lecture 16 full notes

Recap of Signaling Pathways from Lecture 15

G-Protein Coupled Receptors (GPCRs)

• Definition: G-Protein Coupled Receptors (GPCRs) represent the largest and most diverse group of membrane receptors in eukaryotes.

• Function: They act as cell surface receptors for signals in various forms such as light energy, peptides, lipids, sugars, and proteins. These signals inform cells about environmental conditions indicating the presence or absence of life-sustaining resources.

• Role in Medicine: GPCRs are crucial for numerous bodily functions, and advancements in understanding these receptors have significantly influenced modern medicine. Approximately one-third to one-half of all marketed drugs target GPCRs by binding to them.

G Alpha Activation

• Activation Process:

  • In unstimulated cells, G alpha is in a state defined by its binding to GDP.

  • It interacts with G beta-gamma and the GPCR itself.

  • Upon stimulation by a ligand (agonist), the receptor undergoes a conformational change leading to:

  1. Dissociation of G alpha from the receptor and G beta-gamma.

  2. Exchange of GDP for GTP, resulting in the activation of G alpha.

  • Post-activation, G alpha activates other intracellular molecules.

G Proteins Overview

• Definition: G proteins are specialized proteins capable of binding nucleotides, specifically guanosine triphosphate (GTP) and guanosine diphosphate (GDP).

• Structure: The G proteins associated with GPCRs are heterotrimeric, consisting of three different subunits:

  • Alpha subunit

  • Beta subunit

  • Gamma subunit

• Attachment: The alpha and gamma subunits are attached to the plasma membrane via lipid anchors. Some G proteins, like Ras, exist as small proteins with a single subunit.

Epinephrine Binding and Activation Steps

1. Epinephrine Binding: Epinephrine binds to a specific GPCR.

2. Receptor Conformational Change: The binding causes a change in the GPCR's conformation.

3. G-Protein Activation: This change induces a conformational change in the associated G-protein, causing GDP to be replaced by GTP on G alpha.

4. Dissociation of G alpha: G alpha-GTP (active form) separates from G beta-gamma.

Activation of Adenylate Cyclase

1. G alpha Activation: G alpha travels through the membrane to interact with the enzyme Adenylate cyclase.

2. Conformational Change: Interaction with G alpha induces a conformational change, activating Adenylate cyclase.

3. Catalysis: Active Adenylate cyclase catalyzes the reaction:
   $ext{ATP} <br>ightarrow ext{cAMP} + ext{PPi}$

Role of cAMP

• Compound Role: cAMP is a significant signaling molecule that facilitates further downstream signaling.

• Activation of Glycogen Phosphorylase: Investigations into how cAMP activates glycogen phosphorylase led to key findings:

  1. The active form of glycogen phosphorylase is phosphorylated, while the inactive form is not.

  2. The phosphorylation process utilizes ATP.

Mechanism of Phosphorylation

• Catalyzing Enzymes: Enzymes called kinases facilitate the phosphorylation process using phosphate from ATP.

• Regulation: Phosphorylation is a common mechanism for regulating protein activity, particularly enzymes, due to its speed and reversibility.

Specifics of Glycogen Phosphorylase Phosphorylation

• Catalyzing Enzyme: Phosphorylation of glycogen phosphorylase occurs through phosphorylase kinase.

• Conversion Process:

  • Glycogen phosphorylase 'b' (inactive) is converted into glycogen phosphorylase 'a' (active).

  • ATP is consumed in this process, leading to the production of ADP.

Phosphorylase Kinase Activation

• Further Activation: Phosphorylase kinase can also be activated by phosphorylation itself, leading to:

  • Active phosphorylase kinase catalyzing the subsequent phosphorylation of glycogen phosphorylase.

  • Glycogen phosphorylase further catalyzes the conversion of glycogen into glucose.

Signal Amplification through Enzyme Cascades

• Overview: The processes involved can result in significant amplification of the original signal initiated by epinephrine. For instance:

  • One activated GPCR can induce much higher levels of biochemical activity, reflecting signal amplification.

Amplification Example Steps:

1. Single epinephrine molecule activates one receptor, which activates one G protein.

2. Each activated G protein can activate multiple adenylate cyclases (estimated amplification of 20x).

3. The active adenylate cyclase produces cAMP, which further activates multiple protein kinase A enzymes.

4. Each active protein kinase A phosphorylates many phosphorylase kinases, leading to further overall amplification in the path to glucose production.

Types of Cell Responses to Signals

• Responses Include:

  1. Channel Opening: A change in membrane permeability facilitating ion movement.

  2. Production of Second Messenger: Such as cAMP, which facilitates various enzymatic pathways.

  3. Direct Activation of Enzyme Activity: Enzymatic action initiated by receptor binding.

  4. Gene Transcription: Actions such as those initiated by steroid hormones that result in changes in gene expression.

Signaling through Receptor Tyrosine Kinases (RTKs)

1. Growth Factor Binding: Growth factors bind to dimerized receptors of RTKs.

2. Conformational Change: This binding induces a conformational change activating the receptor’s kinase activity.

3. Self-Phosphorylation: The receptor performs self-phosphorylation leading to further downstream signaling.

4. Ras Activation: Heterotrimeric G-proteins (e.g. Ras) undergo GTP-GDP exchange, leading to activation.

5. Enzyme Cascade: The activation initiates a kinase cascade ending with MAPKs entering the nucleus to affect gene transcription associated with proliferation.

Characteristics of Signaling Pathways

• Ligand Affinity: Ligands bind with high affinity and specificity to their receptors.

• Second Messenger Involvement: Some signaling mechanisms involve secondary messengers while others do not.

• Short vs Long-term Changes: Signaling may result in either short-term reversible changes or longer-lasting effects such as gene expression.

• Amplification: Enzyme cascades are prevalent and facilitate signal amplification via conformational changes.

Thermodynamics and Energy in Biology

Basic Thermodynamic Laws

• First Law of Thermodynamics: Energy in a closed system is conserved; energy can convert from one form to another (but total energy remains constant). Entropy cannot decrease in a closed system.

  • Example: Conversion of energy types in biochemical processes.

• Second Law of Thermodynamics: The entropy of a closed system constantly tends to increase, promoting disorder over time.

Gibbs Free Energy

• Definition: The total energy available for work associated with a reaction resides in Gibbs Free Energy (G).

• ΔG: The change in Gibbs Free Energy is essential for determining the energetics of biochemical reactions.

  • Exergonic Reactions: When ext{ΔG} < 0, energy is released (favorable, spontaneous).

  • Endergonic Reactions: When ext{ΔG} > 0, energy is required (unfavorable, non-spontaneous).

• Formula:
  $ext{ΔG} = ext{G}<em>{ ext{products}} - ext{G}</em>{ ext{reactants}}$

Characteristics of Biological Systems

• Essential Properties:

  1. Contain biological macromolecules (L-amino acids, D-monosaccharides).

  2. Are compartmentalized to perform distinct functions.

  3. Take in molecules from the environment and synthesize new ones.

  4. Extract energy from surroundings to perform work.

  5. Maintain homeostasis, ensuring conditions compatible with life.

  6. Contain hereditary information for replication and evolutionary change.

Energy Transduction and Cellular Integrity

• Energy Requirement: Cells continuously require energy to sustain normal functionality and integrity, termed energy transduction. Without energy, cells compromise integrity through breakdown and loss of function.

Summary of Key Points

• Understanding Gibbs Free Energy: Energetics pertinent to biochemical processes is crucial for interpreting reaction favorability through standard conditions, temperature, and concentration effects.

• Energy Coupling: ATP hydrolysis commonly serves as a direct energy source for coupled reactions, making it essential for driving favorable biochemical processes.