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Covalent Bonds Form by the Sharing of

Electrons
➢ All of the characteristics of a cell depend on the molecules it contains.
➢ A molecule is a cluster of atoms held together by covalent bonds
• in which electrons are shared rather than transferred between
atoms.
➢ The shared electrons complete the outer shells of the interacting atoms.
➢ In the simplest possible molecule—a molecule of hydrogen (H2):
• two H atoms:
o each with a single electron
o share their electrons
o thus, filling their outermost shells.
➢ The shared electrons form:
• a cloud of negative charge:
o that is densest between the two positively charged nuclei.
• This electron density
o helps to hold the nuclei together
o by opposing the mutual repulsion between their positive
charges that would otherwise force them apart.
➢ The attractive and repulsive forces are in balance when the nuclei are
separated by a characteristic distance, called the bond length.

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➢ Whereas an H atom can form only a single covalent bond, the other
common atoms that form covalent bonds in cells—O, N, S, and P, as well as
the all-important C— can form more than one.
➢ The outermost shells of these atoms, as we have seen, can accommodate
up to eight electrons, and they form covalent bonds with as many other
atoms as necessary to reach this number.

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➢ Oxygen:
• with six electrons in its outer shell
• is most stable when it acquires two extra electrons by sharing with
other atoms
• and it therefore forms up to two covalent bonds.
➢ Nitrogen:
• with five outer electrons
• forms a maximum of three covalent bonds
➢ carbon:
• with four outer electrons
• forms up to four covalent bonds
• thus, sharing four pairs of electrons
➢ Covalent bonds between multiple atoms are therefore characterized by:
• specific bond angles
• specific bond lengths
• specific bond energies

➢ The four covalent bonds that can form around a carbon atom, for example,
• are arranged as if pointing to the four corners of a regular
tetrahedron.
• The precise orientation of the covalent bonds around carbon
produces the three-dimensional geometry of organic molecules.

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There Are Different Types of Covalent
Bonds
➢ Most covalent bonds involve:
• the sharing of two electrons, one donated by each participating
atom
• these are called single bonds.
➢ Some covalent bonds, however, involve the sharing of more than one pair
of electrons:
• Four electrons can be shared, for example, two coming from each
participating atom; such a bond is called a double bond.
➢ Double bonds are shorter and stronger than single bonds and have a
characteristic effect on the three-dimensional geometry of molecules
containing them.
➢ A single covalent bond between two atoms generally allows the rotation of
one part of a molecule relative to the other around the bond axis.
➢ A double bond prevents such rotation, producing a more rigid and less
flexible arrangement of atoms

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➢ intermediate in character between single and double bonds.
• The highly stable benzene molecule:
o is made up of a ring of six carbon atoms in which the bonding
electrons are evenly distributed

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Types of covalent bonds
1) Polar covalent bonds:
• Are covalent bonds in which the electrons are shared unequally.
• A polar structure (in the electrical sense):
o is one in which the positive charge is concentrated toward one
end of the molecule (the positive pole) and the negative
charge is concentrated toward the other end (the negative
pole).
• Oxygen and nitrogen atoms, for example, attract electrons relatively
strongly, whereas an H atom attracts electrons relatively weakly
o Thus, the covalent bond:
▪ between O and H, O–H
▪ between N and H, N–H
→is polar

2) Nonpolar covalent bond:


• Are covalent bonds in which the electrons are shared equally
o An atom of C and an atom of H attract electrons more equally
o Thus, the bond between carbon and hydrogen, C–H, is
relatively nonpolar.

• C • C
l l

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Covalent Bonds Vary in Strength
➢ Bond strength is measured by the amount of energy that must be supplied
to break the bond, usually expressed in units of either kilocalories per mole
(kcal/mole) or kilojoules per mole (kJ/mole).
• A kilocalorie is the amount of energy needed to raise the
temperature of 1 liter of water by 1°C.
• Thus, if 1 kilocalorie of energy must be supplied to break 6 × 1023
bonds of a specific type (that is, 1 mole of these bonds), then the
strength of that bond is 1 kcal/mole.
• One kilocalorie is equal to about 4.2 kJ
➢ Typical covalent bonds are stronger than the thermal (heat) energies by a
factor of 100
• so, they are resistant to being pulled apart by thermal motions.
➢ In living organisms, they are normally broken:
• only during specific chemical reactions that are carefully controlled
by highly specialized protein catalysts, called enzymes.
➢ When water is present, covalent bonds are much stronger than ionic bonds.
• In ionic bonds, electrons are transferred rather than shared

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Ionic Bonds Form by the Gain and Loss
of Electrons
➢ Ionic bonds are usually formed by donating electrons to—or accepting
electrons from—another atom. For example, we see that:
• a sodium (Na) atom can achieve a filled outer shell by giving up the
single electron in its third shell.
• By contrast, a chlorine (Cl) atom can complete its outer shell by
gaining just one electron.
➢ Consequently, if a Na atom encounters a Cl atom, an electron can jump
from the Na to the Cl, leaving both atoms with filled outer shells.
• The offspring of this marriage between Na and Cl is table salt (NaCl).
• Both atoms become electrically charged ions.
➢ The Na atom:
• that lost an electron now has one less electron than it has protons in
its nucleus
• it therefore has a net single positive charge (Na+).
➢ The Cl atom:
• that gained an electron now has one more electron than it has
protons
• and has a net single negative charge (Cl–).
➢ Because of their opposite charges, the Na+ and Cl– ions are attracted to
each other and are thereby held together by an ionic bond

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Ions held together solely by ionic bonds are generally called salts rather
than molecules

➢ A NaCl crystal contains astronomical numbers of Na+ and Cl


• packed together in a precise three-dimensional array with their
opposite charges exactly balanced
• a crystal only 1 mm across contains about 2 × 1019 ions of each type.
➢ Positive ions are called cations
➢ Negative ions are called anions
➢ Small inorganic ions such as Na+, Cl–, K+, and Ca2+ play important parts in
many biological processes, including the electrical activity of nerve cells

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Noncovalent Bonds Help Bring
Molecules Together in Cells
➢ In aqueous solution:
• ionic bonds are 10–100 times weaker than the covalent bonds that
hold atoms together in molecules.
➢ Much of biology depends on specific but transient interactions between
one molecule and another.
• These associations are mediated by noncovalent bonds.

Electrostatic attractions
➢ The ionic bonds that hold together the Na+ and Cl– ions in a salt crystal:
• are a form of noncovalent bond called an electrostatic attraction.
➢ Electrostatic attractions are strongest when the atoms involved are fully
charged, as are Na+ and Cl–.
➢ But a weaker electrostatic attraction also occurs between molecules that
contain polar covalent bonds.

Polar covalent bonds are thus extremely important in biology


because they allow molecules to interact through electrical forces.

➢ Any large molecule with many polar groups:


• will have:
o a pattern of partial positive and negative charges on its
surface.
• When such a molecule encounters a second molecule with a
complementary set of charges
o the two will be attracted to each other by electrostatic
attraction
➢ When present in large numbers, however, weak noncovalent bonds on the
surfaces of large molecules can promote strong and specific binding.

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Hydrogen Bonds
➢ Hydrogen Bonds Are Important Noncovalent Bonds
➢ For Many Biological Molecules:
• Water accounts for about 70% of a cell’s weight
• most intracellular reactions occur in an aqueous environment.
➢ Life on Earth is thought to have begun in the ocean.
• Thus the properties of water have put a permanent stamp on the
chemistry of living things.
➢ In each molecule of water (H2O), the two H atoms are linked to the O atom
by covalent bonds.
• The two H–O bonds are highly polar:
o because the O is strongly attractive for electrons
o whereas the H is only weakly attractive.

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• Consequently, there is an unequal distribution of electrons in a water
molecule:
o with a preponderance of positive charge on the two H atoms
and negative charge on the O
• When a positively charged region of one water molecule (that is, one
of its H atoms) comes close to a negatively charged region (that is,
the O) of a second water molecule, the electrical attraction between
them can establish a weak bond called a hydrogen bond

➢ These bonds:
• are much weaker than covalent bonds and are easily broken by
random thermal motions.
o Thus each bond lasts only an exceedingly short time.
• But the combined effect of many weak bonds is far from trivial.
➢ Each water molecule
• can form hydrogen bonds through its two H atoms to two other
water molecules,
• producing a network in which hydrogen bonds are being continually
broken and formed.

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➢ It is because of these interlocking hydrogen bonds that water at room
temperature
• is a liquid—with a high boiling point
• and high surface tension—
• and not a gas.
➢ Without hydrogen bonds, life as we know it could not exist.

➢ Hydrogen bonds are not limited to water.


➢ In general, a hydrogen bond can form:
• whenever a positively charged H atom held in one molecule by a
polar covalent linkage comes close to a negatively charged atom—
typically an oxygen or a nitrogen—belonging to another molecule

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➢ Hydrogen bonds can also occur between different parts of a single large
molecule,
• where they often help the molecule fold into a particular shape.
➢ The length and strength of hydrogen bonds and of ionic bonds are
compared to those of covalent bonds in Table 2–1 .

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Hydrophilic
➢ As mentioned previously, molecules carrying positive or negative charges
(ions) likewise dissolve readily in water. Such molecules are termed
hydrophilic, meaning that they are “water-loving.”
➢ Molecules, such as alcohols, that contain polar bonds and that can form
hydrogen bonds mix well with water.
➢ A large proportion of the molecules in the aqueous environment of a cell
fall also into this category, including sugars, DNA, RNA, and a majority of
proteins.

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Hydrophobic
➢ Hydrophobic (“water-fearing”) molecules, by contrast, are uncharged and
form few or no hydrogen bonds, and they do not dissolve in water.
➢ Hydrocarbons are important hydrophobic cell constituents.
• In these molecules, the H atoms are covalently linked to C atoms by
nonpolar bonds. Because the H atoms have almost no net positive
charge, they cannot form effective hydrogen bonds to other
molecules.
• This makes the hydrocarbon as a whole hydrophobic:
o a property that is exploited by cells, whose membranes are
constructed largely from lipid molecules that have long
hydrocarbon tails.
o Because lipids do not dissolve in water, they can form the thin
membrane barriers that keep the aqueous interior of the cell
separate from the surrounding aqueous environment

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Some Polar Molecules Form Acids and
Bases in Water
➢ One of the simplest kinds of chemical reaction, and one that has profound
significance in cells, takes place
• when a molecule possessing a highly polar covalent bond between a
hydrogen and another atom dissolves in water.

➢ The hydrogen atom in such a bond has given up its electron almost
entirely to the companion atom, so it exists as an almost naked positively
charged hydrogen nucleus—in other words, a proton (H+).

➢ When the polar molecule becomes surrounded by water molecules, the


proton will be attracted to the partial negative charge on the oxygen atom
of an adjacent water molecule;
• this proton can dissociate from its original partner and associate
instead with the oxygen atom of the water molecule, generating a
hydronium ion (H3O+).
➢ The reverse reaction also takes place very readily, so one has to imagine an
equilibrium state
• in which billions of protons are constantly flitting to and fro between
one molecule and another in an aqueous solution.

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Acids
➢ Substances that release protons when they dissolve in water, thus forming
H3O+, are termed acids.
➢ The higher the concentration of H3O+, the more acidic the solution.
➢ H3O+ is present even in pure water, at a concentration of 10–7 M, as a
result of the movement of protons from one water molecule to another.

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➢ By tradition, the H3O+ concentration is usually referred to as the H+
concentration, even though most protons in an aqueous solution are
present as H3O+.
➢ To avoid the use of unwieldy numbers, the concentration of H+ is
expressed using a logarithmic scale called the pH scale.
• Pure water has a pH of 7.0 and is thus neutral—that is, neither
acidic (pH < 7) nor basic (pH > 7).

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➢ Acids are characterized as being strong or weak, depending on how readily
they give up their protons to water.
• Strong acids
o such as hydrochloric acid (HCl)
o lose their protons easily.
• Weak acid
o Such as Acetic acid
o it holds on to its proton more tightly when dissolved in water.
o Many of the acids important in the cell—such as molecules
containing a carboxyl (COOH) group—are weak acids.

➢ The H+ concentration inside a cell (the pH) must be closely controlled.


• Because proton dissociation and association can alter the molecules’
character
• Acids—especially weak acid:
o will give up their protons more readily if the H+ concentration
is low
o and will tend to accept them back if the concentration is high.

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Bases (alkaline)
➢ The opposite of an acid is a base, which includes:
• any molecule that accepts a proton when dissolved in water.
• it raises the concentration of hydroxyl (OH–) ions by removing a
proton from a water molecule.
➢ Thus, sodium hydroxide (NaOH) is basic (the term alkaline is also used)
• it dissociates in aqueous solution to form Na+ ions and OH– ions
• because it does so readily, NaOH is called a strong base.
➢ Weak bases:
• which have a weak tendency to accept a proton from water
• are actually more important in cells.
➢ Many biologically important weak bases:
• contain an amino (NH2) group
o which can generate OH
o by taking a proton from water: –NH2 + H2O → –NH3+ + OH
• Because an OH– ion combines with a proton to form a water
molecule:
o an increase in the OH– concentration forces a decrease in the
H+ con- centration, and vice versa.

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Pure water (neutral)
➢ A pure solution of water thus contains an equal concentration (10–7 M) of
both ions, rendering it neutral (pH 7).
➢ The interior of a cell is also kept close to neutral by the presence of buffers:
• mixtures of weak acids and bases
• that can adjust proton concentrations around pH 7
• by releasing protons (acids) or taking them up (bases).
This give-and-take keeps the pH of the cell relatively constant under a variety of conditions.

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SMALL MOLECULES IN CELLS
➢ We now examine the main classes of small molecules found in cells and
their biological roles.

A Cell Is Formed from Carbon


Compounds
➢ If we disregard water, nearly all the molecules in a cell are based on car-
bon.
• Carbon:
o is outstanding among all the elements in its ability to form
large molecules
• Silicon:
o an element with the same number of electrons in its outer
shell
o is a poor second.

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➢ Because a carbon atom:
• is small
• has four electrons and four vacancies in its outer shell
• it can form four covalent bonds with other atoms

➢ Most importantly
• one carbon atom can join to other carbon atoms
o through highly stable covalent C–C bonds
▪ to form chains and rings
o and hence generate large and complex molecules with no
obvious upper limit to their size.

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➢ The small and large carbon compounds made by cells are called organic
molecules.
➢ By contrast, all other molecules, including water, are said to be inorganic.

Chemical groups
➢ Certain combinations of atoms, such as:
• the methyl (–CH3)
• hydroxyl (–OH)
• carboxyl (–COOH).
• carbonyl (–C=O)
• phosphoryl (–PO32– )
• amino (–NH2) groups
→occur repeatedly in organic molecules.

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➢ Each such chemical group:
• has distinct chemical and physical properties:
o that influence the behavior of the molecule in which the group
occurs, including
▪ whether the molecule tends to gain or lose protons
▪ and with which other molecules it will interact.
➢ Knowing these groups and their chemical properties greatly simplifies
understanding the chemistry of life.

Cells Contain Four Major Families of


Small Organic Molecules
➢ The small organic molecules of the cell
• are carbon compounds
• with molecular weights in the range 100–1000
• that contain up to 30 or so carbon atoms.

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➢ They are usually found free in solution in the cytosol and have many
different roles:
• Some are used as monomer subunits
o to construct the cell’s giant polymeric macromolecules, its:
▪ proteins
▪ nucleic acids
▪ large polysaccharides.
• Others serve as energy sources
o which are broken down and transformed into other small
molecules in a maze of intracellular metabolic pathways.
• Many have more than one role in the cell
o acting, for example, as both:
▪ a potential subunit for a macromolecule
▪ and as an energy source.

➢ The small organic molecules are much less abundant than the organic
macromolecules
• accounting for only about one-tenth of the total mass of organic
matter in a cell.

➢ As a rough guess, there may be a thousand different kinds of these small


organic molecules in a typical animal cell.
➢ All organic molecules are synthesized from—and are broken down into—
the same set of simple compounds.
➢ Broadly speaking, cells contain four major families of small organic
molecules:
• the sugars
• the fatty acids
• the amino acids
• the nucleotides.

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➢ Although many compounds present in cells do not fit into these categories,
these four families of small organic molecules, together with the
macromolecules made by linking them into long chains, account for a large
fraction of a cell’s mass.

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Sugars Are Both Energy Sources and
Subunits of Polysaccharides
➢ The simplest sugars—the monosaccharides:
• are compounds with the general formula (CH2O) n
o where n is usually 3, 4, 5, or 6.
➢ Sugars, and the larger molecules made from them, are also called
carbohydrates because of this simple formula.
• Glucose, for example, has the formula C6H12O6.

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Isomers
➢ The formula, however, does not fully define the molecule:
• the same set of carbons, hydrogens, and oxygens:
o can be joined together by covalent bonds in a variety of ways
o creating structures with different shapes.
• Thus, glucose can be converted into a different sugar—mannose or
galactose—
o simply by switching the orientations of specific –OH groups
relative to the rest of the molecule.

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➢ Each of these sugars, moreover, can exist in either of two forms
• called the d -form and the l -form
• which are mirror images of each other.

➢ Sets of molecules with the same chemical formula but different structures
are called isomers
• and mirror-image pairs of such molecules are called optical isomers.
• Isomers:
o are widespread among organic molecules in general
o they play a major part in generating the enormous variety of
sugars.

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Glycosidic bonds:
➢ Monosaccharides can be linked by covalent bonds—called glycosidic
bonds—to form larger carbohydrates.
➢ Two monosaccharides linked together make a disaccharide:
• such as sucrose
o 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:
o molecules made of a small number of monomers, typically 2
to 10 in the case of oligosaccharides.
• Polymers, in contrast, can contain hundreds or thousands of
subunits.

➢ The way sugars are linked together illustrates some common features of
biochemical bond formation.
• 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 subunits in other biological polymers, including nucleic acids and


proteins, are also linked by condensation reactions in which water is
expelled.

➢ 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

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➢ Because each monosaccharide has several free hydroxyl groups that can
form a link to another monosaccharide (or to some other compound)
• sugar polymers can be branched
• and the number of possible polysaccharide structures is extremely
large.

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➢ For this reason, it is much more difficult to determine the arrangement of
sugars in a complex polysaccharide than to determine the nucleotide
sequence of a DNA molecule or the amino acid sequence of a protein, in
which each unit is joined to the next in exactly the same way.

Sugar as an energy source


➢ The monosaccharide glucose has a central role as an energy source for
cells.
• It is broken down to smaller molecules in a series of reactions
o releasing energy that the cell can harness to do useful work
➢ Cells use simple polysaccharides composed only of glucose units—
principally glycogen in animals and starch in plants—as long-term stores
of glucose, held in reserve for energy production.

Sugars as Mechanical support


➢ Sugars do not function exclusively in the production and storage of energy.
➢ They are also used, for example, to make mechanical supports.
• The most abundant organic molecule on Earth—the cellulose:
o that forms plant cell walls—is a polysaccharide of glucose.
• Another extraordinarily abundant organic substance, the chitin of
insect exoskeletons and fungal cell walls, is also a polysaccharide—in
this case, a linear polymer of a sugar derivative called N -
acetylglucosamine.
➢ Other polysaccharides, which tend to be slippery when wet:
• are the main components of slime, mucus, and gristle.

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Glycoproteins & Glycolipids
➢ Smaller oligosaccharides can be covalently linked:
• to proteins to form glycoproteins
• or to lipids to form glycolipids
→which are both found in cell membranes.
➢ The sugar side chains attached to glycoproteins and glycolipids in the
plasma membrane are thought:
• to help protect the cell surface
• and often help cells adhere to one another.
➢ Differences in the types of cell-surface sugars form the molecular basis for
different human blood groups.

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Fatty Acid Chains Are Components of
Cell Membranes
➢ A fatty acid molecule, such as palmitic acid:
• has two chemically distinct regions:
o One is a long hydrocarbon chain:
▪ which is hydrophobic
▪ and not very reactive chemically.
o The other is a carboxyl (–COOH) group:
▪ which behaves as an acid (carboxylic acid): in an
aqueous solution
▪ it is ionized (–COO–)
▪ extremely hydrophilic
▪ and chemically reactive

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➢ 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—that possess both hydrophobic and
hydrophilic regions are termed amphipathic.

Saturated vs unsaturated Fatty acids


➢ The hydrocarbon tail of palmitic acid:
• is saturated:
o =it has no double bonds between its carbon atoms
o and contains the maximum possible number of hydrogens.
➢ Some other fatty acids, such as oleic acid:
• have unsaturated tails

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o = with one or more double bonds along their length.
• The double bonds:
o create kinks in the hydrocarbon tails
o interfering with their ability to pack together

it is the absence or presence of these double bonds that accounts for the
difference between hard (saturated) and soft (polyunsaturated) margarine.

➢ Fatty acid tails are also found in cell membranes:


• where the tightness of their packing: -
o affects the fluidity of the membrane.

Fatty acid Nomenclature:


➢ 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 carbon–carbon double bonds

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18:0 (Stearic Acid) 18:1(Δ9) (Oleic Acid

Fatty acid a source of energy:


➢ Fatty acids serve as a concentrated food reserve in cells:
• they can be broken down to produce about six times as much usable
energy, weight for weight, as glucose.
➢ When a cell needs energy, the fatty acid chains:
• can be released from triacylglycerols
• and broken down into two-carbon units.
➢ These two-carbon units are:
• identical to those derived from the breakdown of glucose
• and they enter the same energy-yielding reaction pathways

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Fatty acid storage:
➢ Fatty acids are stored in the cytoplasm of many cells in the form of:
• fat droplets composed of triacylglycerol molecules:
o compounds made of three fatty acid chains covalently joined
to a glycerol molecule

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➢ Triacylglycerols are the animal fats found in:
• meat
• butter
• cream
• the plant oils such as corn oil and olive oil.

Lipids
➢ Fatty acids and their derivatives, including triacylglycerols:
• are examples of lipids.
➢ Lipids:
• are loosely defined:
o as molecules that are insoluble in water but soluble in fat and
organic solvents such as benzene.
• They typically contain:
o long hydrocarbon chains, as in the fatty acids
o or multiple linked aromatic rings, as in the steroids.

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Formation of the lipid bilayer (cell membrane):
➢ The most unique function of fatty acids:
• is in the formation of the lipid bilayer, which is the basis for all cell
membranes.
o These thin sheets, which enclose all cells and surround their
internal organelles, are composed largely of phospholipids.

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➢ Like triacylglycerols:
• most phospholipids are constructed mainly from:
o fatty acids and glycerol.
➢ In these phospholipids, however, the glycerol
• is joined to two fatty acid chains, rather than to three as in
triacylglycerols.
• The remaining –OH group on the glycerol is linked to a hydrophilic
phosphate group, which in turn is attached to a small hydrophilic
compound such as choline.

➢ With their two hydrophobic fatty acid tails and a hydrophilic, phosphate-
containing head, phospholipids are strongly amphipathic.
• This characteristic amphipathic composition and shape gives them
different physical and chemical properties from triacylglycerols,
which are predominantly hydrophobic.

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➢ In addition to phospholipids, cell membranes contain:
• differing amounts of other lipids, including glycolipids
o which contain one or more sugars instead of a phosphate
group.

➢ Thanks to their amphipathic nature, phospholipids readily form


membranes in water.
• These lipids will spread over the surface of water to form a
monolayer, with their hydrophobic tails facing the air and their
hydrophilic heads in contact with the water.
• Two such molecular layers can readily combine tail-to-tail in water
to form the phospholipid sandwich that is the lipid bilayer.

Essential Cell Biology/Dr.Abdulahi-fuaad Ali Haji Page 46

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