Part I => CARBS and LIPIDS. 1.1 Thermodynamics 1.1a General Principles 1.1b Macromolecular Forces 1.1c Acid-Base Equilibria

Size: px

Start display at page:

Download "Part I => CARBS and LIPIDS. 1.1 Thermodynamics 1.1a General Principles 1.1b Macromolecular Forces 1.1c Acid-Base Equilibria"

Patrick Wilkins
6 years ago
Views:

1 Part I => CARBS and LIPIDS 1.1 Thermodynamics 1.1a General Principles 1.1b Macromolecular Forces 1.1c Acid-Base Equilibria

2 Section 1.1a: General Principles

3 Synopsis 1.1a - Thermodynamics is concerned with changes in heat and temperature as related to energy exchange and work done by living systems the major thermodynamic parameters (or physical quantities) include changes in free energy ( G), enthalpy ( H), entropy ( S), volume ( V), and heat capacity ( C p ) - The laws of thermodynamics provide general constraints that such systems must not violate of the four laws of thermodynamics (zeroth through third), the first and second laws are of particular relevance to understanding living systems - Natural processes are spontaneous ( S > 0) ie they are accompanied by an increase in entropy (S) coupled with a decrease in free energy ( G) the energy available to do useful work at a constant temperature, pressure, and ph - Thermodynamic properties accompanying biochemical processes are usually quoted under the so-called standard state conditions that are defined as: Temperature (T) = 25 C (77 F / 298K) Pressure (P) = 1 atm (10 5 Pa) ph = 7.0 F = (9/5) C + 32 K = C + 273

4 Relationship Between Disorder and Entropy Entropy is a measure of the disorder in a system eg (a) Entrapment of gas in a chamber reduces its overall entropy (b) Release of gas from the chamber increases its entropy

Energy Flow in the Biosphere an Open System - Living organisms are thermodynamically open systems that tend to maintain a steady-state rather than reach equilibrium ( G 0) doing so would equate to

5 Energy Flow in the Biosphere an Open System - Living organisms are thermodynamically open systems that tend to maintain a steady-state rather than reach equilibrium ( G 0) doing so would equate to death! - Steady-state implies that the rates of synthesis and degradation of metabolic intermediates within a cell are more or less equal such that their concentrations change little over time eg the mass of an organism generally remains more or less constant over time irrespective of how much food and water are consumed!

6 Equilibrium vs Steady-State Equilibrium (death) - Consider the following reaction in progress: A + B <=> C - Let us assume that: -d[a]/dt = rate of decay/breakdown of A (into C) -d[c]/dt = rate of decay/breakdown of C (into A and B) - At equilibrium, the forward reaction is exactly balanced by reverse reaction: -d[a]/dt = -d[c]/dt - Concentration of C stabilizes (reaches a constant) at equilibrium the above reaction equilibrium! Steady-State (life) - Consider the following reactions in progress: A + B <=> C C + D <=> E - Let us assume that: d[c1]/dt = rate of formation/synthesis of C (from A and B) -d[c2]/dt = rate of decay/breakdown of C (into E) - At steady-state, the rate of synthesis of C equals its rate of breakdown: d[c1]/dt = -d[c2]/dt - Concentration of C also stabilizes (reaches a constant) but under steady-state conditions neither of the above reactions equilibrium!

Laws of Thermodynamics First law of Thermodynamics Energy is neither created nor destroyed but

energy (of the system) q = Heat exchanged/added (eg to generate steam) w = Work done (eg piston

leading to an increase in disorder or entropy (S) it is mathematically expressed as: S uni = ( S

7 Laws of Thermodynamics First law of Thermodynamics Energy is neither created nor destroyed but only conserved/exchanged it is mathematically expressed as: U = q w U = Change in internal energy (of the system) q = Heat exchanged/added (eg to generate steam) w = Work done (eg piston movement) Steam Engine Second law of Thermodynamics Natural processes are spontaneous ( S > 0), leading to an increase in disorder or entropy (S) it is mathematically expressed as: S uni = ( S sys + S sur ) > 0 S is the change in entropy of the universe (uni), system (sys), and surroundings (sur)

Gibb s Free Energy (G) - Biological manifestation of the first and second laws of thermodynamics is given by the Gibb s equation: where G = H - T S G = Change in free energy (cal/mol) H = Change in

8 Gibb s Free Energy (G) - Biological manifestation of the first and second laws of thermodynamics is given by the Gibb s equation: where G = H - T S G = Change in free energy (cal/mol) H = Change in enthalpy (cal/mol) S = Change in entropy (cal/mol/k) T = Absolute temperature (K) - The sign denotes standard conditions: 25 C, 1 atm, and ph 7 Willard Gibbs ( ) - Gibb s equation provides a measure of the thermodynamic potential of a biological process to do useful work - Biological processes are overall accompanied by a decrease in free energy ie G < 0 - To satisfy the above thermodynamic constraint, endergonic processes ( G > 0) are coupled to exergonic reactions ( G < 0) - Similarly, endothermic processes ( H > 0) are driven by an increase in entropy (T S > 0) ie they are under entropic control

9 Relationship Between H, S and G When G=0 => T= H/ S In thermodynamic terms, thermodynamically favorable reactions ( G < 0) are described as being under: (1) Enthalpic control => H < 0 and T S < 0 (2) Entropic control => H > 0 and T S > 0 (3) Enthalpic and entropic control => H < 0 and T S > 0

10 Equilibrium Thermodynamics - Consider the following reaction with an equilibrium dissociation constant (K d ) of 10 M (10x10-6 M): A + B <=> C - Change in free energy of the reaction ( G) under non-equilibrium setting is given by: G = G + RTlnK a = G - RTlnK d [1] where G = change in free energy of all species under standard state (cal/mol) equilibrium R = Universal molar gas constant (2 cal/mol/k) T = Absolute temperature (K) K a = Equilibrium association constant (M -1 ) K d = Equilibrium dissociation constant (M) - K d is defined as: K d = [A][B]/[C] = 1/K a where letters A-C in [ ] indicate corresponding concentration of each equilibrium - But, forward reaction equals equilibrium ie G = 0 - Thus, Eq [1] can be equilibrium as: G = -RTlnK a [2] => G = RTlnK d [3] => G = (2 cal/mol/k).(298k).ln(10x10-6 M) = (596 cal/mol).ln(10-5 ) = -(596 cal/mol).ln(10 5 ) => G = cal/mol = -7 kcal/mol

11 Exercise 1.1a - Summarize the relationship between energy (U), heat (q), and work (w) - State the first and second laws of thermodynamics - Explain why changes in both enthalpy (ΔH) and entropy (ΔS) determine the spontaneity of a process - What is the free energy change for a reaction at equilibrium? - Write the equation showing the relationship between ΔG and K d - Write the equation showing the relationship between ΔG, ΔG, and the concentrations of the reactants and products - Explain how biochemists define the standard state of a solute

12 Section 1.1b: Macromolecular Forces

13 Synopsis 1.1b - TWO major attractive forces acting on biological molecules include: (1) ionic interactions (2) van der Waals forces (eg hydrogen bonding, dipolar interactions) - Being polar (ie electrostatically polarized), water molecules form hydrogen bonds with other molecules - In terms of attractive forces, water can exist either in a liquid or crystalline (ice) form depending on the nature of hydrogen bonding interactions - The exclusion of nonpolar groups from polar surroundings so as to maximize the entropy of water molecules is the basis of hydrophobic effect - Atomic distances are measured in the units of Ångström (Å)

Structure of Water: van der Waals Envelope Johannes van der Waals (1837-1923) - In chemical terms, water is dihydrogen monoxide (H

chemical (!) in that it can rapidly corrode and destroy most materials!

surrounding cloud of electrons the distance from the center of the molecule to the van der Waals envelope is called the van der

14 Structure of Water: van der Waals Envelope Johannes van der Waals ( ) - In chemical terms, water is dihydrogen monoxide (H 2 O) wherein two hydrogen atoms are covalently bonded to an oxygen atom - While essential to life, dihydrogen monoxide is a lethal chemical (!) in that it can rapidly corrode and destroy most materials! - van der Waals envelope (or surface) is the approximate perimeter of a molecule as demarcated by the outer boundary of the surrounding cloud of electrons the distance from the center of the molecule to the van der Waals envelope is called the van der Waals radius - van der Waals radius (r) of water is 1.4Å two water molecules cannot get closer to each other more than 2r ie the distance from the center of one molecule to the center of the other!

15 Structure of Water: sp 3 Orbitals 2P x y z 2S 4 x SP 3 hybridized orbitals 1S H H O H 2 O Electronic Shell Configurations H 1S 1 O 1S 2.2S 2 2p 4 Tetrahedron Triangular face (x4) Vertex/Corner (x4) Edge (x6) - Water is comprised of four sp 3 hybridized (or mixed) orbitals two of which are associated with H atoms, while the other two arise from the two non-bonding pairs of electrons - The four sp 3 orbitals of water adopt a tetrahedral geometry ie each orbital occupies one of the four vertices (singular vertex) in a tetrahedral arrangement

16 Structure of Water: Hydrogen Bonding - Electrons involved in mediating covalent bonds between a pair of atoms are not equally distributed but rather become slightly polarized toward one or the other bonding partner (depending on their relative electronegativity), thereby resulting in the formation of diploes (or charge separation) - Under such polarization in the context of a covalent bond between a pair of atoms, one atom carries a slightly negative charge ( - ) while the other a slightly positive charge ( + ) interactions between such oppositely charged ends of dipoles are broadly termed van der Waals forces an umbrella term! If such dipole-dipole interactions occur between an electropositive H atom bonded to another highly electronegative atom (such as O or N), the resulting van der Waals forces are called hydrogen bonding ie hydrogen bonding (or H-bonding) is a special case of van der Waals forces due to its rather strong nature coupled with its ubiquity in biological systems - Hydrogen bonding represented by a dotted or dashed line is the supreme attractive force that renders water a liquid at room temperature - Changes in H-bonding pattern impart upon water the ability to exist in a liquid or crystalline (ice) form - Because of charge separation or polarization of electronic clouds of H and O atoms, water is described as being a highly polar molecule such polarity of water enables it to act both as H-bond donor as well as an H-bond acceptor in biochemical processes

Oxygen atom Hydrogen atom ----- H-bond - Ice is a crystal of an highly ordered network of hydrogen-bonded water molecules - In ice, each water molecule interacts tetrahedrally with four other

17 Oxygen atom Hydrogen atom H-bond - Ice is a crystal of an highly ordered network of hydrogen-bonded water molecules - In ice, each water molecule interacts tetrahedrally with four other neighboring (or surrounding) water molecules - In ice, H-bonds are highly stable (static) Structure of Water: Ice crystals - Because of a regular open ordered network of hydrogen bonding, water expands on freezing ie ice (0.92 g/ml) has a lower density than liquid water (1.00 g/ml) - What is the difference between 1, 1.0, and 1.00?! 1 => => =>

18 Structure of Water: Liquid 3-mer 4-mer 5-mer - Liquid water consists of a rather loose network of hydrogen-bonded water molecules ie water molecules rapidly fluctuate and tumble on a picosecond (ps) timescale (1ps = s) - Unlike ice, liquid water thus harbors an highly disordered and irregular structure - In liquid water, H-bonds are highly unstable (dynamic) - Nevertheless, water molecules transiently engage in rings of three (3-mer), four (4-mer), or five (5-mer) molecules in liquid - Because of their irregularity in liquid, water molecules can pack together much more tightly than in ice, thereby rendering water (1.00 g/ml) more dense than ice (0.92 g/ml) cf highlyordered rows of people (ice) versus a random crowd (water)

19 Typical Bond Energies in Biomolecules - Non-covalent forces underlying intermolecular interactions between biological molecules (or biomolecules) can be divided into TWO major categories: (1) Ionic interactions eg between oppositely charged ions such as Na + and Cl - (2) van der Waals forces interactions due to dipoles - Hydrogen bonding is a type of van der Waals interaction albeit of a major significance - The term electrostatic interactions is ambiguous and must be avoided at all costs

Van der Waals Forces: Dipole-Dipole Interactions Van der Waals forces are dipole-dipole interactions that can be divided into three

case of such dipolar interactions) polar polar (b) Dipole-induced-dipole interactions permanent dipoles in groups such as C=O can

cloud (c) London dispersion forces these arise from the fact that the electronic cloud of nonpolar groups such as CH 3 is not static

20 Van der Waals Forces: Dipole-Dipole Interactions Van der Waals forces are dipole-dipole interactions that can be divided into three major categories: (a) Dipole-dipole interactions interactions between permanent dipoles such as a - C=O group (H-bonding is a special case of such dipolar interactions) polar polar (b) Dipole-induced-dipole interactions permanent dipoles in groups such as C=O can also induce a dipole moment in a neighboring group (eg -CH3) by virtue of their ability to distort the distribution of its electronic cloud (c) London dispersion forces these arise from the fact that the electronic cloud of nonpolar groups such as CH 3 is not static but rather experiences rapidly fluctuating motions and, in so doing, generates a small transient dipole polar nonpolar nonpolar nonpolar

Hydration: Solvation of Ionic Substances Cations are shielded by electronegative O atoms Anions are shielded by electropositive H atoms - Water is often described as

ability of water to dissolve polar substances such as NaCl arises from the fact that its dipolar character enables it to weaken attractive forces between oppositely

21 Hydration: Solvation of Ionic Substances Cations are shielded by electronegative O atoms Anions are shielded by electropositive H atoms - Water is often described as a universal solvent due to the fact that its polar character renders it an excellent solvent for hydrophilic substances eg those with polar or ionic character - The ability of water to dissolve polar substances such as NaCl arises from the fact that its dipolar character enables it to weaken attractive forces between oppositely charged Na + and Cl - ions - Multiple water molecules can surround each ion and neutralize its charge in a phenomenon referred to as hydration or solvation in generic terms

22 Hydroxyl Hydration: Solvation of Polar Substances Keto Carboxylate Amino - Water is also an excellent solvent for polar substances for the same reason that it is for ionic substances - The dipolar character of water enables it to engage in H-bonding with other polar groups such as hydroxyl (OH), carboxylate (O=CO - ), keto (C=O) and amino (NH 3+ )

23 Hydrophobic Effect: An Entropic Phenomenon - Apolar (or nonpolar) molecules such as oils and lipids aggregate when in contact with water ie they tend to stick together rather than dissolve in water why?! - Such ability of apolar molecules to minimize contact with water or vice versa is termed the hydrophobic effect what thermodynamic force drives the hydrophobic effect? Enthalpic ( H) or entropic (T S)? - H accompanying the transfer of apolar substances from water to an apolar solvent is unfavorable ( H >= 0), while T S is consistently favorable (T S > 0) - Thus, the hydrophobic effect is largely driven by an entropic force in that the ability of apolar substances to aggregate confers upon surrounding water molecules an entropic advantage ie exclusion of water molecules enables them to move and tumble freely in lieu of being locked or entrapped in an ordered manner with apolar neighbors

Hydrophobic Effect: Orientation of Water Molecules - Maintenance of intramolecular H-bonding network is critical to the random motion of water molecules - Intrusion of apolar solute into water

24 Hydrophobic Effect: Orientation of Water Molecules - Maintenance of intramolecular H-bonding network is critical to the random motion of water molecules - Intrusion of apolar solute into water disrupts such extensive network due to its inability to engage in H-bonding interactions - Accordingly, water molecules orient away from the surface of the apolar solute to engage in H-bonding network with bulk water molecules the surrounding water molecules that are not in direct contact with the solute - Such orientation constitutes an ordering of the water structure (as their degree of freedom or the number of ways in which they can hydrogen bond becomes restricted) - In order to minimize such ordering of water molecules, apolar molecules aggregate so as to minimize their surface area in contact with water and thereby maximize the overall entropy of the system

area in contact with water thereby resulting in lesser loss of entropy Hydrophobic effect is central to many

25 Hydrophobic Effect: Aggregation of Apolar Substances Individual hydration of apolar substances increases their surface area in contact with water thereby resulting in greater loss of entropy Aggregation of apolar substances minimizes their surface area in contact with water thereby resulting in lesser loss of entropy Hydrophobic effect is central to many (bio)physicochemical phenomena: - Separation of oil and water - Membrane bilayer integrity - Folding of proteins in water and lipid bilayer

26 Exercise 1.1b - Sketch a diagram of a water molecule and indicate the ends that bear partial positive and negative charges - Compare the structures of ice and water with respect to the number and geometry of hydrogen bonds - Describe the nature and relative strength of covalent bonds, ionic interactions, and van der Waals forces - Explain why polar substances dissolve in water while nonpolar substances do not - What is the role of entropy in the hydrophobic effect?

27 Section 1.1c: Acid-Base Equilibria

28 Synopsis 1.1c - The acidity of a solution is expressed in terms of a ph value - An acid is a compound that can donate a proton - A base is a compound that can accept a proton - Biological molecules that harbor ionizable groups are sensitive to changes in ph - The relationship between the extent of ionization of a weak acid and the ph of a solution is embodied in the so-called Henderson-Hasselbalch equation

29 - Water is a neutral molecule with a high tendency to ionize into corresponding hydrogen (H + ) and hydroxide (OH - ) ions: HOH <=> H + + OH - Proton Jumping Occurs Rapidly - The hydrogen (H + ) ion is more commonly referred to as a proton - In essence, the proton (H + ) largely exists as an hydronium ion (H 3 O + ) in solution ie the H + is associated with another H 2 O molecule rather than roaming around as a free agent! - The H + of H 3 O + ion is not static but highly dynamic in that it can jump from one H 2 O molecule to another and so on virtually in an infinite (or endless) manner in a phenomenon referred to as proton jumping - Owing to proton jumping, H + and OH - ions exhibit much higher mobilities in bulk water compared to other ions accordingly, acid-base reactions (involving exchange of H + ) rank among the fastest processes occurring in water - For simplicity, the H + is often considered as one of the two dissociative products of ionization of water in lieu of the more complex H 3 O + ion

ph Values: Measure of the acidity of a solution - Consider the ionization of water: HOH <=> H + + OH - - In pure water @ 25 C, the concentration of H + is close to 10-7 M (100nM): [H + ] = [OH - ] =

30 ph Values: Measure of the acidity of a solution - Consider the ionization of water: HOH <=> H + + OH - - In pure 25 C, the concentration of H + is close to 10-7 M (100nM): [H + ] = [OH - ] = 10-7 M = 100nM [H + ] + [OH - ] = 2x10-7 M = 200nM - A solution is described as: Neutral => if [H + ] = 10-7 M => 1M = 1mol/L Acidic => if [H + ] > 10-7 M Alkaline/Basic => if [H + ] < 10-7 M Soren Sorensen ( ) - The measure of acidity (or alkalinity/basicity) of an aqueous solution is defined by the concentration of H + ions expressed in terms of a quantity known as ph - First introduced by Sorensen in 1909, the ph of a solution is defined as: ph = -log[h + ] where [H + ] must be in the units of molar (M) ie moles per liter (or litre in Imperial English) - Thus, the ph is the negative log (to base 10) of the concentration of H + ions in solution - The ph of pure water is: ph = -log[10-7 M] = 7

31 ph Values: Relationship of ph, [H + ], and [OH - ]

32 ph Values: ph of Common Substances

33 pk a Values: Measure of the strength of an acid - Consider the dissociation of an acid HA into its constituent components in hydrogen ion (H + ) and the conjugate base (A - ): HA <=> H + + A - - The equilibrium dissociation constant of the acid (K a ) is defined as: K a = [H + ][A - ]/[HA] [1] - The strength an acid in aqueous solution is expressed in terms of a quantity called the pk a, which is analogous to ph! - pk a is defined as the negative log (to the base 10) of K a : pk a = -logk a [2] where K a must be in the units of molar (M) - The relationship between the ph of a solution and pk a of an acid can be derived as follows: (1) Rearrange Eq [1] for [H+]: [H + ] = K a [HA]/[A - ] (2) Take negative logarithm of each term: -log[h + ] = -logk a - log{[ha]/[a - ]} (3) Substitute the quantities and rearrange: ph = pk a + log{[a - ]/[HA]} [3] - Eq[3] has come to be known as the Henderson-Hasselbalch equation

34 pk a Values: K a and pk a of Common 25 C K a pk a

the ionization of weak acids/bases such as buffers and amino acid sidechain groups in proteins - A buffer with a pk a value of 8 would be most effective @ ph 8! Why? What is a buffer?

35 pk a Values: Henderson-Hasselbalch Equation ph = pk a + log{[a - ]/[HA]} - When [HA] = [A - ], log{[a - ]/[HA]} = 0 => ph = pk a - In other words, the ph of a solution is equivalent to pk a of an 50% dissociation - Note that the Henderson-Hasselbalch equation does not take into account the ionization of water Lawrence Henderson ( ) - Thus, it is only useful for rationalizing the ionization of weak acids/bases such as buffers and amino acid sidechain groups in proteins - A buffer with a pk a value of 8 would be most ph 8! Why? What is a buffer?! - Since buffers resist changes in ph, they are most effective when the concentration of its hydrogen ion (H + ) and conjugate base (A - ) are equal and when they are so, ph = pk a Karl Hasselbalch ( )

- Addition of small amounts of OH - or H + are quickly mopped up with little changes in solution ph: OH - + HA <=> HOH + A - H + + A - <=> HA - A buffer ONLY resists

36 pk a Values: Titration Curves of Weak Acids - A buffer is a mixture of a weak acid (HA) and its conjugate base (A - ): HA <=> H + + A - - Thus, a buffer helps to maintain constant ph. How? - Addition of small amounts of OH - or H + are quickly mopped up with little changes in solution ph: OH - + HA <=> HOH + A - H + + A - <=> HA - A buffer ONLY resists small changes in ph in the region close to its pk a value: ph = pk a 1 Consider acetate buffer (pka ~ 5): (1) When ph < 4, acetate largely exists as HA (undissociated acid form) => thus no good as a buffer! (2) When ph > 6, acetate largely exists as A - (dissociated base form) => again no good as a buffer!

pk a Values: Titration of a Polyprotic Acid pk 3 pk 2 pk 1 - Acids such as phosphoric acid (H 3 PO 4 ) are called polyprotic acids due to the fact that they can lose more than one proton upon

37 pk a Values: Titration of a Polyprotic Acid pk 3 pk 2 pk 1 - Acids such as phosphoric acid (H 3 PO 4 ) are called polyprotic acids due to the fact that they can lose more than one proton upon successive ionizations - Thus, a polyprotic acid has multiple pk a values eg H 3 PO 4 has three pk a values: pk 1 = 2.2 pk 2 = 6.8 pk 3 = Thus, phosphate buffer can be used to resist small changes in ph around ph 2.2, 6.8 and 12.2

38 Exercise 1.1c - What are the products of ionization of water? How are their concentrations related? - Describe how to calculate ph from the concentration of H + or OH - - Define acid and base - What is the relationship between the strength of an acid and its pk a value? - What must a buffer solution include in order to resist changes in ph on addition of acid or base? - Why is it important to maintain biological molecules in a buffered solution?

39 Debunking Alkaline Diet an Alternative Fact Rather Than Alternative Medicine! - Alkaline diet postulates that the consumption of certain fruits and vegetables helps to alkalinize the body fluids to a ph of around 7.4 a ph that cellular homeostasis achieves regardless of alkaline diet! - Thus, alkaline diet is believed to offset acidosis resulting from a typical Western diet, thereby keeping diseases such as cancer at bay indeed, many cancers cells thrive under acidic conditions! - But, the enigma is that the proponents of alkaline diet cannot explain how it helps to alkalinize the body fluids do all foods not go through the stomach?! - If so, then all foods are churned in the a ph of around 2! Does it really matter what the acidity/alkalinity of the intake food is? It represents a small drop in a big ocean does it not? - What about thousands who swear to have benefited from having been on the super-scampensive alkaline diet? nothing but a coincidence and a placebo effect correlation does not imply causation!

Chapter-2 (Page 22-37) Physical and Chemical Properties of Water

Chapter-2 (Page 22-37) Physical and Chemical Properties of Water Introduction About 70% of the mass of the human body is water. Water is central to biochemistry for the following reasons: 1- Biological