1 - Thermodynamics

***How strong are ionic forces?

In the absence of water, ionic forces are very strong. They are responsible for the strength of minerals such as MARBLE and AGATE.

coupling reaction

The Overall ΔG of a reaction is the SUM of free energy changes of the individual steps. Reactions are coupled through common intermediate B.

****8ΔG is independent of path

****ΔG the SAME for the overall process It doesn't matter what route you take to get there

*****How are reactions coupled?

*@ standard state conditions

*********ΔG FOR SPONTANEOUS REACTION

*ΔG < 0 FOR SPONTANEOUS REACTION

******ΔG0'

- Standard-state change in free energy for a process Units - kcal/mol

Enthalpy (H)

1."heat", of system •dH: change in enthalpy for a chemical reaction •dH = H2 - H1 (d - delta)

***how high is the bond strength for covalent bonds?

> 50kcal/mol

equilibrium constant (Keq)

At equilibrium: **Concentrations are not changing •The amounts of products ([C] and [D]) and reactants ([A] and [B]), will be stable at certain ratio called the equilibrium constant (Keq).

Covalent Bonds

Covalent bonding between two atoms results from sharing a pair of electrons such that electron shells overlap. These are strong interactions (ΔG>50)! They do not rupture spontaneously under physiological conditions. Covalent bonds are broken and formed in biological systems by coupling reactions and the involvement of enzymes.

Chemical Bonding

Covalent: strong Non-covalent: weak electrostatic: ionic hydrogen bondind hydrophobic bonds van der Waals interactions

Bioenergetics

Describes energy transfer & utilization in biologic system

Noncovalent -- Ionic Bonds

Electrostatic attraction between 2 atoms or groups with opposite charge Negatively charged groups, such as the carboxylate group (−COO−) in the side chain of aspartate or glutamate, can interact with positively charged groups such as the amino group (−NH3+) in the side chain of lysine

*********G FOR SPONTANEOUS REACTION

G2 < G1 FOR SPONTANEOUS REACTION G DECREASES during approach to equilibrium (A path from state 1 to state 2) G reaches minimum at equilibrium

Noncovalent -- Hydrogen Bonds

Hydrogen Bonds: Occur when a hydrogen atom is partially shared between two other electronegative atoms, usually O or N in biological systems.

Keq and ΔG0 if A → B

If Keq <1 then ΔG0 > 0 and therefore A → B

Keq and ΔG0 if A ↔ B

If Keq = 1 then ΔG0 = 0 and therefore A ↔ B

Keq and ΔG0 if A ← B

If Keq >1 then ΔG0 < 0 and therefore A ← B

Activation free energy (ΔG‡)

In this example, pathway 1 (blue) has greater intermediate energy e.g. ACTIVATION energy is larger RATE would be affected—if only pathway 1 possible, reaction will occur very slowly ΔG same for either pathway Both reactions are spontaneous, but reaction 2 goes faster!

****If noncovalent bonds are weak, why are they important?

Key for the maintenance of 3-D structure of proteins and promoting transient interactions between large molecules Although they are weak, the large numbers of interactions can stabilize macromolecules and supramolecular structures (i.e. combined strength greater than individual bond's strength), while still permitting rapid and dynamic molecular interactions

*****does Keq have a unit?

NO! Keq is a unitless ratio.

******QUESTION - Glucose 6-phosphate (G6P) --> Fructose 6-phosphate (F6P) If [G6P]i = [F6P]i = 5 mM, will the reaction proceed forward?

Need value for ΔG0' , can get it from Keq **plug it in and do the math USE: ΔG0' = -1.36*logKeq ΔG0' = (-1.36)*(-0.30) = +0.4 kcal/mol **plug it in another formula ΔG = ΔG0' + 1.36*(log([product]/[reactant]) ΔG = +0.4 kcal/mol + 1.36*(log1) ***ΔG = +0.4 kcal/mol REACTION WILL NOT PROCEED FORWARD

Noncovalent Bonds

Often electrostatic: occur between the positive nucleus of one atom and the negative electron clouds of another nearby atom; they are very weak and easily disrupted

Adenosine triphosphate (ATP):

Removal of one phosphate produces ADP Removal of two phosphates produces adenosine monophosphate (AMP). •For ATP, the ΔG0 of hydrolysis is approximately -7.3 kcal/mole for EACH of the two terminal phosphate groups. •Because of this LARGE NEGATIVE ΔG0 of hydrolysis, ATP is called a high-energy phosphate compound. •Note: Adenine nucleotides are interconverted (2 ADP ⇄ ATP + AMP) by adenylate kinase.

Relationship Between ΔG0 and Keq

The following equation can be used to connect ΔG0 and Keq mathematically used to make simple predictions Keq = [product]/[reactant] ΔG0' = -1.36*log(Keq)

hydrophobic effect

The increase in the disorder of H2O that results when hydrophobic regions of macromolecules are buried is called the hydrophobic effect. Hydrophobic interactions are a major driving force, but they would not confer specificity on an intermolecular interaction except for the fact that the molecular surfaces MUST BE COMPLEMENTARY to exclude water. The hydrophobic effect is not a bond per se, but A THERMODYNAMIC FACTOR THAT FAVORS MACROMOLECULAR INTERACTIONS.

*******Gecko bonding

The million hairs contained in a dime sized spot could lift a child weighing 45lbs. The researchers believe that the adhesion is based on van der waals interactions. The gecko's bonding capabilities may provide the inspiration for a clean new adhesive.

****Question: If the standard state free-energy (∆Go') for the reaction A → B is -2 kcal/mol, what is the Keq?

USE: ΔG0' = -1.36*logKeq **just plug it in and do the math Keq = 30

****Question: If the Keq for the reaction A → B is 30, what is the standard state free-energy (∆Go') ?

USE: ΔG0' = -1.36*logKeq ΔG0' = -1.36*log30 ΔG0' = -1.36*1.47 ΔG0' = -2 kcal/mol

Entropy (S)

a function of possible states of system •A measure of "disorder" or "randomness" of system •dS: change in entropy

***What are Adenine nucleotides interconverted by?

adenylate cyclase

Thermodynamics

concept of free energy

***Are reactions in an organism reversible?

yes all reactions are reversible

Change in Gibbs free energy (ΔG)

determines whether or not a reaction is spontaneous ΔG - change in gibbs free energy ΔH - change in enthalpy (heat) ΔS - change in entropy (disorder) **G DECREASES during an approach to equilibrium

Gibbs free energy (G)

energy available to do work (dG: change in Gibbs free energy) G = H - TS

**Hydrogen bonding in DNA

holds 2 strands of the double helix together; hydrogen bonds form only between certain nitrogenous bases. These weak bonds allow the structure to separate.

Changes in free energy

provide a measure of the energetic feasibility of a chemical reaction. Therefore, they allow prediction of whether a reaction or process can take place.

***what are unfavorable biosynthetic reactions coupled to?

§Many unfavorable biosynthetic reactions are coupled to ATP hydrolysis ATP → ADP + Pi dGo' = -7.3 kcal/mol

***What thermodynamic quantity measures if a rxn is spontaneous?

ΔG G DECREASES during approach to equilibrium Predicts the direction in which a reaction will proceed spontaneously

**What is the value of ΔG if a reaction occurs spontaneously?

ΔG < 0 Reaction occurs spontaneously

*******QUESTION - Glucose (GLU) + ATP → Glucose 6-phosphate (G6P) + ADP ΔG0' = -4.1 kcal/mol If [GLU] = 1mM, [ATP] = 1mM, [G6P] = 100mM, [ADP] = 100mM, What is ΔG for the reaction?

ΔG = +1.34 kcal/mol **nonspontaneous endothermic

******QUESTION - Glucose 6-phosphate (G6P) --> Fructose 6-phosphate (F6P) If = [G6P]i = 50 mM and [F6P]i = 5 mM, will the reaction proceed forward?

ΔG = -0.96 kcal/mol REACTION WILL PROCEED FORWARD

*******QUESTION - Glucose (GLU) + ATP → Glucose 6-phosphate (G6P) + ADP ΔG0' = -4.1 kcal/mol If [GLU] = 1mM, [ATP] = 100mM, [G6P] = 100 mM, [ADP] = 1mM, What is ΔG for the reaction?

ΔG = -4.1 kcal/mol **spontaneous exothermic

*******QUESTION - Glucose (GLU) + ATP → Glucose 6-phosphate (G6P) + ADP ΔG0' = -4.1 kcal/mol If [GLU] = 100mM, [ATP] = 100mM, [G6P] = 1mM, [ADP] = 1mM, What is ΔG for the reaction?

ΔG = -9.54 kcal/mol **spontaneous exothermic

**What is the value of ΔG if a reaction is at equilibrium?

ΔG = 0 Reaction at equilibrium

****Formula -- ΔG

ΔG = ΔG0' + 1.36*log([product]/[reactant]) ΔG determines if a reaction will proceed!

**What is the value of ΔG if a reaction is non-spontaneously?

ΔG > 0 Reaction will NOT occur spontaneously. ****Energy input is required - a driving force - for reaction to proceed.

**Are reactions in an organism at equilibrium?

ΔG may matter less than rate. ***reactions in an organism are not at equilibrium, because that will mean they are dead

Chemical Equilibrium

•All biochemical reactions are reversible •Living systems are not closed systems •Living systems are not at equilibrium •Life as we know it is headed for equilibrium •We can delay it but we can't prevent it

Biosynthetic reactions tend to be thermodynamically unfavorable. How, then, to make them proceed?

•Can be accomplished by coupling reaction to a favorable reaction •ALSO—principle of mass action (concentrations not standard-state)

**what does the bioenergetics concerns?

•Concerns the initial & final energy states of the reaction components, NOT the reaction mechanism or how much time it takes for the chemical change to occur.

Disulfide bond

•Covalent linkages between sulfhydryl groups (-SH) on cysteines. •They can be intra- or inter-molecular. The 2 cysteines may be separated from each other by many amino acids in the 1° sequence of a polypeptide or may even be located on 2 different polypeptides. • • Polypeptide folding brings the cysteine residues into proximity and permits covalent bonding of their side chains. • •Contribute to the stability of the 3-D shape of the protein molecule and prevents it from becoming denatured in the extracellular environment.

***EXAMPLE 1 - Coupled reaction - direct physical link

•Formation of glucose-6-phosphate from glucose and Pi has positive ΔG0' •Hydrolysis of ATP to Pi has negative ΔG0' •The enzyme hexokinase couples reaction by transferring phosphate directly from ATP to glucose - aided by proximity of both reactants binding to adjacent sites on the enzyme. •Overall ΔG0' is NEGATIVE ****Reaction progress is dependent on the concentration of reactants and products ****Enzyme hexokinase lowers activation energy

Weak Interactions

•Is only 1 - 10% of DG from covalent bonds • •Break spontaneously under physiological conditions • •Are longer than covalent Weak bonds are important in biochemical structures and interactions!

****Hydrogen Bonds Stabilize Proteins & Nucleic Acids

•Right handed α-helix or spiral is stabilized by H-bonding between C=O or carbonyl oxygen with an NH group four residues ahead (N term to C term). •There are 3.6 residues per helical turn (3.6 amino acids per turn/13 atoms between hydrogen bonds.) •The β-sheet is a 2° structure in which ALL of the peptide bond components are involved in hydrogen bonding. •Because the surfaces of β-sheets appear "pleated," they are often called β-pleated sheets.

****what conditions must be met to be considered standard state?

•STANDARD STATE (in biochemistry): •25ºC (Kelvin: 25ºC + 273 = 298.15 K) •solute concentration = 1 M •1 atmosphere pressure •pH = 7

**What determines the spontanity?

•The criterion for spontaneity is ΔG, NOT ΔGº' •Whether ΔG is negative, zero, or positive depends on the exact concentration of reactants and products.

ΔG of the Forward & Back Reactions

•The free energy of the forward reaction (A → B) is EQUAL IN MAGNITUDE but OPPOSITE IN SIGN to that of the back reaction (B → A). •For example, if the forward reaction ΔG= −5 kcal/mol, then the back reaction ΔG= +5 kcal/mol. •Note: ΔG can also be expressed in kilojoules per mole or kJ/mol (1 kcal = 4.2 kJ).

Then B ↔ A unfavorable!

•The product has a HIGHER free energy (G) than the reactant. •ΔG is POSITIVE •There is a net GAIN of energy •Reaction does NOT proceed spontaneously as written (i.e., B → A) •Energy must be added to the system to make the reaction B → A. That is, the reaction must be coupled to an exergonic reaction. •The reaction is said to be endergonic.

If A ↔ B spontaneous:

•The product has a lower free energy (G) than the reactant. •ΔG is negative •There is a net loss of energy •Reaction goes spontaneously as written (i.e., A → B) ****The reaction is said to be exergonic.

At equilibrium, for a reversible reaction:

•The rate of the forward reaction is equal to the rate of the reverse reaction. •The overall reaction rate is zero. A + B ↔ C + D At equilibrium d[A]/dt = d[B]/dt = -d[C]/dt = -d[D]/dt = 0

**Why study Thermodynamics?

•Thermodynamics useful in understanding mechanisms, e.g. •Coupled reactions •Contributions of ΔH, ΔS to binding •Design principles for drug development!

Van der Waals Forces

•Weak forces between neutral atoms due to transient electrostatic interactions. • •They may be attractive or repulsive, depending on the distance between the atoms or groups. • •At close distances any 2 atoms will show a weak attraction due to the dipole generated by the random movement of electrons (neg) around the nuclei (pos). •These are very weak (dGo = -1 kcal/mole), and nonspecific interactions.

***Can a reaction with a positive ΔG0' can proceed in the forward direction if ΔG is negative?

•YES, if the ratio of products to reactants ([B]/[A]) is sufficiently small •That is, the ratio of reactants to products is large to make ΔG negative.

Summary

•dG = dH - TdS •dG = dGo + RTln(Prod/React) • dGo = -RTln(Keq) •Spontaneity (DG < 0) •Coupling reactions to make unfavorable reactions favorable

***EXAMPLE 2 - Coupled reaction - principle of mass action or common intermediate

•ΔG for overall reaction favorable •*@ standard state conditions •Both reactions catalyzed by citrate synthase (ensures they'll occur in same vicinity)

The change in free energy is represented in two ways, ΔG and ΔG0

•ΔGº' is STANDARD-STATE change in free energy (at 25°C/298°K, 1 M, 1 atm, pH = 7) •ΔG is the actual change in free energy observed under whatever conditions are in effect. A negative value for ΔG indicates that the reaction occurs spontaneously (i.e. ΔG < 0).