2.CHEMICAL Foundation 2

7/31/2019 2.CHEMICAL Foundation 2

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CHEMICAL

FOUNDATIONS

Sri Widyarti060309

Polysaccharide chains on the surfaceof cellulose visualized by atomicforce microscopy


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OUTLINE

1. Atomic Bonds and MolecularInteractions

2. Chemical Building Blocks of Cells


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The life of a cell depends on thousands of

chemical interactions

Reactions exquisitely coordinated with one

another in time and space and under the

influence of the cells genetic instructions

and its environment.


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7080 percent by weight of most cells is water

7 percent of the weight of living matter is

composed of

inorganic ions and

small molecules such as

amino acids (the building blocks of proteins),

nucleotides (the building blocks of DNA and RNA),

lipids (the building blocks of biomembranes), and sugars (the building blocks of starches and cellulose)


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The Chemical Nature of

Biomolecules

Hydrophilic or water-liking (e.g., sugars)

Hydrophobic or water-fearing (e.g., fatslike triacylglycerols)

Amphipathic containing both hydrophilicand hydrophobic regions (e.g.,

phospholipids)


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Chemistry of life: key concepts


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Small molecules serve as building blocks for

larger structures.

For example, to generate the information-

carrying macromolecule DNA, the four smallnucleotide building blocks deoxyadenylate (A),

deoxythymidylate (T), deoxyguanylate (G), and

deoxycytidylate (C) are covalently linked

together into long strings (polymers), which thendimerize into the double helix


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Chemical reactions are reversible, and thedistribution of the chemicals between startingcompounds (left) and the products of thereactions (right) depends on the rate constants

of the forward (kf, upper arrow) and reverse (kr,lower arrow) reactions.

In the reaction shown, the forward reaction rateconstant is faster than the reverse reaction,indicated by the thickness of the arrows. Theratio of these Keq, provides an informativemeasure of the relative amounts of products andreactants that will be present at equilibrium.


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Strong and weak attractive forces betweenatoms are the glue that holds them together in

individual molecules and permits interactions

between different biological molecules. Strong forces form a covalent bond when two

atoms share one pair of electrons (single bond)

or multiple pairs of electrons (double bond,

triple bond, etc.).


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The weak attractive forces ofnoncovalentinteractions are equally important indetermining the properties and functions of

biomolecules such as proteins, nucleic acids,carbohydrates, and lipids.

There are four major types of noncovalent

interactions: ionic interactions, hydrogen

bonds, van der Waals interactions, and thehydrophobic effect.


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Covalent Bonds Are Much Stronger and MoreStable Than Noncovalent Interactions


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Bond energies are determined as the energyrequired to break a particular type of linkage.

Covalent bonds are one to two powers of 10

stronger than noncovalent interactions. The latter are somewhat greater than thethermal energy of the environment at normalroom temperature (25 C).

Many biological processes are coupled to theenergy released during hydrolysis of aphosphoanhydride bond in ATP.


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Covalent bonds are very stable because the energiesrequired to break them are much greater than thethermal energy available at room temperature (25 C) orbody temperature (37 C).

For example, the thermal energy at 25 C isapproximately 0.6 kilocalorie per mole (kcal/mol),whereas the energy required to break the carbon-carbonsingle bond (C-C) in ethane is about 140 times larger

Consequently at room temperature (25 C), fewer than 1

in 1012 ethane molecules is broken into a pair ofCH3radicals, each containing an unpaired, nonbondingelectron.


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It takes 84 kcal/mol to break a single C-O bond,

but 170 kcal/mol to break a C=O double bond.

The most common double bonds in biological

molecules are C=O, C=N, C=C, and P=O. The energy required to break noncovalent

interactions is only 15 kcal/mol, much less than

the bond energies of covalent bonds


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Indeed, noncovalent interactions are weak

enough that they are constantly being formed

and broken at room temperature.

Although these interactions are weak and havea transient existence at physiological

temperatures (2537 C), multiple noncovalent

interactions can act together to produce highly

stable and specific associations betweendifferent parts of a large molecule or between

different macromolecules.


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Each Atom Has a Defined Numberand Geometry of Covalent Bonds


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If a carbon atom forms four single bonds,

as in methane (CH4), the bonded atoms

(all H in this case) are oriented in space in

the form of a tetrahedron.

A carbon atom also can be bonded to

three, rather than four, other atoms, as in

formaldehyde (CH2O).


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Electrons Are Shared Unequallyin Polar Covalent Bonds

In many molecules, the bonded atoms exert differentattractions for the electrons of the covalent bond,resulting in unequal sharing of the electrons.

The extent of an atoms ability to attract an electron is

called its electronegativity. A bond between atoms with identical or similar

electronegativities is said to be nonpolar.

In a nonpolar bond, the bonding electrons are essentiallyshared equally between the two atoms, as is the case formost C-C and C-H bonds.

However, if two atoms differ in their electronegativities,the bond between them is said to be polar.


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Ionic Interactions Are AttractionsBetween Oppositely Charged Ions

Ionic interactions result from the attraction of apositively charged iona cationfor anegatively charged ionan anion.

In sodium chloride (NaCl), for example, the

bonding electron contributed by the sodiumatom is completely transferred to the chlorineatom.

Unlike covalent bonds, ionic interactions do not

have fixed or specific geometric orientations,because the electrostatic field around an ionitsattraction for an opposite chargeis uniform inall directions.


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Electrostatic interaction between waterand a magnesium ion (Mg2). Watermolecules are held in place by electrostatic

interactions between the two positive

charges on the ion and the partial negativecharge on the oxygen of each water

molecule. In aqueous solutions, all ions are

surrounded by a similar hydration shell.


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In aqueous solutions, simple ions ofbiological significance, such as Na, K, Ca2,Mg2, and Cl, do not exist as free, isolated

entities. Instead, each is hydrated, surrounded by a

stable shell of water molecules, which areheld in place by ionic interactions betweenthe central ion and the oppositely chargedend of the water dipole.


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Most ionic compounds dissolve readily in

water because the energy of hydration, the

energy released when ions tightly bind

water molecules, is greater than the latticeenergy that stabilizes the crystal structure.

Parts


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Hydrogen Bonds Determine WaterSolubility of Uncharged Molecules

The solubility of uncharged substances in

an aqueous environment depends largely

on their ability to form hydrogen bonds

with water.

For instance, the hydroxyl group (-OH) in

methanol (CH3OH) and the amino group

(-NH2) in methylamine (CH3NH2) can formseveral hydrogen bonds with water.


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Van der Waals Interactions AreCaused by Transient Dipoles

When any two atoms approach each otherclosely, they create a weak, nonspecificattractive force called a van der Waalsinteraction.

These nonspecific interactions result from themomentary random fluctuations in the

distribution of the electrons of any atom, whichgive rise to a transient unequal distribution ofelectrons.


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Two oxygen molecules in vander Waals contact


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The strength of van der Waals interactionsdecreases rapidly with increasing distance; thusthese noncovalent bonds can form only whenatoms are quite close to one another. However,

if atoms get too close together, they becomerepelled by the negative charges of theirelectrons.

When the van der Waals attraction between twoatoms exactly balances the repulsion betweentheir two electron clouds, the atoms are said tobe in van der Waals contact.


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The strength of the van der Waals interaction is

about 1 kcal/mol, weaker than typical hydrogen

bonds and only slightly higher than the average

thermal energy of molecules at 25 C. Thus multiple van der Waals interactions, a van

der Waals interaction in conjunction with other

noncovalent interactions, or both are required to

significantly influence intermolecular contacts.


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Chemical Building Blocks of

Cells


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Covalent and noncovalent linkage of monomers to form biopolymers andmembranes.


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Many molecules in cells contain at leastone asymmetric carbon atom, which isbonded to four dissimilar atoms.

Such molecules can exist as opticalisomers (mirror images), designated D andL, which have different biological activities.

In biological systems, nearly all sugars areD isomers, while nearly all amino acids areL isomers.


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Differences in the size, shape, charge,

hydrophobicity, and reactivity of the side

chains of amino acids determine the

chemical and structural properties ofproteins.


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Amino acids with hydrophobic side chains tend to clusterin the interior of proteins away from the surroundingaqueous environment; those with hydrophilic side chainsusually are toward the surface.

The bases in the nucleotides composing DNA and RNAare heterocyclic rings attached to a pentose sugar.

They form two groups: the purinesadenine (A) andguanine (G)and the pyrimidinescytosine (C),thymine (T), and uracil (U).

A, G, T, and C are in DNA, and A, G, U, and C are inRNA.


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Chemicalstructures of theprincipal bases innucleic acids


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Glucose and other hexoses can exist in

three forms: an open-chain linear

structure, a six-member (pyranose) ring,

and a five-member (furanose) ring.

In biological systems, the pyranose form of

D-glucose predominates.


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Chemicalstructures ofhexoses


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The building blocks of the polysaccharides are

the simple sugars, ormonosaccharides.

Monosaccharides are carbohydrates, which are

literally covalently bonded combinations ofcarbon and water in a one-to-one ratio (CH2O)n,

where nequals 3, 4, 5, 6, or 7.

Hexoses (n= 6) and pentoses (n= 5) are the

most common monosaccharides.


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Glycosidic bonds are usually formed

between a covalently modified sugar and

the growing polymer chain.

Such modifications include a phosphate

(e.g., glucose 6-phosphate) or a

nucleotide (e.g., UDP-galactose):


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Glycosidic bonds are formed between

either the or anomer of one sugar and a

hydroxyl group on another sugar, leading

to formation of disaccharides and otherpolysaccharides


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Formation of the disaccharides lactoseand sucrose

In any glycosidic linkage, the anomeric carbon of one sugar molecule (in

either the or conformation) is linked to a hydroxyl oxygen on another sugar

molecule. The linkages are named accordingly: thus lactose contains a (14)

bond, and sucrose contains an (1

2) bond.


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The long hydrocarbon chain of a fatty acid

may contain no carbon-carbon double

bond (saturated) or one or more double

bonds (unsaturated), which bends thechain.

Phospholipids are amphipathic molecules

with a hydrophobic tail (often two fatty acylchains) and a hydrophilic head


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Phosphatidylcholine, a typical phosphoglyceride.All phosphoglycerides are amphipathic, having a hydrophobic tail (yellow)

and a hydrophilic head (blue) in which glycerol is linked via a phosphategroup to an alcohol.

Either of or both the fatty acyl side chains in a phosphoglyceride may be

saturated or unsaturated. In phosphatidic acid (red), the simplest

phospholipid, the phosphate is not linked to an alcohol.


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In aqueous solution, the hydrophobic effect andvan der Waals interactions organize andstabilize phospholipids into one of threestructures: a micelle, liposome, or sheetlike

bilayer. In a phospholipid bilayer, which constitutes the

basic structure of all biomembranes, fatty acylchains in each leaflet are oriented toward one

another, forming a hydrophobic core, and thepolar head groups line both surfaces and directlyinteract with the aqueous solution.


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Cross-sectional views of the three structures formed by phospholipids inaqueous solutions

M l l


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The complementary shapes, charges, polarity, and hydrophobicity of two protein

surfaces permit multiple weak interactions, which in combination produce a

strong interaction and tight binding. Because deviations from molecular

complementarity substantially weaken binding, any given biomolecule usually

can bind tightly to only one or a very limited number of other molecules. The

complementarity of the two protein molecules on the left permits them to bind

much more tightly than the two noncomplementary proteins on the right.

Molecularcomplementarityand the bindingof proteins via

multiplenoncovalentinteractions.

The DNA double helix


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Hydrogen bonds between the bases are in the center of the structure. The major

and minor groove are lined by potential hydrogen bond donors and acceptors

(highlighted in yellow). This extended schematic shows the two sugar-phosphate

The DNA double helix

2.CHEMICAL Foundation 2

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