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AP Biology
Biochemistry – Chemistry Basics
Atom
The smallest unit of an element that maintains the chemical properties of the element.

Subatomic Particles
Proton – Subatomic particles that carry a positive charge. They are located in the nucleus of an atom.
The number of protons never changes in an element. The number of protons determines the
identity of the element and defines the atomic number of the element.
Neutron - These particles carry NO charge (are neutral). They are also located in the nucleus of
an atom and are similar in size to the [Link] number of neutrons can change. (Atoms of the
same element with different numbers of neutrons are called Isotopes.)
Electrons - These subatomic particles carry a negative charge. They are located in the “Electron cloud”. The
electrons are attracted to the positive protons in the nucleus, but can move within the electron cloud. The
number of electrons associated with an atom can change. (Atoms with different numbers of electrons than the
normal amount for that element are called Ions.)

Molecule
Two or more atoms that are covalently bonded together.

E levels or e- shells – Where the electrons are located within an atom or molecule.
Adding energy to the electrons makes them move farther out, away from the nucleus; losing energy causes
them to move inward, toward the nucleus.
Valence Shell- Where the outer most electrons are located on an atom.
Valence e- - Refers to the outer most electrons. (These are the most important for chemical bonds and the
chemical properties of an element or molecule.) Most elements need 8 valence electrons (an octet) in order
to be chemically stable. Atoms react with other elements in order to obtain a total of 8 valence electrons and
to become chemically stable.

Chemical Bonds (These occur between atoms.)

Covalent Bonds
A type of intramolecular bond.
Results from the sharing of valence electrons between atoms.
Atoms held together by covalent bonds are called molecules.

Polar molecules carry a slight electrical charge at opposite poles (poles refers to the “ends” of the
molecule) and non-polar molecules do not have an electrical charge.

Electronegativity
Refers to an atom’s desire to acquire electrons.
Hydrogen is the least electronegative atom.
Oxygen and Nitrogen are the most biologically important molecules with a high
electronegativity.
Molecules which contain oxygen and nitrogen are likely to be polar.

Ionic Bonds
Ionic bonds form between metal and non-metal atoms.
They form when the metal atoms loses electrons and the non-metal atom gains electrons.

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Both atoms do this in order to have 8 valence electrons.

Compounds held together by ionic bonds are called salts.

Ionic Bonds are very strong when the compound is dry.

Ionic bonds are easily broken in water. This is why many salts dissolve easily in water to form
ions.
Cations – Ions which possess a positive charge because they have more protons than
electrons. The metal atoms in a salt typically become cations.
Anions –Ions which possess a negative charge because they have more electrons than
protons. The non-metal atoms in a salt typically become anions.

Hydrogen Bonds
Hydrogen Bonds are fairly weak (compared to covalent and ionic bonds) intermolecular attractions
that occur between polar molecules. They are often depicted as dots in chemical diagrams.
Hydrogen bonding is very important in water due to its polar nature.

Van der Waals Interactions or London Dispersion Forces

These are temporary intermolecular attractions. (Usually a fraction of a second.)
These interactions are “created” when electrons clump on one side of an atom making that side
temporarily “negative” and the other side “positive”. This allows other charged particles to attach
momentarily. The electrons eventually unclump and the van der waals interactions disappear.

AP Biology
Biochemistry of Water

Water supports life on Earth.

Water makes up over 70% of the bodies of most organisms.

Biogeochemical Cycles--These refer to the cycling of matter.

Water cycle – Water vapor is generated by the sun causing the evaporation of water from oceans, lakes,
rivers, trees, etc…. This water vapor rises and condenses to form rain or snow (referred to as precipitation)
and is returned to the land or ocean. Eventually, the water that lands back on the land, makes its way to plants
or rivers and streams that lead back to the oceans. Plants take in the water and use it for photosynthesis but
also can lose it in the form of transpiration to the air.

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Water is a Polar Molecule.

Because of the high electronegativity of oxygen and the low electronegativity of hydrogen, the oxygen end of
the water molecule has a slight negative charge, while the hydrogen end has a slight positive charge. The
water molecule’s shape is said to be “bent”. This shape means that one side of the molecule “the hydrogen
side” is positive, while the other side “the oxygen side” is negative. The polar water molecules form
hydrogen bonds with each other. These bonds affect many of the biologically important properties ofwater.

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Important Properties of Water for Biology

Water has a high specific heat.

Specific heat refers to the amount of heat needed to change the temperature of 1 gram of a substance by 1
degree. Water’s specific heat is very high due to the hydrogen bonds that hold the water molecules
together.
Due to its high specific heat, water is excellent for helping to maintain a constant internal body
temperature. Large bodies of water have fairly constant temperatures. Water also helps to moderate the
air temperatures of land masses located near large bodies of water.

Water is an excellent solvent.

Water is often referred to as the “Universal Solvent”. This means that it is great at dissolving other materials
(solutes).
Due to its polarity, water is best at dissolving salts and polar molecules.
This is important in Biology, because it allows vital nutrients and gases to be dissolved and transported
through the body and through the ground.

Water has a high heat of vaporization.

Heat of vaporization refers to the amount of heat needed to convert a liquid to a gas. Due to the many
hydrogen bonds which hold water molecules together, the heat of vaporization is very high for water. When
the water does eventually evaporate it carries heat away with it.
This is important in Biology, because it allows processes like sweating and transpiration to cool off organisms
through the process of evaporative cooling.

Water is cohesive and adhesive.

Due to its polarity, water molecules stick to each other (cohesion) and to other polar molecules
(adhesion). This property allows transpiration, the movement of water through the xylem of plants, to
move water from the ground, through the plant, and eventually out into the air.

Water expands as it freezes.

Like most other compounds, the volume of water contracts as it cools down, but unlike most other materials,
the volume of water begins to expand after it cools to temperatures below 4 degrees Celsius. This causes ice
to be less dense than liquid water. This means that ice floats on liquid water.
This happens because the HYDROGEN bonds force the chains of water molecules further apart as the
molecules cool down and slow down. This increased volume causes a decrease in density. This property is
important to life, because as bodies of water freeze, the ice floats and insulates the liquid water underneath.
This allows aquatic life to survive long, cold winters.

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AP Biology
Biochemistry: Carbon Properties
Organic Chemistry
Branch of science dealing with the element carbon and its many properties.
Most of the compounds found in living things, other than water, are organic.
About 30% of an organism’s dry weight (Biomass) is composed of Carbon found in the body’s organic
molecules.
Carbon helps to make the 4 major groups of organic macromolecules: Carbohydrates, Lipids, Proteins, and
Nucleic Acids.
The original source for Carbon in all life forms is Carbon Dioxide. (CO2 - Photosynthesis)

Miller/Urey Experiment (Took place in 1953.)

Miller/Urey took inorganic substances that were thought to have been present in Earth’s early atmosphere
(H2O vapor, H2, NH3, CH4) and created organic amino acids and oils. (CO2 and CH4 are not considered
organic compounds, even though they contain Carbon.) Miller wanted to show that organic molecules, which
are necessary for life, could be created by non-living things.

Important Properties of Carbon for Biology

Carbon has 4 valence electrons

Since carbon has 4 valence electrons, it can form four covalent bonds. This allows carbon to bond with a
variety of molecules and form molecules with an almost infinite variety of shapes and functions.

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Carbon atoms are small

Because carbon is a small atom, its valence electrons are near the nucleus. This means that when carbon
forms covalent bonds, the bonds are strong. This makes carbon an excellent building material for life.

Carbon is abundant on Earth

Carbon isn’t the most abundant element on Earth, but there is a lot of carbon found on the planet. This
makes it a good choice for the building block of life.

Organic Macromolecules
Polymers
These are large molecules that are formed by combining/bonding individual units called
monomers.
The monomers are linked together by covalent bonds. Remember that covalent bonds are strong.

Macromolecules are formed by Dehydration Synthesis (also called Condensation) Reactions.

During these reactions, monomers are covalently bonded together.
The reactions release water as a byproduct.

Macromolecules are broken apart into individual monomers by Hydrolysis reactions. (“lysis” means “to
split.”). In these reactions, water is used as a reactant.

Groups of Organic Macromolecules

Carbohydrates
Carbohydrates are sugars. In living things, carbohydrates serve as sources of quick energy and as
structural/building materials. Most carbohydrate names end in the letters “-ose”.
Monosaccharides - Are the monomers or “building blocks” of carbohydrates. (“sacch” means “sugar”.)
Glucose, fructose, galactose, ribose, and deoxyribose are common monosaccharides. The general
molecular formula for a monosaccharide is (CNH2NON).

Polysaccharides - Are the polymers. These compounds are formed by the bonding together of several
monosaccharides. Biologically important polysaccharides include:

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Starch – Used as an energy storage molecule in plants.

Glycogen – Used as an energy storage molecule in Animals.
Cellulose – Used as a structural component of plant cell walls.
Cellulose is the most abundant organic compound on Earth. Due to the hydrogen bonds that
occur in cellulose, it is very hard for most organisms to digest.
Chitin – Used as a component of the exoskeleton of some animals and also fungal cell walls.

Although starch, cellulose, and glycogen are all polymers of glucose, the molecules have different
shapes. Some of these complex carbohydrates consist of straight chains of monomers, while others
consist of branched chains. Because of the orientation of the glucose monomers, many hydrogen
bonds form in cellulose and cause the molecule to be very strong and hard to digest, while starch is
relatively easy to digest.

Lipids
These macromolecules are fats, oils, waxes, and steroids.
Most lipids are hydrophobic molecules. They contain little oxygen and are mostly nonpolar in nature.
Two Main parts of a lipid:
Fatty Acid—long chain of carbon and hydrogen atoms.
3 Carbon Glycerol molecule (alcohol) to hold the whole molecule together.
Lipids use a covalent bond called an Ester Linkage to hold the fatty acids and glycerol together.

Major Types of lipids:

Triglycerols or Triglycerides (These are your basic fat or oil.)
The degree of saturation (lack of carbon—carbon double bonds) helps to determine the
structure and function of many lipids.
Saturated fats--These fatty acids are saturated with Hydrogen atoms. The molecule has no
open bonds to put any more Hydrogen on. There are no carbon—carbon double or triple
bonds in these chains. Saturated fats are solids at room temp and they usually are associated
with animals. Saturated fats contribute to coronary artery disease.

Unsaturated fats--These fatty acid chains contain some carbon-carbon double or triple
bonds that “could be broken” to add more Hydrogen to the fatty acid. Saturated fats tend to
be liquids at room temperature and they usually are associated with plants (vegetable oil,
sunflower oil, or peanut oil). Unsaturated fats are typically viewed as a healthy part of the
diet.

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Polyunsaturated fats--These fats have many double or triple bonds in their fatty acid chains.
Hydrogenated or Trans fats. These are oils turned solid fats by adding Hydrogen and by
breaking the double or triple bonds in the fatty acids. This was done in the past to change the
texture, stability, and shelf life of fats. Trans fats were common in processed foods. They
have been shown to increase LDL cholesterol levels and to contribute to coronary artery
disease.

Phospholipids
These molecules replace a single fatty acid chain from a triglyceride with a single Phosphate
ion. The phosphate portion of the molecule is Hydrophilic because of the charge on the
phosphate ion.
The remaining fatty acids chains are hydrophobic. They are mostly composed of long chains
of carbon atoms that are also bonded to hydrogens. They are neutral and are not attracted to
water.
Phospholipids are said to be amphipathic since they have both polar and nonpolar sides.
Phospholipid Bi-layers are important for the building of cell and organelle membranes.

Steroids

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A steroid is a lipid composed of 4 carbon rings. Common steroids found in the body include
testosterone, estrogen, progesterone, and cholesterol.
What makes them different from each other are the attached functional groups. These
functional groups help determine the function of the steroid. Most of the steroids are built
from cholesterol. Steroids function in the body as cell signals/hormones. Due to their
lipid/nonpolar nature they can penetrate the cell membrane and bind to intracellular receptors.
They often act to regulate the expression of certain genes.
Cholesterol is an important component of the cell membrane. It helps with cell membrane
flexibility.

Common Steroids

Proteins
Proteins make up greater than 50% of an organism’s dry weight or biomass.

The names of most proteins end in “lin” while the names of most enzymes (which are composed of proteins)
usually end in “ase”.

Proteins are large macromolecules which are composed of monomers “building blocks” called Amino Acids.
There are 20 different Amino Acids used by living things to make proteins. Proteins and enzymes usually have
hundreds to thousands of Amino acids in their structure.

Amino Acids have 4 different parts to them:

Amine end (NH2) – This end can act as a base by accepting a Hydrogen ion.
Carboxyl end (COOH) – This part acts as an acid because it can release a hydrogen ion.
Alpha (α) Carbon – This is the central carbon atom to which all of the other functional groups are attached.
R group - This part is the only part that is different in the 20 different amino acids. The R group gives different
amino acids their distinctive properties.

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Structure of an Amino Acid

Individual Amino Acids (monomers) are bonded together by a covalent bond called a peptide bond. The peptide
bond is a covalent bond and is strong and hard to break.

In order to create a peptide bond, the amino end of one amino acid is positioned to combine with the Carboxyl
end of the second amino acid. The amino acids are joined during dehydration synthesis reactions (also known as
“condensation reactions”).

Two amino acids bonded together are referred to as a dipeptide. When more than two are bonded, the structure is
referred to as a polypeptide chain.

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Because of the structure of the amino acids, a polypeptide chain has directionality, meaning that it has two ends
that are chemically distinct from one another. At one end, the polypeptide has a free amino group, and this end is
called the amino terminus (or N-terminus). The other end, which has a free carboxyl group, is known as
the carboxyl terminus (or C-terminus). The N-terminus is on the left and the C-terminus is on the right for the
very short polypeptide shown above.
New amino acids are always added to the carboxyl terminus of a growing polypeptide chain.

A protein is typically made from several polypeptide chains that are wrapped together into a large 3-D unit.

The function of a protein is largely determined by its shape/structure.

The information included below discusses the four levels of protein structure.

Levels of Protein Structure

Primary Structure (Represented by the symbol - 1’. )

This refers to the sequence of bonded Amino Acids (which amino acids are present and what order are they
in). The primary structure of each protein is coded for by DNA.
A mutation in the DNA can change the primary structure of a protein. This change can vastly change the
overall shape of the protein and cause it to lose its function.

Secondary Structure (2’ )

This refers to the shape of specific sections of each polypeptide chain.
HYDROGEN bonding between polar amino acids allows for overlapping and coiling to occur in the “folding” of
the protein into its 3-D shape. All proteins must be “folded” in order to work. The polarity/nonpolarity of
the “R” groups of the protein’s amino acids determine how the protein will fold.

For proteins that are built by ribosomes located on the rough ER, this folding takes place within the Rough
Endoplasmic Reticulum. These proteins are usually exported from the cell through the process of
exocytosis (secretion).
Other proteins are constructed by ribosomes which float freely in the cytosol. These proteins typically
remain within the cell in which they were made. The folding of these proteins usually takes place within a
chaperonin. Chaperonins are protective structures that allows proteins to fold without water present.

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Two common types of secondary structure are the alpha helix and the beta pleated sheet.

Tertiary Structure (3’ ) (“Tert” means “third”)

This refers to the overall shape of each individual polypeptide chain.
Di-sulfide bridges help stabilize the protein’s folded structure. These bonds form when cysteines (a type of
amino acid) are near each other in a polypeptide. These cysteines form a disulfide bond or bridge which is
much stronger than a hydrogen bond.

The tertiary structure is also partially determined by ionic interactions between certain “R” groups and by
hydrophobic interactions between certain R groups and water.

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Quaternary Structure (4’ )

This is when two or more polypeptides are woven together to form the overall structure of a protein.

Example: Hemoglobin -has four polypeptides woven together to make it.

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Denaturation
The “unraveling” or “unfolding” of a protein or enzyme causing it not to function.
Denaturation can be caused by pH changes, salt concentration changes, and increases in temperature.
Denaturation usually disrupts the secondary and tertiary levels of protein structure by affecting either
the hydrogen bonds or disulfide bonds which stabilize the structure.

Nitrogen Cycle

Although there is plenty of nitrogen found in the air, the amount of usable nitrogen available for life on Earth
is limited. Since the nitrogen atoms in nitrogen gas are held together by triple covalent bonds, atmospheric
nitrogen is difficult for life forms to break apart and use. The nitrogen cycle is the process via which nitrogen
moves from the atmosphere into living things and ultimately back to the atmosphere. Cycles like the nitrogen
cycle, the carbon cycle, the water cycle, and the phosphorus cycle are collectively known as the biogeochemical
cycles. These processes continuously cycle elements throughout the Earth.
Nitrogen is an essential element for the construction of proteins and amino acids. Nitrogen is also an important
component of nucleic acids such as DNA, RNA, and ATP. Some nitrogen is removed from the air by rainwater.
Remember, water is the universal solvent, so the gas is dissolved in the rain. The Nitrogen in the water can be
consumed by Nitrogen Fixing bacteria, in the soil, that convert it into Ammonium ions (NH4+). This process is
referred to as Nitrogen Fixation. The Ammonium ions can then be absorbed by plants to help make proteins and
DNA or RNA. Some Ammonium in the soil is also consumed by Nitrifying Bacteria, and converted to Nitrite (NO2-
) first and then ultimately into Nitrate (NO3-). This process is called Nitrification. The Nitrates are also
absorbed by the plants, just as was the Ammonium ions. Other bacteria, called denitrifying bacteria, in the soil can

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also absorb the nitrates and convert them back into Oxygen gas (O2) and Nitrogen gas (N2). These molecules
are both returned to the air to be used again. This process is called Denitrification. As plants are eaten by
animals, the Nitrogen travels through the food chain. When all life forms die, the bodies decompose and
create Ammonia (NH3), which is why they stink. The Ammonia is converted by bacteria into
Ammonium to be used again by plants and bacteria. This conversion is called
Ammonification. Some Nitrogen is also released by animals in their urine. It too undergoes
Ammonification.

Nucleic Acids

Nucleic Acids function to store genetic information and/or to store and transfer energy. Common nucleic
acids found living organisms include: DNA, RNA, ATP, cAMP, NADH, and NADPH.

The monomers of nucleic acids are called nucleotides. A nucleotide consists of a 5 carbon (pentose) sugar
bonded to a phosphate group and a nitrogenous base.

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DNA and mRNA are both polymers. DNA and RNA are the primary sources of genes and hereditary
information.

1. DNA has Deoxyribose as its 5 Carbon sugar. DNA is double stranded. In eukaryotic cells, DNA is
always stored inside a nuclear membrane or envelope. DNA’s function is to code for proteins.
The sequence of the nitrogenous bases in the DNA determines the order of the amino acids in each
of the body’s proteins.
Watson and Crick were eventually able to determine that the DNA molecule is composed of two strands of
nucleotides that are then twisted into a double helix. The individual strands are built when the phosphate groups
of the nucleotides form covalent bonds with the deoxyribose molecules of adjacent nucleotides. The actual bonds
form when one deoxyribose attaches to another by connecting its 5' carbon to the 3' carbon of the next sugar in the
next nucleotide using a phosphate group. The alternating sugars and phosphates form the “backbone” of the DNA
molecule.

The two strands are connected together by hydrogen bonding between complementary nitrogenous bases. An A on
one strand bonds with a T on the other strand. A G on one strand binds with a C on the other strand. Each A-T base
pair is held together by 2 hydrogen bonds, while each G-C pair is held together by 3 hydrogen bonds. This
means that it is easier to separate DNA strands with lots of A-T base pairs than it is to separate strands with
lots of G-C base pairs. It is important to remember that hydrogen bonds are weak when compared to covalent or
ionic bonds. This is important, because the two DNA strands have to be separated during both the processes of
replication and transcription.
Like a protein, a DNA molecule has directionality. The DNA molecule is composed of two strands of
nucleotides held together by hydrogen bonds. Each strand has two slightly different ends. One end, known as the 5’
end, terminates with an unbound 5’ carbon on the last nucleotide in the chain. The other end, known as the 3’ end,
terminates with an unbound 3’ carbon on the last deoxyribose molecule at its end. When the two strands are
connected together, they are oriented in opposite directions. Because they run parallel to each other, but have
opposite directional orientations, the two strands are said to be antiparallel.

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2. RNA has Ribose as its 5 Carbon sugar. RNA is single stranded. There are several types of RNA.
Messenger RNA (mRNA) is made from the DNA template during the process of transcription.
mRNA’s job is to transmit the protein building directions from the DNA in the nucleus to the
ribosomes in the cytoplasm. Transfer RNA’s (tRNA) job is to deliver and place the appropriate
amino acids into the proteins that are built by the ribosomes. Ribosomal RNA (rRNA) is one ofthe
main building components of the cell’s ribosomes.

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Scientists can now sequence the nucleotide/nitrogenous bases found in genes of an organism and compare this sequence to
the sequence of the same gene found in another organism. The more similar the two sequences are, the more related the
two organisms are.

ATP (Adenosine Triphosphate) is another important nucleic acid. An ATP molecule is composed of a single nucleotide
which consists of the sugar (ribose) bonded to a nitrogenous base (always adenine), and three phosphate groups. ATP’s
role in the body is to store and transfer energy. ATP is made during the process of cellular respiration. It functions to
power almost every activity that occurs in the cell.

Phosphorus Cycle
The phosphorus cycle is another important biogeochemical cycle. Phosphorus is an important component of
DNA, RNA, ATP, phospholipids, and bone. Most of the Earth’s phosphorus is found in rock. As the rock
weathers, some of the phosphorus is released into the soil. Some dissolves into the water as the rains pass through
the soil. This phosphorus makes its way into bodies of water and is available for producers (phytoplankton) to use
to make organic compounds such as phospholipids, DNA, RNA, ATP, etc... Plants can also retrieve the

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phosphorus directly from the soil and use it to make organic compounds. When organisms die, decomposers
break down the bodies and return the phosphorus to the soil so that it can be reused.

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AP Biology

Unit 2

Student Notes

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