Transcript Chapter 2 Homework- 5, 6, 8, 9, 13, 19 Water • Water is the predominate chemical component of living organisms • It is important.

Chapter 2
Homework- 5, 6, 8, 9, 13, 19
Water
• Water is the predominate chemical
component of living organisms
• It is important in Biochemistry because of:
– Ability to solvate due to dipole and H-Bond
capacity
– Interaction of molecules and water helps
dictate structure (ex. Proteins)
– Excellent nucleophile
– Self dissociates to form –OH and H+
• The pH of extracellular fluids is maintained
by buffers, like bicarbonate
• pH of the body can be measured by the
pH of arterial blood and/or the CO2 content
of venous blood
• Acidosis occurs when pH is less than 7.35
• Alkalosis occurs when pH is greater than
7.45
Water forms dipoles
• The geometry of a water molecule is an
irregular, slightly skewed tetrahedron with
the oxygen atom in the center
• It is irregular because the bond angles
between the H’s is only 105o, not 109.5o
• This is due to the stronger repulsion of the
two lone pairs
• Ammonia is also irregular with bond
angles of 107o for the same reasons
• Due to this tetrahedral shape, water
posses a dipole
• Dipole- a molecule with electrical charge
distributed asymmetrically about the
structure
• The strong electronegativity of the oxygen
pulls the electrons from the H’s, which
creates a local positive charge while the
lone pairs constitute a region of local
negative charge
• Due to this dipole, water has a high
dielectric constant
• Coulomb’s law tells us that the strength of
attraction, F, between oppositely charged
particles is inversely proportionate to the
dielectric constant, , of the surrounding
medium.
– Lower , higher attraction
– Higher , lower attraction
 values
• In a vacuum,  = unity
• Other  values:
– Hexane = 1.9
– Ethanol = 24.3
– Water = 78.5
• The strong dipole and high dielectric
constant enable water to dissolve large
quantities of charged and polar
compounds, such as salts
Hydrogen Bonds
• The unshielded hydrogen nuclei
covalently bound to an electron
withdrawing oxygen or nitrogen atom can
interact with an unshared electron pair on
another oxygen or nitrogen to from a
hydrogen bond
• NOTE- this is only an interaction, not a
true bond!!!!
• Breaking a H-bond requires only 4.5
kcal/mol, less than 5% of the energy
required to break a covalent O-H bond
• Remember that O-H covalent bonds are
not even that strong, both water and
alcohols are considered weakly acidic!!
• These H-bonds are also temporary with a
half life of about one microsecond
• However, it is these H-bonds that account
for waters high viscosity, surface tension,
and boiling point.
• Water can act as a H-bond acceptor or
donator, and usually does both!!
• The average water molecule associates to
3.5 other water molecules
• This causes liquid water to self-associate
into very ordered arrays.
Summary
• The H-bonding capacity of water enables it
to dissolve most biomolecules because
they also contain functional groups that
can participate in H-bonding.
Water influences Structure
• While covalent bonds are the strongest
force that holds molecules together,
noncovalent interactions make significant
contributions to the structures, stability,
and functional competence of
biomolecules.
• These include both attractive and
repulsive forces
• Most biomolecules are amhipathic, that is
they contain both hydrophilic regions and
hydrophobic regions
• Most will fold on themselves to leave
hydrophilic regions exposed while
hydrophobic regions remain on the interior
• This occurs because of the media they are
in, water
Types of non-covalent interactions
• Hydrophobic Interactions
• Electrostatic Interactions
• Van der Waals Forces
• Most of the time multiple forces are
present
– Example: DNA
Water as a Nucleophile
• Most metabolic reactions involve a
nucleophile attacking an electrophile
• Biological important Nucleophiles:
– Water
– Oxygens of phosphates, alcohols, carboxylic
acids
– Sulfur of thiols
– Nitrogen of amines and imidazole rings
• Important Electrophiles:
– Carbonyl carbons of amides, esters,
aldehydes, and ketones
– Phosphorus atoms of phosphates
Dissociation of Water
• Water has a slight but important tendency
to dissociate
• Since this reaction is reversible, no
individual H or O is present in ion state
• Instead we talk about the probability to be
in an ion state
• The probability of a hydrogen being in an
ion state is 1.8 x 10-9
• In other words, for every 1 H+, there are
1.8 billion water molecules!!
• For the dissociation of water, we can write
the following equation:
Examples
1) What is the pH of a solution whose
hydrogen ion concentration is 3.2x10-4
2) What is the pH of a solution whose
hydroxide ion concentration is 4.0x10-4
mol/L?
3)What are the pH values of (a) 2.0x10-2
mol/L KOH and of (b) 2.0x10-6 mol/L
KOH?
• This example assumes the complete
dissociation of acids and bases
• This is the case for strong acids and bases
• For weak acids and bases, we have to use
the dissociation constant since they do not
dissociate completely
• Biological systems mainly use weak acids
and bases
• Knowledge of the dissociation of weak
acids and bases is essential in
understanding the influence of intracellular
pH on structure and biological activity
• The protonated species is the acid while
the deprotonated species is the conjugate
base
• Same is true for bases
• Some important acids, conj bases and
pKa’s:
Acid
Conj Base
pH
R-CH2-COOH
R-CH2-NH3+
H2CO3
H2PO4-
R-CH2-COOR-CH2-NH2
HCO3HPO42-
4-5
9-10
6.4
7.2
• For the reaction:
• We can write the expression:
• Ka is the dissociation constant
– These are usually negative exponential
numbers, so instead of Ka, we use pKa
– The lower the pKa, the stronger the acid!
– When acid and conj. Base are present in
equal amounts, pKa = pH
Henderson-Hasselbach Equation
• Describes the behavior of weak acids and
bases
• The HH equation has great predictive
power in protonic equilibria
• It can be used to:
– Calculate conj. base to acid ratios when pH
and pKa are known
– Use ratio and pKa to calculate pH
– Use ratio and pH to calculate pKa
• These solutions of weak acids and their
conj bases act as buffers to resist change
in pH.
• In the body, constant pH involves buffering
by phosphate, bicarbonate and proteins
which accept and donate protons
• In labs and testing, synthetic buffers are
used to maintain pH as in the body
• Most buffers resist changes in pH most
effectively at pH values close to the pKa.
• Why is this?
Own your own
• Tools of Biochemistry 2A, page 52
• Molecules with multiple Ionizing groups
• Interactions between Macroions in
Solution