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HELMIN ELYANI


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Water is the predominant chemical component of livingorganisms.

Its unique physical properties, which include the ability to solvateawide range of organic and inorganic molecules,

derive from waters dipolar structure and exceptional capacity forforming hydrogen bonds.

The manner in which water interacts with a solvated biomoleculeinfluences the structure of each.

An excellent nucleophile, water is a reactant or product in manymetabolic reactions.

Water has a slight propensity to dissociate into hydroxide ions andprotons.

The acidity of aqueous solutions is generally reported usingthe logarithmic pH scale. Bicarbonate and other buffers normallymaintain the pH of extracellular fluid between 7.35 and 7.45.Suspected disturbances of acidbase balance are verified bymeasuring the pH of arterial blood and the CO2 content of venousblood.


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WATER IS AN EXCELLEN NUCLEOPHILEMetabolic reactions often involve the attack by lone pairs of electrons

on electron-rich molecules termed nucleophiles on electron-pooratoms called electrophiles.

Nucleophilic attack by water generally results in the cleavage of theamide, glycoside, or ester bonds that hold biopolymers together. Thisprocess is termed hydrolysis. Conversely, when monomer units are

joined together to form biopolymers such as proteins orglycogen,water is a product,


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Electrostatic InteractionsElectrostatic interactions between oppositely

charged groups within or between

biomolecules are termed salt bridges.Salt bridges are comparable in strengthto hydrogen bonds but act over largerdistances. They thus often facilitate thebinding of charged molecules and ions toproteins and nucleic acids.


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Van der Waals ForcesVan der Waals forces arise from attractions

between transient dipoles generated bythe rapid movement of electrons on allneutral atoms.

Significantly weaker than hydrogen bonds

but potentially extremely numerous, actover very short distances, typically 24 .


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The DNA double helix illustrates the contribution of multiple

forces to the structure of biomolecules.DNA strand is held together by covalent bondsthe two strands of the helix are held together exclusively by

noncovalent interactions.These noncovalent interactions include hydrogen bondsbetween nucleotide bases (Watson-Crick base pairing)

van der Waals interactions between the stacked purine andpyrimidine bases.

The helix presents the charged phosphate groups and polar

ribose sugars of the backbone to water while burying therelatively hydrophobic nucleotide bases inside. The extendedbackbone maximizes the distance between negativelycharged backbone phosphates, minimizing unfavorableelectrostatic interactions.


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The covalent bond is the strongest force that holdsmolecules together (Table 21).Noncovalent forces,while of lesser magnitude, make

significant contributions to the structure, stability,and functional competence of macromolecules inliving cells.

These forces,which can be either attractive orrepulsive, involve interactions both within the

biomolecule and between it and the water thatforms the principal component of the surroundingenvironment.


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Covalent bonds, which bind the atoms composing a molecule in a fixedorientation, consist of pairs of electrons shared by two atoms. Relatively highenergies are required o break them (50200 kcal/mol).

In polar bonds, which link atoms that differ in electronegativity, the bondingelectrons are distributed unequally. One end of a polar bond has a partial

positive charge and the other end has a partial negative charge (see Figure2-3).

Noncovalent interactions between atoms are considerably weaker thancovalent bonds, with bond energies ranging from about 15 kcal/mol (seeFigure 2-4).

Four main types of noncovalent interactions occur in biological systems: ionic

bonds, hydrogen bonds, van der Waals interactions, and interactions due tothe hydrophobic effect.


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Ionic bonds result from the electrostatic attraction between thepositive and negative charges of ions. In aqueous solutions,all cations and anions are surrounded by a shell of boundwater molecules (see Figure 2-5). Increasing the salt (e.g.,NaCl) concentration of a solution can weaken the relative

strength of and even break the ionic bonds betweenbiomolecules.In a hydrogen bond, a hydrogen atom covalently bonded to an

electronegative atom associates with an acceptor atom whosenonbonding electrons attract the hydrogen (see Figure 2-6).

Weak and relatively nonspecific van der Waals interactions are

created whenever any two atoms approach each other closely.They result from the attraction between transient dipolesassociated with all molecules (see Figure 2-8).


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In an aqueous environment, nonpolar molecules or nonpolarportions of larger molecules are driven together by thehydrophobic effect, thereby reducing the extent of their directcontact with water molecules (see Figure 2-9).

Molecular complementarity is the lock-and-key fit between

molecules whose shapes, charges, and other physicalproperties are complementary. Multiple noncovalentinteractions can form between complementarymolecules,causing them to bind tightly (see Figure 2-10), butnot between molecules that are not complementary.

The high degree of binding specificity that results from molecular

complementarity is one of the features that distinguishbiochemistry from typical solution chemistry


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Three major biopolymers are present in cells:proteins, composed of amino acids linked by peptide bonds;Nucleic acids, composed of nucleotides linked by phosphodiester bonds;polysaccharides, composed of monosaccharides (sugars) linked byglycosidic bonds (see Figure 2-11).

Many molecules in cells contain at least one asymmetric carbon atom, which isbonded to four dissimilar atoms. Such molecules can exist as opticalisomers (mirror images), designated D and L, which have different biologicalactivities. In biological systems, nearly all sugars are D isomers, while nearlyall amino acids are L isomers.

Differences in the size, shape, charge, hydrophobicity, and reactivity of the sidechains of amino acids determine the chemical and structural properties ofproteins (see Figure 2-13).

Amino acids with hydrophobic side chains tend to cluster in the interior ofproteins away from the surrounding aqueous environment; those withhydrophilic side chains usually are toward the surface.


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Amino acids with hydrophobic side chains tend to cluster in theinterior of proteins away from the surrounding aqueousenvironment; those with hydrophilic side chains usually aretoward the surface.

The bases in the nucleotides composing DNA and RNA are

heterocyclic rings attached to a pentose sugar. They form twogroups: the purinesadenine (A) and guanine (G)and thepyrimidinescytosine (C), thymine (T), and uracil (U) (seeFigure 2-15). A, G, T, and C are in DNA, and A, G, U, and Care in RNA.

Glucose and other hexoses can exist in three forms: an

open-chain linear structure, a six-member (pyranose) ring, anda five-member (furanose) ring (see Figure 2-16). In biologicalsystems, the pyranose form of D-glucose predominates.


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Glycosidic bonds are formed between either the or anomer of one sugar and ahydroxyl group on another sugar, leading to formation of disaccharides andother polysaccharides (see Figure 2-17).

The long hydrocarbon chain of a fatty acid may contain no carbon-carbondouble bond (saturated) or one or more double bonds (unsaturated), whichbends the chain.

Phospholipids are amphipathic molecules with a hydrophobic tail (often twofatty acyl chains) and a hydrophilic head (see Figure 2-19).

In aqueous solution, the hydrophobic effect and van der Waals interactionsorganize and stabilize phospholipids into one of three structures: micelle,liposome, or sheetlike bilayer (see Figure 2-20).

In a phospholipid bilayer, which constitutes the basic structure of allbiomembranes, fatty acyl chains in each leaflet are oriented toward oneanother, forming a hydrophobic core, and the polar head groups line bothsurfaces and directly interact with the aqueous solution.


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