Transcript Chapter 4 – The Chemistry of Water and Acid

Chapter 2 – The Chemistry of
Water and Acid-Base Chemistry
• Lessons of the past few years-life can
survive just about any conditions
(acidic/basic, hot (now at least 121
°C)/cold, oxidizing/reducing, high/low salt,
relatively high radiation)
• Cannot survive without H2O, can’t
metabolize without liquid H2O
• Water and its unique properties
compound
H2O
boiling point
(°C)
100
H2S
-60
H2Se
-40
H2Te
-10
What’s necessary for H-bonding?
• General pattern:
donor
-X-H | | | | | Y-
acceptor
– Where X,Y = N,O,F (usually)
• Y (acceptor) must have free lone pair(s)
– i.e. nitrogen of a quaternary amine can’t
accept an H-bond
• H-bonds vary in strength from ~5-20 (normal)
kJ/mol (covalent bonds ~150 to 1075 kJ (CO
triple bond))
H2O - 4 H-bonds max (reality ~3.5 in solution) – this means that
very few species are as good at H-bonding as water, so water tends
to want to associate wi/ itself
Distance
usually
referred to
(since
H is
“invisible” in
most protein
structures)
• Bond distance is the major determinant of whether
or not an H-bond has occurred
• H bond distances (distance between hetero atoms
(X and Y), ignoring H) are in the range of 2.5-3.5
Å (covalent bonds are in the range of 1-2 Å and
shorter)
• Linear (i.e. a straight line from the lone pair on Y
to the X-H bond) tend to be stronger than “bent”
H-bonds
SSHB or LBHB
• SSHB “short, strong hydrogen bond”, also known as an LBHB
“low-barrier hydrogen bond,” occurs when the acceptor and
donor share the H equally
donor
-X-H | | | | | Yacceptor
-X| | |H| | |YSSHB or LBHB
• Water will wipe these out (must be isolated at an enzyme
active site)
• Distances of ≤ 2.6 A, stronger than normal H-bond
• pKas between donor/acceptor must be matched
• Implicated in enzymatic catalysis (still controversial)
Other hydrogen bonds (special
cases-don’t write these on a test)
• H can be attached to other atoms
X-C-H | | | | |Y
where X is very e- withdrawing, Y is
Still N, O or F
• X/Y (in X-H||||Y pattern) can be sulfur
(especially if Y is S-) or P
• The real determinant of an H bond is if
an H is being shared (based on bond
distances and strengths)
• The thermodynamics of hydrogen bonding
(especially between water molecules) has a
strong effect on almost everything that
happens in biochemistry
• as an example, see the section in Chapter 2
regarding protein-bound water
X-ray crystal structure of hemoglobin, showing waters that are
tightly bound to the protein (even in the solid state. Removal of
these waters frequently results in loss of protein structure (and
function). In most protein structure illustrations these waters are
not shown – but they are there
Close up of water colored yellow in previous image – water
hydrogen bonded to carbonyl oxygen of protein backbone
(and also H-bonded to another water). Distances are in Å.
Relative strengths of
intermolecular/atomic forces
Interaction
Energy (to break)
London
Low –high
forces/dipole-dipole (London forces
vary greatly based
on size)
H-bonding
8-40 kJ or greater
Ionic attraction(+/-) ~40 kJ
Ionic
~-20 kJ
repulsion(+/+), (-/-)
Covalent bonds
150-1075 kJ
Hydrophobic vs. hydrophilic
• Hydrophilic compounds-dissolve in/are miscible
with H2O
– Hydrophilic compounds like water (and water likes
them) so this term is accurate
• Hydrophibic compounds-do not dissolve in/are not
miscible with H2O
• “the hydrophobic effect”- water tends to want to
associate with water, and exclude other
compounds
– Hydrophobic compounds don’t hate water, water hates
them (therefore the term hydrophobic is a misnomer)
Or facing
head to tail
as in a
membrane
Water and “waters of hydration”
• Salts can dissolve in water because the H2O
“hydrates” the charge
Behavior of buffers and charged
compounds
• pKas – remember:
– Ka = ([H+][A-])/[HA] or ([H+][B])/[BH+]
– pKa = -logKa
– If pH of solution > pKa, species is mostly in the
basic form
– If pH of solution < pKa, species is mostly in
the acidic form
– What about pH = pKa?
• How about pH = pKa± 1 unit? 2 units? 3 units?
• Know the pKa ranges of biologically relevant
functional groups – carboxylic acids, amines,
alcohols (aryl and alkyl), thiols
• Be able to recognize strong acids/bases
– Why do strong acids that have very different
pKas (for example, HCl, HBr and HI) behave
the same in water? How could you determine
their pKas?
• Think about the difference between neutral
acid/anionic base pair and a positive acid/neutral
base pair
– Example: ionization behavior of carboxylates
vs. amines
HI = -10, HBr = -9,
HCl = -7
Amines 9-12
H3O+ = -1.7
Carboxylic acids 2-5
H2O = 15.7
Alcohols
~ 14-16
Phenol ~ 9
Thiols ~ 8
Cocaine and pH
• Cocaine is a stimulant that exerts its effect by inhibiting the
reuptake of neurotransmitters (especially norepinephrin)
• Also has other longer term effects
CH3
O
O
H
ionizable group
H
O
C
H
C
C
H
C
O
H
C
C
C
H
H
N+
H
C
H
H
CH3
H
R
'
R
N+
R''
H
cocaine tertiary amine
pKa = 8.41
R
R
pKa = 8.41
'
R
N+
H
R''
acid formalso known as cocaine HCl
'
R
N
R''
base formalso known as the "free base"
• If cocaine is smoked or otherwise inhaled,
only the neutral form crosses membranes
and enters the blood. Therefore only the
base form (free base) is taken up efficiently
• Both “free base” cocaine and crack cocaine
are cocaine in the neutral (free) base form
Why would tobacco manufacturers add
NH3 (ammonia) to their products?
• Nicotine acid base behavior – nicotine in
the “free base” form will cross membranes
pKa=8 (?)
N+
CH 3
+
H
N
+ 2NH3
CH 3
N
H
pKa= 5
charged, won't cross membranes easily
+2NH4+
N
neutral, will cross membranes
easily
Absorption of aspirin
• Aspirin is neutral in its acidic form, therefore it will only
cross membranes in its acid form
• The pH of the intestine is 6- aspirin is in its –COO- form,
and can’t cross the membrane
• The pH of the stomach is 1.5-aspirin is in its –COOH
form, and can cross the membrane
O
O
C
OH
H3C
aspirin
pKa=3.5
BBS system of blood
• Blood uses the bicarbonate buffer system,
based on HCO3• pKa of H2CO3 = 3.77, while blood is held
precisely at pH 7.4 (pH 7.2-7.3 is acidosis,
<7.1 is severe acidosis)
• How can this system work?
Ka~ 10-4
pKa ~ 4
Koverall = KaKeq ~ 10-7
pKoverall ~ 7
Keq ~ 10-3
catalyzed by
carbonic anhydrase
pKeq~ 3
• If acid is produced, breathing increases,
CO2 is blown off, equilibrium shifts in a
direction that decreases H+
• If base is produced, breathing decreases,
dissolved CO2 increases, increasing H+,
bringing the pH back down
• Respiratory acidosis – what causes it? What
can be done about it?
• Respiratory alkalosis – what causes it?
What is the simple solution?
• If blood is normally ~99-100% saturated
with O2, why does deep breathing before a
sprint or weight lifting improve
performance?
pKa and structural factors affecting pKa
• Inductive effect
– CH3-CO2H vs. CF3-CO2H
• Charge effect – through space (i.e. independent of
above)
– Amino acid -CO2H and –NH3+ vs. N and C
termini of proteins (sort of)
– Enzyme active sites (position of charged
residues in 3 dimensional space)
• Resonance effect
– R-OH vs. R-CO2H
• Atom size (bond strength) effect
– HF vs. HCl vs. HBr vs. HI
Effect of solvent and environment on pKa
• Polar solvents/environments tend to favor charged species
– Example - charged area (especially + charges) on an
enzyme might favor –CO2-, decreasing pKa of a –COOH
group in that area
– The same region would decrease the pKa of an R-NH3+
group
• Non-polar solvents/environments tend to favor uncharged
species
– Example – nonpolar region of an enzyme might favor –
COOH form of a carboxylic acid, increasing pKa
– pKa of R-COOH would be increased, R-NH3+ decreased in
ethanol
– Exception – aromatics can favor anionic species via pi
bond/anionic interactions
pH behavior of buffers
• Buffers have the best “buffering” effect at pHs within 1
unit of their pKa – why?
Solving buffer problems
• Three main types
– Add in buffer in both acid and base forms in
proper ratios
– Start with all of buffer in acid (or base) form
and titrate to proper pH with strong base (or
acid)
– Starting with buffer of known pH, adjust pH to
required pH with strong acid or base