BIOCHEMISTRY
Organization of Life
Atoms
Molecules
Macromolecules
Cells
Tissue
Organs
Organ system
Organism
Atoms
Atom: The smallest unit into
which an element can be
divided and retain its
characteristic properties.
One unit of an element.
Elements
Element:
A substance composed only of
atoms of the same atomic number.
One of more than 100 distinct
types of matter that, singly or in
combination, compose all
materials of the universe.
Atoms: Basic structure
Made up of:
Protons (+)
Neutrons ( )
(Nucleus)
Electrons (-)
Electrically Neutral
if…
Protons =
Electrons
Atomic Number, Symbol, Mass



Atomic Number: The number of protons found in
an atom.
Symbol: The abbreviation for an element.
Atomic Mass: Weight of an atom; approx. the sum
of its protons and neutrons.
Periodic Table of the Elements
Beryllium
Atomic Number: 4
Symbol: Be
Name
Atomic Mass: 9.0112
.
4
Be
Beryllium
9.0112
Periodic Table of the Elements
4
Be
Beryllium
9.0112
9
Be
4
Mass = Protons +
Neutrons
What’s wrong with this
picture?
Elements are arranged:
Vertically into Groups
Horizontally Into
Periods
If you looked at one atom
of every element in a
group you would see…
The group 2 atoms all have 2 electrons in their oute
shells
Be (Beryllium)
Atom
Mg (Magnesium) Atom



The number of outer or “valence” electrons in an
atom effects the way an atom bonds.
The way an atom bonds determines many properties
of the element.
This is why elements within a group usually have
similar properties.
If you looked at an atom from each element in a
period
you would see…
Each atom has the same number of electron
holding shells.
An example…
The period 4 atoms each have 4 electron containing
shells
4th Shell
K (Potassium)
Kr (Krypton)
Atom
Atom
Fe (Iron) Atom
Isotopes
1.
2.
3.
4.
Neutrons do not equal protons.
More neutrons than protons.
Unstable nucleus.
Radioactive Isotope: Isotopes that give off
energy because neutrons peel off their unstable
nucleus.
Ions




Protons do not equal
electrons.
More protons than
electrons = a positive
charge.
More electrons than
protons = a negative
charge.
Na+
Compounds
Definition:
 Two or more elements in definite proportions that
are joined together by a chemical bond.
Two Types of Bonds:
 Ionic
 Covalent
Ionic Bonds


Why do they form?
Octet Rule (Rule of Eight):
Atoms tend to establish completely full outer energy
levels. (K fills with 2, L and M generally fill with 8.)
Ionic Bonds: an example
Chlorine has 17 electrons.
Orbital K takes the first 2.
Orbital L takes the next 8.
Orbital M takes 7.
Sodium has 11 electrons.
Orbital K takes the first 2.
Orbital L takes the next 8.
Orbital M takes 1.
Ionic Bonds: an example
Chlorine needs one more
electron to fill its outer shell
with 8 electrons. (Octet
Rule)
If sodium gives up one
electron it will have
eight in its outer level.
Ionic Bonds: an example
Chlorine:
17 protons
18 electrons
What’s its charge?
-1 (negative ion)
Sodium:
11 protons
10 electrons
What’s its charge?
+1 (positive ion)
What do you
think happens
next?
Ionic Bonds: opposites attract
The sodium atom and the
chloride atoms are
attracted toward one
another because of their
opposite electrical charges.
The combination makes sodiumchloride,
abbreviated NaCl,
commonly known as salt.
Ionic Bonds


Definition:
An attraction between ions of opposite charge.
These bonds are relatively weak and will easily
dissolve in water.
Covalent Bonds



Definition:
A chemical bond formed by the sharing of one or
more pairs of electrons.
These bonds can be very strong.
Most of the structures in the body are made using
these types of bonds.
Molecules


Definition:
A group of elements held
together by covalent
bonds.
Example:
Water
Two hydrogens and one
oxygen share two pairs of
electrons.
Covalent Bonds, cont.


Why do hydrogen and
oxygen want to share?
Answer:
Each wants to fill its outer
shell with electrons.
Hydrogen fills with 2.
Oxygen fills with 8.
Covalent Bonds
Many types of covalent bonds
Single covalent:
shares one
pair.
Triple covalent:
share three
pairs.
Double
covalent:
share two
pairs.
Chemical Reactions

Equation:
A formula that describes what happens during a
chemical reaction.
H + O
•
2
2
Balanced Equation:
H2O + O
The elements on the left side of the
equation are the same as those on the right.
Notice! States of matter (liquid, solid, gas)
may change during a reaction.
Chemical Reactions: Terms
• Reactant- The chemicals before
reaction
• Product- The chemicals after reaction
Elements important for life.




Oxygen (65% of body by weight)
Carbon (18%)
Hydrogen (10%)
Nitrogen (3%)
(N.O.C.H.)
Elements in Human Body






Oxygen (65%)
Carbon (18%)
Hydrogen (10%)
Nitrogen (3%)
Calcium (2%)
Phosphorus (1%)
Other 1%
 Potassium
 Silicon
 Aluminum
 Iron
 Sodium
 Chlorine
 more...
Fortification of elements
Organic Compounds
1.
Pertaining to living things.
2.
The chemistry of compounds containing carbon.
Building Macromolecules


Monomer-smaller unit of large compounds
Polymers-monomer that join together to form
macromolecules
Organic Compounds or Macromolecules
4 Types of Organic Compounds:
1.
Carbohydrates
2.
Lipids
3.
Proteins
4.
Nucleic Acids.
Carbohydrates
Three types:
1.
Monosaccharides
2.
Disaccharides
3.
Polysaccharides
Monosaccharides
One sugar molecule.
Carbon Backbone: Carbon atoms line up near the
center of the molecule and other atoms attach to
them.
Formula for Simple Sugars: C6H12O6
Monosaccharides
Three basic types:
1.
Glucose (general sugar)
2.
Fructose (fruits)
3.
Galactose (milk)
Isomer:
Alternative forms of a molecule that
have the same formula.
Polysaccharides
Many monosaccharides bonded together.
(Storage sugars.)
Three types:
1.
Starches (plants – potato!).
2.
Cellulose (structure – plant cell walls).
3.
Glycogen (animal storage).
Functions of Carbohydrates
1.
2.
3.
Energy source (glucose).
Long-term energy storage (starch, glycogen).
Structure (cellulose).
Organic Compounds
4 Types of Organic Compounds:
1.
Carbohydrates
2.
Lipids
3.
Proteins
4.
Nucleic Acids.
Lipids
Five types:
1.
Fats
2.
Oils
3.
Waxes
4.
Phospholipids
5.
Steroids
Lipids
Functions:

Long-term energy storage (fats, oils).

Insulation (fat).

Protection (waxes waterproof or keep in water).

Cell membrane structure (phospholipids).

Control of body functions (steroids).
Organic Compounds
4 Types of Organic Compounds:
1.
Carbohydrates
2.
Lipids
3.
Proteins
4.
Nucleic Acids.
Proteins
Types:
1.
Amino acids.
2.
Dipeptides.
3.
Polypeptides.
Proteins
Amino Acids:

Building blocks for all proteins.

20 total.

Link together to form “peptide” bonds.
Proteins
Functions:

Movement

Structure

Regulation (catalysts, enzymes)

Transport

Nutrition

Defense
Proteins
(catalysts and enzymes)
Catalyst: Substances used in small amounts which
speed up chemical reactions without themselves
being affected by the reaction.
Enzyme:
Proteins that function as catalysts.
(overhead)
Organic Compounds
4 Types of Organic Compounds:

Carbohydrates

Lipids

Proteins

Nucleic Acids.
Nucleic Acids
Types:

DNA (deoxyribonucleic acid)

RNA (ribonucleic acid)
Functions of Nucleic Acids


Information storage (DNA)
Information transfer (RNA carries genetic
information from DNA to ribosomes)
WATER,
ACIDS, AND BASES
Water
1.
2.
The Cradle of Life:
The Universal Solvent.
The Polarity of Water.
Solutions
Solution:
A homogeneous mixture of the
molecules of two or more
substances.
Ex. Water and glucose mixture.
Solvent
Solvent:
Medium in which a substance is
dissolved (water).
Water is known as the universal solvent
because most of the chemical reactions
necessary for life take place in water (i.e.
water is the solvent).
Solutes
Solutes: A compound dissolved in some
solution.
Ex. The glucose in the water
glucose mixture.
Polarity
For example:
 In a water molecule,
one oxygen atom
shares electrons
with two hydrogen
atoms.
Do they share equally?
Polarity, cont.
 Oxygen and
Hydrogen do not
share electrons
equally.
 Oxygen is more
electronegative (it
attracts electrons
more heavily) than
hydrogen.
Polarity, cont.

The result is that the electrons shared by oxygen
and hydrogen actually spend more of their time
nearer the oxygen atom. This gives the oxygen a
slightly negative charge and leaves hydrogen with
a slightly positive charge.
+
-
Note: The charges are only
partial. (i.e. not as large as a full
proton or electron would be.
The Polarity of Water
1.
2.
3.
4.
Water bonds (hydrogen bonds) to itself.
Water bonds to other molecules.
Water will group non-polar molecules.
Water is a powerful solvent.
Hydrogen Bonds
1.
2.
3.
The positive or negative end of water will be
attracted to other polar molecules.
Weak bonds
Usually last only 1/100,000,000,000 sec., but
their cumulative effect can be great.
Water Clings
Cohesion:
Water attracted to water.
Adhesion:
Water attracted to other polar
molecules.
Capillary Action – water will “climb” by
adhering to a surfaces electrical charges.
Adhesion
Hydrophobic:
Water-fearing
Water tends to form hydrogen bonds. When it
mixes with non-polar molecules, it tends to shun
them and instead cling to other water molecules.
Hydrophilic: Water-loving.
Polar compounds will form hydrogen bonds with
water. This breaks ionic bonds, dissolving the
compound.
pH
1.
2.
3.
4.
A measure of the relative concentration of
hydrogen ions in a solution.
Values range from 0 to 14.
Less than 7 is an acid.
More than 7 is a base.
Acids
1.
2.
3.
A substance that causes an increase in the
concentration of H+ ions.
Tastes sour.
Tingles the skin.
Bases
1.
2.
3.
4.
A substance that causes a decrease in the
relative concentration of H+ ions.
Also called alkaline.
Tastes bitter.
Sometimes slippery or slick feeling.
Chemical Reactions



Catalyst-substance that speed up chemical reaction
Enzyme-is a protein that acts as a biological
catalyst (lock and key model)
Activation Energy (Energy of Activation):
The energy needed to make a reaction occur.