Chapter 6

Chemistry in Biology

Section 6.1Atoms, Elements, & Compounds

Matter!Matter is anything that occupies space and has

mass.

Will this astronaut occupy the same space on the moon as he does on Earth?

Will this astronaut weigh the same on the moon as he does on the Earth?

Mass and weight are not the same.

The Atom –The Simplest of Particles

• The atom is the simplest particle of an element that retains the properties of that element.

The Structure of an Atom Bohr Model – “planetary model”• Proposed by Niels Bohr in 1915• A useful approximation of the structure of

an atom.Consists of two parts:• A central region, or nucleus• Electron cloud – composed of orbitals or

three-dimensional regions around a nucleus

Subatomic ParticlesProtons Positively (+) charged particles Have mass (1 amu = 1 atomic mass unit) Located in the nucleus

+

Neutrons Neutral particles (No charge) Have mass (1 amu) Also located in the nucleus

n

Electrons Negatively (-) charged particles Mass is negligible (1/1840 amu) Remain in constant motion in orbitals

The Bohr ModelBelow is a Bohr Model of a helium (He) atom.

n +n+

Nucleus 2 protons2 neutrons

Electron cloudConsists of orbitals where high-energy electrons orbit the nucleus

Elements

• Elements are substances that cannot be broken down chemically into simpler kinds of matter.

The Elemental Body --The Major Elements

Rank

Chemical

Symbol

Element% of

human body*

1 O Oxygen 62 %

2 C Carbon 23 %3 H Hydrogen 10 %4 N Nitrogen 2.6 %5 Ca Calcium 1.4 %6 P Phosphorus 1.1 %7 K Potassium 0.2 %8 S Sulfur 0.2 %9 Na Sodium 0.1%10 Cl Chlorine 0.1 %11 Mg Magnesium 0.02 %* Based on an average 70 kg (154 lbs.) person

A major element is any element that makes up more than 0.01% of your body mass.

The Elemental Body --The Trace Elements

A trace element is any element that makes up less than 0.01% of your body mass, but is still critical to your health.

Rank

Chemical

Symbol

Element

12 Fe Iron13 F Fluorine14 Zn Zinc15 Si Silicon16 Cu Copper17 I Iodine18 Sn Tin

Rank

Chemical

Symbol

Element

19 B Boron20 Se Selenium21 Cr Chromium22 Mn Manganese

23 Mo Molybdenum

24 Co Cobalt25 V Vanadium

The Periodic Table6

C12.011

Atomic Number

Chemical Symbol

Atomic Mass

Atomically Speaking…• The number of protons in an atom is called the

atomic number.• In an atom, the number of positive protons is

balanced by an equal number of negative electrons. – net electrical charge equals zero

The Bohr model to the left represents an atom of which element?

How many electrons must be in the electron cloud?

= neutron = proton

Atomically Speaking…

• The mass number of an atom is equal to the total number of protons and neutrons of the atom.

What is the mass number of our carbon atom?

= neutron = proton

Isotopes: Not All Atoms are Created Equal

Isotopes are atoms of the same element that have different numbers of neutrons.– therefore they will have different mass numbers– this is the reason for the average atomic mass in the periodic table

= neutron = proton

Click here to compare these two atoms.

These two atoms are both carbon atoms. But the atom on the left has 6 neutrons while the atom on the right has 7 neutrons. Because of this, these two atoms are said to be isotopes of one another.

These two atoms are both carbon atoms. But the atom on the left has 6 neutrons while the atom on the right has 7 neutrons. Because of this, these two atoms are said to be isotopes of one another.

CLOSECLOSE

Radioactive Isotopes

• Sometimes having too many neutrons can make the nucleus of an atom unstable.– Unstable nuclei decay, or break apart.– Particles (usually neutrons) and energy in the form of

radiation are released.– This radiation can be used to calculate the age

of an object or it can be used in medical treatments such as radiation therapy.

A Few Words About Electrons

• High energy particles• Are attracted to (+)ve protons in the nucleus – keeps

them close together• Constant energy of motion prevents them from

collapsing into nucleus• Exact path of travel cannot be known• An electron’s energy confines it to an energy level

within the electron cloud• Electrons with higher energy occupy energy levels

farther from the nucleus

Orbitals• Energy levels contain orbitals which can only

hold a certain number of electrons.

Energy Level

# of orbitals

Maximum # of

electrons1 1 2

2 4 8

3 9 18

Expanding the Bohr ModelExample: A carbon atomWe know:

From periodic table • atomic number of carbon equals six;• therefore the number of electrons equals six Why?

From previous chart• first energy level holds two electrons maximum• second energy level holds eight electrons maximum

= neutron = proton = electron

Expanding the Bohr ModelPutting it all together:

Two of carbon’s electrons will be found in the first energy level of the electron cloud.

The remaining four electrons will be found in the second energy level of the electron cloud.

The second energy level of a carbon atom is not full. It can still accommodate four more electrons.

Compounds

• Compound – substance formed when two or more different elements combine– Form a specific combination of elements in a fixed

ratio– Chemically and physically different from the

elements that comprise them– Cannot be broken down into simpler compounds

or elements by physical means (can be broken down chemically)

Why Combine?

Compounds form because most atoms are not stable in their natural state.

A partially-filled outermost energy level is not as stable as an energy level that is completely filled with the maximum number of electrons it can hold.

Is this carbon atom stable?

= neutron = proton = electron

Two Ways to Bond

Ionic Bonds CovalentBonds

Chemical BondsIonic Bond Covalent Bond

An atom can gain or lose an electron to make a stable energy level. This atom is called an ion and is now charged.

An ionic bond is electrical attraction between two oppositely charged atoms.

Example: sodium chloride

A chemical bond that forms when electrons are SHARED

Example: water

Achieving Stability

Atoms become stable by attaining at least one of the following:– They fill their outermost, or valence, energy level

with the maximum amount of electrons that it will hold.

OR– They fill their outermost energy level with eight

electrons.• The ‘Rule of Eight’

There IS Another Way

Atoms can also share one or more pairs of electrons. – When two atoms share electrons, the shared electrons

occupy orbitals around both of the atoms.– The electrons move so quickly that it is difficult to predict

which atom they are orbiting at any given time.

Water – A Model of Covalent Bonding

Hydrogen1 p0 n

Oxygen8p8n

Hydrogen atom (atomic #: 1) Oxygen atom (atomic #: 8)

How many valence electrons does each atom have?

How many more electrons does each atom need to fill its outermost energy level?

Water – A Model of Covalent Bonding

Hydrogen1 p0 n

Oxygen8p8n

Hydrogen1 p0 n

This is a molecule of water. It can also be referred to by its chemical formula, H2O.

A shared pair of electrons can be considered to be part of the outermost energy level of both atoms that share them.

This is a molecule of water. It can also be referred to by its chemical formula, H2O.

A shared pair of electrons can be considered to be part of the outermost energy level of both atoms that share them.

How might each of these atoms fill its outermost energy level?

Hydrogen1 p0 n

Oxygen8p8n

If each hydrogen atom shares a pair of electrons with oxygen, how many valence electrons does each atom have?

Covalent BondA covalent bond forms when two atoms

share one or more pairs of electrons.– A molecule is the simplest part of a substance

that retains all the properties of that substance

Modeling Ionic Bonds

Activity In your notes, draw a Bohr model of a

sodium atom (atomic number 11). Next to the sodium atom draw a Bohr model of a chlorine atom (atomic number 17).

Activity

1. On the left, draw a neutral sodium atom with a mass number of 23 (atomic number 11).

2. On the right, draw a neutral chlorine atom with a mass number of 35 (atomic number 17).

The Sodium-Chlorine Ionic Bond

Sodium11 p12 n

Chlorine17 p18 n

Sodium atom (atomic #: 11) Chlorine atom (atomic #: 17)

How many electrons does each atom have now?

How does this affect the total charge of each atom?

The Sodium-Chlorine Ionic Bond

Sodium11 p12 n

Chlorine17 p18 n

These atoms are no longer electrically neutral.

Protons +11Electrons -10Charge +1

Protons +17Electrons -18Charge -1

These atoms are stable, but because of their opposite charges they now attract one another.

How many protons does sodium (Na) have?

How many electrons does Na have now?

What is the total charge of this atom of sodium?

The Sodium-Chlorine Ionic BondAn atom with an electrical charge is called an ion. As a result of their opposite charges, sodium ions and chlorine ions attract each other.

Sodium11 p12 n

Chlorine17 p18 n

Sodium ion +1

Chlorine ion-1

An ionic bond is the chemical bond formed between ions with opposite charges.

This new substance is a compound called sodium chloride.

Chapter 6.2Chemical Reactions

Chemical Reactions

• Process by which atoms or groups of atoms in substances reorganize into different substances

• Chemical bonds are broken or formed

• For example – 4 Fe + 3 O2 2 Fe2O3

Reactants and ProductsChemical Equation:

C6H12O6 + O2 CO2 + H20

(Glucose and oxygen react to form carbon dioxide and water)

Reactants (starting substances):C6H12O6 + O2

Products (substances formed):CO2 + H20

Balanced Equation• According to the principle of conservation of

mass, matter cannot be created or destroyed• The number of atoms of each element on the

reactant side must equal the number of atoms of the same element on the product side

For example:

2 H2O2 2 H20 + O2

C6H12O6 + 6 O2 6 CO2+ 6 H20

Energy-Absorbing Reaction Energy-Releasing Reaction

Products

Products

Activation energy

Activation energy

Reactants

Reactants