2.

1 The Nature of Matter

Living materials are made from chemical compounds.

Atoms
atoms are the smallest and basic unit of matter
if you were to break a substance down, the smallest fragment that cant be divided into
something else without changing its properties is an atom
subatomic particles in the atom:
protons (positive charge)
neutrons (neutral charge)
electrons (negative charge)
protons and neutrons are bound together to form the nucleus, at the center of the atom
electrons are 1/1840 the mass of a proton and rotate around the nucleus
electrons are attracted to the positively charged nucleus, but orbit because they are in motion
Elements and Isotopes
An element is a pure substance that consists entirely of one type of atom. Each elements
atomic number is the number of protons in an atom and, consequently, the number of electrons.

Isotopes
atoms of the same element with a different number of neutrons is an isotope
sum of protons and neutrons is the atoms mass number
isotopes are identified by their mass numbers (ex. Carbon-12, Carbon-13, Carbon-14)
Radioactive Isotopes
some isotopes are radioactive - their nuclei are unstable and break down
radiation can be dangerous, but radioactive isotopes have important scientific and practical
uses:
geologists can determine the ages of rocks and fossils by the isotopes found in them
radiation can be used to treat cancer
can kill bacteria that cause food to spoil
can be used as labels or traces to follow the movement of substances in organisms

Chemical Compounds
a chemical compound is a substance formed by the combination of two or more elements in
definite proportions
chemical formula is used to show the composition of a compound (H2O, NaCl)
the physical/chemical properties of a compound differ from the elements from which it was
formed (hydrogen and oxygen, both gases, become liquid when combined)

Chemical Bonds
The atoms in compounds are held together by chemical bonds. Bond formation involves the
electrons that surround each nucleus, called valence electrons.

Ionic Bonds
ionic bonds are formed when one or more electrons are transferred from one atom to another
atoms lose electrons in the bond, giving it a charge - these positively and negatively charged
atoms are known as ions
ex. Sodium loses its one valence electron, Chlorine gains one electron; Na+, Cl-; these ions
have a strong attraction and create the ionic bond

Covalent Bonds
covalent bonds are formed when atoms share electrons (electrons travel in both atoms orbits)
single (covalent) bond: share two electrons; double bond: share four electrons; triple bond:
share six electrons
a molecule, the smallest unit of most compounds, is formed through a covalent bond
Van der Waals Forces
some atoms have a stronger attraction for electrons than other atoms do, creating tiny regions
on a molecule that have a positive or negative charge
molecules can develop a slight attraction to oppositely charged nearby molecules; these
forces are called van der Waals forces
van der Waals forces arent as strong as ionic or covalent bonds, but can hold large molecules
together

2.1 Section Assessment

1. An atom consists of three subatomic particles: protons, neutrons, and electrons. Protons,
which have a positive charge, bind to neutrons, which have no charge, to form the nucleus.
Electrons, which have a negative charge, orbit the nucleus.
2. All isotopes of an element have the same chemical properties because they have the same
number of electrons and protons. Isotopes of an element differ by the number of neutrons
they have.
3. A covalent bond is a bond in which two atoms are held together by shared electrons.
Electrons from each element travel in the orbitals of both atoms, creating molecules. An
ionic bond is a bond in which atoms are held together by the transfer of electrons. The loss
or gain of an electron or electrons gives atoms a positive or negative charge, which holds
the two atoms together.
4. A compound is a combination of two or more elements. An elements molecules are formed
through a covalent bond of atoms and are, in turn, bonded with other elements to form the
compound.
5. Van der Waals forces hold molecules together by attraction between molecules that have a
slight charge to them due to unequal sharing of electrons.

Key Points

1. The subatomic particles that make up atoms are protons, neutrons, and electrons.
2. Because they have the same number of electrons, all isotopes of an element have the
same chemical properties.
3. The chemical bond in which electrons are transferred from one atom to another is
called an ionic bond.
4. The chemical bond in which electrons are shared between atoms is called a covalent
bond.

2.2 Properties of Water

Water molecules are neutral, with 10 protons to balance out 10 electrons.

Polarity
an oxygen atom has a stronger attraction for electrons than the hydrogen atom does
electrons go toward the oxygen atom, creating a slight negative charge at the oxygen end and
a slight positive charge at the hydrogen end
a molecule in which the charges are unevenly distributed is called a polar molecule
Hydrogen Bonds
their partial positive/negative charges allow polar molecules to attract each other
charges of polar molecules are shown in parentheses (+) since they are weaker than the
charges on ions like Na+
hydrogen bonds are bonds between two polar molecules , such as water; they are not as
strong as covalent or ionic bonds
cohesion is an attraction between molecules of the same substance (ex. water)
adhesion is an attraction between molecules of different substances (ex. water and glass)
Solutions and Suspensions
A mixture is a material composed of two or more elements or compounds that are physically
mixed together but not chemically combined.

Solutions
if a crystal of NaCl is put into warm water, the ions are broken from the crystal and dispersed
by the water molecules
all the components of a solution are evenly distributed throughout the solution
the substance in a solution that is dissolved is the solute
the substance in a solution in which the solute dissolves is the solvent
Suspensions
when placed in water, some materials do not dissolve, but separate into pieces so small they
dont settle
movement of water keeps the particles suspended

 mixtures of water and non dissolved material are known as suspensions

Acids, Bases, and pH
A water molecule can react to form ions. However, since the number of positive ions produced is
equal to the number of negative hydroxide ions produced, water is neutral.

The pH Scale
the pH scale is a measurement system indicating the concentration of H+ ions in solution
at a pH of 7, the concentration of H+ ions and OH- ions is equal
solutions with pH > 7 are called basic because they have more OH- ions than H+, vice versa
each step on the pH scale represents a factor of 10 (a solution with pH of 3 has 10x as many
H+ ions as pH of 4)

Acids
an compound that forms H+ ions in solution is an acid
acidic solutions have higher concentrations of H+ ions and have pH values below 7
Bases
a compound that produces hydroxide ions in solution is a base
basic (alkaline) solutions have lower concentrations of H+ ions and have pH values above 7
Buffers
the pH in the body must be kept between 6.5 to 7.5 or it will affect chemical reactions in the
body
the body produces buffers, weak acids or bases that react with strong access or bases to
prevent sudden changes in pH

Chapter 2.2 Assessment

1. The oxygen in a water molecule has a stronger attraction to the electrons than the hydrogen
atoms do, so the electrons are drawn more to the oxygen end of the molecule than the
hydrogen end. The greater number of electrons near the oxygen end makes it slightly
negative, while the fewer number of electrons near the hydrogen make it slightly positive.
2. Acidic solutions have a higher concentration of H+ ions and a lower concentration of OHions, while basic solutions have a lower concentration of H+ ions and a higher concentration
of OH- ions.
3. In a solution, a solute is completely and evenly dissolved into the solution, such as salt in
water. In a suspension, a material that is placed into water separates into smaller pieces, but
does not dissolve.
4. PH measures the concentration level of H+ ions in a solution.

Key Points

1. A water molecule is polar because there is an uneven distribution of electrons

between the oxygen and hydrogen atoms.
2. Acidic solutions contain higher concentration of H+ ions than pure water and have pH
values below 7.
3. Basic (alkaline) solutions contain lower concentration of H+ ions than pure water and
have pH levels above 7.
4. The concentration of H+ ions determines whether solutions are acidic or basic.

2.3 Carbon Compounds

Chemists can apply principles governing the chemistry of nonliving things to living things.

The Chemistry of Carbon

carbon has four valence electrons, so it can bond with itself, creating a chain unlimited in
length
carbon can bond with many elements; including hydrogen, oxygen, phosphorus, nitrogen, etc.
carbon-carbon bonds can be single, double, or triple covalent bonds
carbon can close upon themselves to form rings
Macromolecules
macromolecules are made from thousands or even hundreds of thousands of smaller
molecules
macromolecules are formed through polymerization; large compounds (polymers) are built by
joining smaller ones (monomers) together
monomers that make up a polymer can be identical or different
Carbohydrates
compounds made up of carbon, hydrogen, and oxygen atoms in a ratio of 1:2:1
living things use carbohydrates as the main source of energy, while plants and some animals
use carbs for structural purposes
the breakdown of sugars (ex. glucose) provides immediate energy for call activity
single sugar molecules are called monosaccharides (glucose, galactose, fructose)
large macromolecules are known as polysaccharides
animals store excess sugar in a polysaccharide called glycogen
plants make a different polysaccharide called cellulose that give them their structure
Lipids
lipids are made of carbon and hydrogen atoms and store energy
many lipids are formed when a glycerol molecule combines with compounds called fatty acids
the lipid is saturated if the fatty acids carbon atoms are joined by a single bond
the lipid is unsaturated if the fatty acid contains one carbon-carbon double bond
the lipid is polyunsaturated if the fatty acid contains more than one double carbon bond

Nucleic Acids
nucleic acids are macromolecules containing hydrogen, oxygen, nitrogen, carbon, and
phosphorus
they are polymers made from monomers known as nucleotides: consist of three parts: 1) a 5carbon sugar 2) a phosphate group 3) nitrogenous base
nucleotides can be joined to form a polynucleotide, or a nucleic acid
nucleic acids store and transmit hereditary information in the form of RNA (ribonucleic acid)
and DNA (deoxyribonucleic acid)

Proteins
proteins are macromolecules that contain nitrogen, carbon, hydrogen, and oxygen and made
up of amino acids
amino acids are compounds with an amino group (-NH2) and a carboxyl group (-COOH)
all amino acids contain an amino group, an R-group, and carboxyl group, which allows any
amino acid to be joined to any other amino acid, making it extremely versatile
R-groups vary in acidity and polarity, and decide the job of the protein
Four levels protein is organized:
sequence of amino acids in a protein chain
twisted/folded amino acids
twisted/folded chain of amino acids
position of each chain of amino acids

Chapter 2.3 Section Assessment

1. The four groups of organic compounds found in living things are proteins, nucleic acids,
carbohydrates, and lipids.
2. Proteins help control the rate of reactions and cell functions and also help form bones and
muscles. Nucleic acids form RNA and DNA, which carry hereditary information.
Carbohydrates are the main source of energy for living things. Lipids also store energy.
3. Carbon has four valence electrons, so it can bond with its own atoms in an almost endless
chain. It can also bond with many other common elements, making up many large and
complex structures.

Key Ideas

1. Four groups of organic compounds found in living things are carbohydrates, lipids,
nucleic acids, and proteins.
2. Living things use carbohydrates as their main source of energy. Plants and some
animals also use carbohydrates for structural purposes.
3. Lipids can be used to store energy. Some lipids are important part of biological
membranes and waterproof coverings.
4. Nucleic acids store and transmit hereditary, or genetic, information.
5. Some proteins control the rate of reactions and regulate cell processes. Some
proteins build tissues such as bone and muscle. Other transport materials or help to
fight disease.

2.4 Chemical Reactions and Enzymes

Everything that happens in an organism is based on chemical reactions.

Chemical Reactions
a chemical reaction is a process that changes one set of chemicals into another,
and all energy is conserved; reactions always involve changes in the chemical
bonds that join atoms in compounds
reactants are the elements/compounds that enter the reaction and products are
the elements/compounds produced by the reaction

Energy in Reactions
Energy is released or absorbed whenever there is a chemical reaction.

Energy Changes
exothermic reactions occur spontaneously, while endothermic reactions need a
source of energy to occur
life functions require endothermic reactions that need energy to occur
plants get energy from sunlight
animals get energy by consuming plants or other animals
humans get energy by consuming food
Activation Energy
not all exothermic reactions occur spontaneously; many need a certain level of
energy to start the reaction called activation energy

Enzymes
some chemical reactions needed to live take too long to be practical, so they need a
catalyst, a substance that speeds up the rate of a chemical reaction
enzymes are proteins that are bodily catalysts and they speed up chemical reactions in
cells
catalysts lower the activation energy to speed up the reaction
enzymes are very specific, usually only catalyzing only one chemical reaction

Enzyme Action
Reactants must collide with enough energy so that existing bonds will be broken and new bonds
will be formed.

The Enzyme-Substrate Complex

enzymes provide a place called an active site that reduces the activation energy
reactants of enzyme-catalyzed reactions are called substrates
active sites and substrates have complementary shapes (i.e. puzzle piece)
Regulation of Enzyme Activity
enzymes work best in certain pH values and temperatures
ex. enzymes produced by human cells work best at the normal temperature of
the human body

Chapter 2.3 Section Assessment

1. Chemical bonds are broken and reformed during chemical reactions.

2. During chemical reactions, energy is always preserved. It is either absorbed or released in
the process. A certain amount of energy known as the activation energy is needed to start a
chemical reaction.
3. Enzymes are bodily catalysts that lower the activation energy of certain chemical reactions
and speed them up. Many functions needed for living require endothermic reactions, which
need a high amount of activation energy and take an impractical amount of time to start.
Enzymes lower their activation energy and make the reactions accessible for the body.
4. Enzymes have a place called an active site that lowers the activation energy of the reaction.
Substrates fit into the active site of their respective enzyme perfectly, much like a lock and
key or puzzle pieces.

Key Concepts

1. Chemical reactions always involve changes in the chemical bonds that join atoms in
compounds.
2. Chemical reactions that release energy often occur spontaneously. Chemical
reactions that absorb energy will not occur without a source of energy.
3. Enzymes speed up chemical reactions that take place in cells.