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M1 Water and the Building Blocks of Life
M1L1: pH Review
The definition of pH = -log[H
+
]
o Sorensen, higher H+ more acidic, lower H+ more basic
o Ex: What’s the pH of a solution with 0.1 M H+?
pH=-log(0.1) = -(-1) = 1
o ex: What’s the hydrogen ion concentration of a solution w/a pH of 4?
4=-log[H+]
-4=log[H+]
10^-4 M=H+
o Sea water (pH=8) is 1000x more basic than pH 4. pH 3 is 10x more acidic than
pH 4.
Water rarely dissociates into H
+
and OH
-
and each are present in equal concentrations of
1 x 10
-7
M in pure water.
pH + pOH = 14; thus given the pH of a solution you can calculate the OH
-
ion
concentration.
o Ex: A solution has a pH of 3.6, what is it’s pOH?
14-3.6=10.4 hydroxyl ion concentration
Pure water becomes more acidic when exposed to air because of equilibration with
atmospheric CO
2
.
o Absorbed CO2 reacts with water to become carbonic acid (oceans have become
more acidic over time)
The pH of blood in humans is kept in a narrow range of about pH 7.35 to pH 7.45.
Cells and organelles have pH that can vary from pH of 5 to 7.4.
o Intracellular range is more variable
Pure water is neutral (pH 7) because it has equal amounts of H and OH ions.
M1L2: pH and Buffers
Review: strong bases and acids fully dissociate in water; when weak, they only partially
disassociate/protonate in water
Ex of weak acid: acetic acid (CH3COOH); will stay unless something is added to titrate H’s off
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Buffers are a hydrogen ion reservoirs that can accept or donate protons in response to
metabolic and environmental changes and work to prevent pH fluctuations.
o ½ full reservoir
The pK
a
of a weak acid or weak base is defined as pK
a
= -logK
a
o Ka is the equilibrium constant: Ka=[products H*A]/[substrates HA]
o Low pKa=stronger acid, weaker the acid the stronger the conjugate base
The Henderson-Hasselbalch equation relates pH, pK
a
, and the concentration of ionized
and unionized acids and bases.
o Equation: pH=pka+log[A-]/[HA]
o Ex: The pK of acetic acid is pK = 4.76. For a 0.1 M solution of acetic acid
at a pH = 4.76 what is the concentration of [H
+
]?
[H+] = [CH3COO-] = 0.05 M. For solutions of weak acids and
bases with a pH = pK the concentrations of H+ and OH- are equal.
When pH=pK
a
a buffer has its maximum buffering capacity.
o [A-]=[HA]
The effective range that buffers work is -/+ 1 pH unit of the pK
a
There are three primary buffering systems in our bodies: bicarbonate (blood),
phosphate (intracellular), and proteins (blood and cells).
o Bicarbonate: CO2 is the source
o Proteins: have both carboyl and ammonia groups to use as well as side chains
The bicarbonate buffer system is the major buffer in our blood along with the protein
buffer system. The protein buffer system and phosphate buffer system work to maintain
intracellular pH.
o The bicarbonate buffer helps to maintain a constant blood pH but because
it’s pK is over 1 pH unit from the blood pH of 7.4. Because of this our
bodies have evolved a complex system to prevent build up of CO_2
concentrations in blood by expiring the excess CO_2 from our lungs, and
by excreting it in our urine.
M1L3: Weak Interactions
Weak interactions are about 10-100 fold weaker than strong bonds
The energy of weak interactions is additive so many unstable weak interactions, when
cooperating together, can be very stable
o Weak bonds work by strength in numbers. The energy to break hundreds
or thousands of weak bonds can exceed the energy required to break a
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covalent bond, thus many weak bonds help maintain protein and DNA
structure.
H-bonds form between molecules with charge dipoles
o NH---N (H bond donor to H bond acceptor)
o Water has unusually high boiling, melting, viscosity points and surface tension
due to H bonding network
van der Waals interactions stabilize transient (not lasting) dipoles for attraction
o Depends on how close atoms are together
o Important in base stacking in DNA, binding of ligands to proteins, protein folding
The hydrophobic effect relies on maximizing entropy or disorganization of molecules
o Driven by creation of more entropy, not attraction
o Hydrophobic amino acids internally can displace water/stabilize
o An important example is the formation of cellular membranes between
lipids that are insoluble in water. Aggregation between the long,
uncharged lipid side chains releases the surrounding water molecules back
into bulk water increasing the overall entropy of the system.
These interactions are important for protein, DNA, and RNA stability, for binding of
molecules to proteins, and for enzyme function!
Give 8 examples of key functional groups found in biochemistry.
o An example of a hydrophobic (R-CH3) functional group is within the amino acid
alanine. Alanine has a carbon with 3 hydrogens branched off its structure.
o An example of a hydroxyl group (R-OH) is the amino acid serine, which has an
OH in its structure. An example of an aromatic functional group is in tyrosine,
which has a 6 membered ring with a hydroxyl group.
o An example of an aldehyde (R-CH=O) is glucose, which has a CHO in its
structure.
o An example of a keto (R-C/R=O) group is fructose, which has a CO in its
structure.
o An example of a carboxyl (R-C=O/-OH) group is acetic acid which has a carbon
double bonded with oxygen and a hydroxyl group.
o An example of an amino group (R-NH2) is glycine (as well as the 20 other amino
acids) which has NH2 in its structure.
o There are many phosphate (P=O/O-/O-) group examples. In DNA, there is a
phosphate group located at the 5 prime end.
o Lastly, an example of sulfhydryl (R-SH) is vitamin B1, which has a sulfur bound
to hydrogen in its structure.
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Biomolecules: DNA, Carbohydrates, Lipids, &
Proteins
M2L1: The Central Dogma
The central dogma can be summarized as DNA makes RNA makes protein
This was proposed by Francis Crick as a hypothesis to explain the flow of information
from DNA to protein and anticipated the possibility of an RNA intermediate that could
self replicate
o 1956; proposed: DNA is the storage for cells, proteins could be translated from
DNA, RNA is an intermediate, DNA and RNA can replicate, and
DNARNAprotein
Protein cannot be synthesized directly from DNA
Retroviruses (have an RNA genome and make DNA as an intermediate) are technically
not an exception to the central dogma, because Crick anticipated their unique ability to
replicated their RNA genome
Prions (aggregations of misfolded proteins without RNA/DNA intermediate) are
technically not an exception either, bc they were not even considered
o Prions are proteins that can cause diseases when they are mis-folded.
Mis-folded prion proteins can stabilize other misfolded prion proteins to
make large networks of misfolded proteins that accumulate and are toxic
to neural tissues.
M2L2: Biomolecules - Carbohydrates
Glucose, fructose, and galactose (monosaccharides) are 6-carbon sugars that make up
the disaccharides sucrose, maltose, and lactose
o The aldehyde and keto groups can ‘attack’ an alcohol and crystalize
o Glucose: table sugar
o Fructose: 2x sweet, the isomerization of fructose affects the sweetness (five vs.
six membered ring)
o Galactose: found in lactose
o Sucrose: glucose + fructose (alpha 1,2-beta linkage; ether), therefore a
nonreducing sugar bc it’s ‘tied up’ and cannot open spontaneouely in solution
o Maltose (barley/beer): reducing sugar; can open spontaneously in solution
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o Lactose (milk/dairy): reducing sugar; can open spontaneously in solution
Deoxyribose and ribose are two 5-carbon sugars found in RNA and DNA
o Ribose has a hydroxyl group, deoxyribose does not, therefore sensitive to
hydrolysis (water breaks bond) due to OH group
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