Biochemistry Chapter 5 Quiz

Biochemistry Fundamentals

• BCHE2030 is a course on fundamentals of biochemistry, focusing on thermodynamics and bioenergetics.
• Living cells are complex systems with intricately regulated processes.
• Anabolism is the biosynthetic phase, requiring energy.
• Catabolism is the degradative phase, releasing energy.
• Catabolic pathways release chemical energy in the form of ATP and reduced electron carriers (NADH, NADPH, and FADH2).
• These energy carriers are used in anabolic pathways.
• Biochemistry aims to quantitatively understand energy extraction, storage, and channeling in living cells, considering the laws of thermodynamics.

Thermodynamics

• Thermodynamics studies energy and its effects on matter.
• It allows for the investigation of energy distribution in systems.
• Bioenergetics is the quantitative study of energy transfer in biological systems.
• A goal of biochemistry is to understand energy transformations in living cells in terms of chemical processes and thermodynamics.

Topic Outline

• Laws of thermodynamics and concepts of free energy
• High-energy compounds and coupled reactions
• Cellular energy flow: oxidation-reduction reactions.
• Energetics of biological electron transfers.

Learning Objectives, Laws of Thermodynamics & Free Energy

• Describe the first and second laws of thermodynamics.
• Understand the relationship between free energy (G), enthalpy (H), and entropy (S).
• Understand the concept of spontaneity in a biological process.
• Describe the relationship between the equilibrium constant (K_eq') and free energy.

Key Readings

• Chapter 13, Section 13.1: Bioenergetics and Thermodynamics (Lehninger Principles of Biochemistry, 7th Edition)
• Chapter 1, Section 1.3: Laws of thermodynamics govern biochemical reaction behavior (various textbooks)
• Chapter 8, Section 8.2: Free energy is a useful thermodynamic function for understanding enzymes (various textbooks)

Living Organisms & Dynamic Steady State

• Living organisms are in a dynamic steady state, never at equilibrium with their surroundings.

First Law of Thermodynamics

• Energy is conserved in physical and chemical changes.
• Energy is neither created nor destroyed, but converted from one form to another.
• Potential energy exists in nutrients, sunlight and within cells, going through chemical transformations in different forms of works.

Second Law of Thermodynamics

• The universe tends toward increasing disorder (entropy).
• Natural processes increase the entropy of the universe.
• Entropy (S) is a measure of randomness or disorder.

Free-Energy Change (ΔG)

• ΔG is the change in free energy during a reaction at a constant temperature.
• ΔG= ΔH – TΔS (H = enthalpy change, S= entropy change, T = absolute temperature)..
• If ΔG is negative, the reaction proceeds spontaneously forward.
• If ΔG is positive, the reaction needs energy input to proceed in the forward direction.
• If ΔG is zero, the reaction is at equilibrium.

Exergonic and Endergonic Reactions

• Exergonic reactions proceed with a net release of free energy and occur spontaneously.
• Endergonic reactions absorb free energy from their surroundings and occur non-spontaneously.

Energy Coupling

• Coupling exergonic reaction to endergonic reactions through a shared intermediate.
• This allows non-spontaneous reactions to occur.

Biochemical Reactions as Equilibrium

• Reversible chemical reactions reaching equilibrium.
• Equilibrium constant (K_eq) relates molar concentrations of reactants and products at equilibrium.
• If K_eq > 1, more products than reactants are formed at equilibrium.
• If K_eq < 1, more reactants than products are formed at equilibrium.

Standard Free-Energy Change (ΔG^o)

• Standard conditions are defined initially for reactants and products (1M).
• ΔG^o = -RT ln K_eq' ( R = gas constant, T= temperature, K_eq = equilibrium constant )
• Relationship between ΔG^o and K_eq' is exponential.
• Biochemists use a different standard state (298K=25°C).

Relationship between ΔG and K'_eq

• There's a direct relationship between the equilibrium constant (K_eq') and standard free-energy change (∆G°).
• These values are directly linked, showing whether the reaction proceeds forward or in reverse or remains in equilibrium.

Actual Free-Energy Change (ΔG)

• ΔG is a function of the reactant and product concentrations.
• AG = ΔG^o + RT ln Q, where Q is the mass action ratio (product concentration / reactant concentration).

Standard Free-Energy Changes are Additive

• The standard free-energy change of a reaction is equal to sum of the free energies of component reactions.
• The equilibrium constant of a reaction is equal to product of the equilibrium constants for component reactions.

Thermodynamics & Reaction Rate

• Thermodynamics tells us whether a process is spontaneous (can occur). It doesn't tell us how fast the reaction occurs.

High-Energy Compounds and Coupled Reactions

• Learning objectives focus on ATP coupling to endergonic reactions.
• The chemical logic of ATP hydrolysis.
• High and low-energy compounds and their significance.

High-Energy Phosphate Bonds

• Repulsion between negatively charged phosphates causes the phosphate anhydride bond to act like a coiled spring.
• Energy is released when the bond breaks and phosphates separate rapidly.

Chemical Basis of Large Negative ΔG^o for ATP Hydrolysis

• Charge separation, resonance stabilization of products (Pi and ADP), better hydration of ADP and Pi, relieve electrostatic repulsion among negative charges on ATP.

Actual Free Energy Change (ΔG) in ATP Hydrolysis in Living Cells

• The true substrate for hydrolysis is MgATP²⁻.
• ATP, ADP, and Pi concentrations are typically much lower than 1 M inside cells.

Other Phosphorylated Compounds

• Phosphoenolpyruvate (PEP), 1,3-bisphosphoglycerate, and other compounds also have large free energies of hydrolysis.

Ranking of Biological Phosphate Compounds

• It ranks compounds based on their standard free energies of hydrolysis (high-energy Vs. low-energy compounds)
• This ranking helps to predict whether and how some reactions can proceed.

NADH and NADPH as Universal Electron Carriers

• NAD+ and NADP+ accept a hydride ion (two electrons and one proton) from an oxidizable substrate.
• This process converts them into NADH and NADPH.
• These derivatives are used in cellular oxidation-reduction reactions.

NADH and NADPH as Universal Electron Carriers

• NAD+/NADH often participates in catabolic processes (oxidations).
• NADH/NADPH are used in anabolic processes (reductions).

Dietary Deficiency of Niacin

• Deficiency of niacin leads to pellagra, characterized by dermatitis, diarrhea, and dementia.
• Niacin is a vitamin form of NAD and NADP.
• Humans require niacin from their daily diets.