BIO 203 Biochemistry I

by
Seyhun YURDUGÜL,Ph.D.

Lecture 2
Atoms, Molecules and Water
 Content Outline
• The atom concept
• Ionic and Covalent Bonds
• Hydrogen bonds
• Water
• Hydration shells
 What is an Atom?
• Matter is composed of atoms:
• a consequence of the manner in which the
electrons are distributed throughout space in the
attractive field exerted by the nuclei.
• nuclei act as point attractors immersed in a cloud
of negative charge, the electron density (r).
• electron density: the electronic charge is
distributed throughout real space.
e.g. electron density in the plane containing the two C and four H nuclei of the ethene
molecule, portrayed as a projection in the third dimension and in the form of a contour map.
• Thus a pair of bonded atoms:
• linked by a line along which the electron
density, the glue of chemistry, is maximally
concentrated.
• leads to different conformations
and more….
 Ionic and Covalent Bonds
• Related with distribution of negative charge in a
molecule:
• exhibit varying degrees of asymmetry depending
on the ability of the nuclei to attract and bind the
electronic charge density.
 Ionic and Covalent Bonds
• symmetry or asymmetry of the charge
distribution:
• role in determining the chemical properties
of the molecule
• and this property:
• used for the classification of chemical
bonds.
 Ionic and Covalent Bonding
• We can envisage two extremes for the distribution
of the valance charge density.

• when a bond is formed between two identical

atoms.

• The charge density of the valance electrons will be

delocalized equally over corresponding regions of
each nucleus
 Ionic and Covalent Bonding
• Since both nuclei will attract the electron
density with equal force.
• such an equal sharing of the charge
density: e.g. of covalent binding
• and shown by the molecular charge
distribution of N2.
 Ionic bonding
• The charge distribution of LiF:

• provides an example of the other extreme: ionic

bonding,

• obtained when a bond:

• formed between two atoms with very different

affinities for the electronic charge density.
 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
 Hydrogen bonding
• Polar molecules,
• e.g. water,
• have a weak, partial negative charge at one
region of the molecule (the oxygen atom in
water)
• and a partial positive charge elsewhere (the
hydrogen atoms in water).
 Hydrogen bonding
• When water molecules are close together:
• their positive and negative regions:
• attracted to the oppositely-charged regions
of nearby molecules.
• The force of attraction here: a hydrogen
bond.
• Each water molecule is hydrogen bonded to
four others.
 Hydrogen bonding
• The hydrogen bonds that form between
water molecules:
• account for some of the essential — and
unique — properties of water.
 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.
 Hydrogen bonds
• The energy required to break multiple
hydrogen bonds:
• causes water to have a high heat of
vaporization;
 Hydrogen bonds
• that is, a large amount of energy is needed
to convert liquid water,
• where the molecules are attracted through
their hydrogen bonds, to water vapor,
• where they are not.
 Hydrogen bonds
• Two outcomes of this:
• The evaporation of sweat, used by many mammals
to cool themselves,
• achieves this by the large amount of heat needed to
break the hydrogen bonds between water
molecules.
• Moderating temperature shifts in the ecosystem
(which is why the climate is more moderate near
large bodies of water like the ocean)
 Hydrogen bonds
• The hydrogen bond has only 5% or so of
the strength of a covalent bond.
• However, when many hydrogen bonds can
form between two molecules (or parts of the
same molecule):
• the resulting union can be sufficiently
strong as to be quite stable.
 Multiple hydrogen bonds

• hold the two strands of the DNA double helix

together
• hold polypeptides together in such secondary
structures as the alpha helix and the beta
conformation;
• help enzymes bind to their substrate;
• help antibodies bind to their antigen
• help transcription factors bind to each other;
• help transcription factors bind to DNA
Hydrogen
Bonding
 Water
• a chemical compound
• and polar molecule, which is liquid at
standard temperature and pressure.
• has the chemical formula H2O:
• meaning that one molecule of water is
composed of two hydrogen atoms and one
oxygen atom.
 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 form
anywhere besides Earth, strong evidence of
extraterrestrial life.
• Bonding Arrangement of Water
 General properties

• solid state; known as ice;

• gaseous state : known as water vapor (or steam).
• The units of temperature (formerly the degree
Celsius and now the Kelvin) are defined in terms
of the triple point of water, 273.16 K (0.01 °C)
and 611.2 Pa, the temperature and pressure at
which solid, liquid, and gaseous water coexist in
equilibrium.
 Water
• also exhibits some very strange behaviors,
including the formation of states such as
vitreous ice, a noncrystalline (glassy), solid
state of water.
 Water
• At temperatures greater than 647 K and
pressures greater than 22.064 MPa,
collection of water molecules assumes a
supercritical condition:
• in which liquid-like clusters float within a
vapor-like phase.
• liquid water path is a measure of the
amount of liquid water in an air column.
 Water
• An important feature: its polar nature.
• molecule forms an angle, with hydrogen atoms at the tips
and oxygen at the vertex.
• since oxygen has a higher electronegativity than hydrogen,
the side of the molecule with the oxygen atom has a partial
negative charge:
 Water
• molecule with such a charge difference is
called a dipole.
• charge differences cause water molecules to
be attracted to each other
• and to other polar molecules(hydrogen
bonding)
 Water
• This relatively weak (relative to the covalent
bonds within the water molecule itself) attraction
results in physical properties such as a relatively
high boiling point,
• because more heat is necessary to break the
hydrogen bonds between molecules.
• The extra bonding between water molecules also
gives liquid water a large specific heat capacity.
 Water
• Hydrogen bonding also gives water an unusual
behaviour when freezing,
• the liquid becomes denser with lowering
temperature like other materials
• But; However, unlike most other materials, when
cooled to near freezing point, the presence of
hydrogen bonds form a structure that is actually of
lower density:
• hence the solid form, ice, will float in water.
 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
4°C, water on the surface, as it chills further,
becomes less dense,
• and stays as a surface layer which eventually
forms ice.
 Water as a solvent

• also a good solvent due to its polarity

• solvent properties of water: vital in biology,
• because many biochemical reactions take place
only within aqueous solutions (e.g., reactions in
the cytoplasm and blood).
• In addition, water is used to transport biological
molecules.
 Water as a solvent
• When an ionic or polar compound enters water:
• it is surrounded by water molecules.
• relatively small size of water molecules typically
allows many water molecules to surround one
molecule of solute.
• partially negative dipoles of the water are attracted
to positively charged components of the solute,
and vice versa for the positive dipoles.
 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 are
not.
 Water as a solvent
• Nonpolar molecules stay together in water
• because it is energetically more favorable
for the water molecules to hydrogen bond to
each,
• other than to engage in van der Waals
interactions with nonpolar molecules
 Water as a solvent
• An example of an ionic solute :
• table salt; the sodium chloride, NaCl,
• separates into Na+ cations and Cl- anions, each
being 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 dipolar
regions of the sugar molecule and allow it to be
carried away into solution.
 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 onto
a nonsoluble surface and the water stays together as drops.
• This feature is important when water is carried through
xylem up stems in plants:
• the strong intermolecular attractions hold the water column
together, and prevent tension caused by transpiration pull.
 Conductivity

• Pure water is actually a good insulator (poor

conductor),
• however, it often has some solute dissolved in it,
most frequently salt.
• If water has such impurities, then it can conduct
electricity much better,
• because salt comprise free ions in aqueous
solution by which an electric current can flow.
 Reactivity

• Chemically, water is amphoteric: able to act as an acid or

base.
• Occasionally the term hydroxic acid is used when water
acts as an acid in a chemical reaction.
• At a pH of 7 (neutral), the concentration of hydroxide 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 (higher
concentration of hydroxide ions).
 Reactivity
• Water can act as either an acid or a base in
reactions.
• According to the Brønsted-Lowry system, an acid
is defined as a species which donates a proton (an
H+ ion) in a reaction, and a base as one which
receives a proton.
• When reacting with a stronger acid, water acts as a
base; when reacting with a weaker acid, it acts as
an acid. For instance, it receives an H+ ion from
HCl in the equilibrium:
• HCl + H2O ---> H3O+ + Cl-
 Reactivity
• 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 the
reaction with ammonia, NH3:
• NH3 + H2O ---> NH4+ + OH-
 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 a
solution of carbonic acid, with a limiting pH of
~5.7 (reference: Kendall, J. (1916), Journal of the
American Chemical Society 38 (11): 2460-2466).
 Amphipathic (or amphiphilic,
micelle)

• A compound having both a hydrophilic and

a hydrophobic end.
• e.g., soaps and detergents, behaviour in
water
• depicting amphipathic molecules congregating in a water
solution into a structure known as a micelle.
 Ice floats

• The density of water: actually less than it could

otherwise be.
• because hydrogen bonded water is packed slightly
less favorably than could be achieved without
hydrogen bonding.
• Ice represents a maximal hydrogen bonding of
water, indeed the crystallization of water into the
structure formed upon hydrogen bonding.
 Ice floats
• Thus, ice occupies a greater volume / mass
and, consequently, floats on water.
• Of similar importance, high pressures tend
to inhibit the solidification of water rather
than enhance it.
• Thus, the bottom of oceans and lakes tend
to remain in the liquid phase while the
upper reaches tend to be the first to freeze.
 Cohesion

• The attraction of one water molecule to another

resulting from hydrogen bonding.
• By placing a drop of water on a surface directly:
• observe cohesion in the resistance that water
droplet shows to wetting,
• i.e., water clumps up in a pile despite being a
liquid, rather than spreading out over the surface.
(note that wetting less likely occurs in the absence
of adhesion to the surface being wet.)
 Water is a liquid at typical
ambient temperatures
• By molecular weight (MW), ought to be a
gas:
– CO2 (MW=44), O2 (MW=32), CO (MW=28),
N2 (MW=28), CH4 (MW=16), and H2
(MW=2) are all gases at room temperature.
– Water (MW=18) is a liquid. Why?
 Water is a liquid at typical
ambient temperatures

• Due to water molecules display cohesion

and thus have a much reduced tendency to
fly off into the overlying atmosphere than
these other listed molecules.
 High specific heat of water

• Due to increase in the motion of the molecules and

atoms making up a substance, a temperature
increase is observed in water
• Because of cohesion, water molecules resist
increasing their motion (water molecules resist the
net breaking of hydrogen bonds).

• Consequently, water resists heating; water has a

very high specific heat.
 High specific heat of water

• This tendency to not want to change temperature:

• causes resistance to radical temperature swings
within beings
• and causes bodies of water (e.g., a lake) to
strongly resist rapid changes in temperature.
• This temperature buffering capacity of water is
taken advantage of to a great extent by organisms.
 High heat of vaporization
[evaporation]

• As due to the breaking of hydrogen bonds,

water resists vaporizing (evaporating).
• Consequently, it takes a lot of heat to
evaporate water.
• This high heat of vaporization: utilized by
organisms as a cooling process, e.g., sweat
or panting.
 Hydration shell:

• Particularly, water molecules form a hydrogen bonded

layer, 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 by
hydration shells than to remain within a homogeneous
solid material.
• Thus, hydrophilic substances tend to dissolve in water.
 Hydration shell:
• Any condition that increases the rate at
which water can form a hydration shell
• heating,
• stirring,
• shaking,
• adding an excess of water, the faster a
hydrophilic crystalline substance will
dissolve
 Hydrophobic (non-polar)
substance

• An atom or molecule to which water does not

readily adhere. Hydrophobic substances tend to
not readily dissolve in water.
• Many biological solutes do not like to dissolve in
water, i.e., are hydrophobic.
• These molecules tend to clump together away
from water (hydrophobic exclusion).
• In a sense, these solutes end up "dissolving" in a
solvent consisting of other hydrophobic solutes.
 Hydrophobic exclusion

• Energetically unfavorable hydration shells:

– When dissolved in water, an individual hydrophobic
molecule is, by definition, maximally surrounded by
the water molecules of its hydration shell.
– However, because those water molecules of its
hydration shell do not readily hydrogen bond to the
hydrophobic molecule, the presence of a hydration
shell is energetically unfavorable.
– (that is, the water molecules would much rather be
free to hydrogen bond with one another).
 LITERATURE CITED
• Devlin,T.M. Textbook of Biochemistry with
Clinical Correlations,Fifth Edition,Wiley-Liss
Publications,New York, USA, 2002.
• Lehninger, A. Principles of Biochemistry,
Second edition, Worth Publishers Co., New
York, USA, 1993.
• Matthews, C.K. and van Holde, K.E.,
Biochemistry, Second edition, Benjamin /
Cummings Publishing Company Inc., San
Francisco, 1996.