Chapter 2
CHAPTER 2-THE CHEMICALS OF LIFE
I. CHEMISTRY-the science dealing with the properties and transformations of matter.
II. Matter - anything that occupies space and has a mass. Matter can exist in one of three
forms: solid, liquid or gas. It can be living or non-living
A. Components of Matter
1. Atoms- smallest functional units of matter.
a. Elements cannot be broken down into smaller particles by chemical
reactions. There are 92 natural elements. Those that are required in
large supply for organisms to survive and live are known as Essential
Elements (these include Hydrogen, Nitrogen, Carbon, Oxygen).
b. so small cant see with microscope.
2. Molecules- 2 or more identical atoms that are bonded together.
III. ATOMS-the smallest functional units of matter. All chemical activities revolve around the
properties of atoms.
A. 3 Subatomic Particles that Make Up Atoms
1. Protons- are located in the nucleus (center) of an atom. They have a positive
charge.
2. Neutrons- located in the nucleus and have a neutral charge.
3. Electrons- are located in orbitals (shells) and they have a negative charge.
a. Different atoms have different numbers of electrons and electron
orbitals.
b. Number of Electrons per Orbital
1) First Orbitals- can contain no more than 2 electrons.
2) Second Orbitals-can contain no more than 8 electrons.
3) Third Orbitals- can contain no more than 8 electrons.
c. Atoms attempt to fill their outer orbital with the maximum number of
electrons. Atoms accomplish this through a process known as bonding.
In bonding, atoms can either gain, lose or share electrons with other
atoms.
d. Stable atoms- have an outer orbital that is filled with the maximum
number of electrons.
B. Important Atomic Terms
1. Atomic Number- the number of protons in an atom. Each element has its own
specific atomic number.
a. The number of protons in an atom is equal to the number of electrons in
the atom.
2. Mass Number-the number of protons plus the number of neutrons in the atom.
3. Isotopes- atoms of the same element that contain the same numbers of protons
and electrons but that contain different numbers of neutrons.
a. Hydrogen Isotopes
b. Radioactive Isotopes-decay spontaneously giving off high energy radiation.
C. The Periodic Table of the Elements- a list of all of the known elements.
1. The table is organized by increasing atomic number. Can you read the Table?
> C, N, O, Na, Mg, P, S, Cl, K, Ca, Fe
IV. CHEMICAL BONDING-attractive forces that hold 2 or more atoms together.
A. Chemical bonding allows atoms to fill their outer orbitals with the maximum number
of electrons. This allows atoms to become stable.
B. 2 Types of Chemical Bonds: Ionic Bonds, Covalent Bonds
C. Ionic Bonding- occurs when one atom loses an electron and a second atoms gains the
electron.
1. This type of bonding produces ions- (charged particles.)
2. Oxidation- refers to the loss of an electron. Atoms that lose an electron are said
to be oxidized.
- Atoms that are oxidized are written with a positive charge. Why
is this so? – Because its lost a negative electron. If you lose a negative you become more positive.
3. Reduction- refers to the gain of an electron. Atoms that gain an electron are said
to be reduced. Atoms that are reduced are written with a negative charge. Why
is this so? Because it has gained a negatively charged electron.
4. Sodium Chloride (NaCl)- an example of an ionic bond. Sodium =11 electrons (2 in first orbital, 8 in second, and 1 in third. Chlorine has 2 in 1, 8 in 2, and 7 in 3. It takes electron from sodium to make a full orbital
D. Covalent Bonding- occurs when atoms share 1 or more pairs of electrons. Some can share 2 or 3 pairs of electrons (double and triple bond)
1. There are no charges associated with covalent bonds.
2. These are often very strong bonds and very stable.
3. Examples of Covalent Bonds:
- Double Covalent Bonds- occur when atoms share 2 pairs of electrons.
- Triple Covalent Bonds
- Polar Covalent Bonds- in these bonds, one atom shares the electron stronger than another atom, thus, the atom has a slightly negative charge. Polar molecules tend
to react easily with other molecules. Due to this, polar molecules are said to be hydrophilic (meaning that they dissolve in water).
F. Weak Attractions between atoms:
1. Hydrogen bonds- sometimes hydrogen atoms that are covalently bonded to one
atom can form a weak attraction (with no electrons involved) with atoms in
other molecules.
2. Van der Waals Interactions- very weak attractions that form between slightly
positive and slightly negative molecules.
G. Bond Strength:
1. Covalent Bonds-strongest bonds
2. Ionic Bonds
3. Hydrogen Bonds
4. Van der Waals Interactions-weakest molecular interactions
H. Types of Reactions Related to Bonding that occur in the Human Body:
1. Synthesis (anabolic “building up”) Reactions- occur when atoms bond together to form larger molecules.
2. Decomposition ( catabolic “break down”) Reactions- occur when molecules are broken down into smaller
molecules or atoms.
3. Exchange Reactions- occur when molecules exchange atoms with each other.
V. WATER
A. Water is the most abundant compound in all living organisms. Many of the reactions
that occur in living organisms occur or require water to take place. Without water,
living things (including both plants and animals) would die.
B. Structure of a water molecule
1. Water molecules are composed of 2 hydrogen atoms that are covalently
bonded to a single oxygen atom. What type of bond is this? Polar Covalent bond
a. Overall, water has a very strong and stable structure.
C. Properties of Water
1. Water is a Polar Molecule- this means that the Oxygen atom tends to have a
stronger attraction for the electrons in the covalent bond than do the Hydrogen
atoms. Due to this, the oxygen is slightly more negative than the hydrogens.
Polar molecules tend to react easily with most other molecules.
a. Hydrophilic Compounds- are soluble in water. These compounds
dissolve in water. Examples of hydrophilic compounds include:
b. Hydrophobic Compounds- are not soluble in water. These compounds
do not dissolve in water. Examples include:
2. Water Forms Hydrogen Bonds
a. Hydrogen Bonds-weak attraction between the hydrogen atoms of one
water molecule and the oxygen atom of a second water molecule.
3. Water Stabilizes Temperature
a. Water has a very stable temperature. It takes a tremendous amount of
energy to heat water and a great deal of cold to freeze water.
b. This protects living organisms from rapid temperature changes.
4. Water Participates in Many Reactions
a. Many important biological reactions occur in water. Also, water
initiates many reactions.
5. Water is a powerful solvent. A solvent is a fluid that molecules can dissolve in.
VI. ACIDS, BASES, and pH
A. Acids-release hydrogen ions (H+) when placed in water.
B. Bases-release hydroxide ions (OH-) when placed in water.
C. pH Scale-a measure of how acidic or basic a compound is.
1. Neutral, Strong Acid vs. Weak Acid, Strong Base vs. Weak Base
2. In the real world, small changes in pH can have severe effects on living
organisms. Due to this, most organisms have methods that allow them to
maintain a normal, healthy pH.
D. Buffers-compounds that reduce or minimize changes in pH. These help to maintain a
stable pH.
1. Bicarbonate Buffer System-a major buffering system in living organisms.
a. H2CO3 HCO3 + H+
(Carbonic Acid) (Bicarbonate) (Hydrogen ion)
b. How Bicarbonate Buffers a System
1) In acids (when extra hydrogen ions are present), bicarbonate
will soak up the hydrogen ions to produce a weak acid. This
raises pH towards neutrality.
2) In bases, the hydrogen ions can react with extra hydroxyl ions
to produce water which has a pH of 7. Overall, this lowers pH.
VII. ORGANIC MOLECULES-are molecules that contain the elements carbon and hydrogen.
A. There are four major organic Macromolecules found in all living organisms:
carbohydrates, lipids, proteins and nucleic acids. Often times, numerous smaller
molecules (known as monomers) form covalent bonds to produce larger
macromolecules.
B. Types of Reactions associated with Polymers:
1. Dehydration (Condensation) Reactions-reactions in which monomers bond
together to produce macromolecules. Water is typically lost in these reactions.
2. Hydrolysis Reactions-reactions in which macromolecules are broken down into
monomers.
VIII. Carbohydrates- sugars and related compounds.
A. All carbohydrates are composed of Carbon, Hydrogen and Oxygen. In carbohydrates,
there is always a 1:2:1 ratio of carbon to hydrogen to oxygen.
- All carbohydrates have 1 carbon for every 2 hydrogen for every 1 oxygen
B. Classes of Carbohydrates:
1. Monosaccharides- simple sugars (1)
a. These serve as monomers for many of the larger carbohydrates.
b. Glucose is an example of a monosaccharide. Stored as fat.
2. Disaccharides-sugars that are composed of 2 monosaccharides that are
covalently bonded together. These are formed by dehydration reactions.
a. Types of Disaccharides (2 – two monosaccharides bonded together)
1. Sucrose- table sugar
2. Lactose- milk sugar
3. Maltose- sugar found in beer
3. Polysaccharides-sugars that are composed of more than 2 monosaccharides that
are covalently bonded together. These are often very large molecules.
b. Types of Polysaccharides
1. Starch- a stored form of glucose in plant cells. Plants can use starch for energy under times of need or stress.
2. Glycogen- the storage form of glucose in humans. Humans can
convert glycogen into glucose under times of need or stress. This
glucose can then be used as an energy source. Glycogen is stored in
the liver and in some muscle fibers.
IX. Lipids- fats, oils, waxes.
A. All lipids are hydrophobic- they do not dissolve in water.
B. Lipids serve as a source of stored energy in the human body. Fats also protect and cushion
structures in the human body.
C. Structure of a Typical Lipid
1. Lipids are composed of 2 major components:
a. Glycerol- a 3 carbon alcohol that forms the backbone of a lipid.
b. Fatty Acids attached to each of the carbon
1) Three fatty acid molecules attach to glycerol to form a lipid. Each
fatty acid replaces the hydrogen atom on the hydroxyl groups of the
glycerol molecule. Due to this, there is one fatty acid bonded to
each carbon atom of the glycerol molecule.
a) Due to this arrangement, lipids are often referred to as
triglycerides.
c. Saturated vs. Unsaturated Fatty Acids
D. Types of Lipids
1. Phospholipids-contain only 2 fatty acid tails. These are found in cell membranes.
They have hydrophilic heads and hydrophobic tails.
2. Hormones- chemicals that regulate the growth and functioning of living organisms.
3. Steroids- there are several different types of steroids:
a. Cholesterol-common steroid. This can be used to produce Vitamin D but
large supplies of cholesterol in the diet can cause heart disease.
b. Sex Hormones-including testosterone and estrogen. (anabolic steroids)
X. Proteins
A. Proteins are composed of many amino acids that are covalently bonded together. These
bonds are referred to as peptide bonds.
B. Amino Acids-there are 20 naturally occurring amino acids. They can bond in a variety
of sequences to produce proteins. (share electrons in a covalent bond)
a. All amino acids contain a central carbon atom that is bonded to a hydrogen
atom, a carboxyl group (COOH) and an amino group (NH2). The remaining
carbon bond can form with numerous other molecules to actually produce
a specific amino acid.
b. Some common amino acids include: phenylalanine, tryptophan (amino acid in turkey and chicken that makes you drowsy), asparagine
C. Levels of Protein Structure:
a. Primary Structure-a linear sequence of bonded amino acids.
b. Secondary Structure- coils and slight folding of amino acid structure that
is supported by hydrogen bonds.
c. Tertiary Structure-complex, three-dimensional structure of folded amino
acids. Holds human hair together. Straight hair is less tertiary structures, curly more.
d. Quaternary Structure-aggregation of multiple proteins into a complex
structure.
D. Proteins serve primarily as structural compounds in living organisms. They also make up
enzymes which are proteins that speed up biological reactions. Reactions associated with
enzymes occur at the active site of an enzyme. The molecule that an enzyme reacts with is
known as the substrate.
- Some help to produce blood clots.
VII. Nucleic Acids
A. These are composed of nucleotides that are covalently bonded together.
B. Individual Nucleotides Contain:
1. A 5 Carbon Sugar
2. A Phosphate group
3. A Nitrogen-containing base
C. Types of Nucleic Acids:
1. Deoxyribonucleic Acid (DNA)- primary genetic material in living organisms. Unique double helix shape
2. Ribonucleic Acid (RNA)-involved in building proteins for living cells. Looks like half of a DNA strand. Plays a role in building proteins and in dividing ourselves.
3. Adenosine Triphosphate (ATP)-major energy source for cells.