CHEM 441A Spring 2024
Exam #1 Study Guide – Chapters 2, 3, 4.1, and 4.2
2.1 Energy conversion in biological systems
🞐 Understand the similarities and differences between steady state, homeostasis, and equilibrium 🞐
Be familiar with the characteristics of oxidation and reduction reactions
Can you quickly determine the reduced vs. oxidized molecules in a reaction scheme?
Oxidation reactions decrease the number of hydrogens and increase the oxygens; loss of electrons
Reduction increase hydrogens and decrease the number of oxygens; gain of electrons
🞐 Explain the first and second law of thermodynamics
🞐 Qualitatively and quantitatively describe Gibbs free energy
🞐 Use Gibbs free energy to predict the spontaneity of biochemical processes
Do you know whether enthalpy, entropy, and Gibbs free energy are favorable or unfavorable based on the sign of the term
(positive/negative)? Can you describe each situation appropriately (e.g., exothermic/endothermic, endergonic/exergonic,
etc.)?
B
Can you classify a process as spontaneous vs. non-spontaneous given the favorability/unfavorability of the enthalpy and
entropy terms? Can you predict temperature-dependent spontaneity?
Refer to the table above. If temperature increases, it is non-spontaneous. If temperature decreases, it is spontaneous.
🞐 Relate: mass-action ratio, equilibria constants, actual free energy changes, biochemical standard free energy 🞐
Explain thermodynamic coupling and its role in facilitating biological endergonic reactions 🞐 Provide chemical
,arguments for the thermodynamic spontaneity of ATP hydrolysis and its kinetic stability Can you list reasons for
the thermodynamic favorability of ATP hydrolysis?
Entropy is favored because more products, charge separation, and the resonance is better in inorganic
phosphate
🞐 Calculate the energy charge of a cell and understand its meaning for the energy state of a cell Do you
understand adenylate recycling and the relationship between [ATP], [ADP], and [AMP] in the cell?
2.2 Water is critical for life processes
🞐 Identify hydrogen bond donors and hydrogen bond acceptors
🞐 Differentiate among hydrogen bonds, ionic interactions, and van der Waals interactions Can you predict the most likely
type of interaction that would occur between the sidechains of any two given amino acids?
Hydrogen bonds- acceptors: N, O donors: N-H, O-H
Ionic- between two opposite charges
Van der Waals- occur between two induced dipoles of neutral molecules and are distance dependent
🞐 Explain the concept of the hydrophobic effect and how it impacts protein folding
Can you explain the hydrophobic effect (using protein folding as a model) by describing the contributions of enthalpy and
entropy?
, 🞐 Explain the effects of hypotonic/isotonic/hypertonic solutions on cells
🞐 Calculate [H+] or [OH-] given [OH-] or [H+]
🞐 Relate pH to [H+] and [OH-]
🞐 Differentiate between weak acids and strong acids and weak bases and strong bases
Can you describe the relationship between acid strength, pKa value, and [H+]? Do you understand the log scale (p)?
pH= pKa, more acidic = lower pKa = more protonated, over 7= basic, under 7= acidic
🞐 Relate pH to pKa and the molar ratio of conjugate pairs using the Henderson-Hasselbalch equation 🞐
Navigate titration curves for mono- and polyprotic acids
Are you able to draw the predominant species at a given pH for simple molecules? Could you explain the relationship
between conjugate pairs at conditions of pH = pKa?
Exam #1 Study Guide – Chapters 2, 3, 4.1, and 4.2
2.1 Energy conversion in biological systems
🞐 Understand the similarities and differences between steady state, homeostasis, and equilibrium 🞐
Be familiar with the characteristics of oxidation and reduction reactions
Can you quickly determine the reduced vs. oxidized molecules in a reaction scheme?
Oxidation reactions decrease the number of hydrogens and increase the oxygens; loss of electrons
Reduction increase hydrogens and decrease the number of oxygens; gain of electrons
🞐 Explain the first and second law of thermodynamics
🞐 Qualitatively and quantitatively describe Gibbs free energy
🞐 Use Gibbs free energy to predict the spontaneity of biochemical processes
Do you know whether enthalpy, entropy, and Gibbs free energy are favorable or unfavorable based on the sign of the term
(positive/negative)? Can you describe each situation appropriately (e.g., exothermic/endothermic, endergonic/exergonic,
etc.)?
B
Can you classify a process as spontaneous vs. non-spontaneous given the favorability/unfavorability of the enthalpy and
entropy terms? Can you predict temperature-dependent spontaneity?
Refer to the table above. If temperature increases, it is non-spontaneous. If temperature decreases, it is spontaneous.
🞐 Relate: mass-action ratio, equilibria constants, actual free energy changes, biochemical standard free energy 🞐
Explain thermodynamic coupling and its role in facilitating biological endergonic reactions 🞐 Provide chemical
,arguments for the thermodynamic spontaneity of ATP hydrolysis and its kinetic stability Can you list reasons for
the thermodynamic favorability of ATP hydrolysis?
Entropy is favored because more products, charge separation, and the resonance is better in inorganic
phosphate
🞐 Calculate the energy charge of a cell and understand its meaning for the energy state of a cell Do you
understand adenylate recycling and the relationship between [ATP], [ADP], and [AMP] in the cell?
2.2 Water is critical for life processes
🞐 Identify hydrogen bond donors and hydrogen bond acceptors
🞐 Differentiate among hydrogen bonds, ionic interactions, and van der Waals interactions Can you predict the most likely
type of interaction that would occur between the sidechains of any two given amino acids?
Hydrogen bonds- acceptors: N, O donors: N-H, O-H
Ionic- between two opposite charges
Van der Waals- occur between two induced dipoles of neutral molecules and are distance dependent
🞐 Explain the concept of the hydrophobic effect and how it impacts protein folding
Can you explain the hydrophobic effect (using protein folding as a model) by describing the contributions of enthalpy and
entropy?
, 🞐 Explain the effects of hypotonic/isotonic/hypertonic solutions on cells
🞐 Calculate [H+] or [OH-] given [OH-] or [H+]
🞐 Relate pH to [H+] and [OH-]
🞐 Differentiate between weak acids and strong acids and weak bases and strong bases
Can you describe the relationship between acid strength, pKa value, and [H+]? Do you understand the log scale (p)?
pH= pKa, more acidic = lower pKa = more protonated, over 7= basic, under 7= acidic
🞐 Relate pH to pKa and the molar ratio of conjugate pairs using the Henderson-Hasselbalch equation 🞐
Navigate titration curves for mono- and polyprotic acids
Are you able to draw the predominant species at a given pH for simple molecules? Could you explain the relationship
between conjugate pairs at conditions of pH = pKa?
