Water in Living Systems

Chemical Bonds
A chemical bond is an attraction between atoms that allows the formation
of chemical substances that contain two or more atoms. The bond is caused by
the electrostatic force of attraction between opposite charges, either
between electrons and nuclei, or as the result of a dipole attraction.

Types of Bonding
The different types of chemical bonding are determined by how the
valence electrons are shared among the bonded atoms.

Ionic Bonding
The

valence

electrons

are

completely

transferred from one atom to the other. Ionic bonds

occur between metals and non-metals when there
is a large difference in electronegativity.

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Properties controlled by Ionic Bonding:

Crystalline solid

Very high melting point

Soluble in H2O

Insoluble in nonpolar solvents

Nonconductor of heat and electricity

Conducts electricity in aqueous solutions

Examples: NaCl, CaCO3

Covalent Bonding
The valence electrons are shared as pairs between the bonded atoms.
Pure covalent bonding only occurs when
two nometal atom of the same kind bind
to each other. When two different nonmetal are bonded or a non-metal and a
metal are bonded, then the bond is a
mixture of covalent bonding and ionic
bonding called polar covalent bonding.

Properties controlled by Covalent Bonding:

Gas, liquid, or a soft solid

Low melting point and low boiling point

Insoluble in H2O

Soluble in nonpolar solvents

Nonconductor of heat and electricity and nonlustrous

Examples: Cl2
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Polar Bonding
Electrons are shared but not equally. Many
compounds have the characteristics of both Ionic
and

Covalent

Bonding.

Electronegativity

difference determine the balance of character.

Difference between the three types of bonding:

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Metallic Bonding
The valence electrons are shared among all of the atoms of the substance.
Metallic Bonding occurs when metal bonds to either themselves or mixed other
metals in alloys.

Properties controlled by Metallic Bonding:

Malleable solid

High melting point and boiling point

Insoluble in H2O

Insoluble in nonpolar solvents

Conducts heat and electricity

Lustrous
Examples: gold, copper

In addition there are intermolecular forces which contribute to the stability

of things. These include Dipole-Dipole Forces, Hydrogen Bonding, London
Dispersion Process.

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Dipole-Dipole Forces
Many molecules are electric dipoles, that
is, they have net positive charge on one part of
the molecule and net negative charge on
another part. Since opposite charges attract
and like charges repel, these molecules will
tend to orient themselves so that there is the
most attraction and the least repulsion.

Hydrogen Bonding
A particularly strong and
important variety of dipole-dipole
interaction is called hydrogen
bonding. A hydrogen atom on
one molecule is attracted to a
highly electronegative atom in
another

molecule.

Hydrogen

bonding is strong both because

of the high polarity involved and
because the small size of the hydrogen atom permits a close approach between
it and the electronegative atom.
Hydrogen bonding is particularly noted between water molecules, but from
the description given above you should be able to deduce other substances in
which hydrogen bonding occurs.

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London Dispersion Forces (also known as van der Waals)

Even nonpolar molecules have a random fluctuation of charge making the

molecule temporarily polar. This then induces an opposite fluctuation in a
neighbouring molecules so that the two molecules have opposite charges on
their near sides and attract each other.
The strength of chemical bonds varies considerably; there are strong
bonds and weak bonds. Ionic, Covalent and Metallic Bonding are classified
under strong bonds while most of the intermolecular forces are under the
classification of weak bonds.

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Overview of Macromolecules
A molecule consists of two or more atoms that are covalently bonded in
specific proportions according to weight or stoichiometry, and with a unique
geometry. Both stoichiometry (the chemical formula) and geometry (the
chemical structure) are important.
A macromolecule is literally a large molecule. A biological macromolecule
or biopolymer is typically defined as a large and complex molecule with
biological function. Since these are biopolymers, their size can be defined by the
terms used in polymer chemistry, that is, according to the number of sugar or
amino acid or nucleic acid residues that polymerize to form a single molecule.
Molecules composed of up to 25 residues are called oligomers, while polymers
typically contain more than 25 residues.
The structure of biological macromolecules is hierarchical, with distinct
levels of structure.

Monomers are the simple building blocks that, when polymerized, yield a
macromolecule. These include sugars, amino acids, and nucleic acid residues of
the polymers.
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Primary structure (abbreviated as 1) is the linear arrangement (or

sequence) of residues in the covalently linked polymer.
Secondary structure (abbreviated as 2) is the local regular structure of a
macromolecule or specific regions of the molecule. These are the helical
structures.
Tertiary structure (abbreviated as 3) describes the global 3D fold or
topology of the molecule, relating the positions of each atom and residue in 3D
space. For macromolecules with a single subunit, the functional tertiary structure
is its native structure.
Quaternary structure (abbreviated as 4) is the spatial arrangement of
multiple distinct polymers (or subunits) that form a functional complex.

Configuration and Conformation

The arrangement of atoms or groups of atoms in a molecule is described
by the terms configuration and conformation. These terms are not identical.
The configuration of a molecule defines the position of groups around one
or more nonrotating bonds or around chiral centers, defined as an atom having
no plane or center of symmetry.

For example, the configuration of cis-1,2-dichloroethylene has the two

chlorine atoms on the same side of the nonrotating double bond. To change the
configuration of a molecule, chemical bonds must be broken and remade. A
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conversion from the cis- to trans-configuration of 1,2-dichloroethylene requires

that we first break the carbon-carbon double bond, rotate the resulting single
bond,

then

remake

the

double

bond.

In

biological

macromolecules,

configuration is most important in describing the stereochemistry of a chiral

molecule.

The conformation of a molecule, on the other hand, describes the spatial

arrangement of groups about one or more freely rotating bonds.
For

example,

1,2-dichloroethane,

the

saturated

version

of

dichloroethylene, has no restrictions to rotation about the chemical bonds to

prevent the chlorine atoms from sitting on the same or opposite sides of the
central carbon-carbon bond. These positions define the gauche and anti
structural isomers, respectively. In addition, the conformation can be eclipsed or
staggered, depending on whether the groups are aligned or misaligned relative
to each other on either side of the carbon-carbon bond. The conformation of a
molecule thus describes the structural isomers generated by rotations about
single.

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Water as the Solvent of Life

Water
Water is a chemical compound and
polar molecule, which is liquid at standard
temperature and pressure. It has the
chemical formula H2O, meaning that one
molecule of water is composed of two
hydrogen atoms and one oxygen atom.
Water is found almost everywhere on earth
and is required by all known life. About 70% of the Earth's surface is covered by
water. Water is known to exist, in ice form, on several other bodies in the solar
system and beyond, and proof that it exists (or did exist) in liquid form anywhere
besides Earth would be strong evidence of extraterrestrial life.

Polar covalent bonds in water molecules result in hydrogen bonding

Studied on its own, the water molecule is
deceptively simple. It is shaped like a wide V,
with its two hydrogen atoms joined to the
oxygen atom by single covalent bonds. Oxygen
is more electronegative than hydrogen, so the
electrons of the covalent bonds spend more
time closer to oxygen than to hydrogen; these
are polar covalent bonds.

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This unequal sharing of electrons and waters V-like shape make it a polar
molecule, meaning that its overall charge is unevenly distributed: The oxygen
region of the molecule has a partial negative charge, and each hydrogen has a
partial positive charge.
The properties of water arise from attractions between oppositely charged
atoms of different water molecules: The slightly positive hydrogen of one molecule
is attracted to the slightly negative oxygen of a nearby molecule. The two
molecules are thus held together by a hydrogen bond. When water is in its liquid
form, its hydrogen bonds are very fragile, each about 1/20 as strong as a covalent
bond. The hydrogen bonds form, break, and re-form with great frequency. Each
lasts only a few trillionths of a second, but the molecules are constantly forming
new hydrogen bonds with a succession of partners. Therefore, at any instant, a
substantial percentage of all the water molecules are hydrogen-bonded to their
neighbors. The extraordinary qualities of water are emergent properties resulting
in large part from the hydrogen bonding that organizes water molecules into a
higher level of structural order.

Water as a solvent
Water is also a good solvent due to its polarity. The solvent properties of
water are vital in biology, because many biochemical reactions take place only
within aqueous solutions (e.g., reactions in the cytoplasm and blood). In addition,
water

is

used

to

transport

biological

molecules.

When an ionic or polar compound enters water, it is surrounded by water

molecules. The relatively small size of water molecules typically allows many water
molecules to surround one molecule of solute. The partially negative dipoles of

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the water are attracted to positively charged components of the solute, and vice
versa for the positive dipoles.
In general, ionic and polar substances such as acids, alcohols, and salts are
easily soluble in water, and nonpolar substances such as fats and oils are not.
Nonpolar molecules stay together in water because it is energetically more
favorable for the water molecules to hydrogen bond to each other than to
engage in van der Waals interactions with nonpolar molecules.

An example of an ionic solute is table salt; the sodium chloride, NaCl,

separates into Na+ cations and Cl- anions, each being surrounded by water
molecules. The ions are then easily transported away from their crystalline lattice
into solution. An example of a nonionic solute is table sugar. The water dipoles
hydrogen bond to the dipolar regions of the sugar molecule and allow it to be
carried away into solution.
Also since water preserves chemical equilibrium within living cells. Water
acts as a transport medium within organism for nutrients and wastes and helps to
reduce sudden temperature changes in plants and animals.

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Hydrophilic and Hydrophobic Substances

Any substance that has an affinity for water is said to be hydrophilic (from
the Greek hydro, water, and philios, loving). In some cases, substances can be
hydrophilic without actually dissolving. For example, some molecules in cells are
so large that they do not dissolve. Instead, they remain suspended in the aqueous
liquid of the cell. Such a mixture is an example of a colloid, a stable suspension of
fine particles in a liquid. Another example of a hydrophilic substance that does
not dissolve is cotton, a plant product. Cotton consists of giant molecules of
cellulose, a compound with numerous regions of partial positive and partial
negative charges that can form hydrogen bonds with water. Water adheres to
the cellulose fibers. Thus, a cotton towel does a great job of drying the body, yet
it does not dissolve in the washing machine. Cellulose is also present in the walls
of water-conducting cells in a plant; you read earlier how the adhesion of water
to these hydrophilic walls allows water transport to occur.
There are, of course, substances that do not have an affinity for water.
Substances that are nonionic and nonpolar (or otherwise cannot form hydrogen
bonds) actually seem to repel water; these substances are said to be
hydrophobic (from the Greek phobos, fearing). An example from the kitchen is
vegetable oil, which, as you know, does not mix stably with water-based
substances such as vinegar. The hydrophobic behavior of the oil molecules results
from a prevalence of relatively nonpolar covalent bonds, in this case bonds
between carbon and hydrogen, which share electrons almost equally.
Hydrophobic molecules related to oils are major ingredients of cell membranes.

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Molecular Structure of Living Matter

I.

Polysaccharides
It is estimated that approximately 41011 tons of carbohydrates are

biosynthesized each year on earth by plants and photosynthesizing bacteria. The

majority of these carbohydrates are produced as polysaccharides.
Polysaccharides are polymeric carbohydrate molecules composed of long
chains of monosaccharide units bound together by glycosidic bonds. They range
in structure from linear to highly branched. Examples include storage
polysaccharides such as starch and glycogen, and structural polysaccharides
such as cellulose and chitin.

Functions of Carbohydrates
1. Rapidly Mobilized Source of Energy
Monosaccharides and disaccharides
2. Energy storage
Glycogen in animals
Starch in plants
3. Structural
In cell walls bacteria and plants (Cellulose).
In exoskeletons (Chitin).
4. Coupled with protein to form glycoproteins
Important in cell membranes

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Monosaccharides
Monosaccharides have molecular formulas that are usually multiples of
2
Glucose (6 12 6 ) is the most common monosaccharide
Monosaccharides serve as a major fuel for cells and as raw material for
building molecules
Disaccharides
A disaccharide is formed when a dehydration reaction joins two
monosaccharides
This covalent bond is called a glycosidic linkage

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Polysaccharides
Polysaccharides, the polymers of sugars, have storage and structural roles.
The structure and function of a polysaccharide are determined by its sugar
monomers and the positions of glycosidic linkages.

Types of Polysaccharides
1. Starch
2. Glycogen
3. Cellulose
4. Chitin

Starch, a storage polysaccharide of plants, consists entirely of glucose monomers.

Plants store surplus starch as granules within chloroplasts and other plastids
The simplest form of starch is amylose
Starch form stored in plants, coiled, mainly 1-4 glycosidic linkage. If
branched then will also have 1-6 glycosidic linkage, stored in amyloplasts.
Plants used for energy storage, easy to digest.
Potatoes, rice, carrots, corn
Types of starches:
Amylose not branched
Amylopectin branched, more common

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Glycogen form stored in animals for energy, coiled, mainly 1-4 glycosidic
linkage. It is branched therefore also has 1-6 glycosidic linkage, easy to digest.
Found in animals: stored mainly in liver and Muscle

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Cellulose- The polysaccharide cellulose is a major component of the tough wall

of plant cells.
Like starch, cellulose is a polymer of glucose, but the glycosidic linkages
differ
The difference is based on two ring forms for glucose: alpha () and beta
()
Cellulose straight chains of glucose, -OH groups H-bond to stabilize chains
into tight bundles, 1-4 glycosidic linkage, hard to digest
Used by plants for structure and in cell walls.

Polymers with glucose are helical

Polymers with glucose are straight
In straight structures, H atoms on one strand can bond with OH groups on
other strands

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 Parallel cellulose molecules held together this way are grouped into
microfibrils, which form strong building materials for plants.

Why do we care?
o Enzymes that digest starch by hydrolyzing linkages cant hydrolyze
linkages in cellulose
o Cellulose in human food passes through the digestive tract as insoluble fiber
o Some microbes use enzymes to digest cellulose
o Many herbivores, from cows to termites, have symbiotic relationships with
these microbes

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Chitin, another structural polysaccharide, is found in the exoskeleton of

arthropods.
Contains N-acetyl group which hydrogen bond. Iscross-linked with protein
to form a strongexoskeleton for insects and crustaceans
Chitin also provides structural support for the cellwalls of many fungi

Glycoproteins carbohydrate + protein on outer surface of cell membranes

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II.

Lipids
Lipids are the one class of large biological molecules that does not include

true polymers, and they are generally not big enough to be considered
macromolecules. The compounds called lipids are grouped together because
they share one important trait: They mix poorly, if at all, with water. The
hydrophobic behavior of lipids is based on their molecular structure. Although
they may have some polar bonds associated with oxygen, lipids consist mostly of
hydrocarbon regions.
Important Types of Lipids
1. Fats

Although fats are not polymers, they are large molecules assembled from
smaller molecules by dehydration reactions. A fat is constructed from two kinds
of smaller molecules: glycerol and fatty acids. Glycerol is an alcohol; each of
its three carbons bears a hydroxyl group. A fatty acid has a long carbon
skeleton, usually 16 or 18 carbon atoms in length. The carbon at one end of
the skeleton is part of a carboxyl group, the functional group that gives these
molecules the name fatty acid. The rest of the skeleton consists of a
hydrocarbon chain. The relatively nonpolar C H bonds in the hydrocarbon
chains of fatty acids are the reason fats are hydrophobic. Fats separate from
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water because the water molecules hydrogen bond to one another and
exclude the fats. This is the reason that vegetable oil (a liquid fat) separates
from the aqueous vinegar solution in a bottle of salad dressing.

In making a fat, three fatty acid molecules are each joined to glycerol by
an ester linkage, a bond between a hydroxyl group and a carboxyl group. The
resulting fat, also called a triacylglycerol, thus consists of three fatty acids
linked to one glycerol molecule. (Still another name for a fat is triglyceride, a
word often found in the list of ingredients on packaged foods.) The fatty acids
in a fat can be the same, or they can be of two or three different kinds.
The terms saturated fats and unsaturated fats are commonly used in the
context of nutrition. These terms refer to the structure of the hydrocarbon
chains of the fatty acids.

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If there are no double

bonds between carbon atoms
composing a chain, then as
many

hydrogen

atoms

as

possible are bonded to the

carbon

skeleton.

Such

structure is said to be saturated

with

hydrogen,

and

the

resulting fatty acid therefore

called a saturated fatty acid.

An

unsaturated

fatty

acid has one or more

double bonds, with one
fewer hydrogen atom on
each

double-bonded

carbon. Nearly all double

bonds

in

naturally

occurring fatty acids are

cis double bonds, which
cause

kink

hydrocarbon

in

the
chain

wherever they occur.

The major function of
fats is energy storage. The
hydrocarbon chains of fats are similar to gasoline molecules and just as rich in
energy. A gram of fat stores more than twice as much energy as a gram of a
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polysaccharide, such as starch. In addition to storing energy, adipose tissue

also cushions such vital organs as the kidneys, and a layer of fat beneath the
skin insulates the body. This subcutaneous layer is especially thick in whales,
seals, and most other marine mammals, protecting them from cold ocean
water.
2. Phospholipids
Cells could not exist without another type of lipid phospholipids.
Phospholipids are essential for cells because they make up cell membranes.
Their structure provides a classic example of how form fits function at the
molecular level.

A phospholipid is similar to a fat molecule but has only two fatty acids
attached to glycerol rather than three. The third hydroxyl group of glycerol is
joined to a phosphate group, which has a negative electrical charge in the
cell. Additional small molecules, which are usually charged or polar, can be
linked to the phosphate group to form a variety of phospholipids. The two ends
of phospholipids show different behavior toward water. The hydrocarbon tails
are hydrophobic and are excluded from water. However, the phosphate
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group and its attachments form a hydrophilic head that has an affinity for
water.

At the surface of a cell, phospholipids are arranged in a similar bilayer. The

hydrophilic heads of the molecules are on the outside of the bilayer, in contact
with the aqueous solutions inside and outside of the cell. The hydrophobic tails
point toward the interior of the bilayer, away from the water. The phospholipid
bilayer forms a boundary between the cell and its external environment; in
fact, cells could not exist without phospholipids.
3. Steroids
Steroids are lipids characterized by a carbon skeleton consisting of four
fused rings. Different steroids, such as cholesterol and the vertebrate sex
hormones, are distinguished by the particular chemical groups attached to
this ensemble of rings.

Cholesterol is a crucial molecule in animals. It is a common component of

animal cell membranes and is also the precursor from which other steroids are
synthesized.

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III.

Nucleic Acid
Nucleic acids are polymeric macromolecules, or large biological

molecules, essential for all known forms of life. Nucleic acids, which
include Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA), are made
from monomers known as nucleotides. Each nucleotide is composed of a
nucleoside bonded to a phosphate group, and each nucleoside is composed of
an aldopentose sugar linked through its anomeric carbon to the nitrogen atom
of a heterocyclic amine base. If the sugar is deoxyribose, the polymer is DNA. If
the sugar is ribose, the polymer is RNA.
They are called nucleic acids because scientists first found them in the
nucleus of cells. Now that we have better equipment, nucleic acids have been
found in mitochondria, chloroplasts, and cells that have no nucleus, such as
bacteria and viruses.

Nucleotides

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Their functions include:

Energy (ATP)
Coenzymes that aid enzyme function (NAD+)
Messengers within cells (GTP)
Adenine, Thymine, Uracil, Guanine, Cytosine

Deoxyribonucleic Acid (DNA)

The amino acid sequence of a polypeptide
is programmed by a unit of inheritance called a
gene. Genes are made of DNA, a nucleic acid
made of monomers called nucleotides
DNA contains four different amine bases, two substituted purines (adenine
and guanine) and two substituted pyrimidines (cytosine and thymine). The
sequence of nucleotides in a chain is described by starting at the 5 end and
identifying the bases in order of occurrence, using abbreviations, G,C,A,T. Thus a
typical DNA sequence might be written as TAGGCT.
James Watson and Francis Crick (1953), made their proposal that DNA consists
of a two polynucleotide strands, running in opposite directions and coiled around
each other in a double helix like handrails on a spiral staircase.

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Ribonucleic Acid (RNA)

Ribonucleic Acid is a ubiquitous family of
large

biological

multiple
the

molecules
vital

coding,

that

perform

roles

decoding,

in
regulation,

and expression of genes. Like DNA, RNA is

assembled as a chain of nucleotides, but is
usually

single-stranded.

Cellular

organisms

use messenger RNA (mRNA) to convey genetic

information (often notated using the letters G,
A,

U,

and

for

the

nucleotides guanine, adenine, uracil and cytosine) that directs synthesis of

specific proteins, while many viruses encode their genetic information using an
RNA genome.
Roles of Nucleic Acid

DNA provides directions for its own replication

DNA directs synthesis of messenger RNA (mRNA), which carries genetic
messages from DNA to ribosomes, and, through mRNA, controls protein
synthesis
Protein synthesis occurs on ribosomes
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DNA Replication
As DNA synthesis continues, the original DNA strands continue to unwind on
each side of the bubble, forming a replication fork with two prongs.
The replication fork is a structure that forms within the nucleus during DNA
replication. It is created by helicases, which break the hydrogen bonds holding
the two DNA strands together.

The resulting structure has two branching "prongs", each one made up of a
single strand of DNA. These two strands serve as the template for the leading and

lagging strands, which will be created as DNA polymerase matches

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complementary nucleotides to the templates; the templates may be properly

referred to as the leading strand template and the lagging strand templates.
DNA is always synthesized in the 5' to 3' direction. Since the leading and
lagging strand templates are oriented in opposite directions at the replication
fork, a major issue is how to achieve synthesis of nascent (new) lagging strand
DNA, whose direction of synthesis is opposite to the direction of the growing
replication fork.
The leading strand is the strand of nascent DNA which is being synthesized
in the same direction as the growing replication fork. A polymerase "reads" the

leading strand template and adds complementary nucleotides to the nascent

leading strand on a continuous basis.
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The lagging strand is the strand of nascent DNA whose direction of synthesis
is opposite to the direction of the growing replication fork. Because of its

orientation, replication of the lagging strand is more complicated than that of the
leading strand.
The lagging strand is synthesized in short, separated segments. On the
lagging strand template, a primase "reads" the template DNA and initiates

synthesis of a short complementary RNA primer. A DNA polymerase extends the

primed segments, forming Okazaki fragments. The RNA primers are then removed
and replaced with DNA, and the fragments of DNA are joined together by DNA
ligase.
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As helicase unwinds DNA at the replication fork, the DNA ahead is forced
to rotate. This process results in a build-up of twists in the DNA ahead. This build-up

forms a torsional resistance that would eventually halt the progress of the
replication fork. DNA gyrase is an enzyme that temporarily breaks the strands of
DNA, relieving the tension caused by unwinding the two strands of the DNA helix;
DNA gyrase achieves this by adding negative supercoils to the DNA helix.

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IV.

Amino Acids and the Peptide Bonds

An amino acid is an organic molecule possessing both an amino group and

a carboxyl group. The illustration at the right shows the

general formula for an amino acid. At the center of the
amino acid is an asymmetric carbon atom called the alpha
() carbon. Its four different partners are an amino group, a
carboxyl group, a hydrogen atom, and a variable group
symbolized by R. The R group, also called the side chain,
differs with each amino acid.
The 20 Amino Acids of Proteins
The amino acids are grouped here according to the properties of their side
chains (R groups) and shown in their prevailing ionic forms at pH 7.2.

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The amino acids are grouped according to the properties of their side
chains. One group consists of amino acids with nonpolar side chains, which are
hydrophobic. Another group consists of amino acids with polar side chains, which
are hydrophilic. Acidic amino acids are those with side chains that are generally
negative in charge owing to the presence of a carboxyl group, which is usually
dissociated (ionized) at cellular pH. Basic amino acids have amino groups in their
side chains that are generally positive in charge. Because they are charged,
acidic and basic side chains are also hydrophilic.
Amino Acid Polymers
When two amino acids are positioned so that the carboxyl group of one is
adjacent to the amino group of the other, they can become joined by a
dehydration reaction, with the removal of a water molecule. The resulting
covalent bond is called a peptide bond. Repeated over and over, this process
yields a polypeptide, a polymer of many amino acids linked by peptide bonds.

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The repeating sequence of atoms highlighted in purple in is called the

polypeptide backbone. Extending from this backbone are the different side
chains (R groups) of the amino acids. Polypeptides range in length from a few
amino acids to a thousand or more. Each specific polypeptide has a unique linear
sequence of amino acids. Note that one end of the polypeptide chain has a free
amino group, while the opposite end has a free carboxyl group. Thus, a
polypeptide of any length has a single amino end (N-terminus) and a single
carboxyl end (C-terminus). In a polypeptide of any significant size, the side chains
far outnumber the terminal groups, so the chemical nature of the molecule as a
whole is determined by the kind and sequence of the side chains.

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Proteins: Structure and Function

Nearly every dynamic function of a living being depends on proteins. In
fact, the importance of proteins is underscored by their name, which comes from
the Greek word proteios, meaning first, or primary. Proteins account for more
than 50% of the dry mass of most cells, and they are instrumental in almost
everything organisms do. Some proteins speed up chemical reactions, while
others play a role in defense, storage, transport, cellular communication,
movement, or structural support.
Life would not be possible without enzymes, most of which are proteins.
Enzymatic proteins regulate metabolism by acting as catalysts, chemical agents
that selectively speed up chemical reactions without being consumed by the
reaction. Because an enzyme can perform its function over and over again, these
molecules can be thought of as workhorses that keep cells running by carrying
out the processes of life.
A human has tens of thousands of different proteins, each with a specific
structure and function; proteins, in fact, are the most structurally sophisticated
molecules known. Consistent with their diverse functions, they vary extensively in
structure, each type of protein having a unique three-dimensional shape.
Polypeptides
Diverse as proteins are, they are all unbranched polymers constructed from
the same set of 20 amino acids. Polymers of amino acids are called polypeptides.
A protein is a biologically functional molecule that consists of one or more
polypeptides, each folded and coiled into a specific three dimensional structure.

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Overview of Protein Functions

Protein Structure
Proteins are usually classified as either fibrous or globular, according to their threedimensional shapes. Fibrous proteins, such as the collagen in tendons and
connective tissue and the myosin in muscle tissue, consist of polypeptide chains
arranged side by side in long filaments. Because these proteins are tough and
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insoluble in water, they are used in nature for structural materials. Globular
proteins, by contrast, are usually coiled into compact, roughly spherical shapes.
These proteins are generally soluble in water and are mobile within cells. Most of
the 3000 or so enzymes that have been characterized to date are globular
proteins.

Four Levels of Protein Structure

The primary structure of a protein is simply the amino acid sequence.

The secondary structure of a protein describes how segments of the

peptide backbone orient into a regular pattern.

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The most common secondary structures are the -helix and the -pleated
sheet. An a-helix is a right handed coil of the protein backbone. Each turn of the
helix contains 3.6 amino acid residues, with a distance between coils of 540 pm,
or 5.4 . The structure is stabilized by hydrogen bonds between the amide N H
groups and C=O groups four residues away, with an N H O distance of 2.8 .
The a-helix is an extremely common secondary structure, and almost all globular
proteins contain many helical segments.
A -pleated differs from a-helix in that peptide chain is fully extended rather
than coiled and the hydrogen bonds occur between residues in adjacent chains.
The neighboring chains can run either in the same direction (parallel) or in
opposite directions (antiparallel), although the antiparallel arrangement is more
common and energetically somewhat more favorable.

The tertiary structure describes how the entire protein molecule coils into an
overall three-dimensional shape.

While

secondary

structure

involves

interactions between backbone constituents,

tertiary structure is the overall shape of a
polypeptide resulting from interactions between
the side chains (R groups) of the various amino
acids. One type of interaction that contributes to
tertiary structure issomewhat misleadingly
called

hydrophobic

interaction.

As

polypeptide folds into its functional shape, amino

acids with hydrophobic (nonpolar) side chains usually end up in clusters at the
core of the protein, out of contact with water. Thus, a hydrophobic interaction

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is actually caused by the exclusion of nonpolar substances by water molecules.

Once nonpolar amino acid side chains are close together, van der Waals
interactions help hold them together. Meanwhile, hydrogen bonds between
polar side chains and ionic bonds between positively and negatively charged
side chains also help stabilize tertiary structure. These are all weak interactions in
the aqueous cellular environment, but their cumulative effect helps give the
protein a unique shape.
Covalent bonds called disulfide bridges may further reinforce the shape of
a protein. Disulfide bridges form where two cysteine monomers, which have
sulfhydryl groups (-SH) on their side chains, are brought close together by the
folding of the protein. The sulfur of one cysteine bonds to the sulfur of the second,
and the disulfide bridge (-S-S-) rivets parts of the protein together.

The quaternary structure describes how different protein molecules come

together to yield large aggregate structures.

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