Biochem Office hours exam 1

Overview of Lecture Concepts

  • Contextual Applications of TKA:

    • TKA (theoretical knowledge application) is applied in scenarios like

      • Ion Exchange Chromatography: Understanding movement based on charge (positive/negative).

      • Direct pKa Questions: Can be quantitative and qualitative.

    • Relevant in experiments such as chromatography, emphasizing practical implications of these theories.

General Understanding of pKa and Pi

  • pKa: Influences the isoelectric point (pI), which is critical for understanding protein behavior.

  • Isoelectric Focusing: Involves the concept of pI and its relation to pKa.

Summary of Lecture Six

  • Protein Dynamics:

    • Essential in cellular processes as they dictate actions in biochemical reactions.

  • Kinetics:

    • Driven by energy, differentiating between endergonic (energy input required) vs exergonic (energy released) reactions.

    • Analogous to logistics in planning—having the energy doesn't guarantee execution.

Kinetics Fundamentals

  • Velocity of Reaction:

    • Defined as the change in concentration of reactants/products over time.

  • Influencing Factors:

    • Concentration of reactants and probability of interaction.

  • Rate Constant (k):

    • A critical variable summarizing multiple kinetic factors.

  • Equilibrium (KEQ):

    • Equal velocities in forward and reverse reactions; affected by rate constants.

Kinetic Theory

  • Statistical Nature of Biochemistry:

    • Biochemical changes indicate likelihood rather than certainties.

  • Key Variables:

    • Temperature and Activation Energy (Ea):

      • Ea: Minimum energy needed for the reaction to occur.

      • Temperature: Relates to kinetic energy of molecules.

Enzyme Kinetics

  • Role of Enzymes in Velocity:

    • Enzymes speed up reactions without altering the change in Gibbs Free Energy (ΔG).

    • The enzyme's role reduces the energy barrier between reactants and the transition state.

  • Orders of Reaction:

    • Zero Order: Reaction rate independent of reactant concentration

    • First Order: Rate depends on the concentration of one reactant.

    • Second Order: Rate depends on concentrations of two reactants simultaneously.

Michaelis-Menten Kinetics

  • Michaelis Constant (Km):

    • Reflects affinity between enzyme and substrate; Lower Km indicates higher affinity.

  • Kcat:

    • Represents turnover number of the enzyme, linking enzymatic performance to chemical steps.

  • Catalytic Efficiency:

    • Ideally, enzymes should have high catalytic efficiency optimized for reaction specificity.

Exam Preparation

  • Practical Application:

    • Expect to use the Michaelis-Menten equation for calculations in research contexts.

  • Review Focus:

    • Emphasis on understanding concepts over intensive math; basic algebra applicable.

    • Expect multiple-choice format; familiarize with equations and contextual applications.

Lecture Materials and Resources

  • Suggested videos and channels for additional learning:

    • AK Lectures

    • Orgo Chem Tutor

Final Thoughts

  • Explaining Concepts:

    • Clear understanding is emphasized over rote memorization of equations.

    • Focus on how various thermodynamic principles tie into protein folding and behavior.