•Be able to recognize common functional groups;
•Characteristics of H-bonds: H-bond donor and acceptor; the relevance of H-
bonds in the structures of DNA and proteins; the relevance of H-bonds in
determining the properties of water.
H-bond: sharing the H between 2 electronegative atoms
H-bonds being strongest when all three of the involved atoms, i.e., the two electronegative
atoms and the hydrogen atom, are collinear.
H-bonds are important in Shaping the Structure of DNA and Proteins
o there is hydrogen bonding in peptide bonds and in the tertiary structure.
Networks of H-bonding make water highly cohesive
o The oxygen pulls the electrons in the two hydrogens
Hydrogen bond is highly directional
•Hydrophobic interaction: is it a type of electrostatic interaction?
Nonpolar molecules tend to associate with one another in water. The water molecules in
contact with these nonpolar molecules form cages around them becoming more well-ordered
than water molecules.
, Non-specific: not much because hydrophobic molecules like each other but rather they are
excluded by the highly connected water network.
Powerful organizing force in biological systems: driving the formation of membrane, as well as
spontaneous folding of the polypeptide chain.
they are about 2% the strength of a carbon-carbon bond (8 vs. 350 kJ/mole);
It is not an electrostatic interaction instead an entropy driven association
•What drives the folding of proteins and the assembly of membranes?
Hydrophobic effects drive a protein to fold into a compact conformation
•For a given weak acid, be able to distinguish its acid form and its conjugate
base form.
Weak acids have only a modest tendency to shed their protons (definition of an acid)
When they do, the corresponding species becomes a willing proton acceptor, and is called the
conjugate base
Ex: CH3COOH H+ + CH3COO-
•The H-H equation as how the difference between pH of a solution and the pKa of
a weak acid determines the relative abundance of the weak acid in its acid
form and in its base form.
pKa: a measure of the strength of an acid. The lower the pKa vlaue, the easire to lose the
proton, the stronger the acid
When pH=pKa log ([A-]/[HA]) has to be 0, [A-] = [HA]
When pH> pKa A- (i.e., base form) predominates.
When pH<pKa HA (i.e., acid form) predominates.
pH= pKa + log[A-]/[HA]
•Why is the –COOH group in alanine has a much lower pKa value than the –
COOH group in acetic acid?
The –COOH group in alanine is attached to CH3-CH-NH2 R group, which contains one
inductive electron withdrawing group, this increases the strength of the acid and the pKa value
decreases since the lower the pKa the stronger the acid
The –COOH group in acetic acid is attached to CH3 group, which is a inductive electron
donating group. With the donating electron group, the tendency to donate a proton decreases
so does the acidic nature. If it has an electron donating group it wants to accept protons not
donate them. The pKa value increases
•Why is it important to finely control pH in living systems as well as in
biochemical experiments?
Living cells have a VERY narrow range of tolerance for pH, i.e. [H+]. Changes in pH in cells or
body fluids can have profound clinical significance, and if untreated can be fatal.
Changes in pH can disrupt the double helix
, Changes in pH can alter the surface charge of proteins, which could impact their functions
Protein molecules in aqueous solution become increasingly protonated and more positively
charged as the pH decreases. -NH3 -COOH
Protein molecules in aqueous solution become increasingly de-protonated and more
negatively charged as the pH increases. -NH2 –COO-
•What are the three major buffering systems for biological pH control?
Organisms use buffer systems to maintain the pH of cells and body fluids in the appropriate
range
Buffer solutions function because the pH of a weak acid-base solution is least sensitive to
added acid or base near the pKa where the conjugate acid and conjugate base of the buffer
are both present in nearly equal molar concentrations.
Three important buffer systems for biological pH control:
–The carbonic acid-bicarbonate buffer system is very important for the pH control of blood
and body fluids
–The dihydrogen phosphate-hydrogen phosphate system plays a major role in controlling
intracellular pH because it has pKa value near 7.0 and it is abundant in cells.( in the
cytoplasm?)
–Proteins contain many weakly acidic or basic groups, and some of these have pKa values
near 7.0. Because proteins are abundant both in cells and in body fluids, pH buffering is very
strong.
The histidine side chains in proteins also contribute to the cytoplasmic buffering
•Identification of chiral centers in amino acids and be able to distinguish L- & D-
form of amino acids; which form is used in the ribosomal synthesis of
protein?
When a carbon atom has four different substituents attached to it, the carbon is said to be
chiral, or a stereocenter, or an asymmetric carbon.
•Characteristics of H-bonds: H-bond donor and acceptor; the relevance of H-
bonds in the structures of DNA and proteins; the relevance of H-bonds in
determining the properties of water.
H-bond: sharing the H between 2 electronegative atoms
H-bonds being strongest when all three of the involved atoms, i.e., the two electronegative
atoms and the hydrogen atom, are collinear.
H-bonds are important in Shaping the Structure of DNA and Proteins
o there is hydrogen bonding in peptide bonds and in the tertiary structure.
Networks of H-bonding make water highly cohesive
o The oxygen pulls the electrons in the two hydrogens
Hydrogen bond is highly directional
•Hydrophobic interaction: is it a type of electrostatic interaction?
Nonpolar molecules tend to associate with one another in water. The water molecules in
contact with these nonpolar molecules form cages around them becoming more well-ordered
than water molecules.
, Non-specific: not much because hydrophobic molecules like each other but rather they are
excluded by the highly connected water network.
Powerful organizing force in biological systems: driving the formation of membrane, as well as
spontaneous folding of the polypeptide chain.
they are about 2% the strength of a carbon-carbon bond (8 vs. 350 kJ/mole);
It is not an electrostatic interaction instead an entropy driven association
•What drives the folding of proteins and the assembly of membranes?
Hydrophobic effects drive a protein to fold into a compact conformation
•For a given weak acid, be able to distinguish its acid form and its conjugate
base form.
Weak acids have only a modest tendency to shed their protons (definition of an acid)
When they do, the corresponding species becomes a willing proton acceptor, and is called the
conjugate base
Ex: CH3COOH H+ + CH3COO-
•The H-H equation as how the difference between pH of a solution and the pKa of
a weak acid determines the relative abundance of the weak acid in its acid
form and in its base form.
pKa: a measure of the strength of an acid. The lower the pKa vlaue, the easire to lose the
proton, the stronger the acid
When pH=pKa log ([A-]/[HA]) has to be 0, [A-] = [HA]
When pH> pKa A- (i.e., base form) predominates.
When pH<pKa HA (i.e., acid form) predominates.
pH= pKa + log[A-]/[HA]
•Why is the –COOH group in alanine has a much lower pKa value than the –
COOH group in acetic acid?
The –COOH group in alanine is attached to CH3-CH-NH2 R group, which contains one
inductive electron withdrawing group, this increases the strength of the acid and the pKa value
decreases since the lower the pKa the stronger the acid
The –COOH group in acetic acid is attached to CH3 group, which is a inductive electron
donating group. With the donating electron group, the tendency to donate a proton decreases
so does the acidic nature. If it has an electron donating group it wants to accept protons not
donate them. The pKa value increases
•Why is it important to finely control pH in living systems as well as in
biochemical experiments?
Living cells have a VERY narrow range of tolerance for pH, i.e. [H+]. Changes in pH in cells or
body fluids can have profound clinical significance, and if untreated can be fatal.
Changes in pH can disrupt the double helix
, Changes in pH can alter the surface charge of proteins, which could impact their functions
Protein molecules in aqueous solution become increasingly protonated and more positively
charged as the pH decreases. -NH3 -COOH
Protein molecules in aqueous solution become increasingly de-protonated and more
negatively charged as the pH increases. -NH2 –COO-
•What are the three major buffering systems for biological pH control?
Organisms use buffer systems to maintain the pH of cells and body fluids in the appropriate
range
Buffer solutions function because the pH of a weak acid-base solution is least sensitive to
added acid or base near the pKa where the conjugate acid and conjugate base of the buffer
are both present in nearly equal molar concentrations.
Three important buffer systems for biological pH control:
–The carbonic acid-bicarbonate buffer system is very important for the pH control of blood
and body fluids
–The dihydrogen phosphate-hydrogen phosphate system plays a major role in controlling
intracellular pH because it has pKa value near 7.0 and it is abundant in cells.( in the
cytoplasm?)
–Proteins contain many weakly acidic or basic groups, and some of these have pKa values
near 7.0. Because proteins are abundant both in cells and in body fluids, pH buffering is very
strong.
The histidine side chains in proteins also contribute to the cytoplasmic buffering
•Identification of chiral centers in amino acids and be able to distinguish L- & D-
form of amino acids; which form is used in the ribosomal synthesis of
protein?
When a carbon atom has four different substituents attached to it, the carbon is said to be
chiral, or a stereocenter, or an asymmetric carbon.
