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Chapter 2
The Chemistry
of the Cell
Lectures by
Kathleen Fitzpatrick
Simon Fraser University
© 2012 Pearson Education, Inc.
The Chemistry of the Cell
• Five principles important to cell biology
– Characteristics of carbon
– Characteristics of water
– Selectively permeable membranes
– Synthesis by polymerization of small molecules
– Self assembly
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The Importance of Carbon
• Study of all classes of carbon-containing
compounds is organic chemistry
• Biological chemistry (biochemistry) is the study of
the chemistry of living systems
• The carbon atom (C) is the most important atom in
biological molecules
• Specific bonding properties of carbon account for
the characteristics of carbon-containing compounds
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Bonding properties of the carbon atom
• The carbon atom has a valence of 4 (outermost
electron shell lacks 4 of 8 electrons needed to fill it),
so can form 4 chemical bonds with other atoms
• Carbon atoms are most likely to form covalent
bonds with one another and with oxygen (O),
hydrogen (H), nitrogen (N), and sulfur (S)
• Covalent bonds - the sharing of a pair of electrons
between two atoms
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Figure 2-1A
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Covalent bonding of carbon atoms
• Sharing one pair of electrons between two atoms
forms a single bond
• Double and triple bonds involve two atoms sharing
two and three pairs of electrons, respectively
• Whether carbon atoms form single, double or triple
bonds with other atoms, the total number of
covalent bonds per carbon is four
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Figure 2-1B-D
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Carbon-Containing Molecules Are
Stable
• Stability is expressed as bond energy - the amount
of energy required to break 1 mole (~6x 1023) of
bonds
• Bond energy is expressed as calories per mole
(cal/mol)
• A calorie is the amount of energy needed to raise
the temperature of 1g of water by 1oC
• A kcal (kilocalorie) is equal to 1000 calories
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Bond energies of covalent bonds
• A lot of energy is needed to break covalent bonds
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C-C, 83 kcal/mol
C-N, 70 kcal/mol
C-O, 84 kcal/mol
C-H, 99 kcal/mol
• Double and triple bonds are even harder to break
– C=C, 146 kcal/mol
– C≡C, 212 kcal/mol
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Figure 2-2
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Strong covalent bonds necessary for life
• Solar radiation has an inverse relationship between
wavelength and energy content
• The visible portion of sunlight is lower in energy
than C-C bonds
• So, visible light cannot break the bonds of organic
molecules
• Higher energy, ultraviolet light, is more hazardous
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Figure 2-3
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Carbon-Containing Molecules Are
Diverse
• A large variety of compounds can be formed by
relatively few kinds of atoms
• Rings or chains of carbon atoms can form
• Chains may branch and may have single or double
bonds between the carbons
• Variety of structures possible is due to the
tetravalent nature of the carbon atom
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Hydrocarbons
• Hydrocarbons are chains or rings composed only of
carbon and hydrogen
• They are economically important, because
petroleum products, including gasoline and natural
gas, are hydrocarbons
• In biology, they are of limited importance because
they are not soluble in water
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Figure 2-4
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Biological compounds
• These normally contain carbon, hydrogen, and one
or more atoms of oxygen, as well as nitrogen,
phosphorus, or sulfur
• These (O, N, P, S) are usually part of functional
groups, common arrangements of atoms that
confer specific chemical properties on a molecule
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Functional groups
• Important functional groups include
– Carboxyl and phosphate groups (negatively
charged)
– Amino groups (positively charged)
– Hydroxyl, sulfhydroxyl, carbonyl, aldehyde
(uncharged; but polar)
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Figure 2-5A,B
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Bond polarity
• In polar bonds electrons are not shared equally
between two atoms
• Polar bonds result from a high electronegativity
(affinity for electrons) of oxygen and sulfur
compared to carbon and hydrogen
• Polar bonds have high water solubility compared to
C-C or C-H bonds, in which electrons are shared
equally
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Figure 2-5C
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Activity: Functional Groups
Right click on animation / Click play
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Carbon-Containing Molecules Can
Form Stereoisomers
• The carbon atom is a tetrahedral structure
• When four atoms are bonded to the four corners of
the tetrahedron, two spatial configurations are
possible
• These non-superimposable configurations are
mirror images, called stereoisomers
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Figure 2-6
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Activity: Isomers – Part 1
Right click on animation / Click play
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Activity: Isomers – Part 2
Right click on animation / Click play
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Activity: Isomers – Part 3
Right click on animation / Click play
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Asymmetric carbon atoms
• An asymmetric carbon atom has four different
substituents
• Two stereoisomers are possible for each
asymmetric carbon atom
• A compound with n asymmetric carbons will have
2n possible stereoisomers
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Figure 2-7A
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Figure 2-7B
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The Importance of Water
• Water has an indispensable role as the universal
solvent in biological systems
• It is the single most abundant component of cells
and organisms
• About 75-85% of a cell by weight is water
• Its chemical characteristics make water
indispensable for life
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Water Molecules Are Polar
• Unequal distribution of electrons gives water its
polarity
• The water molecule is bent rather than linear
• The oxygen atom at one end of the molecule is
highly electronegative, drawing the electrons
toward it
• This results in a partial negative charge at this end
of the molecule, and a partial positive charge
around the hydrogen atoms
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Figure 2-8A
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Water Molecules Are Cohesive
• Because of their polarity, water molecules are
attracted to each other and orient so the
electronegative oxygen of one molecule is
associated with the electropositive hydrogens of
nearby molecules
• Such associations, called hydrogen bonds, are
about 1/10 as strong as covalent bonds
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Hydrogen bonds and cohesiveness
• Water is characterized by an extensive network of
hydrogen-bonded molecules, which make it
cohesive
• The combined effect of many hydrogen bonds
accounts for water’s high
–
–
–
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Surface tension
Boiling point
Specific heat
Heat of vaporization
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Surface tension of water
• Is the result of the collective strength of vast
numbers of hydrogen bonds
• Allows insects to walk along the surface of water
without breaking the surface
• Allows water to move upward through conducting
tissues of some plants
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Figure 2-9
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Water Has a High TemperatureStabilizing Capacity
• High specific heat gives water its temperaturestabilizing capacity
• Specific heat - the amount of heat a substance
must absorb to raise its temperature 1oC
• The specific heat of water is 1.0 calorie per gram,
much higher than most liquids
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Temperature-stabilizing capacity
• Heat that would raise the temperature of other
liquids is first used to break numerous hydrogen
bonds in water
• Water therefore changes temperature relatively
slowly, protecting living systems from extreme
temperature changes
• Without this characteristic of water, energy released
in cell metabolism would cause overheating and
death
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Heat of vaporization
• Heat of vaporization is the amount of energy
required to convert one gram of liquid into vapor
• This value is high for water because of the many
hydrogen bonds that must be broken
• The high heat of vaporization of water makes it an
excellent coolant
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Water Is an Excellent Solvent
• A solvent is a fluid in which another substance, the
solute, can dissolve
• Water is able to dissolve a large variety of
substances, due to its polarity
• Most of the molecules in cells are also polar and
so can form hydrogen bonds, or ionic bonds with
water
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Solutes
• Solutes that have an affinity for water and dissolve
in it easily are called hydrophilic (generally polar
molecules or ions)
• Many small molecules - sugars, organic acids,
some amino acids - are hydrophilic
• Molecules not easily soluble in water - such as
lipids and proteins in membranes are called
hydrophobic (generally nonpolar molecules)
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NaCl in water
• A salt, such as NaCl, exists as a lattice of Na+ cations
(positively charged) and Cl- anions (negatively
charged)
• To dissolve in a liquid, the attraction of anions and
cations in the salt must be overcome
• In water, anions and cations take part in electrostatic
interactions with the water molecules, causing the
ions to separate
• The polar water molecules form spheres of hydration
around the ions, decreasing their chances of
reassociation
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Figure 2-10
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Figure 2-10A
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Figure 2-10B
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Solubility of molecules with no net charge
• Some molecules have no net charge at neutral pH
• Some of these are still hydrophilic because they
have some regions that are positively charged
and some that are negatively charged
• Water molecules will cluster around such regions
and prevent the solute molecules from interacting
with each other
• Hydrophobic molecules, such as hydrocarbons
tend to disrupt the hydrogen bonding of water and
are therefore repelled by water molecules
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The Importance of Selectively
Permeable Membranes
• Cells need a physical barrier between their
contents and the outside environment
• Such a barrier should be
– impermeable to much of the cell contents
– not completely impermeable, allowing some materials
into and out of the cell
– insoluble in water to maintain the integrity of the barrier
– permeable to water to allow flow of water in and out of
the cell
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Membranes surround cells
• The cellular membrane is a hydrophobic
permeability barrier
• Consists of phospholipids, glycolipids, and
membrane proteins
• Membranes of most organisms also contain
sterols - cholesterol (animals), ergosterols (fungi),
or phytosterols (plants)
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Membrane lipids are amphipathic
• Membrane lipids are amphipathic; they have both
hydrophobic and hydrophilic regions
• Amphipathic phospholipids have a polar head,
due to a negatively charged phosphate group
linked to a positively charged group
• They also have two nonpolar hydrocarbon tails
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Figure 2-11
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Figure 2-11A
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Figure 2-11B
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Video: Dynamics of a Lipid Bilayer
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A Membrane Is a Lipid Bilayer with
Proteins Embedded in It
• In water, amphipathic molecules undergo
hydrophobic interactions
• The polar heads of membrane phospholipids face
outward toward the aqueous environment
• The hydrophobic tails are oriented inward
• The resulting structure is the lipid bilayer
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Figure 2-12
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Figure 2-13A
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Figure 2-13B
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Membrane proteins
• Membrane proteins may play a variety of roles
– Transport proteins, for moving specific substances
across an otherwise impermeable membrane
– Enzymes, that catalyze reactions associated with the
membrane
– Receptors on the cell’s surface, and other proteins in
mitochondrial or chloroplast membranes
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Membranes Are Selectively Permeable
• Because of the hydrophobic interior, membranes
are readily permeable to nonpolar molecules
• However, they are quite impermeable to most polar
molecules and very impermeable to ions
• Cellular constituents are mostly polar or charged
and are prevented from entering or leaving the cell
• However, very small molecules diffuse
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Ions must be transported
• Even the smallest ions are unable to diffuse across
a membrane
• This is due to both the charge on the ion and the
surrounding hydration shell
• Ions must be transported across a membrane by
specialized transport proteins
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Transporter proteins
• Transport proteins act as either hydrophilic
channels or carriers
• Transport proteins of either type are specific for a
particular ion or molecule or class of closely related
molecules or ions
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The Importance of Synthesis by
Polymerization
• Most cellular structures are made of ordered arrays
of linear polymers called macromolecules
• Important macromolecules in the cell include
proteins, nucleic acids, polysaccharides
• Lipids share some features of macromolecules, but
are synthesized somewhat differently
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Macromolecules Are Responsible for
Most of the Form and Function in Living
Systems
• Cellular hierarchy: biological molecules and
structures are organized into a series of levels,
each building on the preceding one
• Most cellular structures are composed of small
water-soluble organic molecules, obtained from
other cells or synthesized from nonbiological
molecules (CO2, NH4, PO4, etc.)
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Hierarchical assembly
• The small organic molecules then polymerize to
form biological macromolecules
• Biological macromolecules may function on their
own, or assemble into a variety of supramolecular
structures
• The supramolecular structures are components of
organelles and other subcellular structures that
make up the cell
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Figure 2-14
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Fundamental principle of biological
chemistry
• The macromolecules that are responsible for most
of the form and order of living systems are
generated by the polymerization of small organic
molecules
• The repeating units are called monomers;
examples include the glucose present in sugar or
starch, amino acids in proteins, and nucleotides in
nucleic acids
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Figure 2-15
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Cells Contain Three Different Kinds of
Macromolecules
• The major macromolecular polymers in the cell are
proteins, nucleic acids, and polysaccharides
• Nucleic acids and proteins have a variety of
monomers that may be arranged in nearly limitless
ways; the order and type of monomer are critical for
function
• Polysaccharides, composed of one or two
monomers, have relatively few types
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Table 2-1
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Informational macromolecules
• Nucleic acids are called informational
macromolecules because the order of the four
kinds of nucleotide monomers in each is nonrandom and carries important information
• DNA and RNA serve a coding function, containing
the information needed to specify the precise
amino acid sequences of proteins
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Proteins
• Proteins are composed of a nonrandom series of
amino acids
• Amino acid sequence determines the threedimensional structure, thus the function, of a
protein
• With 20 different amino acids, a nearly infinite
variety of protein sequences is possible
• Proteins have a wide range of functions including
structure, defense, transport, catalysis, and
signaling
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Polysaccharides
• Polysaccharides typically consist of single
repeating subunits or two altering subunits
• The order of monomers carries no information and
is not essential for function
• Most polysaccharides are structural
macromolecules (e.g., cellulose or chitin) or storage
macromolecules (e.g., starch or glycogen)
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Figure 2-16A
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Figure 2-16B
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Macromolecules Are Synthesized by
Stepwise Polymerization of Monomers
• Despite some differences, the production of most
polymers follows basic principles
– 1. Macromolecules are always synthesized by the
stepwise polymerization of monomers
– 2. The addition of each monomer occurs by the removal
of a water molecule (condensation reaction)
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Basic principles (continued)
– 3. The monomers must be present as activated
monomers before condensation can occur
– 4. To become activated, a monomer must be coupled to
a carrier molecule
– 5. The energy to couple a monomer to a carrier molecule
is provided by adenosine triphosphate (ATP) or a related
high-energy compound
– 6. Macromolecules have directionality; the chemistry
differs at each end of the polymer
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Figure 2-17
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Figure 2-17A
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Figure 2-17B
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Figure 2-17C
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Carrier molecules
• A different kind of carrier molecule is used for each
kind of polymer
– For protein synthesis, amino acids are linked to carriers
called transfer RNA (tRNA)
– Sugars (often glucose) that form polysaccharides are
activated by linking them to ADP (adenosine
diphosphate), or UDP (uridine diphosphate)
– For nucleic acids the nucleotides themselves are highenergy molecules (ATP, GTP)
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Condensation and hydrolysis
• Activated monomers react with one another in a
condensation reaction, then release the carrier
molecule
• The continued elongation of the polymer is a
sequential, stepwise process
• Degradation of polymers occurs via hydrolysis,
breaking the bond between monomers through
addition of one H+ and one OH- (a water molecule)
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The Importance of Self-Assembly
• After macromolecules are synthesized, further
steps are needed for assembly into higher-order
structures
• The principle of self-assembly states that
information needed to specify the folding of
macromolecules and their interactions to form
complex structures is inherent in the polymers
themselves
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Many proteins self-assemble
• The immediate product of amino acid
polymerization is a polypeptide
• Once the polypeptide has assumed its correct three
dimensional structure, or conformation, it is called a
protein
• The native (natural) conformation of a protein can
be altered by changing conditions such as the pH
or temperature or treating with certain chemical
agents
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Denaturation and renaturation
• The unfolding of polypeptides, denaturation, leads
to loss of biological activity (function)
• When denatured proteins are returned to conditions
in which the native conformation is stable, they may
undergo renaturation, a refolding into the correct
conformation
• In some cases, renaturation is associated with the
return of the protein function (e.g., ribonuclease)
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Figure 2-18A
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Figure 2-18B
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Molecular Chaperones Assist the
Assembly of Some Proteins
• Some proteins require molecular chaperones,
which assist the assembly process by inhibiting
interactions that would produce incorrect structures
• Under lab conditions, such proteins do not regain
their native conformation after the conditions of
denaturation are reversed
• Molecular chaperones are not components of the
completed structures and they convey no
information
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Types of self-assembly and chaperones
• Strict self-assembly - no factors other than the
polypeptide sequence itself are needed
• Assisted self-assembly - requires a specific
molecular chaperone to ensure that the correct
conformation predominates over incorrect forms
• Chaperone proteins are abundant, and even
moreso under stresses such as high temperature
• Many chaperones fall into one of two categories of
heat shock proteins
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Noncovalent Bonds and Interactions
Are Important in the Folding of
Macromolecules
• Covalent bonds link the monomers of a polypeptide
together and can stabilize the three-dimensional
structure of many proteins
• However, four other types of interactions are
important for the folding of proteins
– Hydrogen bonds (previously discussed)
– Ionic bonds
– Van der Waals interactions
– Hydrophobic interactions
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Ionic bonds
• Ionic bonds are noncovalent electrostatic
interactions between two oppositely charged ions
• They form between negatively charged and
positively charged functional groups
• Ionic bonds between functional groups on the same
protein play an important role in the structure of the
protein
• Ionic bonds may also influence the binding between
macromolecules
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Van der Waals interactions
• Van der Waals interactions (or forces) are weak
attractions between two atoms that only occur if the
atoms are very close to one another and oriented
appropriately
• Atoms that are too close together will repel one
another
• The van der Waals radius of an atom defines how
close other atoms can come to it, and is the basis
for space-filling models of molecules
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Figure 2-19
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Hydrophobic interactions
• Hydrophobic interactions describes the tendency of
nonpolar groups within a macromolecule to
associate with each other and minimize their
contact with water
• These interactions commonly cause nonpolar
groups to be found in the interior of a protein or
embedded in the nonpolar interior of a membrane
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Self-Assembly Also Occurs in Other
Cellular Structures
• The same principles of self-assembly that apply to
polypeptides also apply to the assembly of more
complex structures
• Many such structures are composed of complexes
of two or more kinds of polymers
• Ribosomes, membranes, primary cell wall (plants)
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The Tobacco Mosaic Virus Is a Case
Study in Self-Assembly
• A virus is a complex of nucleic acids and proteins
that uses living cells to produce more copies of
itself via self-assembly
• A good example is the tobacco mosaic virus (TMV)
• It is a rodlike particle, with a single RNA strand and
about 2130 copies of a coat protein that form a
cylindrical covering for the RNA
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Figure 2-20
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Self-assembly of TMV is quite complex
• The unit of assembly is a two-layered disc of coat
protein that changes conformation (from cylinder to
helix) as it interacts with the central RNA molecule
• This conformational change allows another disc to
bind and to interact with the RNA, and thus change
its conformation as well
• The process repeats until the end of the RNA
molecule is reached
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Figure 2-21A,B
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Figure 2-21C,D
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Video: Tobacco mosaic virus (TMV)
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Self-Assembly Has Limits
• Some assembly systems depend additionally on
information provided by a preexisting structure
• Examples
– Membranes
– Cell walls
– Chromosomes
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Hierarchical Assembly Provides
Advantages for the Cell
• Hierarchical assembly is the dependence on
subassemblies that act as intermediates of the
process of assembly of increasingly complex
structures
• Biological structures are almost always assembled
hierarchically
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Advantages of hierarchical assembly
• Chemical simplicity - relatively few subunits are
used for a wide variety of structures
• Efficiency of assembly - a small number of kinds of
condensation reactions are needed
• Quality control - defective components can be
discarded prior to incorporation into higher-level
structure, reducing the waste of energy and
materials
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