Werkcolleges
H1
1. As will be seen in succeeding chapters, enzymes provide a specific binding site for substrates
where one or more chemical steps can be carried out. Often these sites are designed to
exclude water. Suppose that at a binding site, a negatively charged substrate interacts with a
positively charged atom of an enzyme.
a. Using Coulomb’s equation, show how the presence of water might affect the
interaction. What sort of environment might be preferable for an ionic interaction?
Note that a numerical answer is not required here.
b. How would an ionic interaction be affected by the distance between the oppositely
charged atoms?
2. Water molecules have an unparalleled ability to form hydrogen bonds with one another.
Water also has an unusually high heat capacity, as measured by the amount of energy
required to increase the temperature of a gram of water by 1ºC. How does hydrogen bonding
contribute to water’s high heat capacity?
3. Double-helix-formation entropy. For double-helix formation, ΔG can be measured to be −54
kJ mol−1 (−13 kcal mol−1) at pH 7.0 in 1 M NaCl at 25° C (298 K). The heat released indicates
an enthalpy change of −251 kJ mol−1 (−60 kcal mol−1). For this process, calculate the entropy
change for the system and the entropy change for the surroundings.
4. What is the ratio between the concentration H 2PO4 − en HPO4 2− at the given pH’s:
a. pH=7.0
b. pH=7.5
c. pH=8.0
5. Human blood maintains a very tight pH range (about 7.35–7.45). It accomplishes this
homeostasis partly through what is known as the bicarbonate buffering system. Blood
has large amounts of bicarbonate, HCO3 − , a weak acid with a pKa near
physiological pH. As the equilibrium below shows, bicarbonate can pick up H+ and
form carbonic acid. Carbonic acid is dehydrated by enzymes to form CO2, which can
exit via the lungs.
CO2 + H2O <>H2CO3 <> H+ + HCO3-
Uncontrolled diabetes can result in ketoacidosis, a condition in which metabolic acids
such as b-hydroxybutyric acid (a substance known as a ketone body) build up. b -
hydroxybutyric acid has a pKa below that of physiological pH. A characteristic of
, ketoacidosis is deep and rapid breathing. Why would ketoacidosis lead to this
symptom?
6. You need to make a buffer with an pH of 5,8. You have a 0,1 M acetic acid (CH3COOH)
solution and a 0,1 M sodium acetate (NaCH3COO) solution (pKa=4,8). How much of each
solution do you need to mix to make 1 liter 0,1 M buffer?
H2 + H7
WERKCOLLEGE H2/H7
7. Given the peptide Glu-Met-Arg-Thr-Gly
a. Which of the residues is the carboxy terminus
b. What is the number of charged groups (not residues!) at pH=7
c. Sketch the charge of the peptide on a pH scale from 0 to 14.
8. Why does histidine act as a buffer at pH 6.0? What can you say about the buffering
capacity of histidine at pH 7.6?
9. Calculate the pH at which a solution of cysteine would have no net charge (see table 2.1 on
page 36 for the pKa values).
10. Glycophorin A is a glycoprotein that extends across the red blood cell membrane. The portion
of the polypeptide that extends across the membrane bilayer contains 19 amino acid residues
and is folded into a helix.
a. What is the width of the bilayer that could be spanned by this helix?
The interior of the bilayer includes long acyl chains that are nonpolar.
b. Which of the 20 amino acids would you expect to find among those in the portion of
the polypeptide that traverses the bilayer?
11. Suppose you are studying the conformation of a monomeric protein that has an unusually
high proportion of aromatic amino acid residues throughout the length of the polypeptide
chain. Compared with a monomeric protein containing many aliphatic residues, what might
you observe for the relative α-helical content for each of the two types of proteins? Would
you expect to find aromatic residues on the outside or the inside of a globular protein? What
about aliphatic residues?
12.An effective respiratory carrier must be able to pick up oxygen from the lungs and
deliver it to peripheral tissues. Oxygen dissociation curves for substances A and B are
shown in the following figure.
a) What would be the disadvantage of each of these substances as a respiratory carrier?
b) Where would the curve for an effective carrier appear in the figure?
H1
1. As will be seen in succeeding chapters, enzymes provide a specific binding site for substrates
where one or more chemical steps can be carried out. Often these sites are designed to
exclude water. Suppose that at a binding site, a negatively charged substrate interacts with a
positively charged atom of an enzyme.
a. Using Coulomb’s equation, show how the presence of water might affect the
interaction. What sort of environment might be preferable for an ionic interaction?
Note that a numerical answer is not required here.
b. How would an ionic interaction be affected by the distance between the oppositely
charged atoms?
2. Water molecules have an unparalleled ability to form hydrogen bonds with one another.
Water also has an unusually high heat capacity, as measured by the amount of energy
required to increase the temperature of a gram of water by 1ºC. How does hydrogen bonding
contribute to water’s high heat capacity?
3. Double-helix-formation entropy. For double-helix formation, ΔG can be measured to be −54
kJ mol−1 (−13 kcal mol−1) at pH 7.0 in 1 M NaCl at 25° C (298 K). The heat released indicates
an enthalpy change of −251 kJ mol−1 (−60 kcal mol−1). For this process, calculate the entropy
change for the system and the entropy change for the surroundings.
4. What is the ratio between the concentration H 2PO4 − en HPO4 2− at the given pH’s:
a. pH=7.0
b. pH=7.5
c. pH=8.0
5. Human blood maintains a very tight pH range (about 7.35–7.45). It accomplishes this
homeostasis partly through what is known as the bicarbonate buffering system. Blood
has large amounts of bicarbonate, HCO3 − , a weak acid with a pKa near
physiological pH. As the equilibrium below shows, bicarbonate can pick up H+ and
form carbonic acid. Carbonic acid is dehydrated by enzymes to form CO2, which can
exit via the lungs.
CO2 + H2O <>H2CO3 <> H+ + HCO3-
Uncontrolled diabetes can result in ketoacidosis, a condition in which metabolic acids
such as b-hydroxybutyric acid (a substance known as a ketone body) build up. b -
hydroxybutyric acid has a pKa below that of physiological pH. A characteristic of
, ketoacidosis is deep and rapid breathing. Why would ketoacidosis lead to this
symptom?
6. You need to make a buffer with an pH of 5,8. You have a 0,1 M acetic acid (CH3COOH)
solution and a 0,1 M sodium acetate (NaCH3COO) solution (pKa=4,8). How much of each
solution do you need to mix to make 1 liter 0,1 M buffer?
H2 + H7
WERKCOLLEGE H2/H7
7. Given the peptide Glu-Met-Arg-Thr-Gly
a. Which of the residues is the carboxy terminus
b. What is the number of charged groups (not residues!) at pH=7
c. Sketch the charge of the peptide on a pH scale from 0 to 14.
8. Why does histidine act as a buffer at pH 6.0? What can you say about the buffering
capacity of histidine at pH 7.6?
9. Calculate the pH at which a solution of cysteine would have no net charge (see table 2.1 on
page 36 for the pKa values).
10. Glycophorin A is a glycoprotein that extends across the red blood cell membrane. The portion
of the polypeptide that extends across the membrane bilayer contains 19 amino acid residues
and is folded into a helix.
a. What is the width of the bilayer that could be spanned by this helix?
The interior of the bilayer includes long acyl chains that are nonpolar.
b. Which of the 20 amino acids would you expect to find among those in the portion of
the polypeptide that traverses the bilayer?
11. Suppose you are studying the conformation of a monomeric protein that has an unusually
high proportion of aromatic amino acid residues throughout the length of the polypeptide
chain. Compared with a monomeric protein containing many aliphatic residues, what might
you observe for the relative α-helical content for each of the two types of proteins? Would
you expect to find aromatic residues on the outside or the inside of a globular protein? What
about aliphatic residues?
12.An effective respiratory carrier must be able to pick up oxygen from the lungs and
deliver it to peripheral tissues. Oxygen dissociation curves for substances A and B are
shown in the following figure.
a) What would be the disadvantage of each of these substances as a respiratory carrier?
b) Where would the curve for an effective carrier appear in the figure?
