Biochemistry Quiz on Enzymes and Proteins

Protein Misfolding, Enzymes, and Protein Regulation

• This week's topics cover protein folding perturbation, protein function, enzyme mechanisms, and protein regulation.
• Students will learn how cells respond to unfolded or misfolded proteins.
• They will also explore protein-ligand interactions, enzyme function, and chemical reaction acceleration by enzymes.

Unit Objectives

• Describe the impact of environmental factors on protein folding and the cellular stress response when proteins misfold.
• Explain how the strength of protein-ligand interactions is determined and measured using the dissociation constant (Kd).
• Explain why cells need enzymes and how they speed up chemical reactions.
• Describe general mechanisms of enzyme-catalyzed chemical reactions.
• Identify and describe the general mechanisms of protein function regulation.

Reading and Resources

• Consult provided lecture slides and diagrams for visual aids.
• Utilize the recommended online resources for further in-depth knowledge and clarification of concepts.
• Review supplemental videos for context and alternative explanations of subjects.

Protein-Ligand Interactions

• Protein-ligand interactions involve chemical bonds between a protein and a ligand (molecule).
• The strength of these interactions, or affinity, is determined by the number and strength of chemical bonds.
• Dissociation constant (Kd) is a measure of the average rate of protein dissociation/separation from its ligand.
• A small Kd suggests a high affinity, meaning the protein binds strongly to the ligand.

Denaturation by Acid or Base

• Environmental factors such as heat, salt concentration, pH, and high-intensity light (like X-rays) can affect the stability of non-covalent bonds in proteins.
• Destabilization of bonds can lead to protein unfolding or misfolding, resulting in a loss of function.
• Thermal energy or heat can also impact rates of diffusion and interaction among molecules.
• Cells regulate factors like temperature, pH, and salt concentration to maintain protein stability.

Enzymes

• Enzymes are proteins that accelerate chemical reactions by lowering the activation energy.
• They typically stabilize the transition state, leading to faster reactions.
• Enzymes are crucial in biological systems to speed up specific reactions essential for proper cellular functioning.
• Enzymes can facilitate reactions by positioning reactants to enhance bond formation, providing favorable charge environments around reacting groups, and changing reactant conformation to better promote the transition state.

Reaction Progress Diagram

• Reaction progress diagrams track free energy during a reaction over time.
• The y-axis represents free energy, and the x-axis represents the progression of the reaction.
• Reactants possess higher energy than products in an exergonic (spontaneous) reaction, resulting in energy release.
• In an endergonic reaction, the products require higher energy than the reactants, requiring energy input from the environment.
• Enzymes accelerate reactions by lowering the activation energy barrier.

Protein Folding

• The environment significantly impacts protein folding.
• Factors like temperature (thermal energy), pH, and salt concentration affect the stability of a protein's structure.
• Proteins can unfold (denature) and misfold due to unfavorable environmental conditions or cellular stresses.
• Specialized proteins called chaperones aid in preventing misfolding/unfolding and assisting in the proper folding of other proteins.

Protein Regulation and Allostery

• Proteins are regulated by post-translational modifications like modification of amino acid side chains.
• Allostery involves a conformational change in a protein in response to binding at one site, affecting its activity in another part/area.
• Post-translational modifications can alter protein structure, activity, and/or localization and can either positively or negatively affect protein function.

GTP-Binding Proteins

• GTP-binding proteins (like Ran and Ras) typically cycle between active and inactive conformations via GTP hydrolysis, influencing cellular processes like signal transduction, and transport.
• GTPases switch between GTP-bound and GDP-bound states, regulating various cellular functions such as protein activity, transport, and cellular communications.
• Motor proteins utilize stepwise ATP binding, hydrolysis, and release to facilitate movement across cellular structures.

Post-translational Modifications

• Proteins can be modified after their synthesis via covalently adding molecules to their structure.
• These adjustments often impact protein stability, activity, localization, and/or interaction with other molecules.