Tymoczko • Berg • Stryer
Biochemistry: A Short Course
Third Edition
Lecture 2: 8/22
CHAPTER 2
Water, Weak Bonds, and the Generation of Order Out of Chaos
8/22/16
© 2015 W. H. Freeman and Company
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Summary of Lecture 1
• An organism requires a limited number of atoms and molecules
• Four commons atoms and their abundance are;
– Hydrogen > oxygen > carbon > nitrogen
• There are four major classes of biomolecules;
– Proteins, Nucleic acids, Lipids and Carbohydrates
• The central dogma is key to biological information transfer
• Cell membranes define cell and play critical role in cellular functions
• Learn the differences between prokaryotic and eukaryotic as well as plant cells
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Chapter 2 Outline
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Weak bonds permit dynamic interactions that form the basis of biochemistry and life itself.
Brownian motion is the movement of molecules powered by random fluctuations of environmental energy.
Brownian motion of water initiates many biochemical interactions.
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Water is a polar molecule because the oxygen atom carrying a slightly negative charge and the hydrogen atoms carrying slightly positive charges.
H2O
Chemical Structure
of Water
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The polarity of water allows the formation of hydrogen bonds between water molecules and accounts for the cohesiveness of water.
The polarity of water also accounts for its ability to dissolve many important biochemicals.
The inability of water to dissolve nonpolar molecules results in an important organizing principle called the hydrophobic effect.
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The Hydrogen Bounding in Water
Hydrogen bonds (shown as dashed green lines) are formed between water molecules to produce a highly ordered and open structure.
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Electrostatic interactions are also called ionic bonds or salt bridges.
The energy of an electrostatic interaction between two charges is give by Coulomb’s law:
E is the energy, q1 and q2 are the charges on the ions, D is the dielectric constant, r is the distance between the two ions, and k is a proportionality constant.
The dielectric constant is 1 in a vacuum, and 80 in water. Thus, water weakens electrostatic interactions.
The distance for maximal bond strength is about 3Ao
Example: Energy of the electrostatic interaction between two ion bearing single opposite charges separated by 3Ao in water is ‐5.8 kJ mol‐1 (‐1.4 kcal mol‐1). However, the same two ions separated by 3Ao in a nonpolar solvent such hexane, (has a dielectric constant of 2) has a energy of ‐231 kJ mol‐1 (‐55 kJ mol‐1
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Sodium chloride dissolves in water
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Hydrogen Bonds Form Between an Electronegative Atom and Hydrogen
Hydrogen bonds are not unique to water molecules and can occur whenever hydrogen is covalently bonded to an electronegative atom.
Water disrupts hydrogen bonds between two molecules by competing for the hydrogen bonding capability.
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Hydrogen bonds between nitrogen and oxygen atoms
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Disruption of hydrogen bonds
Water disrupts hydrogen bonds between two molecules by competing for the hydrogen bonding capability.
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van der Waals Interactions Depend on Transient Asymmetry in Electrical Charge
Nonpolar and uncharged molecules can interact electrostatically with van der Waals interactions.
The basis of the van der Waals interaction is that transient asymmetry in one molecule will induce complementary asymmetry in a nearby molecule.
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The energy of a van der Waals interaction as two atoms approach each other.
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The power of van der Waals interactions
Geckos can cross a ceiling, held only by weak bonds called van der Waals forces
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Weak Bonds Permit Repeated Interactions
Hydrogen bonds contribute to the stability of the DNA double helix. However, these bonds are weak enough to be broken by the enzymes of DNA metabolism, thereby allowing access to the genetic information.
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Hydrophobic molecules such as benzene tend to cluster together in aqueous solutions.
Hydrophobic effect. Entropy‐driven interaction of nonpolar molecule Definition: This clustering of hydrophobic molecules in water is called the hydrophobic effect.
The hydrophobic effect is powered by the increase in the entropy of water that results when hydrophobic molecules come together.
Chemical and biological significance of the hydrophobic effect:
The hydrophobic effect is a powerful organizing force in biological systems.
Polar molecules: Charged or ionized molecules. These molecules can interact with water Nonpolar molecules: Nonionic or hydrophobic molecules. These molecules cannot interact with water
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The hydrophobic effect
The aggregation of nonpolar groups in water leads to an increase in entropy owing to the release of water molecules into bulk water.
Entropy is a measure of randomness. Hydrophobic interactions form spontaneously and no input of energy is required 8/22/16
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Membrane Formation is Powered by the Hydrophobic Effect
Phospholipids have hydrophilic and hydrophobic properties. When exposed to water, phospholipids form membranes. Hydrophobic Effect is important for membrane formation
A molecule such as lipid, with distinct chemical properties is called amphipathic or
amphiphilic molecule. When such a molecule exposed to water hydrophilic head group Interact with the aqueous medium, while hydrophobic tails are sequestered away from the water and interact with only one another. The hydrophobic interaction is stabilized by
Van der Waals interactions.
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Protein Folding is Powered by the Hydrophobic Effect
Hydrophobic effect is important for protein folding
How does hydrophobic effect favor
protein folding?
Some amino acids in the protein have nonpolar groups. These nonpolar amino acid have strong tendency to interact with 8/22/16
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Functional Groups Have Specific Chemical Properties
Although there are many different biomolecules, only a limited number of functional groups are found in these molecules.
Functional groups are arrays of atoms that have distinctive chemical properties.
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Some key functional groups in Biochemistry
All of these groups have hydrogen binding potentials or ability to form ionic bonds, except for the hydrophobic groups, which can interact with other hydrophobic group through van der Waals interaction.
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Quizzes: 8/22/16
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pH Meter
Definition: pH is the measure of H+ concentration of a solution.
Significance: Controlling pH is a crucial function in biological systems. Gastric esophageal reflux disease (GERD) is a pathological condition that results when the esophagus is exposed to the acid of the stomach.
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Water Ionizes to a Small Extent
The equilibrium constant Keq for the dissociation of water is given by: Kw, the ion constant of water, is given by: This can be simplified to:
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Water Ionizes to a Small Extent
How cab make use of this equation? This equation will allow us to calculate molar concentration of H and OH ions in solution.
The ion constant of water at 25oC is:
The pH of any solution is defined as:
pH+pOH=14
Concentration of H+ and OH‐ are reciprocally related. If [H+] is high, then [OH‐]
must be low and vice versa.
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An Acid Is a Proton Donor
A Base Is a Proton Acceptor
Acids ionize to form a proton and a base.
Conjugate Base: The ionization of an acid yield its conjugate base.
Conjugate Acid: The protonation of a base results in its a conjugate acid.
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Acids Have Differing Tendencies to Ionize
How can we measure a strength of an acid in a given biochemical environment?
The ionization equilibrium of a weak acid is given by:
The equilibrium constant for this reaction is:
The larger Ka, the stronger the acid.
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Acids Have Differing Tendencies to Ionize
What is the relationship between pH and the ration of acid to base? We can derive a relationship between pH and the ratio of acid to base by first manipulating the formula for the ionization of the acid.
Taking the logarithm of both sides gives:
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Acids Have Differing Tendencies to Ionize
The log(1/Ka) is called the pKa of the acid.
Substituting pH for log(1/H+) and pKa for log of (1/Ka) yields the Henderson‐Hasselbalch equation: 8/22/16
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Acids Have Differing Tendencies to Ionize
Henderson‐Hassellbalch equation
When [A‐] = [HA], log ([A‐]/[HA]) equals 0, and pH =pKa.
For any acid, at pH > pKa, A‐ predominates. At pH < pKa, HA predominates.
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A variety of conjugate acid–base pairs.
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Buffers Resist Changes in pH
An acid‐base conjugate pair resists changes in the pH of a solution. In other words, it acts as a buffer. A buffer is most effective at a pH near its pKa. The titration curve for acetic acid.
Near the pKa of acetic acid, the pH does not change much with the addition of more base
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Buffer action
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The titration curves of three important weak acids
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Buffers Are Crucial in Biological Systems
The CO2 produced in aerobic respiration (Chapter 19) reacts with water to produce the weak acid carbonic acid. Carbonic acid then ionizes to produce a proton and bicarbonate.
The conjugate acid‐base pair of carbonic acid and bicarbonate (H2CO3/HCO3‐) maintains the pH (7.4) of blood constant. This mechanism of blood‐pH control is
known as compensatory respiratory alkalosis
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Making Buffers Is a Common Laboratory Practice
Buffers that resist pH changes over range of pH can be made by using the Henderson‐Hasselbalch equation and simple chemistry. Henderson‐Hasselbalch equation 8/22/16
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Summary of Lecture 2
• Thermal motions or Brownian motion play a vital role in biological interactions and cellular biology
• Biochemical interactions take place in aqueous solution
• There are three common types of week interactions found in biochemical system: – Ionic bonds or Electrostatic interactions, Hydrogen bonds and van der Waals interactions.
• Weak interactions are important biochemical properties
• Hydrophobic molecules cluster together, which is biologically important • Hydrophobic effect is critical for membrane formation and protein folding • pH, a common laboratory practice, is an important parameter of biochemical system
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Tymoczko • Berg • Stryer
Biochemistry: A Short Course
Third Edition
Lecture 3: 8/24
CHAPTER 3
Amino Acids
8/22/16
© 2015 W. H. Freeman and Company
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