Chemical components

of cell
(2nd half)

Molecules in cells
A Cell is Formed from Carbon Compounds:
If disregard waternearly all of the molecules in a cell are
based on carbon (C)outstanding among all the elements
in its ability to form large moleculesbecause C is small,
has four electrons and four vacancies in its outermost shell
can form four covalent bonds with other atoms.
One carbon atom can join to other carbon atoms through
highly stable covalent CC bonds to form chains and rings
and hence generate large & complex molecules with no
obvious upper limit to their sizecalled organic molecules
Certain combinations of atoms, such as the methyl (CH 3),
hydroxyl (OH), carboxyl (COOH), carbonyl (C=O),
phosphoryl (PO32-), and amino (NH2) groups, occur
repeatedly in organic molecules Each such group has
distinct chemical and physical properties influencing the
behaviour of the molecule in which the group occurs.

Cells contain four major families of

small organic molecules
Carbon compoundsmolecular weights in the range
1001000contain up to 30 or so (C) atomsusually
found free in solution in the cytoplasmSome are
used as monomer subunits to construct the giant
polymeric macromolecules (the proteins, nucleic acids,
& large polysaccharidesof the cellOthers act as
energy sources & are broken down and transformed
into other small molecules.
All organic molecules are synthesized fromand are
broken down intothe same set of simple compounds.
Cells contain four major families of small organic
molecules: the sugars, the fatty acids, the amino
acids, and the nucleotides

Sugars are energy sources for cells

and subunits of polysaccharides
The simplest sugarsthe monosaccharides
are compounds with the general formula
(CH2O)n, where n is usually 3, 4, 5, or 6.
Sugars, and the molecules made from them,
are also called carbohydratesGlucose, for
example, has the formula C6H12O6Carbons,
hydrogens, and oxygens can be joined
together by covalent bonds in a variety of
ways, creating structures with different
shapes (E.g glucose, galactose, mannose)

 Each of these sugars, moreover, can exist in either of two

formsthe d-form and the l-formmirror images of each
other.
Sets of molecules with the same chemical formula but
different structures called isomers & mirror-image pairs
of molecules called optical isomers widespread among
organic molecules.
Monosaccharides can be linked by covalent bonds
called glycosidic bondsto form larger carbohydrates. Two
monosaccharides linked together make a disaccharide,
such as sucrose, which is composed of a glucose and a
fructose unit.
Larger sugar polymers range from the oligosaccharides
(trisaccharides, tetrasaccharides, and so on) up to giant
polysaccharides, which can contain thousands of
monosaccharide units. In most cases, the prefix oligo- is
used to refer to macromolecules made of a small number of
monomers, between 3 and 50 or so. Polymers, in contrast,

 A bond is formed between an OH group on one

sugar and an OH group on another by a
condensation reaction, in which a molecule of
water is expelled as the bond is formed. The
bonds created by all of these condensation
reactions can be broken by the reverse process
of hydrolysis, in which a molecule of water is
consumed.
Each monosaccharideseveral free hydroxyl
groupscan form a link to another
monosaccharide (or to some other compound)
the number of possible polysaccharide structures
is extremely largedifficult to determine the
arrangement of sugars in a polysaccharide.

 The glucose a central role as an energy source

for cells is broken down to smaller molecules in
a series of reactions releasing energy that the
cell can harness to do useful work.
Cells use simple polysaccharides composed only
of glucose unitsprincipally glycogen in animals
and starch in plantsas long-term stores of
glucose, held in reserve for energy production.
Sugars do not function exclusively in the
production and storage of energyalso used,
e.g , to make mechanical supportsthe cellulose
that forms plant cell wallsis a polysaccharide of
glucose. The chitin of insect exoskeletons and
fungal cell walls, is also a polysaccharide.

 Smaller oligosaccharides can be

covalently linked to proteins to form
glycoproteins, or to lipids to form
glycolipidsboth found in cell
membranes.
These sugar side chains are often
recognized selectively by other cells.
Differences in the types of cellsurface sugars form the molecular
basis for different human blood
groups.

Fatty acids are components of cell

membranes
A fatty acid molecule (such as palmitic acid)
has two chemically distinct regionsOne is a
long hydrocarbon chain (hydrophobic and not
very reactive chemically) & a carboxyl (COOH)
group, which behaves as an acid (carboxylic
acid): it is ionized in solution (COO), extremely
hydrophilic, and chemically reactive.
Almost all the fatty acid molecules in a cell are
covalently linked to other molecules by their
carboxylic acid group. Molecules such as fatty
acids, which possess both hydrophobic and
hydrophilic regions, are termed amphipathic.

 The hydrocarbon tail of palmitic acidsaturated

i.e no double bonds between its carbon atoms
Stearic acid (fatty acids in animal fat)
saturated.
Some other fatty acids, such as oleic acid, have
unsaturated tails, with one or more double bonds
along their length which create kinks in the
molecules interfering with their ability to pack
together in a solid mass.
Fatty acids are also found in cell membranes,
where the tightness of their packing affects the
fluidity of the membrane. The many different
fatty acids found in cells differ only in the length
of their hydrocarbon chains and in the number
and position of the carboncarbon double bonds.

 Fatty acids serve as a concentrated food

reserve in cellscan be broken down to
produce about six times as much usable
energy, weight for weight, as glucose. Fatty
acids are stored in the cytoplasm of many
cells in the form of droplets of triacylglycerol
moleculescompounds made of three fatty
acid chains joined to a glycerol molecule.
These molecules are the animal fats found in
meat, butter, and cream, and the plant oils
such as corn oil and olive oil.
When a cell needs energy, the fatty acid
chains can be released from triacylglycerols
and broken down into two-carbon units.

 Fatty acids and their derivatives, including

triacylglycerols, are examples of lipids. This
class of biological molecules is loosely defined,
with the common feature that the molecules in
the class are insoluble in water and soluble in fat
and organic solvents such as benzene. Lipids
typically contain long hydrocarbon chains, as in
the fatty acids and isoprenesor multiple linked
aromatic rings, as in the steroids.
The most important function of fatty acids in
cells is in the formation of membranes
composed largely of phospholipids, which are
small molecules that, like triacylglycerols, are
constructed mainly from fatty acids and glycerol.

 In phospholipids, however, the glycerol is joined to

two fatty acid chains, rather than to three as in
triacylglycerols. The third site on the glycerol is
linked to a hydrophilic phosphate group, which in
turn is attached to a small hydrophilic compound
such as choline Phospholipids are strongly
amphipathic: each phospholipid molecule has a
hydrophobic tail, composed of the two fatty acid
chains, and a hydrophilic head, where the
phosphate is located.
Other lipids present in the cell membrane contain
one or more sugars instead of a phosphate group.
Several of these glycolipids play an important role
in intracellular cell signaling.

 The membrane-forming property of

phospholipids results from their
amphipathic nature. Phospholipids will
spread over the surface of water to form
a monolayer of phospholipid molecules,
with the hydrophobic tails facing the air
and the hydrophilic heads in contact
with the water. Two such molecular
layers can readily combine tail-to-tail in
water to make a phospholipid sandwich,
or lipid bilayer, which forms the
structural basis of all cell membranes.

Figure: Phospholipids aggregate

to
form cell membranes.

Figure: Cell membrane

Amino acids are the subunits of

proteins
Amino acidsall possess a carboxylic acid group and
an amino group, both linked to the same carbon
atom called the -carbon.
Their chemical variety comes from the side chain that
is also attached to the -carbon. Cells use amino
acids to build proteinspolymers of amino acids
joined head-to-tail in a long chainfolded into a
three-dimensional structure unique to each type of
protein.
The covalent linkage between two adjacent amino
acids in a protein chain is called a peptide bond; the
chain of amino acids is also known as a polypeptide.

 Peptide bonds are formed by condensation

reactions that link one amino acid to the next.
Regardless of the specific amino acids from
which it is made, the polypeptide always has an
amino (NH2) group at one end (its N-terminus)
and a carboxyl (COOH) group at its other end
(its C-terminus). This gives a protein or
polypeptide a definite directionalitya
structural (as opposed to electrical) polarity.
Twenty types of amino acidsfound in proteins
each with a different side chain attached to
the a-carbon atom. The same 20 amino acids
occur over and over again in all proteins,
whether they hail from bacteria, plants, or
animals.

 Like sugars, all amino acids (except glycine)

exist as optical isomers in d and l-forms. But
only l-forms are ever found in proteins
(although d-amino acids occur as part of
bacterial cell walls and in some antibiotics).
Five of the 20 amino acids have side chains
that can form ions in solution and can
therefore carry a charge (lysine and
glutamic acid, for example. The others are
uncharged.
Some amino acids are polar and hydrophilic,
and some are non polar and hydrophobic

Nucleotides are the subunits of DNA

and RNA
A nucleosidemade of a nitrogencontaining ring compound linked to a fivecarbon sugar(either ribose or deoxyribose).
NucleotideA nucleoside sporting one or
more phosphate groups attached to its
sugar.
RibonucleotidesNucleotides containing
ribose.
Deoxyribonucleotidesthose containing
deoxyribose.

 The nitrogen-containing rings are generally

referred to as bases for historical reasons:
under acidic conditions they can each bind a
H+ (proton) and thereby increase the
concentration of OH ions in aqueous solution.
There is a strong family resemblance between
the different nucleotide bases. Cytosine (C),
thymine (T), and uracil (U) are called
pyrimidines because they all derive from a
six-membered pyrimidine ring; guanine (G)
and adenine (A) are purine compounds,
which bear a second, five-membered ring
fused to the six-membered ring. Each
nucleotide is named after the base it
contains.

 Nucleotides can act as short-term carriers of

chemical energy. Above all others, the
ribonucleotide adenosine triphosphate, or ATP,
participates in the transfer of energy in hundreds
of cellular reactions. ATP is formed through
reactions that are driven by the energy released
by the breakdown of foodstuffs. Its three
phosphates are linked in series by two
phosphoanhydride bonds. Rupture of these
phosphate bonds releases large amounts of
useful energy. The terminal phosphate group in
particular is frequently split off by hydrolysis. In
many situations, transfer of this phosphate to
other molecules releases energy that drives
energy-requiring biosynthetic reactions.

 The most fundamental role of nucleotides in the

cell is in the storage and retrieval of biological
information. Nucleotides serve as building blocks
for the construction of nucleic acidslong
polymers in which nucleotide subunits are
covalently linked by the formation of a
phosphodiester bond between the phosphate
group attached to the sugar of one nucleotide
and a hydroxyl group on the sugar of the next
nucleotide.
Nucleic acid chains are synthesized from energyrich nucleoside triphosphates by a condensation
reaction that releases inorganic pyrophosphate
during phosphodiester bond formation.

 Two main types of nucleic acidsThose based on

the sugar ribose are known as ribonucleic acids,
or RNA, and contain the bases A, G, C, and U.
Those based on deoxyribose (in which the
hydroxyl at the 2 position of the ribose carbon
ring is replaced by a hydrogen are known as
deoxyribonucleic acids, or DNA, and contain
the bases A, G, C, and T (T is chemically similar to
the U in RNA).
RNA usually occurs in cells in the form of a single
stranded polynucleotide chain, but DNA is virtually
always in the form of a double-stranded molecule:
the DNA double helix is composed of two
polynucleotide chains running antiparallel to each
other, being held together by hydrogen-bonding
between the bases of the two chains.

 The two nucleic acids, however, have

somewhat different roles in the cell.
DNA, with its more stable, hydrogenbonded helices, acts as a long-term
repository for hereditary information,
while single-stranded RNA is usually a
more transient carrier of molecular
instructions. The ability of the bases in
different nucleic acid molecules to
recognize and pair with each other by
hydrogen-bonding (called base pairing)
G with C, and A with either T or U
underlies all of heredity and evolution.

Macromolecules in Cells
On the basis of weight, macromolecules
are by far the most abundant of the
carbon-containing molecules in a living
cell. They are the principal building blocks
from which a cell is constructed and also
the components that confer the most
distinctive properties on living things.
Macromoleculespolymersconstructed
simply by covalently linking small organic
molecules (called monomers, or subunits)
into long chains, or polymers.

Figure: Polymers are made up of many

small, repeating molecular units known
as monomers

 Proteinsversatile & perform thousands of distinct

functions in cellsact as enzymes that catalyze
the chemical reactions in the cell, also required to
synthesize the many different molecules that a cell
needsFor example, an enzyme called ribulose
bisphosphate carboxylase, found in chloroplasts,
converts CO2 to sugars in plants; this protein
thereby creates most of the organic matter used by
the rest of the living world.
Other proteinsused to build structural
componentstubulin self-assembles to make the
cells long, stiff microtubulesHistone proteins pack
the cells DNA in chromosomes.
Other proteinsact as molecular motors
produce force and movement, as in the case of
myosin in muscle.

Macromolecules contain a specific

sequence of subunits
Each polymer grows by the addition of a monomer onto one
end of the polymer chain via a condensation reaction, in
which a molecule of water is lost with each subunit added.
In all cases the reactions are catalyzed by specific enzymes,
which ensure that only monomers of the appropriate type
are incorporated. The stepwise polymerization of monomers
into a long chain is a simple way because the subunits are
added by the same reaction performed over and over again
by the same set of enzymes. In a sense, the process
resembles the repetitive operation of a machine in a factory
with some important differences. First, apart from some of
the polysaccharides, most macromolecules are made from a
set of monomers that are slightly different from one
another, for example, the 20 different amino acids from
which proteins are made.

 Second, and most important, the polymer

chain is not assembled at random from these
subunits; instead the subunits are added in a
particular order, or sequence.
The possibility of varying the sequence of
subunits creates enormous diversity in the
polymeric molecules that can be produced.
Thus, for a protein chain 200 amino acids
long, there are 20200 possible combinations
(20 x 20 x 20 x 20... multiplied 200 times).
Thus the machinery of polymerization must
be subject to a sensitive control that allows it
to specify exactly which subunit should be
added next to the growing polymer end.

Non-covalent bonds specify the

precise shape of a macromolecule
Most of the single covalent bonds in a
macromolecule allow rotation of the atoms they
join, so that the polymer chain has great
flexibility. In principle, this allows a
macromolecule to adopt an almost unlimited
number of shapes, or conformations, as the
polymer chain writhes and rotates under the
influence of random thermal energy. However,
the shapes of most biological macromolecules
are highly constrained because of weaker
noncovalent bonds that form between different
parts of the molecule.

 If these weaker bonds are formed in sufficient

numbers, the polymer chain may preferentially
adopt one particular conformation, determined
by the linear sequence of monomers in its chain.
Most protein molecules and many of the RNA
molecules found in cells fold tightly into one
highly preferred conformation in this way.
The non-covalent bonds important in biological
molecules include two types: electrostatic
attractions and hydrogen bonds. Electrostatic
attractions, although strong on their own, are
quite weak in water. This is because charged or
partially charged (polar) groups are shielded by
their interactions with water molecules or with
other salts present in the aqueous solution.

 Electrostatic attractions, however, are very important

in biological systems. An enzyme that binds a positively
charged substrate will often use a negatively charged
amino acid side chain to guide its substrate into the
proper position.
Hydrogen bonds also hold the two strands of the DNA
double helix together. Because individual hydrogen
bonds are weak, enzymes can easily unzip the helixfor
example, when a cell needs to copy its genetic material.
A third type of weak bond results from van der Waals
attractions, which are a form of electrical attraction
caused by fluctuating electric charges that arise
whenever two atoms come within a very short distance
of each other. Although van der Waals interactions are
weaker than hydrogen bonds, in large numbers they play
an important role in the attraction between large
molecules with complementary shapes.

 Another important non-covalent force

is created by the three-dimensional
structure of water, which forces
hydrophobic groups together in order
to minimize their disruptive effect on
the hydrogen-bonded network of water
molecules. This expulsion from the
aqueous solution generates what is
sometimes thought of as a fourth kind
of weak noncovalent bond, called a
hydrophobic interaction. This
interaction forces phospholipid
molecules together in cell membranes.

Non-covalent bonds allow a macromolecule

to bind other selected molecules
Although non-covalent bonds are individually very weak,
they can add up to create a strong attraction between two
molecules when these molecules fit together very closely,
like a hand in a glove, with many non-covalent bonds
between them. Binding of this type underlies all biological
catalysis, making it possible for proteins to function as
enzymes. Non-covalent bonds can also stabilize
associations between two different macromolecules if their
surfaces match closely. These bonds thereby allow
macromolecules to be used as building blocks for the
formation of much larger structures. For example, proteins
often bind together into multiprotein complexes, thereby
forming intricate machines with multiple moving parts that
perform such complex tasks as DNA replication and protein

Figure: Non-covalent bonds mediate

interactions between macromolecules.

Applications
Abiosensor is a device for the detection of an analyte that
combines a biological component with a physicochemical
detector component. It consists of 3 parts:
(1): The ''sensitive biological element'' (biological material (eg.
tissue, microorganisms, organelles, cell receptors,
enzymes,antibodies, nucleic acids, etc), a biologically derived
material or biomimic) The sensitive elements can be created
by biological engineering.
(2): The ''transducer'' or the ''detector element'' (works in a
physicochemical way; optical, piezoelectric, electrochemical,
etc.) that transforms the signal resulting from the interaction of
the analyte with the biological element into another signal (i.e.,
transducers) that can be more easily measured and quantified;
(3): Associated electronics or signal processors that are
primarily responsible for the display of the results in a userfriendly way.

Avidin:Biotin Binding
Biotin
Biotin, also known as vitamin H, is a small molecule (MW
244.3) that is present in tiny amounts in all living cells. The
valeric acid side chain of the biotin molecule can be
derivatized to incorporate various reactive groups that are
used to attach biotin to other molecules. Once biotin is
attached to a molecule, the molecule can be affinitypurified using an immobilized version of any biotin-binding
protein. Alternatively, a biotinylated molecule can be
immobilized through interaction with a biotin-binding
protein, then used to affinity-purify other molecules that
specifically interact with it. Pierce offers biotin-labeled
antibodies and a number of other biotinylated molecules,
as well as a broad selection of biotinylation reagents to
label any protein.

 Avidin
Avidin is a glycoprotein derived from
both avians and amphibians that
shows considerable affinity for biotin, a
co-factor that plays a role in multiple
eukaryotic biological processes. Avidin
and other biotin-binding proteins,
including streptavidin and NeutrAvidin
Protein, have the ability to bind up to
four biotin molecules, as shown in the
diagram, making this interaction ideal
for both purification and detection
strategies.

 Advantages of using Avidin-Biotin Systems

The avidin-biotin complex is the strongest known noncovalent interaction (Kd= 10-15M) between a protein and
ligand. The bond formation between biotin and avidin is
very rapid, and once formed, is unaffected by extremes
of pH, temperature, organic solvents and other
denaturing agents. These features of biotin and avidin
features that are shared by streptavidin and NeutrAvidin
Protein are useful for purifying or detecting proteins
conjugated to either component of the interaction.
Applications for which the avidin-biotin interaction is used
include:
Enzyme linked immunosorbent assay (ELISA)
Western, Northern and Southern blotting
Cell-surface labeling
Affinity purification
Electromobility shift assays (EMSA)