Podcast
Questions and Answers
How does water affect the strength of ionic interactions between biomolecules?
How does water affect the strength of ionic interactions between biomolecules?
- Water weakens ionic interactions by shielding charged groups. (correct)
- Water enhances ionic interactions by forming salt bridges.
- Water strengthens ionic interactions through hydrophobic effects.
- Water has no impact on the strength of ionic interactions.
Which characteristic of water molecules makes them effective hydrogen bonding partners?
Which characteristic of water molecules makes them effective hydrogen bonding partners?
- Their ability to serve as either hydrogen bond donors or acceptors due to their polarity. (correct)
- Their non-polar nature, which repels other molecules.
- Their inability to interact with charged molecules.
- Their large size and inability to donate protons.
What happens when two atoms are separated by the sum of their van der Waals radii?
What happens when two atoms are separated by the sum of their van der Waals radii?
- The atoms repel each other strongly.
- The attractive force between them is maximal. (correct)
- The atoms form a covalent bond.
- The attractive force between them is minimal.
In protein folding, where do non-polar side chains typically cluster?
In protein folding, where do non-polar side chains typically cluster?
What property primarily determines the solubility of a molecule in water?
What property primarily determines the solubility of a molecule in water?
Why do non-polar gases like $O_2$ and $CO_2$ present a challenge for biological transport?
Why do non-polar gases like $O_2$ and $CO_2$ present a challenge for biological transport?
How does the folding of a polypeptide affect the entropy of the surrounding water molecules?
How does the folding of a polypeptide affect the entropy of the surrounding water molecules?
Which of the following is a characteristic of van der Waals forces?
Which of the following is a characteristic of van der Waals forces?
What occurs when amphipathic molecules are mixed with water?
What occurs when amphipathic molecules are mixed with water?
What are the forces that hold the non-polar regions of amphipathic molecules together in water called?
What are the forces that hold the non-polar regions of amphipathic molecules together in water called?
How does the hydrophobic effect contribute to protein folding?
How does the hydrophobic effect contribute to protein folding?
What is the impact of introducing non-polar molecules in water?
What is the impact of introducing non-polar molecules in water?
What role does hydrophobic drive play in biomolecular structures?
What role does hydrophobic drive play in biomolecular structures?
What did the Nature paper suggest about water regarding biomolecules?
What did the Nature paper suggest about water regarding biomolecules?
What type of interactions primarily determine the three-dimensional structures formed by stable polymers of covalently linked building blocks?
What type of interactions primarily determine the three-dimensional structures formed by stable polymers of covalently linked building blocks?
Which statement is true regarding biomolecules and their interactions?
Which statement is true regarding biomolecules and their interactions?
Why is water considered essential for life as we know it, even when exploring the possibility of life on other planets?
Why is water considered essential for life as we know it, even when exploring the possibility of life on other planets?
How does water's interaction with hydrophobic molecules influence the structure of biomolecules, such as proteins?
How does water's interaction with hydrophobic molecules influence the structure of biomolecules, such as proteins?
In peptide bond formation, what role does water play, and how does this affect the overall biochemical process?
In peptide bond formation, what role does water play, and how does this affect the overall biochemical process?
Considering the electronegativity difference between oxygen and hydrogen in a water molecule, how does this polarity contribute to water's unique properties?
Considering the electronegativity difference between oxygen and hydrogen in a water molecule, how does this polarity contribute to water's unique properties?
Water molecules can form hydrogen bonds with each other. What is the maximum number of hydrogen bonds one water molecule can theoretically form?
Water molecules can form hydrogen bonds with each other. What is the maximum number of hydrogen bonds one water molecule can theoretically form?
If scientists were to discover a planet with an atmosphere primarily composed of formamide instead of water, what primary characteristic would make formamide a viable alternative to water for supporting life?
If scientists were to discover a planet with an atmosphere primarily composed of formamide instead of water, what primary characteristic would make formamide a viable alternative to water for supporting life?
Considering water's role as a solvent, how does its polarity affect the interactions between charged biomolecules?
Considering water's role as a solvent, how does its polarity affect the interactions between charged biomolecules?
What is the relationship between the electronegativity of an atom and its ability to attract electrons in a chemical bond, and how does oxygen fit into this?
What is the relationship between the electronegativity of an atom and its ability to attract electrons in a chemical bond, and how does oxygen fit into this?
What is the approximate hydrogen ion concentration, $[H^+]$, in a solution with a pH of 8?
What is the approximate hydrogen ion concentration, $[H^+]$, in a solution with a pH of 8?
What is the role of weak acids in a solution?
What is the role of weak acids in a solution?
If a weak acid, HA, has a pKa of 4.5, at what pH will the concentrations of HA and $A^−$ be equal?
If a weak acid, HA, has a pKa of 4.5, at what pH will the concentrations of HA and $A^−$ be equal?
Why does homeopathy lack scientific validity?
Why does homeopathy lack scientific validity?
Given $K_w = [H^+][OH^-] = 1.0 \times 10^{-14} M^2$, what is the hydroxide ion concentration $[OH^-]$ in a solution where $[H^+] = 1.0 \times 10^{-4} M$?
Given $K_w = [H^+][OH^-] = 1.0 \times 10^{-14} M^2$, what is the hydroxide ion concentration $[OH^-]$ in a solution where $[H^+] = 1.0 \times 10^{-4} M$?
If the pH of a solution changes from 3 to 5, what is the change in the hydrogen ion concentration?
If the pH of a solution changes from 3 to 5, what is the change in the hydrogen ion concentration?
What does a titration curve reveal about a weak acid?
What does a titration curve reveal about a weak acid?
How does the high specific heat capacity of water contribute to maintaining a stable internal environment in living organisms?
How does the high specific heat capacity of water contribute to maintaining a stable internal environment in living organisms?
Why does ice float on liquid water, and what is the biological significance of this property?
Why does ice float on liquid water, and what is the biological significance of this property?
Based on the text, what was Nature's conclusion regarding the claims that water can retain a 'memory' of past solutes in the context of homeopathy?
Based on the text, what was Nature's conclusion regarding the claims that water can retain a 'memory' of past solutes in the context of homeopathy?
Why was there initial concern regarding 'polywater' and its potential impact?
Why was there initial concern regarding 'polywater' and its potential impact?
What ultimately debunked the claims surrounding 'polywater?'
What ultimately debunked the claims surrounding 'polywater?'
How does water's ability to form hydration layers around ions contribute to biological processes?
How does water's ability to form hydration layers around ions contribute to biological processes?
Considering water's properties, which scenario would MOST likely occur due to its high surface tension?
Considering water's properties, which scenario would MOST likely occur due to its high surface tension?
If a hypothetical liquid was discovered with a significantly lower specific heat capacity than water, what would be the MOST likely consequence for organisms using this liquid as their primary internal fluid?
If a hypothetical liquid was discovered with a significantly lower specific heat capacity than water, what would be the MOST likely consequence for organisms using this liquid as their primary internal fluid?
How does the density change of water when it transitions from liquid to solid impact aquatic ecosystems in cold climates?
How does the density change of water when it transitions from liquid to solid impact aquatic ecosystems in cold climates?
Using the Henderson-Hasselbalch equation, calculate the pH of a solution containing 0.2 M of a weak acid (HA) with a pKa of 6.0, and 0.5 M of its conjugate base (A-).
Using the Henderson-Hasselbalch equation, calculate the pH of a solution containing 0.2 M of a weak acid (HA) with a pKa of 6.0, and 0.5 M of its conjugate base (A-).
A buffer solution contains a weak acid and its conjugate base. If the ratio of the conjugate base to weak acid is 10:1 and the pH of the buffer is 5.0, what is the pKa of the weak acid?
A buffer solution contains a weak acid and its conjugate base. If the ratio of the conjugate base to weak acid is 10:1 and the pH of the buffer is 5.0, what is the pKa of the weak acid?
If the pKa of a certain weak acid is 4.5, at what pH will the concentration of the acid be equal to the concentration of its conjugate base?
If the pKa of a certain weak acid is 4.5, at what pH will the concentration of the acid be equal to the concentration of its conjugate base?
A solution contains 0.05 M benzoic acid and 0.15 M benzoate. The pKa of benzoic acid is 4.2. What is the pH of this solution?
A solution contains 0.05 M benzoic acid and 0.15 M benzoate. The pKa of benzoic acid is 4.2. What is the pH of this solution?
What is the ratio of acetic acid to acetate required to create a buffer of pH 5.0, given that the pKa of acetic acid is 4.76?
What is the ratio of acetic acid to acetate required to create a buffer of pH 5.0, given that the pKa of acetic acid is 4.76?
Determine the pKa of a weak acid if a solution containing 0.05 M of the acid and 0.25 M of its conjugate base has a pH of 6.0.
Determine the pKa of a weak acid if a solution containing 0.05 M of the acid and 0.25 M of its conjugate base has a pH of 6.0.
A chemist needs to create a buffer solution with a pH of 7.4. They have access to a weak acid with a pKa of 7.0 and its conjugate base. What ratio of conjugate base to weak acid should they use?
A chemist needs to create a buffer solution with a pH of 7.4. They have access to a weak acid with a pKa of 7.0 and its conjugate base. What ratio of conjugate base to weak acid should they use?
A buffer solution is prepared with a weak acid (pKa = 4.0) and its conjugate base. If the pH of the buffer is 3.7, which of the following statements is true?
A buffer solution is prepared with a weak acid (pKa = 4.0) and its conjugate base. If the pH of the buffer is 3.7, which of the following statements is true?
Flashcards
Isothermic Function
Isothermic Function
Helps maintain a stable internal temperature due to water's high specific heat capacity.
Ice Structure
Ice Structure
Each water molecule forms four hydrogen bonds, creating a less dense, ordered structure.
Ice Insulation
Ice Insulation
Ice floats, insulating the water below and preventing it from freezing solid.
Polywater
Polywater
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Water as a Solvent
Water as a Solvent
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Water's Versatility
Water's Versatility
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Electrostatic Interactions
Electrostatic Interactions
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Water's Solvent Properties
Water's Solvent Properties
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Water's Role in Life
Water's Role in Life
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Passive Role of Water
Passive Role of Water
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Active Role of Water
Active Role of Water
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Water as a Polar Molecule
Water as a Polar Molecule
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Electronegativity
Electronegativity
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Partial Charges in Water
Partial Charges in Water
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Water's Dipole Influences
Water's Dipole Influences
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Hydrogen Bonding Capacity of Water
Hydrogen Bonding Capacity of Water
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Hydrogen Bonds in Biomolecules
Hydrogen Bonds in Biomolecules
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Solubility in Water
Solubility in Water
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Hydrophilic Molecules
Hydrophilic Molecules
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Hydrophobic Molecules
Hydrophobic Molecules
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Amphipathic Molecules
Amphipathic Molecules
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Hydrophobic Interactions
Hydrophobic Interactions
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Non-Covalent Interactions
Non-Covalent Interactions
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Hydrophobic Drive
Hydrophobic Drive
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Water Shielding
Water Shielding
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Maximal van der Waals Attraction
Maximal van der Waals Attraction
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Hydrophobic Effect
Hydrophobic Effect
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Hydrophobic Effect & Entropy
Hydrophobic Effect & Entropy
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Non-polar association
Non-polar association
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van der Waals Forces
van der Waals Forces
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Hydrophobic Effect
Hydrophobic Effect
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Polypeptide Folding and Entropy
Polypeptide Folding and Entropy
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Homeopathic remedies
Homeopathic remedies
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Water 'memory'
Water 'memory'
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Ionization of Water
Ionization of Water
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Kw (Ion Product of Water)
Kw (Ion Product of Water)
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pH Scale
pH Scale
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Weak Acids and Bases
Weak Acids and Bases
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Ka (Acid Dissociation Constant)
Ka (Acid Dissociation Constant)
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Buffer
Buffer
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Henderson-Hasselbalch Equation
Henderson-Hasselbalch Equation
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What is pKa?
What is pKa?
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pKa of Acetic Acid
pKa of Acetic Acid
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Lactic Acid Mixture
Lactic Acid Mixture
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Calculating pKa
Calculating pKa
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pKa of Lactic Acid
pKa of Lactic Acid
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pH > pKa
pH > pKa
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Acetic Acid Solution pH
Acetic Acid Solution pH
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Study Notes
- Water is the most abundant molecule in living organisms and has both passive and active roles in biochemistry.
Water's Passive Role
- Biomolecules form in response to interaction with water.
- Protein folding is driven by burying hydrophobic residues.
Water's Active Role
- Water participates in many biochemical reactions.
- Peptide bond formation releases a water molecule.
- The presence of water on other planets is a critical determinant of their habitability by humans.
- Scientists contemplate alternate liquids like ammonia or formamide for life.
Water Molecular Structure/Function Relationship
- Oxygen and hydrogen differ in their electronegativities.
- Oxygen is more electronegative than hydrogen, giving water a permanent dipole.
- Oxygen has a partial negative charge, and each hydrogen has a partial positive charge.
- Each water molecule can donate or accept two hydrogen bonds.
- The dipole of a water molecule influences its ability to form electrostatic interactions with charged molecules and hydrogen bonds with other water molecules.
Hydrogen Bonds
- Hydrogen bonds are electrostatic interactions between an electronegative atom with a covalently linked hydrogen (donor) to another electronegative atom with a free electron pair (acceptor).
- Oxygen and nitrogen are common hydrogen bonders within biomolecules.
- Oxygen and nitrogen can each serve as hydrogen bond donors and acceptors.
- The significance of hydrogen bonds for physiology is greater than that of any other single structural feature.
Hydrogen Bond Strength and Geometry
- Hydrogen bonds are relatively weak, ~5% of the strength of a covalent bond.
- Hydrogen bonds are about double the length of a covalent bond.
- Hydrogen bond strength depends on its geometry.
- Anti-parallel beta sheets are more stable than parallel due to better hydrogen bonding geometry.
Unusual Properties of Water
- Each water molecule can donate and accept two hydrogen bonds.
- Each water molecule can potentially participate in four hydrogen bonds with four other water molecules.
- In liquid water, each molecule participates in an average of 3.4 hydrogen bonds in dynamic "flickering clusters".
- Hydrogen bonds between water molecules confer great internal cohesion, influencing water's properties.
- Water has a high heat of vaporization, which is the amount of heat required to vaporize a liquid at its boiling temperature.
- Water has a high specific heat capacity, which is the amount of heat required to raise the temperature of a substance by one degree.
- Water has a higher melting point, boiling point, and heat of vaporization than most common solvents.
- Living organisms burn tremendous amounts of energy, which results in heat.
- Most living organisms are isothermic and need to regulate and maintain their temperatures.
- The high composition of water within bodies, coupled with its high specific heat capacity, aids in temperature regulation.
- In ice, each water molecule participates in four hydrogen bonds with other water molecules.
- Ice has a lower density than liquid water, causing it to float.
Polywater
- A Soviet physicist studied water forced through quartz tubes, finding that this resulted in a new water form (polywater) with a higher boiling point, lower freezing point, and much higher viscosity than ordinary water.
- Original theories suggested this was due to a novel arrangement of interaction between water molecules.
- It was later proven to be "bad science" when an American scientist found its properties were due to the influence of impurities, such as sweat.
Water as a Solvent
- Water molecules can interact and dissolve charged solutes through the formation of layers of hydration.
- Water molecules can greatly interact with both positively and negatively charged ions, due to their small size and permanent dipole.
Water's Ability to Act as a Solvent
- Biomolecules have functional groups that can form hydrogen bonds.
- These groups can hydrogen bond within the same molecule, other biomolecules, or with water.
- Water molecules are ideal hydrogen bonding partners because of their small size and ability to serve as either donors or acceptors.
Solubility of Dissolved Molecules
- The solubility of molecules in water depends on the ability to interact with water molecules.
- Molecules with charges (+ or -) or that participate in hydrogen bonds have high solubility in water.
- Hydrophilic (water-loving) molecules are polar.
- Hydrophobic (water-fearing) molecules are non-polar.
- Amphipathic molecules contain both hydrophobic and hydrophilic portions, like fatty acids.
- Gases such as CO2 and O2 are non-polar and have limited solubility in water.
- Limited solubility presents transport challenges. Specialized transport proteins and strategies are required for their transport.
Behavior of Amphipathic Substances
- When an amphipathic molecule mixes with water, hydrophilic regions interact favorably with the water, but hydrophobic regions cluster together to minimize their surface area that is exposed to the water.
- Forces holding non-polar regions of the molecule together are called hydrophobic interactions.
- Most biomolecules are amphipathic.
- Hydrophobic drive is the primary driving force in the formation and stabilization of biomolecular structures.
Weak Interactions
- Most biomolecules are stable polymers of covalently linked building blocks.
- Three-dimensional structures are largely determined through non-covalent interactions.
- Interactions between biomolecules are also largely determined by non-covalent interactions.
- Non-covalent interactions enable transient, dynamic interactions and structure/function flexibility.
- Non-covalent forces influence the formation and stabilization of structures of biomolecules, recognition/interactions between biomolecules, and binding of reactants to enzymes. Non-covalent interactions include hydrogen bonds, ionic (electrostatic) interactions, hydrophobic interactions, and van der Waals interactions.
Hydrogen Bonds in Detail
- Functional groups with biomolecules hydrogen bonding capacity.
- These can form hydrogen bonds with water molecules, groups in the same molecule (intramolecular), and groups in other molecules (intermolecular).
- Hydrogen bonds are critical for the specificity of biomolecular interactions but less so for the formation of biomolecular structures.
- In the unfolded state, groups can hydrogen bond with water.
- There is little to be gained, from a hydrogen bonding perspective, with the formation of higher-order structures.
Ionic (Electrostatic) Interactions
- Electrostatic interactions between charged groups can be attractive (oppositely charged groups) or repulsive (similarly charged groups).
- The magnitude of contribution of ionic interactions to biomolecular structures is reduced by the shielding of these groups by water molecules.
- Water tends to shield the charged groups, greatly diminishing the strength of the interaction.
- The strength of electrostatic interactions depends on the distance separating the atoms and the nature of the intervening medium
Van der Waals Forces
- Interactions between permanent and induced dipoles occur and are short-range, low-magnitude interactions.
- When two atoms are separated by the sum of the van der Waals radii, the attraction is maximal.
- A large number of atoms are brought into van der Waals contact when two surfaces of complementary shapes come together.
- These are abundant in the core of folded proteins.
Hydrophobic Effect
- Drives polar groups to interact with water and non-polar regions shielded away from water.
- In protein folding, for example, non-polar side chains cluster in the protein's interior away from water, while polar and charged side chains remain on the outer surface facing water.
- The folding of a protein notably involves creating a more ordered state, contradicting the Second Law of Thermodynamics.
Thermodynamics of the Hydrophobic Effect
- Water molecules around hydrophobic molecules become more ordered, decreasing the entropy of water.
- The association of non-polar molecules (or regions) releases some ordered water molecules, which increases the entropy of water.
- Polypeptide folding decreases the entropy of the polypeptide but increases the entropy of the associated water.
Water Memory
- In 1988, a paper reported that an extreme dilution of a biomolecule retains some biological activity.
- The extent of dilution was such that there was no possibility that a single molecule remained.
- Authors suggested water molecules could “remember” what the original molecule looked like through retention of interactions between water molecules, in the presence of an active ingredient.
- It was disproved shortly after it was published by the scientific community
Bad Science
- Homeopathic remedies are prepared by repeatedly diluting a chosen substance, often 30 sequential dilutions of 1 in 100.
- This corresponds to a dilution of 1 in an astronomically large number.
- By current understanding, homeopathy makes no sense,. Countless investigations have failed to find any scientific merit in homeopathy.
- The disproven theory that water molecules remember molecule shapes supports homeopathy.
Ionization of Water
- In solution, the structure of water is more complicated than H2O.
- Water has a limited tendency to ionize to hydrogen ions (H+) and hydroxide ions (OH-).
- Kw is the ion product of water.
The pH Scale
- pH = -log [H+] = log 1/[H+]
- pH is a log scale, such that a one pH unit difference equals a tenfold difference in [H+].
Characteristic Dissociation Constants
- Strong acids and bases dissociate completely in water.
- Weak acids and bases do not completely dissociate in water.
- Weak acids can serve as buffers.
- Ka values are often expressed as pKa's (pKa = -log Ka).
Titration Curves
- The ratio of the acid to the conjugate base changes over the course of the titration curve.
- When pH = pKa, then [A-] = [HA].
- When pH = pKa, the solution can best resist changes in pH.
- Buffering region extends one pH unit on either side of the pKa point.
- For a weak acid of pKa 4.76, the buffering range would be 3.76 to 5.76.
- The line in red represents the weakest acid.
- The line in blue represents the strongest acid.
- The lower the pKa, the stronger the acid.
Buffers
- Organisms need to be able to maintain a constant pH.
- Changes to pH could alter the protonation state of biomolecules, potentially changing their structure and function.
- A number of weak acids serve to buffer biological systems.
- For example, blood pH is maintained by a bicarbonate buffer system.
- Compensatory respiratory alkalosis maintains the H2CO3/HCO3- ratio to maintain a constant pH.
The Henderson-Hasselbalch Equation
- Describes the relationship between the pH of the solution, the pKa of the weak acid and the relative concentrations of the weak acid (HA) and conjugate base (A-).
- Given any two of these variables, it is possible to calculate the third.
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Description
Explore the impact of water on biomolecular interactions, hydrogen bonding, and solubility. Understand van der Waals forces, hydrophobic effects in protein folding, and challenges in transporting non-polar gases. Learn about the behavior of amphipathic molecules in water and the hydrophobic drive.