)

Electrons

This model represents theelectrons as a cloud ofnegative charge, as if we hadtaken many snapshots of the 2electrons over time, with eachdot representing an electron‘sposition at one point in time.

Simplified models of an atom

Atomic Number and Atomic Mass• Atoms of the various elements• Differ in their number of subatomic particles

• The atomic number of an element• Is the number of protons

• Is unique to each element

• Is equal to the number of electrons for neutral atoms

• Atoms of the various elements• Differ in their number of subatomic particles

• The atomic number of an element• Is the number of protons

• Is unique to each element

• Is equal to the number of electrons for neutral atoms

Atomic Number and Atomic Mass• The mass number of an element• Is the sum of protons plus neutrons in the

nucleus of an atom

• Is an approximation of the atomic mass of an atom

• The mass number of an element• Is the sum of protons plus neutrons in the

nucleus of an atom

• Is an approximation of the atomic mass of an atom

Atomic Number and Atomic Mass• If you know some facts about an atom,

you can figure out the rest• For example, Boron (B) has an atomic

number of 5 and a mass number of 11.• How many protons does Boron have?

• How many neutrons?

• How many electrons?

• If you know some facts about an atom, you can figure out the rest

• For example, Boron (B) has an atomic number of 5 and a mass number of 11.• How many protons does Boron have?

• How many neutrons?

• How many electrons?

Atomic Number and Atomic Mass• Another example: Magnesium (Mg) has

atomic number of 12 and mass number of 24.• How many protons does Mg have?

• How many neutrons?

• How many electrons?

• Another example: Magnesium (Mg) has atomic number of 12 and mass number of 24.• How many protons does Mg have?

• How many neutrons?

• How many electrons?

Isotopes• Atoms of a given element may occur in

different forms called isotopes• Atoms of a given element may occur in

different forms called isotopes

Isotopes• Atoms of a given element may occur in

different forms called isotopes• Isotopes of a given element• Differ in the number of neutrons in the atomic

nucleus

• Have the same number of protons

• Atoms of a given element may occur in different forms called isotopes

• Isotopes of a given element• Differ in the number of neutrons in the atomic

nucleus

• Have the same number of protons

Isotopes• Atoms of a given element may occur in

different forms called Isotopes• Isotopes of a given element• Differ in the number of neutrons in the atomic

nucleus

• Have the same number of protons

• Radioactive isotopes• Spontaneously give off particles and energy

• Atoms of a given element may occur in different forms called Isotopes

• Isotopes of a given element• Differ in the number of neutrons in the atomic

nucleus

• Have the same number of protons

• Radioactive isotopes• Spontaneously give off particles and energy

Isotopes of Hydrogen

Radioactive Dating• Isotopes can be used to

date biological samples• In Carbon 14 dating, the

ratio of C-12 and C-14 in a biological sample gives an estimate of when that organism died

• C-14 dating works for specimens less than 60,000 years old

• Isotopes can be used to date biological samples• In Carbon 14 dating, the

ratio of C-12 and C-14 in a biological sample gives an estimate of when that organism died

• C-14 dating works for specimens less than 60,000 years old

Energy Levels of Electrons

• An atom’s electrons• Vary in the amount of energy they possess

• Energy• Is defined as the capacity to cause change

• Potential energy• Is the energy that matter possesses because

of its location or structure

Energy Levels

• The electrons of an atom• Differ in the amounts of potential energy

they possess depending on their location

Electron Shells• Energy levels

• Are represented by electron shells

Third energy level (shell)

Second energy level (shell)

First energy level (shell)

Energyabsorbed

Energylost

Atomic nucleus

More potential energy to reside here

Less potential energy to reside here

Electron Configuration and Chemical Properties

• Valence electrons• Are those in the outermost, or valence shell• Determine the chemical behavior of an atom

• The valence number of an atom is the number of unpaired electrons in its valence shell • This valence number determines the number

of bonds the atom can form

Periodic Table• The periodic table of the elements• Shows the electron distribution for all the

elements

Secondshell

Helium

2He

Firstshell

Thirdshell

Hydrogen1H

2He

4.00Atomic mass

Atomic numberElement symbol

Electron-shelldiagram

Lithium3Li

Beryllium

4Be

Boron5B

Carbon6C

Nitrogen7N

Oxygen8O

Fluorine9F

Neon10Ne

Sodium11Na

Magnesium

12Mg

Aluminum

13Al

Silicon14Si

Phosphorus15P

Sulfur16S

Chlorine17Cl

Argon18Ar

Orbitals• An orbital• Is the three-dimensional space

where an electron is found 90% of the time

Orbitals• Each electron shell• Consists of a specific number of orbitals

Electron orbitals.Each orbital holds

up to two electrons.

1s orbital 2s orbital Three 2p orbitals 1s, 2s, and 2p orbitals

(a) First shell

(maximum 2 electrons)

(b) Second shell

(maximum 8 electrons)

(c) Neon, with two filled shells

(10 electrons)

Electron-shell diagrams.Each shell is shown withits maximum number of

electrons, grouped in pairs.

x

Z

Y

Combining Atoms into Bigger Structures: Molecules & Compounds

•A molecule consists of two or more atoms held together by chemical bonds

•A compound is specifically 2 more more different kinds of atoms held together by chemical bonds

Examples of Molecules:

Specifically compounds

Types of Chemical Bonds

•Chemical bonds form because atoms “desire” to complete their valence shell•Atoms can get full valence shells by different methods:

• Sharing electrons• Losing/gaining electrons

•Note: Inert elements already have complete valence shells and thus do not form bonds with other atoms (Ex. Helium)

Covalent Bonds•A covalent bond (co- = sharing)• Is the sharing of a pair of valence electrons between 2 atoms• Each atom involved appears to have a complete valence shell

therefore

•A single bond• Is the sharing of one pair of valence electrons

•A double bond• Is the sharing of two pairs of valence electrons

•Covalent bonds are strong, stable bonds• Create the diverse molecules of biology

Formation of a covalent bond2 Hydrogen atoms (2 H)

1 Hydrogenmolecule (H2)

+ +

+ +

+ +

3

Name(molecularformula)

Electron-shell

diagram

Structuralformula

Space-fillingmodel

Hydrogen (H2). Two hydrogen atoms can form a single bond.

Oxygen (O2). Two oxygen atoms share two pairs of electrons to form a double bond.

H H

O O

Single and Double Covalent bonds

Name(molecularformula)

Electron-shell

diagram

Structuralformula

Space-fillingmodel

Methane (CH4). Four hydrogen atoms can satisfy the valence ofone carbonatom, formingmethane.

Water (H2O). Two hydrogenatoms and one oxygen atom arejoined by covalent bonds to produce a molecule of water.

HO

H

H H

H

H

C

Covalent Bonding in Molecules

Electronegativity• Electronegativity• Is the attraction a particular kind of

atom has for the electrons in a covalent bond

• The more electronegative an atom• The more strongly it pulls shared

electrons toward itself

• Electronegativity• Is the attraction a particular kind of

atom has for the electrons in a covalent bond

• The more electronegative an atom• The more strongly it pulls shared

electrons toward itself

Electronegativity• Electronegativity values can vary

between elements causing different types of covalent bonds

• In a nonpolar covalent bond:• The atoms have similar electronegativities • Share the electrons equally

• In a polar covalent bond:• One of the atoms has a higher

electronegativity value than the other atom

• The shared electrons are pulled towards the atom with the higher value

• Electronegativity values can vary between elements causing different types of covalent bonds

• In a nonpolar covalent bond:• The atoms have similar electronegativities • Share the electrons equally

• In a polar covalent bond:• One of the atoms has a higher

electronegativity value than the other atom

• The shared electrons are pulled towards the atom with the higher value

Polar vs. Nonpolar Covalent Bonds

Ionic Bonds• In some cases, atoms don’t share but

strip electrons away from their bonding partners• This will also create complete valence

shells of the atoms involved

• Electron transfer between two atoms creates ions

• Ions• Are atoms with more or fewer electrons

than usual (charged atoms)

• In some cases, atoms don’t share but strip electrons away from their bonding partners• This will also create complete valence

shells of the atoms involved

• Electron transfer between two atoms creates ions

• Ions• Are atoms with more or fewer electrons

than usual (charged atoms)

Ions• An anion• Atom that gains electrons• Is negatively charged

• A cation• Atom that lost electrons• Is positively charged

• An anion• Atom that gains electrons• Is negatively charged

• A cation• Atom that lost electrons• Is positively charged

Ionic Bonds

Cl–

Chloride ion(an anion)

–

The lone valence electron of a sodiumatom is transferred to join the 7 valenceelectrons of a chlorine atom.

1

Each resulting ion has a completedvalence shell. An ionic bond can formbetween the oppositely charged ions.

2

Na NaCl Cl

+

NaSodium atom

(an unchargedatom)

ClChlorine atom(an uncharged

atom)

Na+

Sodium on(a cation)

Sodium chloride (NaCl)

• An ionic bond• Is an attraction between anions and

cations

Ionic Bonds• In ions, the number of protons and

electrons will be unequal• For example: Cl has an atomic

number of 17• Regular Cl would have 17 protons and

17 electrons

• The Cl anion still has 17 protons but will have 18 electrons making it Cl-

• In ions, the number of protons and electrons will be unequal• For example: Cl has an atomic

number of 17• Regular Cl would have 17 protons and

17 electrons

• The Cl anion still has 17 protons but will have 18 electrons making it Cl-

Ionic Bonds

Na+

Cl–

• Ionic compounds• Are often called salts, which may form crystals

Sodium Chlorine Sodium Chloride

+

Reminder of Emergent Properties Concept