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BIO 203 Biochemistry I
bySeyhun YURDUGL,Ph.D.
Lecture 2Atoms, Molecules and Water
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Content Outline The atom concept
Ionic andC
ovalent Bonds Hydrogen bonds
Water
Hydration shells
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What is an Atom? Matter is composed of atoms:
a consequence of the manner in which the
electrons are distributed throughout space in theattractive field exerted by the nuclei.
nuclei act as point attractors immersed in a cloudof negative charge, the electron density (r).
electron density: the electronic charge isdistributed throughout real space.
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e.g. electron density in the plane containing the two C and four H nuclei of the ethenemolecule, portrayed as a projection in the third dimension and in the form of a contour map.
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Thus a pair of bonded atoms:
linked by a line along which the electrondensity, the glue of chemistry, is maximallyconcentrated.
leads to different conformations
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and more.
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Ionic and Covalent Bonds
Related with distribution of negative charge in amolecule:
exhibit varying degrees of asymmetry dependingon the ability of the nuclei to attract and bind theelectronic charge density.
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Ionic and Covalent Bonds
symmetry or asymmetry of the chargedistribution:
role in determining the chemical propertiesof the molecule and this property: used for the classification of chemical
bonds.
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Ionic and Covalent Bonding
We can envisage two extremes for the distributionof the valance charge density.
when a bond is formed between two identicalatoms.
The charge density of the valance electrons will bedelocalized equally over corresponding regions ofeach nucleus
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Ionic and Covalent Bonding
Since both nuclei will attract the electrondensity with equal force.
such an equal sharing of the chargedensity: e.g. ofcovalent binding
and shown by the molecular charge
distribution of N2.
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Ionic bonding The charge distribution of LiF:
provides an example of the other extreme: ionicbonding,
obtained when a bond:
formed between two atoms with very differentaffinities for the electronic charge density.
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Ionic bonds the bond in LiF corresponds : complete
transfer of the valance charge density of
lithium to fluorine, resulting in a molecule best described as: Li+F-. a considerable charge transfer: has occurred
in the formation of the LiF molecule
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Hydrogen bonding Polar molecules,
e.g. water,
have a weak, partial negative charge at oneregion of the molecule (the oxygen atom inwater)
and a partial positive charge elsewhere (thehydrogen atoms in water).
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Hydrogen bonding When water molecules are close together:
their positive and negative regions:
attracted to the oppositely-charged regionsof nearby molecules.
The force of attraction here: a hydrogen
bond. Each water molecule is hydrogen bonded to
four others.
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Hydrogen bonding The hydrogen bonds that form between
water molecules:
account for some of the essential andunique properties of water.
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Hydrogen bonding attraction formed by hydrogen bonds:
keeps water liquid over a wider range of
temperature, than is found for any other molecule its size.
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Hydrogen bonds that is, a large amount of energy is needed
to convert liquid water,
where the molecules are attracted throughtheir hydrogen bonds, to water vapor,
where they are not.
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Hydrogen bonds
Two outcomes of this:
The evaporation of sweat, used by many mammalsto cool themselves,
achieves this by the large amount of heat neededto break the hydrogen bonds between watermolecules.
Moderating temperature shifts in the ecosystem(which is why the climate is more moderate nearlarge bodies of water like the ocean)
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Hydrogen bonds The hydrogen bond has only 5% or so of the
strength of a covalent bond.
However, when many hydrogen bonds canform between two molecules (or parts of thesame molecule):
the resulting union can be sufficientlystrong as to be quite stable.
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Multiple hydrogen bonds
hold the two strands of the DNA double helixtogether
hold polypeptides together in such secondarystructures as the alpha helix and thebetaconformation;
help enzymesbind to their substrate;
help antibodies bind to their antigen help transcription factorsbind to each other; help transcription factors bind to DNA
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Hydrogen
Bonding
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Water a chemical compound
andpolar molecule, which is liquid atstandard temperature and pressure.
has the chemical formula H2O:
meaning that one molecule of water iscomposed of two hydrogen atoms and oneoxygen atom.
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Water found almost everywhere on earth and is
required by all known life.
70% of the Earth's surface: water. known to exist, in ice form, on several other
bodies in the solar system and beyond,
proof : exists (or did exist) in liquid formanywhere besides Earth, strong evidence ofextraterrestrial life.
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Bonding Arrangement of Water
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General properties
solid state; known as ice;
gaseous state : known as water vapor(orsteam).
The units of temperature (formerly the degreeCelsius and now the Kelvin) are defined in termsof the triple point of water, 273.16 K (0.01 C)and 611.2 Pa, the temperature and pressure atwhich solid, liquid, and gaseous watercoexist inequilibrium.
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Water also exhibits some very strange behaviors,
including the formation of states such as
vitreous ice, a noncrystalline (glassy), solidstate of water.
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Water At temperatures greater than 647 Kand
pressures greater than 22.064 MPa,
collection of water molecules assumes asupercriticalcondition:
in which liquid-like clusters float within avapor-like phase.
liquid water path is a measure of the amountof liquid water in an air column.
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Water An important feature: itspolarnature. molecule forms an angle, with hydrogen atoms at the tips
and oxygen at the vertex.
since oxygen has a higherelectronegativity than hydrogen,the side of the molecule with the oxygen atom has a partialnegative charge:
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Water molecule with such a charge difference is
called a dipole.
charge differences cause water molecules tobe attracted to each other
and to other polar molecules(hydrogen
bonding)
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Water This relatively weak (relative to the covalent
bonds within the water molecule itself) attraction
results in physical properties such as a relativelyhighboiling point,
because more heat is necessary to break thehydrogen bonds between molecules.
The extra bonding between water molecules alsogives liquid water a large specific heat capacity.
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Water In other words, water expands as it freezes (most
other materials shrink on solidification). Liquid water reaches its highest density at a
temperature of 4 C: an interesting consequence for water life in winter. but when the temperature of the lake water reaches
4C, water on the surface, as it chills further,
becomes less dense, and stays as a surface layer which eventually
forms ice.
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Water as a solvent
also a good solvent due to its polarity
solvent properties of water: vital inbiology, because many biochemical reactions take place
only within aqueous solutions (e.g., reactions inthe cytoplasm andblood).
In addition, water is used to transportbiologicalmolecules.
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Water as a solvent When an ionic or polar compound enters water:
it is surrounded by water molecules.
relatively small size of water molecules typicallyallows many water molecules to surround onemolecule ofsolute.
partially negative dipoles of the water are attractedto positively charged components of the solute,and vice versa for the positive dipoles.
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Water as a solvent In general, ionic and polar substances such as
acids, alcohols, and salts are easily soluble in
water, and nonpolar substances such as fats and oils arenot.
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Water as a solvent Nonpolar molecules stay together in water
because it is energetically more favorable
for the water molecules to hydrogen bond toeach,
other than to engage in van der Waalsinteractions with nonpolar molecules
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Water as a solvent An example of an ionic solute : table salt; the sodium chloride, NaCl,
separates into Na+
cations and Cl-
anions, eachbeing surrounded by water molecules. The ions are then easily transported away from
their crystalline lattice into solution. e.g. for a nonionic solute: table sugar.
The water dipoles hydrogen bond to the dipolarregions of the sugar molecule and allow it to becarried away into solution.
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Cohesion and surface tension
The strong hydrogen bonds give water a high cohesiveness
and, consequently, surface tension.
This is evident when small quantities of water are put ontoa nonsoluble surface and the water stays together as drops.
This feature is important when water is carried throughxylem up stems in plants:
the strong intermolecular attractions hold the water columntogether, and prevent tension caused by transpiration pull.
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Conductivity
Pure water is actually a good insulator(poorconductor),
however, it often has some solute dissolved in it,most frequently salt.
If water has such impurities, then it can conductelectricity much better,
because salt comprise free ions in aqueoussolution by which an electric current can flow.
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R
eactivity
Chemically, water is amphoteric: able to act as an acid orbase.
Occasionally the term hydroxic acidis used when wateracts as an acid in a chemical reaction. At a pH of 7 (neutral), the concentration ofhydroxide ions
(OH-) is equal to that of the hydronium (H3O+) or
hydrogen ions (H+) ions.
If the equilibrium is disturbed, the solution becomes acidic(higher concentration of hydronium ions) or basic (higherconcentration of hydroxide ions).
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R
eactivity Water can act as either an acid or a base in
reactions. According to the Brnsted-Lowry system, an acid
is defined as a species which donates a proton (anH+ ion) in a reaction, and a base as one whichreceives a proton.
When reacting with a stronger acid, water acts as a
base; when reacting with a weaker acid, it acts asan acid. For instance, it receives an H+ ion fromHCl in the equilibrium:
HCl + H2O ---> H3O+ + Cl-
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R
eactivity Here water is acting as a base, by receiving
an H+ ion. An acid donates an H+ ion, and
water can also do this, such as in thereaction with ammonia, NH3:
NH3 + H2O ---> NH4+ + OH-
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pH of water in practice
In theory, pure water has a pH of 7.
In practice, pure water is very difficult to produce. Water left exposed to air for any length of time
will rapidly dissolve carbon dioxide, forming asolution of carbonic acid, with a limiting pH of~5.7 (reference: Kendall, J. (1916), Journal of the
American Chemical Society 38 (11): 2460-2466).
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Amphipathic (or amphiphilic,
micelle)
A compound having both a hydrophilic anda hydrophobic end.
e.g.,soaps and detergents, behaviour inwater
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depicting amphipathic molecules congregating in a water
solution into a structure known as a micelle
.
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Ice floats
The density ofwater: actually less than it couldotherwise be.
because hydrogen bonded wateris packed slightlyless favorably than could be achieved withouthydrogen bonding.
Ice represents a maximal hydrogen bonding of
water, indeed the crystallization of water into thestructure formed upon hydrogen bonding.
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Ice floats
Thus, ice occupies a greater volume / massand, consequently, floats on water.
Of similar importance, high pressures tendto inhibit the solidification of water ratherthan enhance it.
Thus, the bottom of oceans and lakes tendto remain in the liquid phase while theupper reaches tend to be the first to freeze.
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Cohesion
The attraction of one water molecule to anotherresulting from hydrogen bonding.
By placing a drop ofwateron a surface directly: observe cohesion in the resistance that waterdroplet shows to wetting,
i.e., waterclumps up in a pile despite being aliquid, rather than spreading out over the surface.(note that wettingless likely occurs in the absenceofadhesion to the surface being wet.)
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High specific heat of water
Due to increase in the motion of the molecules andatoms making up a substance, a temperatureincrease is observed in water
Because ofcohesion, water molecules resistincreasing their motion (water molecules resist thenet breaking ofhydrogen bonds).
Consequently, waterresists heating; waterhas avery high specific heat.
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High specific heat of water
This tendency to not wantto change temperature:
causes resistance to radical temperature swings
within beings and causes bodies ofwater(e.g., a lake) to
strongly resist rapid changes in temperature.
This temperature buffering capacity ofwateristaken advantage of to a great extent by organisms.
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High heat of vaporization
[evaporation]
As due to the breaking ofhydrogen bonds,
water resists vaporizing (evaporating). Consequently, it takes a lot of heat to
evaporate water.
This highheat of vaporization: utilized byorganisms as a cooling process, e.g., sweator panting.
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Hydration shell:
Particularly, water molecules form a hydrogen bondedlayer, called a hydration shell, that surrounds hydrophilic
substances This shell adheres so powerfully: actually more energetically favorable for many polar
substances to exist as individual molecules surrounded byhydration shells than to remain within a homogeneoussolid material.
Thus, hydrophilic substances tend to dissolve in water.
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Hydrophobic (non-polar)
substance
An atom or molecule to which water does notreadily adhere. Hydrophobic substances tend tonotreadily dissolve in water.
Many biological solutes do not like to dissolve inwater, i.e., are hydrophobic.
These molecules tend to clump togetheraway
from water (hydrophobic exclusion). In a sense, these solutes end up "dissolving" in asolvent consisting of other hydrophobic solutes.
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Hydrophobic exclusion
Energetically unfavorable hydration shells: When dissolved in water, an individual hydrophobic
molecule is, by definition, maximally surrounded bythe water molecules of its hydration shell.
However, because those water molecules of itshydration shell do not readily hydrogen bond to thehydrophobic molecule, the presence of a hydration
shell is energetically unfavorable. (that is, the water molecules would much rather befree to hydrogen bond with one another).
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