biology lesson document 2

8/6/2019 biology lesson document 2

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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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