CHAPTER 3: THE MOLECULES OF

CELLS

Carbon the versatile atom at the center of lifes molecules

INTRODUCTION TO ORGANIC COMPOUNDS

3.1 Lifes molecular diversity is based on the properties of carbon

Carbon is unparalleled in its ability to form large and complex

molecules, which build the structures and carry out the functions
required for life.
Organic compounds carbon-based molecules
A carbon atom has 4 electrons in a valence shell that holds 8. Thus,
each carbon atom is a connecting point from which a molecule can
branch in up to four directions.
CH4 - methane, one of the simplest organic molecules
Hydrocarbons compounds composed of only carbon and
hydrogen (e.g. methane, propane)
o As components of fats, longer hydrocarbons provide fuel to
your body cells.
Carbon skeleton the chain of carbon atoms in an organic molecule
o can vary in length
o can be unbranched or branched
o may also include double bonds
o some are arranged in rings
Isomers compounds with the same formula but different structural
arrangements

3.2 A few chemical groups are key to the functioning of biological molecules
CHEMICAL GROUPS

Hydroxyl Group

Carbonyl Group

DESCRIPTION
Consists of a hydrogen atom bonded
to an oxygen atom, which in turn is
bonded to the carbon skeleton (e.g.
ethanol). Other organic compounds
containing hydroxyl groups are
called alcohols.
A carbon atom is linked by a double
bond to an oxygen atom. If the
carbonyl group is at the end of a
carbon skeleton, the compound is

Carboxyl Group

Amino group

Phosphate Group

Methyl Group

called an aldehyde; if it is within

the chain, the compound is called a
ketone (e.g. sugars).
Consists of a carbon double-bonded
to an oxygen atom and also bonded
to a hydroxyl group. Acts as an acid
by contributing an H+ to a solution.
Compounds with carboxyl groups
are called carboxylic acid (e.g.
acetic acid in vinegar)
Has a nitrogen bonded to two
hydrogens and the carbon skeleton.
Acts as a base by picking up an H+
from a solution. Organic compounds
with an amino group are called
amines. The building blocks of
proteins are called amino acids
because they contain an amino and
a carboxyl group.
Consists of a phosphorus atom
bonded to four oxygen atoms.
Usually ionized and attached to the
carbon skeleton by one of its oxygen
atoms. Compounds with phosphate
groups are called organic
phosphates and are often involved
in energy transfers (e.g. ATP)
Consists of a carbon bonded to three
hydrogens. Compounds with methyl
groups are called methylated
compounds. (e.g. DNA)

The first five groups are called functional groups. They affect a
molecules function by participating in chemical reactions in characteristic
ways. These groups are polar and hydrophilic (water-loving) and therefore
soluble in water.
The sixth group is nonpolar and not reactive, but it affects
molecular shape and thus function.
3.3 Cells make a huge number of large molecules from a limited set of small
molecules

FOUR MAIN CLASSES OF THE IMPORTANT MOLECULES OF

LIVING THINGS:
1.
2.
3.
4.

Carbohydrates (macromolecules)
Lipids
Proteins (macromolecules)
Nucleic Acids (macromolecules)

Polymer a large molecule consisting of many identical or

similar building blocks strung together.
Monomers the building blocks of polymers
(Making Polymers) Dehydration reaction through this,
monomers together for polymers; a reaction that removes a
molecule of water; are the same regardless of the specific
monomers and the type of polymer the cell is producing
(Breaking Polymers) Hydrolysis a digestion process; the
reverse of a dehydration reaction; means to break (lyse) with
water (hydro-)
Enzymes are specialized macromolecules that speed up
chemical reactions in cells

Points:

The diversity of macromolecules in the living world is vast.

A cell makes all its thousands of different macromolecules
from a small list of ingredients about 40 to 50 common
components and a few others that are rare.
Proteins are built from only 20 kinds of amino acids.
Your DNA is built from just four kinds of monomers called
nucleotides.
Arrangement is the key to great diversity of polymers and is
the variation in the sequence in which monomers are strung
together.
The monomers themselves are essentially universal.

CARBOHYDRATES
3.4 Monosaccharides are the simplest carbohydrates

Carbohydrates refers to a class of molecules ranging from the small

sugar molecules to large polysaccharides
Monosaccharides from the Greek monos, single, and sacchar,
sugar; the carbohydrate monomers
Glucose is an aldose and fructose is a ketose. (Most names for
sugars end in ose. Most names of enzymes and in ase.)

Glucose and fructose are isomers; they differ only in the arrangement
of their atoms (in this case, the positions of carbonyl groups)
Fructose taste considerably sweeter than glucose.
The carbon skeletons of both glucose and fructose are six carbon
atoms long.
Other monosaccharides may have three to seven carbons. Fivecarbon sugar, called pentoses, and six-carbon sugars, called
hexoses, are among the most common.
In aqueous solutions, many monosaccharides form rings, as shown in
glucose.
Monosaccharides, particularly glucose, are the main fuel molecules for
cellular work.
Dextrose an aqueous solution of glucose
Cells use the carbon skeletons of monosaccharides as raw material for
making other kinds of organic molecules, such as amino acids and
fatty acids.

3.5 Two monosaccharides are linked to form a disaccharide

Disaccharide constructed by cells from two monosaccharide

monomers by dehydration reaction (e.g. maltose and sucrose)
The most common disaccharide is sucrose, which is made of a glucose
monomer linked to a fructose monomer. Sucrose provides a source of
energy and raw materials to all parts of the plant.

3.6 What is high-fructose corn syrup, and is it to blame for obesity?

Sugar is the disaccharide sucrose. Sugars have been described as

empty calories because they contain only negligible amounts of
other nutrients.
High fructose corn syrup is reported to be linked to the obesity
epidemic Its main carbohydrate is starch, a polysaccharide.

3.7 Polysaccharides are long chains of sugar units

Polysaccharides
o are macromolecules, polymers of hundreds to thousands of
monosaccharides linked together by dehydration reactions.
o May function as storage molecules or as structural
compounds
3 Common Polysaccharides
o Starch a storage polysaccharide in plants, consists
entirely of glucose monomers. Starch molecules coil into a
helical shape and may be unbranched or branched. Starch

granules serve as carbohydrate banks from which plant

cells can withdraw glucose for energy or building materials.
o Glycogen is more highly branched than starch; here,
animals store glucose
o Cellulose the most abundant organic compound on
Earth; a major component of the tough walls that enclose plant
cells; also a polymer of glucose. However, cellulose in not a
nutrient for humans, although it does contribute to digestive
system health. The cellulose that passes through your digestive
tract is referred to as insoluble fiber (e.g. fiber of fresh fruits,
vegetables, and grains).
o Chitin is used by insects and crustaceans to build their
exoskeleton (the hard case enclosing the animal). Also found in
the cell walls of fungi. Humans use chitin to make a strong and
flexible surgical thread that decomposes after a wound or
incision heals.
LIPIDS
3.8 Fats are lipids that are mostly energy-storage molecules

Lipids
o Diverse compounds that are grouped together because they
share one trait: They do not mix well with water.
o They consist mainly of carbon and hydrogen atoms linked by
nonpolar covalent bonds.
o They are hydrophobic (water-fearing).
o They are neither large macromolecules nor polymers built from
similar monomers.
Fat
o Is a large lipid made from two kinds of smaller molecules:
glycerol and fatty acids.
o The nonpolar hydrocarbon chains are the reason fats are
hydrophobic.
o The synonym for fat is triglyceride.
o An unsaturated fatty acid has one fewer hydrogen atom on
each carbon of the double bond (e.g. corn oil, olive oil, and other
vegetable oils).
o A saturated fatty acid has no double bonds in their
hydrocarbon chain have the maximum number of hydrogen
atoms (are saturated with hydrogens) (e.g. beef fat and
butter).
o Unsaturated fats can be converted to saturated fats by adding
hydrogen. Hydrogenation, however, also creates trans fats, a

form of fat that recent research associates with health risks. They
may contribute to atherosclerosis.
o The main function of fats is long-term energy storage. A gram
of fat stores more than twice as much energy as a gram of
polysaccharide.
3.9 Phospholipids and steroids are important lipids with a variety of functions

Phospholipids the major component of cell membranes, are

structurally similar to fats.
The hydrophilic and hydrophobic ends of multiple molecules assemble
in a bilayer of phospholipids to form a membrane.
Steroids lipids in which the carbon skeleton contains four fused rings
Cholesterol is a common component in animal cell membranes, and
animal cells also use it as a starting material for making other steroids,
including sex hormones. Too much cholesterol in the blood may
contribute to atherosclerosis.

3.10 Anabolic steroids pose health risks

Anabolic steroids
o Are synthetic variants of the male hormone testosterone
o The word anabolic comes from anabolism, the building of
substances by the body
o As prescription drugs, anabolic steroids are used to treat general
anemia and diseases that destroy body muscle.

3.11 Proteins are made from amino acids linked by peptide bonds

Nearly every dynamic function in your body depends on proteins.

You have tens of thousands of different proteins, each with a specific
structure and function.
Of all lifes molecules, proteins are structurally the most elaborate and
diverse.
A protein is a polymer of amino acids.
Protein diversity is based on differing arrangements of a common set
of 20 amino acid monomers.
Amino acids all have an amino group and a carboxyl group (which
makes it an acid, hence the name amino acid).
o Both of these functional groups are covalently bonded to a
central carbon atom, called the alpha carbon.
o Also bonded to the alpha carbon is a hydrogen atom and a
chemical group symbolized by the letter R.
o The R group, also called the side chain, differs with each amino
acid.

o In the simplest amino acid (glycine), the R group is just a

hydrogen atom.
The amino acids have two main types, hydrophobic and hydrophilic.
Amino acids with polar and charged R groups help proteins dissolve in
the aqueous solutions inside cells.
How are amino acids linked to form polymers?
o Cells join amino acids together in a dehydration reaction that
links the carboxyl group of one amino acid to the amino group of
the next amino acid as a water molecule is removed.
o The resulting linkage is called a peptide bond.
o The product of the reaction shown in the figure is called a
dipeptide, because it was made from two amino acids.
o Additional amino acids can be added by the same process to
form a chain of amino acids, a polypeptide.
o To release amino acids from the polypeptide by hydrolysis, a
molecule of H2O must be added back to break each peptide
bond.

3.12 A proteins specific shape determines its function

Probably proteins most important role is as enzymes, the chemical

catalysts that speed and regulate virtually all chemical reactions in
cells.
Types of proteins:
o Structural (hair, fibers that make up connective tissues)
o Contractile (in muscle cells)
o Defensive (antibodies)
o Signal (hormones)
o Receptor (in cell membranes, transmit signals)
o Transport (hemoglobin)
o Storage (ovalbumin)
Shape
o Globular (most enzymes and other proteins)
o Fibrous (structural proteins)
In a process called denaturation, polypeptide chains unravel, losing
their specific shape and, as a result, their function.
Changes in salt concentration and pH can denature many proteins, as
can excessive heat.

3.13 A proteins shape depends on four levels of structure

The primary structure of a protein is its unique sequence of amino

acids.

o Even a slight change in primary structure may affect a proteins

overall shape and thus its ability to function.
o For instance, a single amino acid change in hemoglobin, the
oxygen-carrying blood protein, causes sickle-cell disease, a
serious blood disorder.
In the second level of protein structure, part of the polypeptide coil or
fold into local patterns called secondary structure.
The term tertiary structure refers to the overall three-dimensional
shape of a polypeptide, which determines the function of a protein.
o A proteins shape may be reinforced further by covalent bonds
called disulfide bridges.
Many proteins consist of two or more polypeptide chains aggregated
into one functional macromolecule. Such proteins have a quaternary
structure, resulting from the association of these polypeptides, which
are known as subunits (e.g. collagen).

3.14 DNA and RNA are the two types of nucleic acids

The amino acid sequence of a polypeptide is programmed by a discrete

unit of inheritance known as gene.
The name nucleic comes from their location in the nuclei of eukaryotic
cells.
Unique among molecules, DNA provides directions for its own
replication.
The genes present in DNA do not build proteins directly.
o They work through an intermediary the second type of nucleic
acid, known as ribonucleic acid (RNA).

3.15 Nucleic acids are polymers of nucleotides

The monomers that make up nucleic acids are nucleotides.

The sugar in DNA is deoxyribose, whereas RNA has a slightly different
sugar called ribose.
Each DNA nucleotide has one of four different nitrogenous bases:
adenine (A), thymine (T), cytosine (C), and guanine (G).
RNA nucleotides also contain the bases A, C, and G; but the base
uracil (U) is found instead of thymine.
Like polysaccharides and polypeptides, a nucleic acid polymer a
polynucleotide is built from its monomers by dehydration reactions.
RNA usually consists of a single polynucleotide strand, but DNA is a
double helix, in which two polynucleotides wrap around each other.
Because of the base-pairing rules, the two strands of the double helix
are said to be complementary, each a predictable counterpart of the
other.

Complementary base pairing is the key to how a cell makes two

identical copies of each of its DNA molecules every time it divides.

3.16 Lactose tolerance is a recent event in human evolution