CHAPTER 2 – The Chemistry of Life
2.1
The Nature of Matter
Since living things are made of chemical compounds, a biologist must understand the chemistry of
life.
Atoms
The atom is the basic unit of matter.
The Greek word atomos means “unable to be cut,” and was used by the Greek philosopher
Democritus nearly 2500 years ago to describe the smallest fragment of a substance that could not be
divided.
Copy Figure 2-1 on Page 35 (Helium Atom)
The subatomic particles that make up atoms are protons, neutrons, and electrons.
Protons are positively charged (+) and neutrons carry no charge, but both have approximately the
same mass.
Protons and neutrons are bound together by strong forces to form the nucleus, or center of an atom.
Electrons are negatively charged particles (-) that are much lighter than protons and neutrons.
Electrons are attracted to the nucleus, but stay in constant motion in the space surrounding the
nucleus.
Atoms are neutral because they have equal numbers of protons (+) and electrons (-).
Elements and Isotopes
An element is a pure substance that consists entirely of one type of atom.
Elements are represented by either one capital letter (like H for hydrogen and C for carbon) or one
capital and one lower-case letter (like Na for sodium).
The number of protons in an atom of an element is the element’s atomic number.
The Periodic Table (Appendix G) – find oxygen
Atoms of the same element that differ in the number of neutrons they contain are called isotopes.
The sum of protons and neutrons in the nucleus of an atom is called its mass number.
For example, there are 3 isotopes of carbon: C-12, C-13, and C-14 (see Figure 2-2 on Page 36).
The atomic mass of an element is equal to the weighted average of the masses of all its isotopes.
Because they have the same number of electrons, all isotopes of an element have the same chemical
properties.
Radioactive isotopes have unstable nuclei that break down at a constant rate over time.
What are some practical uses for radioactive isotopes?
Chemical Compounds
A chemical compound is a substance formed by the chemical combination of two or more elements
in definite proportions.
These proportions can be written as a chemical formula.
What is the chemical formula for water? For table salt?
The physical and chemical properties of a compound are usually very different from those of the
elements that form it.
Chemical Bonds
Atoms in compounds are held together by chemical bonds that involve their available electrons
(called valence electrons).
The main types of chemical bonds are ionic bonds and covalent bonds
Ionic Bonds
Atoms are electrically neutral because they have equal numbers of electrons and protons.
If an atom loses or gains an electron, it is known as an ion. Ions have a positive or negative charge.
An ionic bond is formed when one or more electrons are transferred from one atom to another.
An ionic bond is formed between sodium and chlorine in table salt. A sodium atom loses one
valence electron and becomes a sodium ion (Na+). A chlorine atom loses one valence electron and
becomes a chlorine ion (Cl-).
The oppositely charged ions have a strong attraction that results in an ionic bond.
Covalent Bonds
A covalent bond forms when electrons are shared between atoms (the electrons travel in the orbitals
of both atoms).
There can be single covalent bonds (share 2 electrons), double bonds (4 shared), and triple bonds (6
shared).
Molecules are formed when atoms are joined together by covalent bonds. The molecule is the
smallest unit of most compounds.
Copy Figure 2-4 on Page 38 (Water Molecule)
Van der Waals Forces
Regions on molecules may have a slight positive or negative charge. So when molecules are close
together, a slight attraction can develop between the oppositely charged regions of nearby
molecules.
These intermolecular attractions are called van der Waals forces. They are not as strong as ionic or
covalent bonds.
2.2
Properties of Water
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The water in oceans covers 3/4ths of the Earth’s surface.
Water is the single most abundant compound in most living things.
Water is liquid at room temperature.
Water expands when it freezes (ice is less dense than water and floats on water).
The Water Molecule
A water molecule is neutral. How many protons and electrons are there in a water molecule?
Because oxygen has 8 protons in its nucleus and hydrogen has only 1 proton, oxygen has a much
stronger attraction for electrons than hydrogen.
Water molecules have a bent shape (see Figure 2-6).
The oxygen end of an H2O molecule has a slight (-) charge and the hydrogen end has a slight (+)
charge.
A water molecule is polar because there is an uneven distribution of electrons between the oxygen
and hydrogen atoms.
Any molecule that has an uneven distribution of charges is called a polar molecule (think of the north
and south poles on a magnet).
Hydrogen Bonds
Since opposites attract, the opposite charges of water molecules allows them to attract each other.
This attraction between water molecules is an example of hydrogen bonds (Figure 2-7 on Page 41).
Hydrogen bonds are not as strong as covalent or ionic bonds.
A single water molecule may have as many as four hydrogen bonds at one time, which gives water
several of its properties.
Water is extremely cohesive and produces a force that is sometimes called surface tension.
Cohesion is the attraction between molecules of the same substance.
Adhesion is an attraction between molecules of different substances.
Adhesion between water and glass causes water to rise in a narrow tube against the force of gravity
(called capillary action).
Capillary action helps plants draw water from their roots into their stems and leaves.
Will two pieces of wet glass sick together? Why?
Solutions
Sodium chloride (NaCl) is an ionic compound. What happens when you place table salt in water?
Water molecules surround and separate the positive Na+ ions and negative Cl- ions. When the ions
become evenly dispersed in the water, you have a solution.
All the components of a solution are evenly distributed throughout the solution.
The substance that is dissolved (for example - table salt) is called the solute.
The substance in which the solute dissolves is called the solvent (water is the universal solvent).
Since water is polar, it is able to dissolve both ionic compounds and other polar molecules (like
sugar).
Suspensions
Some materials separate into very small pieces when placed in water. These pieces do not dissolve,
but instead of settling to the bottom, they stay suspended.
These mixtures of water and non-dissolved materials are called suspensions.
Your red and white blood cells remain in suspension as your blood moves through your body.
Some medicines are also sold as suspensions. (Why do medicine containers say “Shake well before
using” )
Acids, Bases, and pH (see Figure 2-10 on Page 43)
A water molecule can also react and form ions.
H20
H+
+
OH-
Where H20 is water, H+ is a hydrogen ion, OH- is a hydroxide ion, and the double arrows indicate that
the reaction can occur in either direction.
The pH scale ranges from 0 to 14 and indicates the concentration of H+ ions in a solution.
At a pH of 7, the concentration of H+ ions and OH- ions are equal and the solution is neutral.
Solutions with pH values below 7 have more H+ ions than OH- ions and are called acidic.
An acid is any compound that forms hydrogen ions (H+ ions) in solution.
Solutions with pH values above 7 have more OH- ions than H+ ions and are called basic (or alkaline).
A base is any compound that produces hydroxide ions (OH - ions) in solution.
Strong acids have low pH values (1-3, example HCl); while strong bases have high pH values (11-14,
example lye).
Buffers are weak acids or bases that react with strong acids or bases to prevent sharp, sudden
changes in pH.
2.3
Carbon Compounds
Organic chemistry is the study of all compounds that contain bonds between carbon atoms.
The Chemistry of Carbon
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Carbon has 4 valence electrons, which allows it to form 4 covalent bonds.
Carbon can bond with many different elements, including: hydrogen, oxygen, phosphorous,
sulfur, and nitrogen.
A carbon atom can also bond to other carbon atoms, which allows it to form long chains, or
even rings.
Carbon to carbon bonds can be single, double, or triple covalent bonds.
Carbon has the ability to form millions of different large and complex structures (Figure 2-11).
Macromolecules
Macromolecules are “giant molecules” that are made from thousands or even hundreds of
thousands of smaller molecules.
Macromolecules are formed by joining smaller molecules together in a process called
polymerization.
The smallest molecules or units are called monomers. Monomers are joined together to form larger
units called polymers (see Figure 2-12).
The organic compounds found in living things can be classified into four groups:
 Carbohydrates
 Lipids
 Nucleic Acids
 Proteins
Sometimes these organic compounds are referred to as biomolecules.
Carbohydrates
Carbohydrates are compounds that are made up of C, H, and O atoms, usually in a ratio of 1:2:1 (for
example, the formula for glucose, a sugar, is C6H12O6)
Living things use carbohydrates as their main source of energy (that’s why eating sugar gives us
energy).
Plants and some animals also use carbohydrates for structural purposes (for example, cell walls of
plants).
Reminder: small molecules called monomers join together to make larger molecules called polymers.
Single sugar molecules are called monosacharides; and examples are glucose, galactose, and
fructose.
Monosacharides can join and form macromolecules called polysaccharides (example: glycogen produced by your liver is used by your muscles for movement).
Plants produce a polysaccharide known as cellulose, which is the major component of paper and
wood.
Lipids
Lipids are macromolecules that are primarily made up of carbon and hydrogen atoms. They are
usually not soluble in water, and include fats, oils, waxes, and steroids.
Lipids are also used to store energy for living things, and some are important parts of biological
membranes and waterproof coverings.
Lipids form when a glycerol molecule combines with compounds called fatty acids.
If each of the carbon atoms in the lipid’s fatty acid chains is joined to another carbon atom by a
single covalent bond, the lipid is said to be saturated.
If even one carbon-to-carbon double bond is present, the fatty acid is said to be unsaturated.
What would you call a fatty acid with many carbon-to-carbon double bonds?
Lipids which contain unsaturated or polyunsaturated fatty acids tend to be liquid at room
temperature. Examples are olive oil, corn oil, sesame oil, canola oil, and peanut oil.
Nucleic Acids
Nucleic acids are macromolecules that contain hydrogen, oxygen, nitrogen, carbon, and
phosphorus.
The monomers that make up nucleic acids are called nucleotides.
Each nucleotide consists of three parts:
 a 5-carbon sugar
 a phosphate group, and
 a nitrogenous base
(copy Figure 2-15 on Page 47)
Individual nucleotides can be joined by covalent bonds to form a polynucleotide, or nucleic acid.
Nucleic acids store and transmit hereditary, or genetic, information.
There are two kinds of nucleic acids:
RNA – ribonucleic acid, and
DNA – deoxyribonucleic acid.
The main difference between RNA and DNA is the 5-carbon sugar. RNA contains the sugar ribose
and DNA contains the sugar deoxyribose.
Proteins
Proteins are macromolecules that contain nitrogen as well as carbon, hydrogen, and oxygen.
Amino acids are the monomers of proteins.
All amino acids have an amino group (-NH2) at one end, a carboxyl group (-COOH) at the other end,
and a side chain called an R-group. (see Figure 2-16 on Page 47)
Proteins are very diverse macromolecules, and more than 20 different amino acids are found in
nature. (Note: the difference is in the R-group.)
Any amino acid can bond to any other amino acid.
The instructions for arranging amino acids into different proteins are stored in an organism’s DNA.
Each protein has a specific role. For example:
 Some proteins control the rate of reactions and regulate cell processes.
 Some are used to form bones and muscles.
 Others transport substances into or out of cells, or help fight disease.
Proteins can have up to four levels of organization, starting with a protein chain and then becoming
more twisted, folded, and complex.
Van der Waals forces and hydrogen bonds help proteins maintain their shape.
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 set of chemicals.
The elements or compounds that enter into a chemical reaction are called reactants.
The elements or compounds that are produced by a chemical reaction are called products.
Chemical reactions always involve the breaking of bonds in reactants and the formation of new
bonds in products.
An example of a chemical reaction is when carbon dioxide (CO2) reacts with water (H20) in your blood
to produce a water-soluable compound called carbonic acid (H2CO3).
CO2
+
H2O
→
H2CO3
(CO2 & H20 are the reactants and H2CO3 is the product)
This chemical reaction allows the bloodstream to carry CO2 to your lungs.
In your lungs, the reverse chemical reaction takes place, and you release CO 2 and H2O when you
exhale.
H2CO3 →
CO2
+
H2O
Energy in Reactions
Energy is either released or absorbed whenever chemical bonds are broken.
Chemical reactions involve the breaking and forming of chemical bonds, so they involve changes in
energy.
Chemical reactions that release energy (give off energy as heat, light, sound) often occur
spontaneously and are called exothermic reactions (Figure 2-19, bottom).
Chemical reactions that absorb energy (take energy in) will not occur without a source of energy and
are called endothermic reactions (Figure 2-19, top).
An example of an energy-releasing reaction is:
2H2
+
O2
→
2H2O
Where hydrogen gas (2H2) reacts or burns with oxygen (O2) to produce water vapor (2H2O) and heat.
Reversing this reaction would require energy.
Therefore, in order to stay alive, all organisms need to carry out chemical reactions that require
energy.
Plants get their energy by trapping sunlight and storing the energy as carbohydrates.
Animals (like us) get their energy by consuming plants and/or animals.
Activation Energy
Not all exothermic chemical reactions occur spontaneously.
For example, even though paper is flammable, it does not burst into flame on hot days. Energy in the
form of a match or spark is needed. What energy is released?
The energy that is needed to get a chemical reaction started is called the activation energy.
Enzymes
If the activation energy for a reaction is too high, or if the reaction occurs to slowly, a catalyst is
needed.
A catalyst is a substance that speeds up the rate of a chemical reaction by lowering the activation
energy needed so start that reaction.
Enzymes are proteins that act as biological catalysts by speeding up chemical reactions that take
place in cells.
As shown in Figure 2-20, the addition of an enzyme lowers the activation energy needed, which
speeds up the reaction.
For example, we talked up the build-up of CO2 in blood. An enzyme called carbonic anhydrase
removes CO2 at a rate that is 10 million times faster than without it.
NOTE: enzymes are very specific and usually only catalyze one chemical reaction.
Enzyme Action
The reactants of a chemical reaction must collide with enough energy to so that the existing
chemical bonds will be broken and new bonds can be formed.
Enzymes provide a site where reactants can be brought together to react. This site also lowers the
activation energy needed for the reaction.
The reactants of enzyme-catalyzed reactions are known as substrates.
See Figures 2-21 and 2-22 on Pages 52 and 53
The Enzyme-Substrate Complex
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Each protein has a specific and complex shape.
The substrates bind to a place on the enzyme called the active site.
The substrates and enzyme fit together so well that this is often referred to as the lock and
key model.
Once the reaction is complete, the products of the reaction are released.
The enzyme is also released and can be used over and over again (it is not used up by the
reaction).
Regulation of Enzyme Activity
The effectiveness of an enzyme can be affected by any variable that can influence a chemical
reaction.
For example, many enzymes work best within certain pH and temperature ranges.
Most cells also contain proteins that help turn enzymes “on” or “off.”
Enzymes play important roles in organisms. Examples?