Chemistry for Biology

Part 1 - Elements and Atoms

What is Chemistry?

All substances are made of chemicals. Chemistry is the study of those chemicals.

Chemistry also studies:• Chemical changes - how substances

change from one substance to another.

• What is contained in food.• What is contained in our bodies. • How to purify chemicals and make

new chemicals.

Why Study Atoms? All chemicals are made of smaller

substances called atoms. Understanding atoms explains why

chemicals do what they do. For example:

• Why do 2 hydrogen atoms join with 1 oxygen atom to form a molecule of water (H2O)?

• Why does Sodium (an explosive white metal), join with Chlorine (a deadly gas), to form harmless table salt (NaCl)?

Elements

There are about 112 kinds of elements which are listed on the Periodic Table.Examples: Hydrogen, Gold, Carbon,

OxygenThese elements combine to make

up all the substances we know of.

Most substances contain more than 1 type of element and are called Compounds. For example: Water, Soap, CO2, & DNA.

The smallest particles of an element are the atoms of that element. So, the atoms are the smallest building blocks of all substances.

3 Parts of an Atom

In the middle of an atom is a tiny nucleus which contains 2 types of particles - protons and neutrons

The nucleus is surrounded by orbiting electrons.

Sample Atom

From World Book © 2002 World Book, Inc., 233 N. Michigan Avenue, Suite 2000, Chicago, IL 60601. All rights reserved. World Book illustration by Leonard Morgan

The Atomic Nucleus The nucleus is 100,000 times smaller than

the diameter of the atom.• E.g. An ant in a football stadium, or a tennis

ball and 2 miles on each side. Protons and neutrons are about the same

size. Protons have a charge of +1 (a “positive”

charge). Neutrons have no charge (they are

“neutral”).

Electrons Electrons are much smaller than protons and

neutrons. In fact, it takes 1800 electrons to equal the

mass of just 1 proton. Electrons have a charge of -1 (they are

“Negatively” charged) Electrons only orbit in certain energy levels

(specific spaces around the nucleus). They orbit so fast, the energy levels are

more like an ‘electron cloud’.

Atomic Size Aluminum foil is about 50,000 atoms

thick. Even a dust particle contains millions of

atoms. The mass of a proton is 1.7 x 10-24

grams. .0000000000000000000000017 grams

To make it easier, the SI unit of a proton is 1 AMU (Atomic Mass Unit)

Atoms compared Atoms vary a lot in mass, but little in size.

From World Book © 2002 World Book, Inc., 233 N. Michigan Avenue, Suite 2000, Chicago, IL 60601. All rights reserved. World Book illustration by Leonard E. Morgan

Plutonium-Atomic Mass = 244.1

Hydrogen -Atomic Mass = 1.0

How atoms differ The number of protons in an atom

determines which element it is. All atoms of a certain element have the same number of protons. Example: All gold atoms have 79 protons

Note: Atoms of the same element “may” have different numbers of Neutrons.

The number of Protons in an atom is called the ‘Atomic Number’, and is the top (left) number in the boxes of the Periodic Table.

2 Simple Atoms Hydrogen atoms always

have 1 proton. They also have 1 electron and usually have no neutrons.

Helium atoms always have 2 protons. They have 2 electrons and usually have 2 neutrons.

P

e

PPN

N

e

e

H

He

Isotopes Atoms of the same element that have

different numbers of neutrons are called Isotopes.

Even Hydrogen has different Isotopes. One version has no neutrons, and one version has 1 neutron.

Some isotopes are radioactive.

P

e

P

e

NH-1 H-2

Mass Number The Mass Number is the sum of the protons

plus neutrons in an atom. Below are two Lithium Isotopes. Each has

3 protons which makes them Lithium. One isotope has 3 neutrons, with a Mass

Number of 6 (3P+3N) One isotope has 4 neutrons, with a Mass

Number of 7 (3P+4N).

Li-6 Li-7

Protons

Neutrons

Question

What is the atomic number of this atom? What element is this? What is the mass number of this atom?

Proton

Neutron

Atomic Mass The Atomic Mass of an element is the

weighted average of the masses of its isotopes found in nature.

For example:50% Li - 6 = 3.020% Li - 7 = 1.420% Li - 8 = 1.610% Li - 9 = .9

100% 6.9 (Atomic Mass)

Atomic Mass The Atomic Mass is the larger number

in the Element Boxes on the Periodic Table.

Calculating the # of Neutrons

Sorry, it’s not in the boxes of the Periodic Table.

If you are given the Atomic Number (# of protons) and the Mass Number (# of protons + neutrons), you can easily calculate the number of neutrons.

Example:

If the Mass Number (#P + #N) =45,

and the Atomic Number (#P) =20

that atom must have 25 neutrons

(45 - 20 = 25)

Calculating the Number of Electrons

It’s the Same as the number of Protons! That’s why an atom is Electrically Neutral overall.

E.g. for Carbon, 6 P’s = +6, 6 e-’s = -6, so +6 and -6 = 0 Total charge.

When an atom loses or gains electrons from normal, it is called an Ion.

More on Ions when we discuss Chemical Bonding.

The Periodic Table The Zig Zag Line - Divides Metals to the Left,

from Non-Metals to the Right. Along the Zig Zag Line are the Metalloids. Rows = “Periods” Columns = “Groups” or “Families”

Elements in a group have the same number of electrons in their outermost shell (energy level)

So, members of a group tend to act the same in chemical reactions.

Group Similarities Group 1 elements all have 1 electron in their

outermost energy level (shell). Group 2 has 2 electrons in their outermost

shell. Group 18 has 8 electrons in their outermost

shells, (so their outermost shells are full.) Group 17 has 7 electrons in the outermost

shells. (Tip-subtract 10 from the group number.)

Chemical Bonding

Part 2

What is a Chemical Bond ???

A force of attraction that holds atoms together due to their electrical charges.

3 Types of Bonds

Covalent

Ionic

Metallic

Energy Levels Electrons are located in areas around the

nucleus called Energy Levels. Only a certain number of electrons can

occupy each Energy Level. The first level can hold 2. The second level can hold 8. The energy levels are often drawn as circles.

(It’s actually much more complicated)

Electron Configurations One way to show the electrons in an

Atom is to draw Electron Dot Diagrams. Here is an electron dot diagram for

Nitrogen:

N

The Essence of Chemical Bonding

Atoms are “happiest” and most “content” when their outermost energy levels are Full of Electrons.

Atoms can borrow, give away, or share electrons with other atoms to reach a full outermost level.

Electrons in the outermost level are called Valence Electrons.

Full!

Electron Dot Diagram - Nitrogen

For Nitrogen, first determine the Atomic Number for Nitrogen - 7

That means it has 7 Protons.Therefore, it must also have 7

Electrons.Start filling energy levels with

electrons from the inside out.

The first energy level can hold only 2 electrons

For Nitrogen, that leaves 5 more electrons for the next level. (7-2 = 5)

N

The second energy level can hold 8 electrons.

So, Nitrogen has room for 3 more electrons in its 2nd energy level.

N

The last 5 electrons of Nitrogen all fit in the 2nd energy level.

Remember, Atoms prefer to have full outer energy levels . . .

So, Nitrogen would be “Happier” if it could find a way to get 3 more electrons to bring it’s outer level up to 8 Electrons.

That’s where Bonding comes in. Nitrogen will seek out a willing-partner; an Atom, or Atoms, that want to share, or give away, 3 of their electrons.

N

Giving Away Electrons Some atoms can reach a full outer level more

easily by giving away electrons. For example, a Sodium Atom has 1 electron in

its outermost energy level.

If it gives one away, it has a Full outer level.

Na Na

Covalent Bonds

Covalent Bonds occur when atoms ‘Share’ electrons.

The resulting substance is called a Molecule.

Most organic molecules (molecules of living things) have this type of bond.

This is usually the type of bond between non-metals.

For a simple Example, lets look at

Chlorine . . . 2 Chlorine Atoms bond together to

form a Chlorine Molecule. The Chemical Formula is Cl2

Each Cl Atom has 7 valence electronsEach atom needs 1 more electron to

have a full outer shell

Cl Cl

By sharing electrons, each now has a full outer level

Cl Cl

DNA MOLECULE

‘Polar’ Covalent Bonds

Sometimes, the electron sharing isn’t exactly equal. One atom hogs them.Example: In a water molecule, the shared

electrons spend more time around Oxygen than the two Hydrogen atoms.

This makes one end slightly negative.And the other end slightly positive. O

H H

(+)(+)

(-)

Next, Ionic BondsOne type of atom gives away

(donates) electrons, the atom other receives (gains) electrons.

They aren’t “sharing”.After the exchange, Both types

of atoms are called Ions.

Types of IonsAtoms who received electrons are

called negative ions. Their “total” charge becomes “more

negative”. E.g. Cl atom has 17 P’s and 17 e-’s. If

gains 1 e-, now 17 P’s and 18 e-’s. (+17 - 18 = -1) Total charge now -1.

Atoms who donated electrons are called positive ions. Their “total” charge becomes “more

positive”.E.g. K atom has 19 P’s and 19 e-’s. If

lose 1 e-, now 19 P’s and 18 e-’s. (+19 - 18 = +1) Total charge now +1.

Positive Ions Atoms with few electrons in their

outermost level usually like to donate electrons.

This includes metals. They are on the left side of the Periodic

Table.

Na

Negative Ions Atoms with almost full outermost

levels don’t give them away easily. They prefer to gain electrons.

These include non-metals. They are on the right side of

The Periodic Table. Cl

Ionic Bond Positive and Negative Ions have an

electrical attraction for each other. In other words, they form an Ionic Bond.

ClNa

Positive Ion Negative Ion

Cl-

IonNa+

Ion

Why are Ions attracted? In nature - opposite electrical

charges attract. A positive and negative ion have

opposite charges, so they are naturally attracted to each other.

The resulting substance isn’t a molecule. It’s an ionic compound.

Bonding and the Periodic Table

Group 18 doesn’t like to bond with any other elements, Why?

Group 1 forms Ionic Bonds with Group 17. Why?

Group 2 forms Ionic Bonds with which Group? Carbon has 4 electrons in its outermost shell.

How many covalent bonds does it usually make?

Chemical Reactions

Part 3

Chemical Reactions Defined

The process by which substances change to produce different substances.

The new substances have different properties from the original substances.

Chemical Reaction Terminology

‘Yield’

C + O2 CO2

‘Reactants’ ‘Products’

In common English:

The reactants Carbon and Oxygen combine to yield a product called Carbon Dioxide.

How do substances change? Chemical bonds break Atoms rearrange New chemical bonds form

Common Chemical Reactions

Burning Fuel Converting the energy of Food into ATP A bomb explosion Photosynthesis - plants creating food Rusting iron

2 Types of Reactions

1. Synthesis

two or more one

2. Decomposition

one two or more

Chemical Formulas They are a shorthand notation for

chemically combined atoms. They use chemical symbols and numbers

- H2O CO2 3C6H12O6

The small numbers after the symbols are called Subscripts.

Numbers placed in front of a formula are called Coefficients.

Coefficients A Coefficient means there are that

number of whatever follows. Example: 2H2SO4 means there are

2 H2SO4’s How many atoms are in that

formula? 14.

Each “H2SO4” has 7 atoms, and there are 2 of them.

How many atoms are in these Chemical Formulas?

CO2

MgCl2 2C3H8

C6H12O6

3AgNO3