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Questions and Answers
What type of bond is a disulfide bond?
What type of bond is a disulfide bond?
Why are disulfide bonds important for protein stability?
Why are disulfide bonds important for protein stability?
Which amino acid is highlighted for its role as a 'pH sensor'?
Which amino acid is highlighted for its role as a 'pH sensor'?
What is the significance of the pKa in relation to hydrogen bonds?
What is the significance of the pKa in relation to hydrogen bonds?
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What was concluded about the strongest hydrogen bond based on pKa?
What was concluded about the strongest hydrogen bond based on pKa?
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What is the role of tryptophan in relation to ultraviolet absorbance?
What is the role of tryptophan in relation to ultraviolet absorbance?
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Which statement about hydrogen bonds is true?
Which statement about hydrogen bonds is true?
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What does a lower pKa indicate about a substance's affinity for protons?
What does a lower pKa indicate about a substance's affinity for protons?
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How does the pKa of a leaving group influence its ability to leave in a chemical reaction?
How does the pKa of a leaving group influence its ability to leave in a chemical reaction?
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What occurs during the formation of clathrate structures involving hydrogen bonds?
What occurs during the formation of clathrate structures involving hydrogen bonds?
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How does the pKa of acetic acid in water compare to its pKa in DMSO?
How does the pKa of acetic acid in water compare to its pKa in DMSO?
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In what way does a solvent with a low pKa influence protonatable groups?
In what way does a solvent with a low pKa influence protonatable groups?
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What factor allows acetate ions to stabilize their negative charge more effectively in water?
What factor allows acetate ions to stabilize their negative charge more effectively in water?
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What occurs when a functional group is easier to protonate?
What occurs when a functional group is easier to protonate?
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Why is it less favorable for acetic acid to deprotonate in DMSO compared to water?
Why is it less favorable for acetic acid to deprotonate in DMSO compared to water?
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What is the buffering range defined in terms of pKa?
What is the buffering range defined in terms of pKa?
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How can the folding of a protein affect its pKa values?
How can the folding of a protein affect its pKa values?
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How does the concept of pKa relate to protein folding and function?
How does the concept of pKa relate to protein folding and function?
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What is one effect of the native protein structure on hydrogen bonding?
What is one effect of the native protein structure on hydrogen bonding?
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What does Charles Tanford suggest about hydrogen bonds in protein folding?
What does Charles Tanford suggest about hydrogen bonds in protein folding?
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What happens to a functional group's pKa when it becomes easier to protonate?
What happens to a functional group's pKa when it becomes easier to protonate?
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In the context of protein stability, what role do salt bridges play?
In the context of protein stability, what role do salt bridges play?
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What might happen when the pKa of an -OH group decreases upon protein folding?
What might happen when the pKa of an -OH group decreases upon protein folding?
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What happens to a protein as it becomes desolvated during folding?
What happens to a protein as it becomes desolvated during folding?
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Why is water the primary solvent of concern in biochemistry regarding pKa?
Why is water the primary solvent of concern in biochemistry regarding pKa?
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How does hemoglobin sense changes in blood pH?
How does hemoglobin sense changes in blood pH?
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What must occur for a protein to achieve a low-energy folded state?
What must occur for a protein to achieve a low-energy folded state?
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What occurs when blood pH becomes too basic?
What occurs when blood pH becomes too basic?
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Which of the following best describes the relationship between pKa and proton affinity in a protein core?
Which of the following best describes the relationship between pKa and proton affinity in a protein core?
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What role does stabilizing negative charge on a conjugate base play in acid-base reactions?
What role does stabilizing negative charge on a conjugate base play in acid-base reactions?
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Why might pKa values of proteins differ from standard values found in textbooks?
Why might pKa values of proteins differ from standard values found in textbooks?
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What is the primary role of histidine residues in hemoglobin?
What is the primary role of histidine residues in hemoglobin?
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What happens to the binding of protons to hemoglobin as blood pH increases?
What happens to the binding of protons to hemoglobin as blood pH increases?
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At which blood pH would a person be at risk of death due to protonation of hemoglobin?
At which blood pH would a person be at risk of death due to protonation of hemoglobin?
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According to the discussed topics, what is the extinction coefficient calculated for the enzyme?
According to the discussed topics, what is the extinction coefficient calculated for the enzyme?
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Using Lambert-Beer Law, if the absorbance of the enzyme solution is 0.85 and the extinction coefficient is 4790 M-1 cm-1, what is the concentration of the protein in the solution?
Using Lambert-Beer Law, if the absorbance of the enzyme solution is 0.85 and the extinction coefficient is 4790 M-1 cm-1, what is the concentration of the protein in the solution?
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What is the physiological pH of blood typically found in humans?
What is the physiological pH of blood typically found in humans?
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What does a 50:50 ratio of deprotonated to protonated histidine indicate?
What does a 50:50 ratio of deprotonated to protonated histidine indicate?
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Which of the following is a correct statement regarding the pKa of histidine relative to physiological pH?
Which of the following is a correct statement regarding the pKa of histidine relative to physiological pH?
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What is the primary role of salt bridges in a folded protein?
What is the primary role of salt bridges in a folded protein?
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How do salt bridges and hydrogen bonds affect the free energy change (dG) during protein folding?
How do salt bridges and hydrogen bonds affect the free energy change (dG) during protein folding?
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What is a significant factor that drives protein folding according to the discussion?
What is a significant factor that drives protein folding according to the discussion?
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Which statement best describes the energy states of a protein during folding?
Which statement best describes the energy states of a protein during folding?
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In the context of protein folding, what is meant by a 'two-state model'?
In the context of protein folding, what is meant by a 'two-state model'?
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What happens to the energy absorbed when hydrogen bonds in clathrate cages are broken?
What happens to the energy absorbed when hydrogen bonds in clathrate cages are broken?
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What are 'intermediate states' in protein folding?
What are 'intermediate states' in protein folding?
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Why might hydrogen bonding and Van der Waals interactions be significant in protein stability?
Why might hydrogen bonding and Van der Waals interactions be significant in protein stability?
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Study Notes
VSG #2 - Chapter 2 Review
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Tryptophan UV Absorbance: Tryptophan is used for UV absorbance.
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Disulfide Bonds in Protein Stability:
- Proteins are composed of covalently linked amino acids.
- Disulfide bonds are covalent.
- They contribute to protein stability.
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Protein Composition: Proteins are made of covalently linked amino acids; disulfide bonds are a type of covalent bond.
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pKa Values & Titratable Protons:
- Know the pKa of H, K, R, E, D, C, Y.
- Know the titratable protons of residues.
- pKa values for overall protein structure (not all side chains) are required for quiz 4.
- Histidine pKa values are needed now and used to make a pH sensor.
Hydrogen Bonds
- Hydrogen Bond Strength: The hydrogen bond on the right is considered stronger because the donor and the protonated form of the acceptor have the same pKa value. This results in greater covalent character in the molecule.
Endergonic & Exothermic Reactions
- Temperature & Spontaneity: An endothermic, exothermic reaction cannot be made spontaneous by increasing temperature. Decreasing temperature may make it spontaneous.
ATP Hydrolysis
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Standard Free Energy Change: The standard free energy change for ATP hydrolysis at 37°C is -30.5 kJ/mol.
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Q (Reaction Quotient): Q = [ADP][Pi]/[ATP]
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ΔG (Gibbs Free Energy): ΔG = ΔG° + RTlnQ
Protein Folding
- Two-State Model: The two-state model for protein folding considers folded and unfolded states.
- Rule of Thumb: A ratio of 1000:1 (folded:unfolded) corresponds to approximately -3.4 kcal/mol for AGfolding.
Protein Folding and Mutations
- Surface vs. Buried Residues: The effect on folding equilibrium differs when a charged residue is on the protein surface compared to buried in the core. A buried charge will have a greater influence on the folding equilibrium because of the cost of desolvation.
Non-Covalent Interactions
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Ranking:
- Ionic bonds are the strongest.
- Dipole-dipole interactions.
- Van der Waals forces are the weakest.
H-Bonding
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Donor/Acceptor: A ROH group is a good H-bond donor compared to a RCH3 as there is a differing pKa value. This means ROH's oxygen is more electronegative than the H of a RCH3, which means there is a partial charge on ROH, making it a better dipole compared to RCH3 which doesn't have a partial charge.
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Ice vs. Liquid Water: H-bonds between water molecules are stronger in ice than in liquid water due to less "flickering'' in ice.
Buffering of Blood
- Carbonic Acid-Bicarbonate Buffer: The carbonic acid-bicarbonate buffer system maintains blood pH through a reversible reaction, in which the concentration of carbon dioxide and water affect the equilibrium.
- Hyperventilation and pH: Hyperventilation expels more CO2 than is produced, which causes a deviation away from equilibrium resulting in blood becoming more basic (increase in pH) .
pKa and Solvent Effects
- Solvent DMSO: pKa values for acetic acid are different in water vs DMSO. Solvent will influence the ease of protonation or deprotonation.
- Protein Environments: The pKa of an acid buried in a protein core is likely higher than in solution due to reduced solvation of the conjugate base.
- Salt Bridges: Salt bridges involve interactions between oppositely charged groups in protein structure. The ratio of protonation vs deprotonation are factors to determine whether salt bridges will form.
Conformational Change of Hemoglobin
- Hemoglobin and pH: Hemoglobin binds or releases protons based on blood Ph changes. Protons bind to hemoglobin at histidine residues when the blood pH is low and can be released when the blood pH is high.
Other
- Absorption Calculations: To determine protein concentration given absorbance, use the formula: A = εLC
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Description
This quiz covers key concepts from Chapter 2 of the VSG, focusing on protein structure, including tryptophan UV absorbance, disulfide bonds, pKa values, and hydrogen bonds. Additionally, it delves into reactions such as endergonic and exothermic processes. Review these important topics to ensure a solid understanding of protein chemistry.
