Untitled Flashcards Set

Flashcard Set: Myoglobin, Hemoglobin, & Immune System

Protein-Ligand Binding

Q: What equation describes reversible protein-ligand binding?
A: The equilibrium equation with dissociation constant (Kd) and association constant (Ka).

Q: How is fractional occupancy (Y or θ) defined?
A: Fraction of protein P that exists in a protein-ligand complex (PL) divided by the total protein (P + PL).

Q: How can you determine Kd experimentally?
A: By plotting Y (fraction bound) vs. ligand concentration [L].

Myoglobin & Hemoglobin

Q: What are the structural differences between myoglobin (Mb) and hemoglobin (Hb)?
A: Mb is a monomer with 1 heme and 1 O₂ binding site, while Hb is a tetramer with 4 hemes and 4 O₂ binding sites.

Q: What is the role of the heme group in oxygen binding?
A: It contains Fe²⁺, which binds O₂ reversibly in a stable oxidation state.

Q: What is the role of histidine residues in oxygen binding?
A: Proximal His F8 coordinates Fe²⁺, while distal His E7 stabilizes bound O₂.

Q: What is the Hill coefficient (nH), and what does it indicate?
A: nH describes the degree of cooperativity in ligand binding:

• nH = 1 (no cooperativity)

• nH > 1 (positive cooperativity)

• nH < 1 (negative cooperativity)

Cooperativity & Allosteric Regulation

Q: What is the difference between the T and R states of hemoglobin?
A:

• T (tense) state: More interactions, more stable, lower O₂ affinity.

• R (relaxed) state: Fewer interactions, more flexible, higher O₂ affinity.

Q: What triggers the T → R conformational change?
A: O₂ binding breaks ion pairs at the α1-β2 interface, increasing O₂ affinity.

Q: What is an allosteric modulator?
A: A molecule that influences protein function by binding at a site other than the active site.

Q: What are examples of positive and negative allosteric effectors of Hb?
A:

• Positive effectors: O₂ (homotropic), CO (heterotropic).

• Negative effectors: 2,3-BPG, CO₂, H⁺ (heterotropic).

Carbon Monoxide (CO) Binding

Q: How does CO binding affect hemoglobin function?
A: CO binds to Fe²⁺ ~20,000x better than O₂ (in free heme) and 40x better in Mb/Hb, increasing O₂ affinity but preventing its release.

Q: Why is CO poisoning dangerous?
A: Hb with bound CO does not release O₂ effectively, leading to tissue hypoxia.

2,3-BPG & O₂ Release

Q: How does 2,3-BPG affect hemoglobin?
A: Binds in the central cavity of Hb, stabilizing the T-state and promoting O₂ release.

Q: How does altitude affect 2,3-BPG levels?
A: Higher altitudes increase 2,3-BPG levels, enhancing O₂ unloading in tissues.

Bohr Effect & CO₂ Transport

Q: What is the Bohr effect?
A: A decrease in pH (increase in H⁺ or CO₂) lowers Hb’s O₂ affinity, promoting O₂ release in tissues.

Q: How does CO₂ bind to hemoglobin?
A: Forms carbaminohemoglobin by reacting with N-terminal amino groups, stabilizing the T-state.

Sickle-Cell Anemia

Q: What mutation causes sickle-cell anemia?
A: Glutamate (E) → Valine (V) substitution at position 6 in the β chain of Hb.

Q: How does the E6V mutation affect red blood cells?
A: Causes Hb polymerization, leading to rigid, sickle-shaped cells that block capillaries.

Immune System & Antibodies

Q: What are the two main branches of the adaptive immune system?
A:

• Humoral immunity: B cells produce antibodies that recognize antigens.

• Cell-mediated immunity: T cells directly attack infected cells.

Q: What are the components of an antibody (immunoglobulin)?
A:

• Y-shaped structure with heavy and light chains.

• Two antigen-binding sites formed by variable domains.

Q: What is an epitope?
A: The specific region on an antigen that an antibody recognizes and binds to.

Q: How does antibody diversity arise?
A: Through genetic recombination of immunoglobulin gene segments.

Flashcard Set: Myoglobin, Hemoglobin, & Oxygen Transport

Protein-Ligand Binding

Q: What equation describes reversible protein-ligand binding?
A: The equilibrium equation with constants for ligand dissociation (Kd) and association (Ka).

Q: How is fractional occupancy (Y or θ) defined?
A: Fraction of protein (P) that exists in a protein-ligand complex (PL) divided by total protein (P + PL).

Q: How can Kd be determined experimentally?
A: By plotting Y (fraction bound) vs. ligand concentration [L].

Myoglobin & Hemoglobin Structure & Function

Q: What is the structural difference between myoglobin (Mb) and hemoglobin (Hb)?
A:

• Mb: Monomer with 1 heme and 1 O₂ binding site.

• Hb: Tetramer with 4 hemes and 4 O₂ binding sites.

Q: What is the role of histidine residues in oxygen binding?
A:

• Proximal His F8 coordinates Fe²⁺.

• Distal His E7 stabilizes bound O₂.

Q: How does Fe²⁺ contribute to O₂ binding?
A: Fe²⁺ in the heme group binds O₂ reversibly in a stable oxidation state.

Hemoglobin Cooperativity & Oxygen Binding

Q: What is the difference between the T and R states of hemoglobin?
A:

• T (tense) state: More interactions, stable, low O₂ affinity.

• R (relaxed) state: Fewer interactions, flexible, high O₂ affinity.

Q: What is the Hill coefficient (nH), and what does it indicate?
A:

• nH = 1: No cooperativity.

• nH > 1: Positive cooperativity (e.g., Hb).

• nH < 1: Negative cooperativity.

Q: What effect does O₂ binding have on hemoglobin structure?
A: O₂ binding shifts Fe²⁺ into the plane of the porphyrin ring, triggering T → R transition.

Allosteric Regulation of Hemoglobin

Q: What are examples of allosteric effectors of Hb?
A:

• Positive effectors: O₂ (homotropic), CO (heterotropic).

• Negative effectors: 2,3-BPG, CO₂, H⁺ (heterotropic).

Q: What is the Bohr effect?
A: A decrease in pH (increase in H⁺ or CO₂) lowers Hb’s O₂ affinity, promoting O₂ release in tissues.

Q: How does 2,3-BPG affect Hb function?
A:

• Binds the central cavity of Hb.

• Stabilizes the T-state.

• Enhances O₂ release at high altitudes.

Q: How does CO poisoning affect Hb function?
A:

• CO binds to Fe²⁺ ~40x better than O₂ in Hb.

• Increases O₂ affinity but prevents O₂ release.

• Leads to tissue hypoxia.

Flashcard Set: Antibody Structure & Immune System

Basic Antibody Structure

Q: What are antibodies (Abs)?
A: Immune system proteins that recognize and neutralize foreign molecules.

Q: What is the general structure of an antibody?
A:

• 4 polypeptide chains (2 heavy, 2 light).

• "Y"-shaped quaternary structure.

• Antigen-binding sites at the tips of the arms.

Q: What are the key regions of an antibody?
A:

• Variable (V) domains: Bind antigens.

• Constant (C) domains: Interact with immune cells.

• Complementarity Determining Region (CDR): Recognizes specific epitopes.

Q: How are antibodies held together?
A: By disulfide bonds between chains.

Antibody Classes & Function

Q: What are the five antibody isotypes?
A:

1. IgG: Most abundant, secondary immune response.

2. IgA: Mucosal immunity (saliva, tears, gut lining).

3. IgM: First produced, pentameric structure.

4. IgE: Involved in allergic reactions.

5. IgD: Function not well understood.

Q: How does IgG activate the immune response?
A:

• Binds pathogens.

• Activates macrophages via Fc receptor binding.

• Promotes phagocytosis.

Antibody-Antigen Interactions

Q: What forces mediate antibody-antigen binding?
A:

• Van der Waals forces

• Hydrophobic interactions

• Dipole interactions

• Hydrogen bonds

Q: What is the induced fit model in antibody binding?
A: Both the antigen and antibody undergo conformational changes upon binding.

Q: What is a hapten?
A: A small molecule that is non-immunogenic alone but elicits an immune response when attached to a larger protein.

Antibody Diversity & Immune Memory

Q: How is antibody diversity generated?
A:

• V(D)J recombination: DNA rearrangement of immunoglobulin genes.

• Hypermutation: Introduces additional variability in binding sites.

Q: What is immunological memory?
A: The ability of the immune system to remember and respond quickly to previously encountered pathogens.