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Unit 2 Ecological Biochemistry
Unit 2A: Basic Chemistry
Atoms are the Basic Units of Matter
 Atoms are incredibly
small. Placed side by
side, 100 million atoms
would make a row only
about 1 centimeter
long—about the width
of your little finger!
What are Atoms made of?
 Atoms are made of particles
called protons, neutrons, and
electrons.
 Protons have a positive (+)
charge
 Electrons have a negative (-)
charge
 Neutrons are neutral (no
charge)
 Atoms normally have equal
numbers of electrons and
protons, making them neutral
Elements
 Elements are pure substances made of only one type of
atom
 Elements are listed in the periodic table of elements
 They are arranged in order of their atomic numbers
 An atom is the smallest unit of an element that has the
properties of that element
Atomic Number and Mass Number
 The atomic number of an
element is the number of
protons (typically the same as
the number of electrons)
 The mass number of an
element is the number of
protons plus the number of
neutrons
Element
Symbol
Atomic
Number
Mass
Number
Helium
He
2
4
Magnesium
Mg
12
Zinc
Zn
30
Bromine
Br
Aluminum
Al
Number
of
Protons
Numbers
of
Neutrons
Number
of
Electrons
2
12
65
35
80
45
13
14
35
Important Elements for Biology
 The five most abundant elements in living things are:
1. Hydrogen – 10%
2. Oxygen – 65%
3. Nitrogen – 4%
4. Carbon – 19%
5. Phosphorus – 1%
H
Molecules, Compounds, and
Chemical Formulas
 A molecule is made when 2 or more of any atom
are joined together (Ex: O2, H2O)
 A compound is a substance formed by the
combination of two or more different elements
(Ex: H2O, C6H12O6)
 All compounds are molecules, but not all
molecules are compounds
 Chemical Formula- written shorthand showing
the composition of a compound
Chemical Formulas
 Coefficient: tells how many molecules of that substance (the
large number BEFORE the formula)
 Subscript: goes with the element symbol preceding the
number; tells how many atoms of that element within one
molecule of the substance (small number WITHIN the formula).
6
 Example 2: 6CO2




What is the coefficient? _______
What is carbon’s subscript? ________
What is oxygen’s subscript? ________
How many molecules of this compound are
represented by this formula? _________
 How many atoms TOTAL are present in this molecule?
______
Chemical Bonds
 The atoms in compounds are held together by
chemical bonds.
 Making bonds involves the electrons that
surround each nucleus.
 The electrons that are available to form bonds
are called valence electrons.
Valence Electrons
 The electrons of an atom are
spread out in different layers
around the nucleus to make an
“electron cloud”
 These layers are called energy
levels
 2 electrons go in the first energy
level
 8 electrons can go in the second
energy level and beyond (octet rule)
This type of drawing is called a
Bohr model
Valence Electrons (cont.)
 If there are not 8 electrons for
the outer level, these empty
spots are called vacancies and
some electrons are thus
unpaired
 The unpaired electrons in the
outer layer are the valence
electrons
 The valence electrons can pair
with those from other atoms to
“fill” the vacancy
 This creates a molecule
Bohr Model vs. Lewis Dot Structure
Bohr Model: shows all of the
electrons in their energy
levels
Lewis Dot Structure: shows
just the valence electrons in
the outer energy level
Reactive vs. Stable
 The reactivity of an atom is
determined by the number of
vacancies in its outer energy
level
 If there are vacancies, the atom
is reactive/unstable
 If there are no vacancies, the
atom is nonreactive/stable
 If the vacancies are filled due to
bonding, the molecule is stable
The main types of chemical bonds are
1. ionic bonds
2. covalent bonds
 There are other types of bonds and
interactions but they are not as strong as
these two types
1. Ionic Bonds
 An ionic bond is formed when one or more
electrons are transferred from one atom to
another.
 An atom that loses electrons becomes positively
charged.
 An atom that gains electrons has a negative
charge.
 These positively and negatively charged atoms
are known as ions.
 These oppositely charged ions have a strong
attraction for each other, forming an ionic bond.
2. Covalent Bonds
 When electrons are
shared by atoms instead
of transferred.
 The moving electrons
travel about the nuclei of
both atoms, forming a
covalent bond.
A covalent bond can be a…
 Single Covalent Bond: atoms share 2
electrons (1 pair)
 Double Covalent Bond: atoms share 4
electrons (2 pairs)
 Triple Covalent Bond: atoms share 6
electrons (3 pairs)
HONC
This is the number
of bonds each of
these can form!
 Bonds between the most
important biological atoms
will be covalent
 The number of bonds each
can make is important for
the compounds that will be
created using these atoms
H O N C
1 2 3 4
Hydrogen -can form 1 single bond
Oxygen- can form 2 single bonds or
one double bond
Nitrogen- can form 3 single bonds or
1 double bond and 1 single bond
Carbon- can form 4 single bonds or 2
double bonds, or 1 double bond and
2 single bonds (no quadruple bond!)
Structural formulas
 Show you
 the types of elements in the
molecule
 the number of atoms of each
element AND
 the arrangement of atoms and
location of covalent bonds. Shows
the two dimensional shape of the
molecule.
Chemical Reactions
 Chemical Reactions: process that changes or transforms one set of
chemicals into another set of chemicals. Involves changes to the
chemical bonds that join atoms in compounds.
 Reactants: elements or compounds that enter into a chemical reaction
 Products: elements or compounds produced by a chemical reaction
 HINT: Reactants react to produce products!
 Bonds of the reactants are broken and new bonds form in the products
Chemical Equations
What
process is
this equation
for?
 Chemical Equation: a mathematical representation of
a chemical reaction. It shows the numbers and types
of compounds involved.
6O2
+
C6H12O6

6CO2
+
6H2O
+ ___
Balancing Chemical Equations
 The Law of Conservation of Matter:
matter (atoms and elements) in a
chemical reaction cannot be created or
destroyed. Only the arrangement of the
atoms is changed, NOT the number or
types.
 Therefore both sides of a chemical
equation must be “balanced” (have the
same number of atoms).
Are these equations balanced?
C + 2H2 --> CH4
Na2SO4 + CaCl2 --> CaSO4 + NaCl
C2H6 + O2 --> CO2 + H2O
2Al2O3 --> 4Al + 3O2