CH250: Chapter 2

Define the 3 different types of work

1. Osmotic work: Maintains varying solute concentrations across biological membranes 

2. Chemical work: Biosynthesis (anabolism) and degradation (catabolism) of organic molecules 

3. Mechanical work: Muscle contraction in animals 

Compare homeostasis (4) vs equilibrium (4)

• Homeostasis 

  • The state of steady internal, physical, and chemical conditions

  • Highly ordered steady state in terms of temperature, [biomolecules], etc.

  • Requires energy and delays equilibrium

  • Example: living organisms

• Equilibrium 

  • Substances transition between the reactants and products at equal rates, meaning there is no net change in concentrations

  • Homeostasis is no longer maintained

  • Macromolecules tend to equilibrate to their surroundings

  • Example: non-living organisms

Oxidation-reduction rxns: Why are they important? + Define each

• Redox rxns often coupled in biological systems 

  • Important in biochemical processes bc electron transfer makes energy available, which can be used to perform chemical work

• Oxidation = Loss of electrons

• Reduction = Gain of electrons 

What are the zeroth, first, second, and third laws of thermodynamics?

• Zeroth law: If two thermodynamic systems are each in thermal equilibrium w a third, then they are in equilibrium w e/o 

  • I.e., there is no heat flow b/w objects that are the same temp 

• First law: Energy can neither be created nor destroyed, it can only change forms 

  • In any process in an isolated system, the total energy remains the same 

  • For a thermodynamic cycle, the net heat supplied to the energy system equals the net work done by the system 

  • I.e., heat can neither be created nor destroyed 

• Second law: The entropy of an isolated system consisting of 2 regions in space, isolated from one another, each in thermodynamic equilibrium in itself, but no in equilibrium w e/o, will, when the isolation that separates the two regions is broken so that the two regions become able to exchange matter or energy, tend to increase over time, approaching a max value when the jointly communicating system reaches thermodynamic equilibrium 

  • I.e., “entropy” is a quantifiable measure of how evenly heat is distributed 

    • Every time heat flows from hot spot to cold spot → entropy increases 

    • Every time heat flows from cold spot to hot spot → entropy decreases 

• Third law: As temp approaches absolute 0, the entropy of a system approaches a constant minimum 

  • I.e., an ideal engine would convert 100% of heat into useful work only if its exhaust temp was absolute zero (therefore, 100% efficiency is impossible)

Ice melting at room temp is dominated by which thermodynamics law? + Explain

• Dominated by second law 

• Explanation 

  • Solid water (ice) has lower entropy than liquid water bc water molecules in ice have limited motion 

  • Gas phase of water (steam) has highest entropy bc of the increased motion of its water molecules

• Gibbs free energy (G): Expresses the amt of energy capable of doing work during a rxn at constant temperature and pressure

  • ΔG < 0 = Gibbs energy released + Rxn is exergonic

  • ΔG > 0 = Gibbs energy is gained + Rxn is endergonic

  • Units = joules/mole (J mol^-1) for ΔG

• Enthalpy (H): Heat content of the reacting system (reflects the number and kind of chemical bonds in the reactants and the products)

  • ΔH < 0 = Heat released + Rxn is exothermic

  • ΔH > 0 = Heat absorbed + Rxn endothermic 

  • Units = joules/mole (J mol^-1) for ΔH

• Entropy (S): Quantitative expression of the randomness or disorder of a system

  • ΔS < 0 = Prods more complex and more ordered than reactants + Rxn has loss of entropy 

  • ΔS > 0 = Prods less complex and more disordered than reactants + Rxn has gain of entropy 

What is the ΔG_system and ΔS_universe in spontaneous rxns?

• All processes that occur spontaneously → decrease in Gibbs energy of system 

• All processes that occur spontaneously → increase in entropy of the universe (ΔS_universe > 0)

Exergonic vs endergonic processes: Energy relationship + ΔG_system + Spontaneous? + Example

• Exergonic processes (ΔG_system < 0)

  • Energy-yielding 

  • Proceed spontaneously (but may be very slow)

  • Ex: C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + energy

• Endergonic processes (ΔG_system > 0)

  • Energy-requiring 

  • Cannot proceed spontaneously 

  • Ex: 6CO₂ + 6H₂O + energy → C₆H₁₂O₆ + 6O₂

	ΔH < 0	ΔH  > 0
ΔS > 0
ΔS < 0

Fill in this table

	ΔH < 0 (favourable)	ΔH  > 0 (unfavourable)
ΔS > 0 (favourable)	ΔG < 0 at all temperatures Process spontaneous at any temp	ΔG > 0 when T low (T < HS) ΔG < 0 when T low (T < HS) Process only spontaneous at high temp
ΔS < 0 (unfavourable)	ΔG < 0 when T low (T < HS) ΔG > 0 when T low (T < HS) Process only spontaneous at low temp	ΔG > 0 at all temps Process nonspontaneous at all temps

Define: Equilibrium constant + Units

• Equilibrium constant (K_eq): Ratio of product concentrations to reactant concentrations at equilibrium 

• Units = moles/litre (mol litre^-1) at 25°C

What are the conditions and symbols of standard state in biochem?

• Conditions of standard state used in biochemistry 

  • [H⁺] = 10^-7 M

    • pH = 7.0

  • [H₂O] = 55.5 M

  • If Mg²⁺ present, then [Mg²⁺] is constant at 1 mM

  • When H₂O, H⁺, and/or Mg²⁺ are reactants or prods, their concentrations are incorporated into ΔG°’ and K’_eq 

• Symbols 

  • Standard Gibbs energy change = ΔG°’

  • Standard equilibrium constant = K’_eq 

Mass action ratio (Q): Define + Relationship w K

• Mass action ratio (Q): Reflects the actual concentrations of reactants and products under steady-state conditions (e.g., in a living cell)

• A comparison of the mass action ratio (Q) to the equilibrium constant (K) predicts the direction in which a rxn will proceed 

  • Q < K → Rxn proceeds in forward (product-forming) direction 

  • Q > K → Rxn proceeds in reverse (reactant-forming) direction 

  • Q = K → Rxn is at equilibrium  

Water: Unique chemical and physical properties of water (9) + What is the reason for most of these properties? + What is the geometry of water? + What is special abt H-bonding in water? 

• Properties

  1. Water is less dense as a solid than as a liquid

  2. Water is a liquid over a wide range of temperatures on earth

  3. Water is an excellent solvent

  4. Heat capacity: Extremely high heat capacity

     • Useful for heating and cooling

  5. Latent heats of fusion and vaporization: Latent heats of fusion and vaporization are both unusually high

     • Ice for cooling, steam for heating

  6. “Universal” solvent

     • More substances dissolve in water than other liquids

  7. More substances dissolve in water than other liquids (“universal” solvent)

  8. Surface tension: Highest surface tension of any liquid (besides mercury)

  9. Solid phase

     • Water expands as it cools below 4°C

     • Becomes less dense to 0°C

     • Below 0°C, it becomes solid (ice)

• Reason = H-bonding

• Geometry = tetrahedral

• H-bonding: Can act as H-bond donor and H-bond acceptor

Biochemical rxns depend on___ + Examples (4)

• Biochemical rxns depend on weak interactions

• Ex: 

  • 3D structure of proteins and nucleic acids

  • Enzyme–substrate interactions

  • Hormone binding to receptors (e.g., insulin binding to insulin receptors)

  • Stability of DNA double helix

Define the 4 basic types of noncovalent interactions in biomolecules

1. Hydrogen bonds: A weak noncovalent bond in which a hydrogen is shared b/w 2 electronegative atoms 

   • Involves a partial positive charge in the donor H and a partial negative charge in the acceptor atom 

2. Ionic interactions: A weak interaction b/w oppositely charged atoms or groups 

   • Ex: attraction b/w pos amino grp NH₃⁺ and neg charged carboxylate grp COO^- in a protein 

3. Van der Waals interactions: A weak interaction b/w the dipoles of nearby electrically neutral molecules 

   • Most favourable when atoms are at a distance slightly greater than when they’re covalently bonded 

     • Too close → repulsion; Too far → van der Waals interaction energy decreases 

4. Hydrophobic effects: A weak molecular interaction b/w fully-reduced hydrocarbon molecules (i.e., C and all C bonds saturated w H)

   • Due to the tendency of hydrophobic molecules to pack closely tg to try to minimize interactions w water (e.g., olive oil floats to top of water)

     • Explanation: Bc hydrophobic molecs can’t form H-bonds w water, the water surrounding a hydrophobic region becomes more ordered to satisfy its H-bonding potential through interactions w other water molecs, forming cage-like structures

       • Energetically unfavourable bc entropy of water molecs decreased bc their motion is restricted 

       • When hydrophobic regions cluster tg, they have less exposed surface area so less water molecs need to be ordered, which is more energetically favourable so hydrophobic regions tend to pack tg 

   • Nonionic and nonpolar 

   • Cannot form H bonds w water 

   • Water molecules form an ordered shell around hydrophobic molecules (similar to ordered molecules in surface tension)

   • Not the same as other noncovalent interactions bc they’re due to avoiding water rather than true molecular attraction 

Define: Hydrogen bond donor vs acceptor

• Hydrogen-bond donor: An electronegative atom covalently bonded to a hydrogen atom, which carries a partial positive charge (bc of the electronegative atom) and can be donated to form the hydrogen bond 

  • Essentially all H-bond donors are H bonded to O or N bc these are only situations that result in partially pos charge on H strong enough to interact w the neg charge of an acceptor atom 

• Hydrogen-bond acceptor: An electronegative atom w a lone pair of electrons that attracts the partially positive hydrogen of a hydrogen-bond donor, thereby accepting it to form the hydrogen bond

How do hydrophobic effects contribute to the structure and function of biomolecules?

• hydrophobic effects b/w nonpolar amino acids in proteins important for proper folding of newly synthesized proteins 

  • Nonpolar amino acids collapse into core of folded protein, leaving polar amino acids on surface to increase protein solubility 

  • As nonpolar amino acids pack closer tg due to hydrophobic effects, additional weak interactions b/w polar and nonpolar amino acids (h bonds, ionic interactions, van der Waals interactions) serve to stabilize overall 3D structure of protein

Define: Osmosis, Hypotonic, Hypertonic, Isotonic + What are the effects of placing an RBC in each type of solution? 

• Osmosis: The diffusion of solvent molecules from a region of lower solute concentration to one of higher solute concentration (or diffusion of H₂O molecules from a solution of high H₂O concentration to one of low H₂O concentration)

• Hypotonic: Solution w lower solute concentration than that of another solution (such as the solution inside a cell)

• Hypertonic: Solution w higher solute concentration than that of another solution (such as the solution inside a cell)

• Isotonic: Solution w same solute concentration as that of another solution (such as the solution inside a cell)

• Effects of placing an erythrocyte (RBC) into diff solutions 

  • RBC in hypotonic solution = H₂O diffuses from solution into RBC → RBC lyses (ruptures)

  • RBC in hypertonic solution = H₂O diffuses out of RBC into solution → RBC shrinks

  • RBC in isotonic solution = H₂O diffusion into cell equal to H₂O diffusion out of cell → cell is balanced