Biomolecules and Water Interactions
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Questions and Answers

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?

  • 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?

  • 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?

<p>In the interior of the protein, away from water. (A)</p> Signup and view all the answers

What property primarily determines the solubility of a molecule in water?

<p>Its ability to interact with water molecules through charge or hydrogen bonds. (D)</p> Signup and view all the answers

Why do non-polar gases like $O_2$ and $CO_2$ present a challenge for biological transport?

<p>They have limited solubility in water and blood. (B)</p> Signup and view all the answers

How does the folding of a polypeptide affect the entropy of the surrounding water molecules?

<p>It increases the entropy as some ordered water molecules are released. (C)</p> Signup and view all the answers

Which of the following is a characteristic of van der Waals forces?

<p>Short range, low magnitude interactions (C)</p> Signup and view all the answers

What occurs when amphipathic molecules are mixed with water?

<p>The hydrophilic regions interact favorably with the water, while the hydrophobic regions cluster together. (B)</p> Signup and view all the answers

What are the forces that hold the non-polar regions of amphipathic molecules together in water called?

<p>Hydrophobic interactions. (A)</p> Signup and view all the answers

How does the hydrophobic effect contribute to protein folding?

<p>It promotes the clustering of non-polar side chains in the protein interior. (D)</p> Signup and view all the answers

What is the impact of introducing non-polar molecules in water?

<p>Water molecules around hydrophobic molecules become more ordered (C)</p> Signup and view all the answers

What role does hydrophobic drive play in biomolecular structures?

<p>It is a primary driving force in the formation and stabilization of biomolecular structures. (D)</p> Signup and view all the answers

What did the Nature paper suggest about water regarding biomolecules?

<p>Water molecules can retain the interactions that existed between water molecules in the presence of active agent (B)</p> Signup and view all the answers

What type of interactions primarily determine the three-dimensional structures formed by stable polymers of covalently linked building blocks?

<p>Non-covalent interactions. (C)</p> Signup and view all the answers

Which statement is true regarding biomolecules and their interactions?

<p>Interactions between biomolecules are largely determined by non-covalent interactions. (B)</p> Signup and view all the answers

Why is water considered essential for life as we know it, even when exploring the possibility of life on other planets?

<p>Water's ability to act as a solvent and participate in biochemical reactions is critical. (A)</p> Signup and view all the answers

How does water's interaction with hydrophobic molecules influence the structure of biomolecules, such as proteins?

<p>Water promotes the clustering of hydrophobic residues in the interior, minimizing their exposure. (D)</p> Signup and view all the answers

In peptide bond formation, what role does water play, and how does this affect the overall biochemical process?

<p>Water is released as a product, contributing to the overall entropy of the system. (D)</p> Signup and view all the answers

Considering the electronegativity difference between oxygen and hydrogen in a water molecule, how does this polarity contribute to water's unique properties?

<p>It gives water molecules a permanent dipole, enabling electrostatic and hydrogen bond interactions. (A)</p> Signup and view all the answers

Water molecules can form hydrogen bonds with each other. What is the maximum number of hydrogen bonds one water molecule can theoretically form?

<p>Four, two through its hydrogen atoms and two through its oxygen atom. (C)</p> Signup and view all the answers

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?

<p>Formamide's ability to form hydrogen bonds and act as a solvent. (C)</p> Signup and view all the answers

Considering water's role as a solvent, how does its polarity affect the interactions between charged biomolecules?

<p>Water shields charged biomolecules, weakening their electrostatic interactions and promoting dissolution. (C)</p> Signup and view all the answers

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?

<p>Electronegativity indicates an atom's electron-attracting ability; oxygen is highly electronegative, pulling electrons towards it. (C)</p> Signup and view all the answers

What is the approximate hydrogen ion concentration, $[H^+]$, in a solution with a pH of 8?

<p>$1 \times 10^{-8} M$ (C)</p> Signup and view all the answers

What is the role of weak acids in a solution?

<p>They serve as buffers, resisting changes in pH upon addition of acid or base. (C)</p> Signup and view all the answers

If a weak acid, HA, has a pKa of 4.5, at what pH will the concentrations of HA and $A^−$ be equal?

<p>pH = 4.5 (D)</p> Signup and view all the answers

Why does homeopathy lack scientific validity?

<p>Because the extreme dilutions used typically result in none of the original substance remaining. (B)</p> Signup and view all the answers

Given $K_w = [H^+][OH^-] = 1.0 \times 10^{-14} M^2$, what is the hydroxide ion concentration $[OH^-]$ in a solution where $[H^+] = 1.0 \times 10^{-4} M$?

<p>$1.0 \times 10^{-10} M$ (C)</p> Signup and view all the answers

If the pH of a solution changes from 3 to 5, what is the change in the hydrogen ion concentration?

<p>Decrease by a factor of 100. (B)</p> Signup and view all the answers

What does a titration curve reveal about a weak acid?

<p>It reveals the pKa of the weak acid. (D)</p> Signup and view all the answers

How does the high specific heat capacity of water contribute to maintaining a stable internal environment in living organisms?

<p>By buffering temperature changes, preventing drastic shifts due to metabolic processes or environmental exposure. (C)</p> Signup and view all the answers

Why does ice float on liquid water, and what is the biological significance of this property?

<p>Ice floats because it is less dense than liquid water due to hydrogen bonding creating a more open structure; this insulates aquatic environments, preventing them from freezing solid. (A)</p> Signup and view all the answers

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?

<p>The claims were considered to have no substantial basis and were regarded as fanciful and unnecessary. (C)</p> Signup and view all the answers

Why was there initial concern regarding 'polywater' and its potential impact?

<p>Because its unusual properties, like higher boiling point and viscosity, suggested it could self-propagate and potentially replace normal water with catastrophic consequences. (A)</p> Signup and view all the answers

What ultimately debunked the claims surrounding 'polywater?'

<p>Further analysis revealed it was simply ordinary water contaminated with impurities, affecting its properties. (C)</p> Signup and view all the answers

How does water's ability to form hydration layers around ions contribute to biological processes?

<p>It facilitates the transport of ions across cell membranes and prevents their aggregation, maintaining proper ionic balance and enabling nerve impulse transmission. (D)</p> Signup and view all the answers

Considering water's properties, which scenario would MOST likely occur due to its high surface tension?

<p>A small insect being able to walk on the surface of a pond. (A)</p> Signup and view all the answers

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?

<p>Increased sensitivity to temperature fluctuations, making it harder to maintain a stable internal environment. (D)</p> Signup and view all the answers

How does the density change of water when it transitions from liquid to solid impact aquatic ecosystems in cold climates?

<p>The decreased density of ice causes it to float, insulating the water below and allowing aquatic life to survive. (B)</p> Signup and view all the answers

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-).

<p>6.40 (D)</p> Signup and view all the answers

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?

<p>4.0 (B)</p> Signup and view all the answers

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?

<p>4.5 (D)</p> Signup and view all the answers

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?

<p>4.7 (A)</p> Signup and view all the answers

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?

<p>0.55 (D)</p> Signup and view all the answers

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.

<p>5.30 (B)</p> Signup and view all the answers

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?

<p>2.51 (C)</p> Signup and view all the answers

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?

<p>The concentration of the acid is greater than the concentration of the conjugate base. (B)</p> Signup and view all the answers

Flashcards

Isothermic Function

Helps maintain a stable internal temperature due to water's high specific heat capacity.

Ice Structure

Each water molecule forms four hydrogen bonds, creating a less dense, ordered structure.

Ice Insulation

Ice floats, insulating the water below and preventing it from freezing solid.

Polywater

False claim of a new water form with unusual properties; later disproven as impurity effects.

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Water as a Solvent

Water molecules surround and dissolve charged solutes through electrostatic interactions and hydration layers.

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Water's Versatility

Due to their small size and permanent dipole, water molecules effectively interact with both positive and negative ions.

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Electrostatic Interactions

Dissolves charged solutes through layers of hydration, interacting with positive and negative ions.

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Water's Solvent Properties

Water's ability to dissolve many substances due to its polarity and small size.

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Water's Role in Life

Most abundant molecule in living organisms; plays passive and active roles in biochemistry.

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Passive Role of Water

Biomolecule structure adapts based on water interaction (e.g., hydrophobic residues bury themselves).

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Active Role of Water

Water participates directly in reactions (e.g., peptide bond formation releases water).

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Water as a Polar Molecule

A molecule with a permanent dipole due to unequal sharing of electrons. Oxygen is more electronegative than Hydrogen.

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Electronegativity

The measure of an atom's ability to attract electrons in a chemical bond.

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Partial Charges in Water

Oxygen has a partial negative charge; hydrogen has a partial positive charge.

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Water's Dipole Influences

Electrostatic interactions with charged molecules and hydrogen bonds.

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Hydrogen Bonding Capacity of Water

Each water molecule can donate/accept up to TWO hydrogen bonds.

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Hydrogen Bonds in Biomolecules

Functional groups on biomolecules that can form hydrogen bonds with water, other biomolecules, or within the same molecule.

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Solubility in Water

The degree to which a substance can dissolve in water, dependent on its ability to interact with water molecules.

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Hydrophilic Molecules

Molecules that are attracted to water, typically polar and able to form hydrogen bonds.

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Hydrophobic Molecules

Molecules that are repelled by water, typically non-polar and unable to form hydrogen bonds.

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Amphipathic Molecules

Molecules possessing both hydrophilic and hydrophobic regions.

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Hydrophobic Interactions

The clustering of hydrophobic regions of molecules away from water.

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Non-Covalent Interactions

Non-covalent interactions are crucial for determining the three-dimensional structures of biomolecules

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Hydrophobic Drive

A primary driving force in the formation and stabilization of biomolecular structures.

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Water Shielding

Electrostatic interactions diminish due to water shielding charged groups.

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Maximal van der Waals Attraction

Attraction maximizes when atoms are separated by the sum of their van der Waals radii.

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Hydrophobic Effect

Non-polar groups cluster away from water, while polar groups interact with water.

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Hydrophobic Effect & Entropy

Folding increases water's entropy by releasing ordered water molecules.

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Non-polar association

The association of non-polar molecules releases some of the ordered water molecules, resulting in an increase in the entropy of water.

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van der Waals Forces

Short range, low magnitude interactions between permanent and induced dipoles.

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Hydrophobic Effect

Drive for polar groups to interact with water and non-polar regions to be shielded away from water.

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Polypeptide Folding and Entropy

The folding of a polypeptide decreases the entropy of the polypeptide but increases the entropy of the associated water.

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Homeopathic remedies

The preparation of remedies by repeatedly diluting a substance, often to the point where there are no original molecules left.

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Water 'memory'

The (disproven) idea that water retains a 'memory' of substances previously dissolved in it, even after extreme dilution.

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Ionization of Water

The limited process where water molecules can break down into hydrogen ions (H+) and hydroxide ions (OH-).

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Kw (Ion Product of Water)

The equilibrium constant for the autoionization of water. Kw = [H+][OH-] = 1.0 x 10-14 M2 at 25°C

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pH Scale

A scale used to specify the acidity or basicity of an aqueous solution. It is the negative logarithm of the hydrogen ion concentration.

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Weak Acids and Bases

Acids and bases that do not fully dissociate into ions when dissolved in water.

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Ka (Acid Dissociation Constant)

The dissociation constant for a weak acid, indicating the extent of its dissociation in water.

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Buffer

A solution that resists changes in pH upon the addition of small amounts of acid or base.

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Henderson-Hasselbalch Equation

pH equals pKa plus the log of [A-]/[HA], useful for relating pH, pKa, and concentrations of acid/base forms.

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What is pKa?

The pH at which the concentrations of the acid and its conjugate base are equal. It indicates the strength of an acid.

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pKa of Acetic Acid

Acetic acid's pKa is 4.76.

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Lactic Acid Mixture

A mixture of 0.01 M lactic acid and 0.087 M lactate has a pH of 4.80.

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Calculating pKa

pKa = pH - log([A-]/[HA]).

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pKa of Lactic Acid

Lactic acid has a pKa of 3.86.

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pH > pKa

When pH is greater than pKa, the base form [A-] predominates.

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Acetic Acid Solution pH

pH of 5.76

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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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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.

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