UNIT 1.

1: FOUNDATIONAL CHEMISTRY THE CHEMISTRY OF LIFE

Topic 1 Review of Important Chemistry Concepts
Identify three examples of matter – a solid, Matter
liquid, and gas – that are found in the • Matter refers to anything that has mass and takes up space
human body. (has volume).
• Matter exists in three states: solid, liquid, and gas.
• All matter (both living and non-living) is composed of basic
substances called elements.
What are the six main elements found in all
living things? Elements
• An element is a substance that cannot be broken down by
chemical means into any simpler substances; elements are
composed of only one type of atom.
According to the pie charts in the slides, • The six main elements found in all living organisms are Carbon
what element is most abundant in living (C), Oxygen (O), Hydrogen (H), Nitrogen (N), Phosphorus (P),
things? and Sulfur (S).
o Acronym to remember: CHNOPS
According to the pie charts in the slides, o They make up more than 97% of the human body.
what element makes up the majority of • Trace elements - such as Potassium (K), Sodium (Na), Calcium
Earth’s atmosphere? (Ca), Chlorine (Cl), and a handful of others - make up the
remaining small percent of living things.

Trace elements are elements that are Atoms

required by an organism, but only in • An atom is the smallest unit of matter that still retains the
minute quantities. Iron (Fe) is one of those properties of an element.
elements in humans; your body is only • Composed of three subatomic particles: protons, neutrons,
about 0.006% iron. What important use electrons
does iron have in humans? (Google if you • In the nucleus:
do not know) o Protons (positively charged) and neutrons (no charge).
• In orbiting clouds (electron shells) around the nucleus:
o Electrons (negatively charged)
• The number of protons determines which element an atom is.
• On the Periodic Table:
o Atomic Number = # of protons
o Avg. Atomic Mass Number = # of protons and neutrons

Isotopes
• Isotopes are atoms of the same element (have the same
Complete the following table for two of
number of protons), but have a different number of neutrons.
carbon’s isotopes:
Carbon-12 Carbon-14 • Some isotopes are radioactive, meaning they are unstable.
o Radioactive decay is when the nucleus of a radioactive
# Protons
isotope breaks down into a more stable atom.
# Electrons • Ex: Carbon has three isotopes.
# Neutrons o Carbon-14 is radioactive and over thousands of years will
Radioactive? decay into Nitrogen-14

The half-life of Carbon-14 is 5,730 years. If Uses of Isotopes in Biology

an archaeologist finds a fossil that contains • Radioactive isotopes have many uses in science.
0.04mg of C-14, and estimates that the • Using the half-life of certain isotopes, scientists can determine
amount of C-14 would’ve been 0.32mg the age of fossils, rocks, and other relics in a process called
when the organism was alive, how old is radioactive dating.
the fossil? o Half-life is the amount of time it takes for half a sample of
radioactive isotopes to decay into more stable isotopes.
o Ex: Carbon-14 has a half-life of 5,730 years. If you had 10g
of C-14, after 5,730 years only 5g of the sample would still
be C-14. After another 5,730 years (11,460 total years), only
2.5g would still be C-14, and so on.

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UNIT 1.1: FOUNDATIONAL CHEMISTRY THE CHEMISTRY OF LIFE
Analyze the example in the slides of • Radioactive isotopes can also be used as tracers in biological
radioactive isotopes being used as tracers. molecules, allowing scientists to monitor and investigate
What happened when the DNA of the virus biological processes.
was radioactively labeled and then allowed o A tracer is a molecule that was synthesized (“labeled”) using
to infect bacteria cells? a certain radioactive isotope. The radioactivity of that
isotope can then be tracked by scientists to see where that
molecule ended up.
o Ex: When viruses (phages) were made using DNA that was
labeled with radioactive phosphorus, scientists found that
bacteria cells become radioactive after being infected by
the viruses. This proved that virus transmit their DNA to the
infected bacteria cells. (SEE IMAGE ON NEXT SLIDE)

Compounds
• A compound is two or more elements bonded together.
Looking at a diagram of a carbon atom, o Ex: H2O , CO2 , NaCl , C6H12O6
how many valence electrons does carbon • Atoms chemically bond to other atoms to gain a full valence
have? shell (an atom’s outermost shell of electrons). Atoms typically
need 8 valence electrons to have a “full” valence shell.
o Valence Electrons: electrons in outer electron shell.
Mark each statement as ionic compound • Two types of chemical bonds that allow atoms to gain a full
(I), covalent compound (C), or both (B). valence shell:
____ Atoms transfer electrons 1. Ionic Bonds: Form when atoms transfer electrons to one
another and become ions (positively or negatively charged
____ Atoms share electrons atoms).
____ Called molecules 2. Covalent Bonds: Form when atoms share electrons with
other atoms.
____ Called salts
____ Can dissolve in water Ionic Compounds
• Ionic bonds form ionic compounds, generally known as “salts.”
____ Bonds break when dissolved in water • Consist of positively and negatively charged ions (charged
____ Requires a chemical reaction for atoms or particles), typically a metal and a nonmetal element.
bonds to be broken • Ionic compounds can usually dissociate in water - meaning
water can separate the ions from one another, breaking the
____ Forms charged atoms called ions ionic bonds between them. This allows the compound to
dissolve in water.
Photosynthesis is a chemical reaction. o Ex: Salt (NaCl) in water
What types of bonds are being broken and
reformed between the atoms during the Covalent Compounds (Molecules)
reaction? • Covalent bonds form covalent compounds, generally known as
“molecules”.
• Covalent compounds do not dissociate in water - meaning
water does not break the covalent bonds between the atoms
Explain the difference between polar and within each molecule.
nonpolar molecules. o However, individual molecules can separate from one
another, allowing some covalent compounds to dissolve in
water.
o Ex: Sugar (C6H12O6) in water
• A chemical formula tells the number of each kind of atom in a
molecule.
• Chemical reactions are REQUIRED to break covalent bonds
between atoms in a molecule and to form new ones between
atoms, allowing molecules to become new molecules.
o Ex: Photosynthesis a chemical reaction:
6 CO2 + 6 H2O → 6 O2 + C6H12O6

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UNIT 1.1: FOUNDATIONAL CHEMISTRY THE CHEMISTRY OF LIFE
As shown in the slides, glucose (sugar) is a Polar and Nonpolar Molecules
molecule that dissolves in water. Is glucose • Covalent compounds (molecules) can be classified as polar or
a polar or nonpolar molecule? How do you nonpolar.
know? • Nonpolar Molecules:
o Atoms share electrons equally.
o There is no partial positive or partial negative region on the
molecule.
o Ex: fats and oils
Label each of the following as hydrophobic • Polar Molecule:
or hydrophilic: o Atoms do not share electrons evenly
_______________ polar molecules o This creates a partial positive and a partial negative region
on the molecule.
_______________ nonpolar molecules o Ex: water
_______________ dissolves in water • “Like Dissolves Like”: Polar substances (and charged
substances, such as ions) like to associate with other polar
_______________ repels water substances, while nonpolar substances like to associate with
_______________ ions other nonpolar substances.
• Nonpolar molecules are hydrophobic: repel from or do not mix
_______________ oil with water
Endorphins are hormone molecules that • Polar molecules and ions are hydrophilic: mix or dissolve in
relieve pain and produce euphoria in times water
of stress, such as exercise. Morphine is a
drug that mimics the effects of endorphins. Molecular Shape
Why is this? Explain. • The covalent bonding that forms among atoms in a molecule,
give molecules unique 3-dimensional shapes.
• A molecule’s shape is key to its function in the cell.
• Molecular shape determines how biological molecules
recognize and respond to one another.
• Molecules with similar shapes can have similar biological
effects.
• Ex: Because a morphine molecule has a region that has a very
similar shape to a region on an endorphin molecule, they both
can bind to the same cell receptors.
Topic 2 Properties of Water
Draw two water molecules. Label the Hydrogen Bonding
positive and negative regions on the • Water is a very polar molecule, allowing it to form hydrogen
molecules. Then label a hydrogen bond. bonds.
• Hydrogen bonding is possible when hydrogen is bonded to
nitrogen (N), oxygen (O), or fluorine (F) in a molecule.
o This causes the hydrogen to take on a strong partial positive
charge and the atom its bonded to (N, O, or F) to take on a
strong partial negative charge.
• A hydrogen bond is the attraction between the positively
charged hydrogen atom of one molecule and the negatively
charged atom (N, O, or F) of another molecule.
o A single hydrogen bond is easily broken, but many can be
Explain how cohesion and adhesion are collectively strong.
being shown in the picture below.
Properties of Water
• Hydrogen bonding gives water many unique chemical
properties that are essential to life on Earth.
1. Water molecules are cohesive and adhesive:
o Cohesion is the ability of water molecules to “cling” to each
other due to hydrogen bonding.
 Ex: Water forming droplets
o Adhesion is the ability of water molecules to “cling” to
other polar surfaces due to hydrogen bonding.

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UNIT 1.1: FOUNDATIONAL CHEMISTRY THE CHEMISTRY OF LIFE
How does water travel up a tree from its  Ex: Water drops sticking to glass.
roots in the soil to the leaves at the top? o Cohesion and adhesion create capillary action: water’s
ability to “climb” narrow spaces.
o Biological Example: Cohesion and adhesion allows water to
be transported up plants against gravity, through
microscopic “tunnels” and pores in plant tissue.

2. Water has a high surface tension:

o Cohesion also causes water to have high surface tension.
o Surface tension is the force created from the molecules at
A paperclip sinks when placed in a cup of the surface of a liquid being attracted to the molecules
water. However, if it is rested very gently below the surface.
and carefully on the surface of the water, it o Surface tension causes water to form droplets, so that it can
will float. How is this possible? minimize surface area as much as possible (allowing for
maximum hydrogen bonding between water molecules)
o Surface tension also creates a force at the surface of water
that is resistant to breaking when objects are carefully
placed on it.
 Biological Example: Some insects can “walk” on water.

3. Water has a high specific heat capacity:

Look at the picture of a map in the slides o Water absorbs lots of thermal energy without a great
showing the temperatures in different change in temperature.
regions of southern California. Explain why o Biological Examples:
the temperature in Palm Springs is much  Organisms are made of mostly water, which allows them
higher than the temperature in Los Angeles to maintain normal internal temperatures and protects
during the summer. them from rapid temperature change.
 Coastal habitats have a more stable climate with less
fluctuating temperatures, because the nearby ocean
absorbs a lot of heat.

4. Water has a high heat of vaporization:

o Liquid water has to absorb a lot of thermal energy to break
its hydrogen bonds so that it can evaporate into vapor.
Elephants spray water on themselves to o Biological Example: Evaporative cooling.
cool down their bodies. What property of  When animals sweat or get splashed, their body heat is
water makes this possible? used to evaporate the water, taking away heat from their
bodies.

If water did not form hydrogen bonds, 5. Water expands when it freezes:
what would happen to organisms living in o Due to its hydrogen bonds, water expands when it freezes,
lakes during freezing temperatures in the causing it to be less dense as a solid.
winter? o Biological Example:
 When bodies of water freeze, the ice floats, insulating
the water beneath, allowing life to still exist. Prevents
lakes from completing freezing.

6. Water is the “universal solvent”:

o A solution is made up of a solute (the substance being
dissolved) and a solvent (the substance it’s dissolved in).
Lysozymes are large protein molecules o Because of its polarity, water is able to dissolve many
found in tears and saliva that kill bacteria. different substances.
Would you predict that a lysozyme o Biological Example:
molecule is polar or nonpolar? Why?  Blood and cells are mainly composed of water, which
allows many essential substances to dissolve and be
transported throughout the body (such as proteins,
nutrients, minerals, and waste).

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UNIT 1.1: FOUNDATIONAL CHEMISTRY THE CHEMISTRY OF LIFE
Topic 3 Acids and Bases
Fill in the beakers with appropriate Hydrogen and Hydroxide Ions
amounts of H+ and OH— ions to show one • A very small amount of water molecules will dissociate into
as acidic, one as basic, and one as neutral. hydrogen ions (H+) and hydroxide ions (OH−).
o In pure water, the concentration of H+ ions is equal to the
Acidic Basic concentration of OH−, or [H+] = [OH−]
• When substances are dissolved in water, it changes the the
concentration of H+ and OH− ions.
o Acids increase the [H+] when dissolved in water (and lower
the [OH−] ).
o Bases increase the [OH−] when dissolved in water (and
lower the [H+] )

Neutral The pH Scale

• The acidity of a solution is determined by the concentration of
H+ ions, [H+].
• Acidity is often measured in terms of pH, which ranges on a
scale from 0-14.
o The [H+] determines the pH of the solution, according to the
equation: pH = −log [H+]
(You do not need to know this formula or be able to use it)
Which beaker has the highest pH? Which o Ex: In water, [H+] = 1.0 x 10−7 M
one has the lowest pH? pH = −log (1.0 x 10−7) → pH = 7
• The greater the concentration of H+, the lower the pH value
(and vice versa).

There are different types of biological fluids Acidic and Basic Solutions
found in the human body, each with • In neutral solutions, like pure water, [H+] = [OH−] and the pH
different acidities. For example, the pH of equals 7.
blood is 7.4, the pH of stomach acid is 2.0, • In acidic solutions, [H+] > [OH−] and the pH is less than 7.
and the pH of urine is 6.0. Rank these fluids o The more acidic a solution is, the higher the [H+], the lower
in order of increasing acidity. the [OH−], and the lower the pH.
• In basic solutions (also called alkaline solutions), [H+] < [OH−]
and the pH is greater than 7
o The more alkaline a solution is, the lower the [H+], the
In which fluid described above would you higher the [OH−], and the higher the pH.
find the highest concentration of H+ ions?
In which fluid would you find the highest
concentration of OH− ions?

Topic 4 Introduction to Organic Chemistry

Organic compounds are ones that contain Organic Chemistry
which element? • Aside from water, living organisms consist mostly of carbon-
based compounds
In order to have a full valance shell (8 • Organic molecules are carbon-containing molecules that exist
valence electrons), how many covalent because of living things.
bonds does a carbon atom have to form • Organic compounds found in living things fall into four main
with other atoms? classes: Carbohydrates, Lipids, Proteins, and Nucleic Acids.
These are the focus of the next set of notes (Unit 1.2)
Draw a molecule of benzene (a picture of
which you will find in the slides). The Carbon Atom
• Having four valence electrons, a carbon atom will form four
covalent bonds, allowing it to build a huge diversity of large and
complex molecules.
• The bonds between carbon atoms are very stable.

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UNIT 1.1: FOUNDATIONAL CHEMISTRY THE CHEMISTRY OF LIFE
Examine the functional group table in the • Long hydrogen-carbon chains called hydrocarbons, can be
slides. What do the six common biological formed between carbon atoms
functional groups all have in common? • Hydrocarbons can create branching structures as well as ring
structures

Label all the functional groups you can find Functional Groups
in each of the following molecules: • Chemical groups can replace one or more of the hydrogens
bonded to the carbon backbone skeleton of a hydrocarbon.
Glucose (a sugar molecule) • By themselves, hydrocarbons are nonpolar (hydrophobic)
molecules.
• Functional groups are clusters of specific atoms bonded to the
carbon skeleton with special structures and chemical
properties.
o They determine the chemical reactivity and polarity of
organic molecules.
o Ex: Replacement of an H with an -OH on ethane (C2H6) turns
Valine (an amino acid molecule; found in it into ethanol (C2H5OH). This turns it from hydrophobic to
proteins) hydrophilic.
o Ex: The hydrocarbon backbone between estrogen and
testosterone is almost identical, but the difference in their
functional groups is what causes these two hormones to
have dramatically different effects on the human body.

Macromolecules
• Organic molecules found in living things form huge molecules,
called macromolecules.
Thymine (a nucleotide molecule; found in • Macromolecules usually consist of many repeating units
DNA) bonded together. Each repeating unit is called a monomer.
• A molecule composed of many monomers bonded together is
called a polymer.

Synthesis of Macromolecules
• A dehydration reaction is a chemical reaction in which subunits
are joined together by the formation of a covalent bond,
• Each new covalent bond formed through a dehydration
reaction results in the production of a water molecule.
• Dehydration reactions are used to connect monomers together
to make polymers
Which of the molecules above would you
predict to be the least polar? Explain why. Degradation of Macromolecules
• A hydrolysis reaction is a chemical reaction in which a water
molecule is added to cleave (break) a covalent bond between
two subunits.
• Each covalent bond cleaved through a hydrolysis reaction
requires a water molecule.
• Hydrolysis reactions are used to break down polymers into
What type of reaction would be needed to monomers.
bond the following monomers (squares)
together to form a polymer? Enzymes
• Special molecules called enzymes are required for cells to carry
out chemical reactions, including dehydration synthesis and
hydrolysis reactions.
• An enzyme is a catalyst, a molecule that speeds up a chemical
Is water needed or produced in the reaction.
reaction above? o Enzymes are not consumed in the reaction.
o Enzymes are not changed by the reaction.
How many water molecules?