Chapter 3: Biologically Important Molecules (Introduction to

Biological Science Reviewer)

Cells contain many complex molecules called macromolecules. Carbohydrates, lipids, proteins,
and nucleic acids are all examples of large molecules necessary for life.

Carbohydrates, lipids, proteins, and nucleic acids are all organic molecules. Organic molecules
generally refer to those molecules that have carbon as the principal element, bonded to
hydrogen and other carbon atoms. Molecules that do not contain carbon and hydrogen, such
as water, are classified as inorganic.

Carbon atoms are the fundamental components for all carbohydrates, lipids, proteins, and
nucleic acids. Carbon atoms can form up to four covalent bonds with other atoms to satisfy the
octet rule. Hydrocarbons are organic molecules consisting entirely of carbon and hydrogen,
such as methane described above. We often use hydrocarbons in our daily lives. Fuels like the
propane in a gas grill, or the butane in a lighter, are classified as hydrocarbons.

Hydrocarbons form the backbones of large macromolecules and may be linear chains, carbon
rings, or a combination of both. Furthermore, carbon-carbon bonds may be single, double, or
triple bonds, with each type of bond affecting the molecule's three-dimensional shape in a
specific way. When carbon forms single bonds with other atoms, the shape is tetrahedral.
When two carbon atoms form a double bond, the shape is planar, or flat. Single bonds, like
those in ethane, can rotate. Double bonds, like those in ethene, cannot rotate.

The bonds that hold a molecule together help dictate its three-dimensional shape. Isomers are
molecules that have the same chemical formula but differ from one another in the
arrangement of their atoms and or chemical bonds. Structural butane and isobutane isomers
have a different covalent arrangement of atoms.

Functional groups are groups of atoms that are found within macromolecules and confer
specific chemical properties to those molecules. The functional groups in a macromolecule are
usually attached to the carbon backbone at one or several different places along its chain and
or ring structure. Carbohydrates, lipids, proteins, and nucleic acids each have their own
characteristic set of functional groups that contributes significantly to its differing chemical
properties and its function in living organisms. They include hydroxyl, methyl, carbonyl,
carboxyl, amino, phosphate, and sulfhydryl groups. We usually classify functional groups as
hydrophobic or hydrophilic depending on their charge or polarity. An example of a
hydrophobic group is the nonpolar methyl molecule, which is hugely prevalent in lipids.

hydrocarbon: organic molecules consisting entirely of carbon and hydrogen.

functional group: groups of atoms that occur within molecules and confer specific chemical
properties to those molecules

hydrophilic: describes a substance that dissolves in water; “water-loving".

hydrophobic: describes a material that does not dissolve in water; “water-fearing".

isomers: molecules that share the same chemical formula but differ in the placement
(structure) of their atoms and/or chemical bonds.

organic molecule: any carbon-containing liquid, solid, or gas.

Most biologically important molecules are made from single subunits, or building blocks, called
monomers. The monomers combine using covalent bonds to form larger molecules known as
polymers. When monomers combine, water is released as a by-product. This type of reaction is
called a dehydration synthesis, a condensation reaction, which means “to put together while
losing water". When a hydrolysis reaction occurs, a water molecule is used to break a chemical
bond. In dehydration synthesis, two monomers are covalently bonded. In a hydrolysis reaction,
the covalent bond between two monomers is split apart.

In a dehydration synthesis, the hydrogen of one monomer combines with the hydroxyl group of
another monomer, forming a water molecule. At the same time, the monomers then come
together and share electrons resulting in the formation of a covalent bond. In the dehydration
synthesis reaction above, two glucose molecules link to form the disaccharide maltose. In the
process, it forms a water molecule. Polymers can be broken down into monomers during
hydrolysis reactions. Hydrolysis reactions occur when a water molecule is used to break a
chemical bond. During these reactions, the polymer breaks into two components: one part
gains a hydrogen atom (H+), and the other gains a hydroxyl molecule (OH–). Both the hydrogen
and hydroxyl ions are a result of splitting a water molecule. Dehydration synthesis and
hydrolysis reactions can occur quickly with the help of molecules called enzymes. In
dehydration reactions, enzymes help with the formation of new bonds, while enzymes used in
hydrolysis reactions break bonds apart. Enzymes called proteases, such as pepsin and
peptidase, break down proteins, whereas enzymes called lipases break down lipids.

dehydration synthesis: a reaction where monomers combine with the help of water (and often
an enzyme) to form polymers.

hydrolysis reactions: a reaction where a water molecule (and usually an enzyme) is used to
break a chemical bond within a polymer.

monomers: the single subunits, or building blocks that make up polymers.

polymers: larger molecules that are formed by combining monomers using covalent bonds.

There are four major biological macromolecule classes (carbohydrates, lipids, proteins, and
nucleic acids). Carbohydrates are macromolecules that students may be familiar with. To lose
weight, some individuals adhere to “low-carb” diets. Athletes, in contrast, often “carb-load”
before competitions to ensure that they have sufficient energy to compete at a high level.
Carbohydrates are classified into three subtypes: monosaccharides, disaccharides, and
polysaccharides.

Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple sugars, the most common of
which is glucose. In monosaccharides, the number of carbon atoms usually ranges from three to
six. Most monosaccharides have names ending with the suffix -ose, such as glucose, galactose,
and fructose. During cellular respiration, glucose is used as a source of energy, when its
covalent bonds are broken. The energy released is used to make adenosine triphosphate (ATP),
an energy-rich molecule that powers most cellular activity. Plants can synthesize their glucose
using light energy, carbon dioxide, and water through the process of photosynthesis. Galactose
(part of lactose, or milk sugar) and fructose (found in fruit) are other common
monosaccharides. Glucose, galactose, and fructose are all isomers meaning they have the same
chemical formula (C6H12O6) but differ structurally.

Disaccharides (di- = “two”) form when two monosaccharides undergo a dehydration synthesis.
During this process, the hydroxyl group (–OH) of one monosaccharide combines with a
hydrogen atom of another monosaccharide, releasing a water molecule (H2O). A covalent bond
forms between the atoms in the two sugar molecules. A polysaccharide (poly- = "many") is a
chain of three or more monosaccharides linked together by covalent bonds. The chain may be
branched or unbranched and is typically very large (i.e. thousands of monosaccharides). Starch,
glycogen, cellulose, and chitin are all examples of polysaccharides. Plants can synthesize
glucose through the process of photosynthesis. Any excess glucose that is not used to make ATP
is stored as starch in different parts of the plant, including its roots and seeds.

Humans and many other vertebrates store their excess glucose as glycogen. Glycogen is made
up of glucose monomers and is the animal equivalent of starch. It is a highly branched molecule
and most often stored in liver cells. In humans, two important hormones, insulin and glucagon,
govern these two processes of glycogen formation and glycogen breakdown. Cellulose is one of
the most abundant natural polysaccharides. The cell walls of plants are mostly made of
cellulose, which provides structural support for the cell. Wood and paper are also mostly
cellulose in nature. Cellulose passing through the human digestive system is called dietary
fiber. Cellulose can break cellulose down into glucose monomers that are then used to
synthesize ATP. Exoskeletons are made of a polysaccharide called chitin. Chitin is also found in
the scales of fish and the cell walls of fungi.

carbohydrate: a biological macromolecule in which the ratio of carbon to hydrogen to oxygen is

1:2:1; carbohydrates serve as energy sources and structural support in cells.

cellulose: a polysaccharide that makes up the cell walls of plants and provides structural
support to the cell.

chitin: a type of carbohydrate that forms the outer skeleton of arthropods, such as insects and
crustaceans, and the cell walls of fungi.

dehydration synthesis: a reaction where monomers combine with the help of water (and often
an enzyme) to form polymers.

disaccharide: two sugar monomers that are linked together by a peptide bond.

glycogen: a storage carbohydrate in animals.

monosaccharide: a single unit or monomer of carbohydrates.

polysaccharide: a long chain of monosaccharides; may be branched or unbranched. starch: a

storage carbohydrate in plants.

Lipids include a diverse group of compounds. All lipids share one major characteristic: they are
all hydrophobic (or at least have a hydrophobic region, as in phospholipids). Lipids are mostly
hydrocarbons, meaning they have large proportions of nonpolar carbon-carbon or carbon
hydrogen bonds. Lipids are also smaller in molecular size when compared to polymers of
carbohydrates, proteins, and nucleic acids and therefore some sources do not consider them
large macromolecules. Lipids include fats, phospholipids, steroids, and waxes. Many cells store
energy for long-term use in the form of fats. Triglycerides, an example of a fat molecule, is a
naturally occurring fat that can be found in many of the foods we consume. A glycerol molecule
is an organic compound with three carbon atoms, five hydrogen atoms, and three hydroxyl (–
OH) groups. Each fatty acid consists of a long chain of hydrocarbons with an attached acidic
carboxyl group, hence the name “fatty acid."

Fatty acids may be saturated or unsaturated. If there are only single bonds between
neighboring carbon atoms, the fatty acid is "saturated." Saturated fatty acids are saturated
with hydrogen. In other words, the number of hydrogen atoms attached to the carbon skeleton
is maximized. When the hydrocarbon chain contains a double bond, it is called an unsaturated
fatty acid. They are called unsaturated fatty acids because when carbon atoms form double
bonds between them, the two carbon atoms in that bond each has one less hydrogen atom
attached to it. Therefore, it is said to be "unsaturated." Most unsaturated fats are liquid at
room temperature and are called oils. Examples of unsaturated fats include olive oil and canola
oil. Examples of saturated fats include palmitic acid, which can be found in meat, and butyric
acid, which is found in butter. Unsaturated fats help to improve blood cholesterol levels,
whereas saturated fats contribute to plaque formation in blood vessels, which increases the risk
of a heart attack. Mammals store fats in specialized cells called adipocytes, where globules of
fat occupy most of the space in the cell. In plants, fats or oils are stored in seeds and used as
sources of energy during embryonic development. During the hydrogenation process the
orientation around the double bonds is changed, which changes the chemical properties of the
molecule. This forms a trans-fat.

Like fats, phospholipids are composed of fatty acid chains attached to a glycerol molecule.
Unlike a triglyceride, a phospholipid only has two fatty acid chains instead of three. The third
carbon of the glycerol backbone is bound to a phosphate group. The addition of alcohol
modifies the phosphate group. Because of this arrangement, a phospholipid has both
hydrophobic and hydrophilic regions. The fatty acid chains are hydrophobic and exclude
themselves from water, whereas the phosphate "head" is hydrophilic and interacts with water.
Phospholipids are the major component of the plasma membrane. They come together and
organize themselves in what is called a phospholipid bilayer. The phospholipid bilayer consists
of two adjacent layers of phospholipids arranged tail to tail. The hydrophobic tails associate
with one another, forming the interior of the cell membrane. The polar heads interact with the
fluid inside and outside of the cell.

Unlike the phospholipids and fats discussed earlier, steroids have a ring structure. Steroids do
not structurally resemble other lipids; however, they are all hydrophobic. All steroids have four
linked carbon rings. Some steroids, like cholesterol, have a short tail. Cholesterol is the most
common steroid. In animals, the liver synthesizes cholesterol, which acts as the precursor for
many steroid hormones, including testosterone and estradiol. Testosterone and estradiol are
crucial hormones that lead to the sexual maturation and secondary sex characteristics of males
and females. A hormone is a chemical signaling molecule, usually a protein or steroid, secreted
by an endocrine gland or group of endocrine cells. It acts to control or regulate specific
physiological processes. Another example of a steroid hormone is cortisol. Cortisol is released
by the adrenal gland and can affect glucose regulation and inflammation. Waxes are also
classified as lipids. They are composed of a hydrocarbon molecule with an alcohol (–OH) group
and a fatty acid chain. Examples of animal waxes include beeswax and lanolin, both of which
can be used to prevent and treat dry skin. Plants also have waxes. The superficial waxy cuticle
that covers leaves helps prevent plants from drying out.

fat: a lipid molecule composed of three fatty acids and glycerol (triglyceride) that typically exists
in a solid form at room temperature.

hormone: a chemical signaling molecule, usually a protein or steroid, secreted by an endocrine

gland or group of endocrine cells; acts to control or regulate specific physiological processes.

hydrophilic: describes a substance that dissolves in water; water-loving.

hydrophobic: describes a substance that does not dissolve in water; water-fearing.

lipids: a class of macromolecules that are nonpolar and insoluble in water.

oil: an unsaturated fat that is a liquid at room temperature.

phospholipid: a major constituent of the membranes of cells; composed of two fatty acids and
a phosphate group attached to the glycerol backbone.

Saturated fatty acid: a long-chain hydrocarbon with single covalent bonds in the carbon chain;
the number of hydrogen atoms attached to the carbon skeleton is maximized.

steroid: a type of lipid composed of four fused hydrocarbon rings. trans-fat: a form of
unsaturated fat with the hydrogen atoms neighboring the double bond across from each other
rather than on the same side of the double bond.

triglyceride: a fat molecule; consists of three fatty acids linked to a glycerol molecule.

unsaturated fatty acid: a long-chain hydrocarbon that has one or more than one double bonds
in the hydrocarbon chain.

waxes: a type of lipid made up of a hydrocarbon chain with an alcohol (–OH) group and a fatty
acid.

Proteins are one of the most abundant organic molecules in living systems and have the most
diverse range of functions of all macromolecules. Proteins may be structural, regulatory,
contractile, or protective. They may serve in transport, storage, or they may be used as toxins
or enzymes. Each cell in a living system may contain thousands of different proteins, each with
a unique function. The structures of proteins, like their functions, vary greatly. All proteins,
however, are polymers made up of amino acids arranged in a linear sequence. Enzymes are
proteins that speed up the rate of chemical reactions. Enzymes do this by decreasing the
amount of activation energy needed to start the chemical reaction. Enzymes are usually
complex proteins. Each enzyme has a specific substrate, a reactant that binds to the enzyme.
An enzyme may assist in hydrolysis reactions or dehydration synthesis reactions. Enzymes that
break down their substrates are called catabolic enzymes, whereas those that build more
complex molecules are called anabolic enzymes. Salivary amylase is an example of a catabolic
enzyme. Salivary amylase hydrolyzes starch into simple sugars like glucose. An example of an
anabolic enzyme is rubisco, which plants use during photosynthesis to make sugar from carbon
dioxide. Some enzymes function as hormones. Hormones are molecules that are important for
chemical signaling between cells. Hormones regulate specific physiological processes, including
growth, development, metabolism, and reproduction. For example, insulin is a protein
hormone that helps regulate blood glucose levels. Not all hormones are protein-based. Some
hormones, such as estradiol and testosterone, are made of lipids.

Amino acids are the monomers that make up proteins. Each amino acid has the same
fundamental structure which consists of a central carbon atom bonded to an amino group
(NH2), a carboxyl group (COOH), and a hydrogen atom. Every amino acid has a side chain called
the R group. The R group is a side chain that can be made up of several different atoms. The R
groups are very diverse and ultimately give each amino acid its defining characteristics. There
are 20 common amino acids commonly found in proteins, each with a different R group (variant
group) that determines its chemical nature. he chemical nature of the side chain determines
the amino acid's nature (that is, whether it is acidic, basic, polar, or nonpolar). For example, the
amino acids valine, methionine, and alanine are nonpolar or hydrophobic. Amino acids such as
serine, threonine, and cysteine, are polar and have hydrophilic side chains. The sequence and
the number of amino acids ultimately determine the protein's shape, size, and function. Amino
acids can be linked together using a dehydration synthesis reaction. One amino acid’s carboxyl
group and the incoming amino acid’s amino group combine, releasing a water molecule. The
resulting bond that forms is covalent and called a peptide bond. As two amino acids are linked
together they form a peptide chain. As more amino acids are added it is called a polypeptide
chain. The primary structure is simply the polypeptide chain--the sequence of amino acids
bonded together via peptide bonds. A protein’s primary structure is not rigid, but rather is
flexible because of the nature of the bonds that hold the amino acids together.

Due to chemical bonding, the polypeptide chain begins to fold in some regions giving rise to the
secondary structure of the protein. The most common secondary structures are the αhelix
and β-pleated sheet structures. The polypeptide's unique three-dimensional shape is its
tertiary structure. This structure is in part due to chemical interactions within the polypeptide
chain. Some proteins consist of several separate polypeptide chains. These proteins function
only when all polypeptide chains are present and appropriately configured. The interactions
that hold these subunits together leads to what is referred to as the quaternary structure of
the protein. When a protein loses its three-dimensional shape and is no longer functional, the
protein is said to be denatured. Denaturation is often reversible because the polypeptide's
primary structure may be conserved during the process. If the denaturing agent is removed,
and the primary structure was preserved, the protein can refold and resume its normal
function. Proteins associated with the plasma membranes of cells are classified as peripheral or
integral. Peripheral proteins are associated with one side of the membrane, whereas integral
proteins are embedded in the membrane. The most common pathogens found in the lungs of
patients with cystic fibrosis are Pseudomonas aeruginosa and Burkholderia cepacia.
Pseudomonas differentiates within the biofilm in the lung and forms large colonies, called
“mucoid” Pseudomonas.

amino acid: a monomer of a protein

denaturation: loss of shape in a protein that may be a result of changes in temperature, pH, or
chemical exposure.

enzyme: a catalyst in a biochemical reaction that is usually a complex or conjugated protein.

hormone: a chemical signaling molecule, usually a protein or steroid, secreted by an endocrine
gland or group of endocrine cells; acts to control or regulate specific physiological processes.

hydrophilic: describes a substance that dissolves in water; water-loving.

hydrophobic: describes a substance that does not dissolve in water; water-fearing.

peptide bond: a covalent bond that forms between one amino acids carboxyl group and
another amino acids amino group.

polypeptide chain: a long chain of amino acids linked by peptide bonds.

primary structure: a linear sequence of amino acids in a protein.

protein: a biological macromolecule composed of one or more chains of amino acids.

quaternary structure: association of different polypeptide chains in a protein.

secondary structure: structure that proteins form by hydrogen bonding between the oxygen
atom of one amino acid and the hydrogen attached to the nitrogen atom of another amino
acid.

substrate: a reactant that binds to a specific enzyme.

tertiary structure: a protein's three-dimensional conformation, including interactions between

secondary structural elements.

Nucleic acids are essential macromolecules that allow cells to survive. They carry the cell's
genetic blueprint and contain instructions that allow cells to function properly. The two main
types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the
genetic material found in all living organisms. DNA contains the "instructions" on how the cell
makes different proteins necessary for maintaining homeostasis. DNA is located in the nucleus
of eukaryotes and in two eukaryotic organelles, chloroplasts and mitochondria. Prokaryotes
also possess DNA, however it is not enclosed in a membrane-bound organelle. DNA and RNA
are polymers made up of monomers called nucleotides. The nucleotides combine with each
other to form a polynucleotide, DNA or RNA. Each nucleotide is made up of three components:
a nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group. Each nitrogenous
base in a nucleotide is attached to a sugar molecule, which is attached to a phosphate group.
Structurally, DNA is shaped like a double helix, RNA is usually singled stranded and performs
several different roles important for generating proteins. DNA is shaped like a double helix . It is
composed of two strands of nucleotides. Each DNA strand is formed with covalent bonds
between the phosphate and sugar groups of adjacent nucleotides. The bonds between the
sugar and phosphate make up the "sugar” phosphate backbone." The two separate DNA
strands are held together by hydrogen bonds between nitrogenous bases . The strands usually
coil, hence the “double helix” description. DNA and RNA are both examples of nucleic acids
that perform unique functions that allow cells to survive. The flow of information within a cell
or organism usually begins with DNA, which is used to make RNA, which is necessary to
synthesize protein. DNA dictates the structure of mRNA in a process called transcription, and
RNA dictates the protein's structure in a process called translation.

deoxyribonucleic acid (DNA): a double-stranded polymer of nucleotides that carries the

hereditary information of the cell.
nucleic acid: a biological macromolecule that carries the genetic information of a cell and
carries instructions for the functioning of the cell.

nucleotide: a monomer of nucleic acids; contains a pentose sugar, a phosphate group, and a

nitrogenous base.

ribonucleic acid (RNA): a single-stranded polymer of nucleotides that are involved in protein
synthesis.

transcription: the process of making RNA from DNA.

translation: the process of making protein from mRNA.