BICD 110

Midterm 2 Notes

Which of the following best describes phagocytosis?

A. A clathrin-dependent pathway used to internalize small molecules
B. An actin-independent process used for the constitutive internalization of fluids
C. An ancient, actin-dependent mechanism for engulfing large particles >500 nm
D. A type of exocytosis used to secrete lysosomal enzymes

C. C. An ancient, actin-dependent mechanism for engulfing large particles >500 nm

What is the role of Fc receptors in phagocytosis?

A. They hydrolyze target particles during phagosome maturation
B. They bind to antibodies that are attached to targets, initiating uptake
C. They synthesize V-ATPases in the early phagosome
D. They directly convert Rab5 to Rab7 during maturation

B. They bind to antibodies that are attached to targets, initiating uptake.

During phagosome maturation, which of the following events occurs first?

A. Fusion with lysosomes
B. Recruitment of LAMP proteins
C. Conversion from Rab5 to Rab7
D. Fusion with early endosomes delivering V-ATPases

D. Fusion with early endosomes delivering V-ATPases

What is the correct sequence of events during phagocytosis?

A. Signal termination → cup formation → NADPH oxidase activation → opsonized target detection
B. Opsonized target detection → phagocytic cup formation → phagosome maturation → phagosome closure
C. Cup formation → opsonized target detection → actin remodeling → exocytosis
D. Early endosome fusion → Rab7 recruitment → antibody binding → pseudopod extension

B. Opsonized target detection → phagocytic cup formation → phagosome maturation → phagosome closure

What function does the NADPH oxidase complex serve during phagosome maturation?

A. Tags phagosomes for lysosome fusion
B. Synthesizes LAMP proteins
C. Generates reactive oxygen species to help destroy engulfed material
D. Pumps protons into the phagosome to lower pH

C. Generates reactive oxygen species to help destroy engulfed material

Describe how Rab proteins regulate phagosome maturation.

Rab proteins regulate phagosome maturation by sequentially labeling the vesicle’s identity. Rab5 is first recruited to the early phagosome and promotes fusion with early endosomes. Then, Rab5 is replaced by Rab7, which promotes further acidification and fusion with lysosomes, marking the transition to a late phagosome.

Explain the role of actin in phagocytosis

Actin plays a critical role in forming the phagocytic cup and extending pseudopods around the engulfed particle. Actin remodeling is essential for membrane deformation, allowing the plasma membrane to surround and eventually internalize the target into a phagosome.

What triggers the termination of signaling during phagocytosis?

Signaling is terminated after the phagosome is fully enclosed and begins to mature. Termination likely occurs due to removal or inactivation of receptor-ligand interactions, changes in the membrane composition, and progression into the degradative pathway.

What is a defining feature of macropinocytosis?

A. It selectively internalizes specific ligands via clathrin-coated vesicles
B. It requires the presence of Fc receptors to initiate uptake
C. It is an actin-dependent process that nonspecifically engulfs extracellular fluid
D. It is triggered exclusively by pathogen detection

C. It is an actin-dependent process that nonspecifically engulfs extracellular fluid

Which of the following correctly pairs a protein or lipid with its role in clathrin-mediated endocytosis?

A. Clathrin – hydrolyzes cargo for degradation
B. PI(4,5)P₂ – binds directly to LDL particles
C. AP-2 – adaptor complex that recognizes sorting motifs on receptors
D. Auxilin – inserts receptors into plasma membrane

C. AP-2 – adaptor complex that recognizes sorting motifs on receptors

What happens to clathrin-coated vesicles (CCVs) after budding from the plasma membrane?

A. They fuse immediately with lysosomes
B. They remain coated to protect the cargo
C. They are uncoated by Hsc70 and auxilin using ATP
D. They are destroyed by proteasomes

C. They are uncoated by Hsc70 and auxilin using ATP

What is the functional role of V-type ATPases in lysosomes?

A. They degrade misfolded proteins
B. They prevent lysosomal enzymes from becoming active in the cytoplasm
C. They pump calcium ions into lysosomes for signaling
D. They recycle clathrin-coated vesicles

B. They prevent lysosomal enzymes from becoming active in the cytoplasm

What experimental strategy was used to visualize LDL uptake?

A. Fluorescent tagging of clathrin
B. GFP-tagging of early endosomes
C. Labeling LDL with ferritin
D. Immunoprecipitation of ApoB

C. Labeling LDL with ferritin

Describe how macropinosomes are formed and their role.

Macropinosomes form via actin-driven membrane ruffling, where the cell engulfs large volumes of extracellular fluid. The ruffles collapse inward, trapping fluid into vesicles ranging from 200 nm to 10 µm. This process allows the cell to "sample" its environment and is constitutive in some cell types.

What triggers the open conformation of AP-2 in clathrin-mediated endocytosis?

Binding of PI(4,5)P₂ and cargo triggers AP-2 to adopt an open conformation, enabling it to interact with both membrane lipids and receptor motifs (such as NPXY or LL), initiating vesicle budding.

Outline the pathway for receptor-mediated endocytosis of LDL particles.

1. LDL receptors bind to ApoB on LDL particles.

2. The complex is recruited into clathrin-coated pits via AP-2.

3. Vesicle buds off and is uncoated by Hsc70 and auxilin.

4. Vesicle fuses with early endosomes; LDL and receptor separate in acidic pH.

5. Receptor recycles to the surface; LDL is sent to lysosomes for degradation.

Which of the following statements about caveolin-dependent endocytosis is TRUE?

A. It uses actin polymerization to form phagocytic cups
B. It forms vesicles coated in clathrin
C. It involves the protein caveolin and flask-shaped invaginations of the plasma membrane
D. It is primarily responsible for engulfing pathogens

C. It involves the protein caveolin and flask-shaped invaginations of the plasma membrane

What is the current consensus on the structure once referred to as "caveosomes"?

A. They are specialized lysosomes
B. They are distinct and well-defined organelles for caveolar trafficking
C. They are likely experimental artifacts
D. They are derived from the Golgi apparatus

C. They are likely experimental artifacts

Which of the following is a feature of clathrin- and caveolin-independent endocytic pathways?

A. They require both clathrin and caveolin for vesicle formation
B. They are triggered exclusively by pathogens
C. Their mechanisms are poorly understood and may vary depending on the cargo and cell type
D. They use Fc receptors and tyrosine kinase activation

C. Their mechanisms are poorly understood and may vary depending on the cargo and cell type

What is caveolin, and what role does it play in endocytosis?

Caveolin is a membrane-associated protein that forms flask-shaped invaginations in the plasma membrane known as caveolae. These structures help mediate caveolin-dependent endocytosis, which internalizes select cargo molecules without the use of clathrin.

Why are “caveosomes” considered artifacts in modern cell biology?

Early studies proposed “caveosomes” as distinct organelles involved in caveolar trafficking, but later research showed they lack clear markers, structure, and reproducibility. They are now widely regarded as artifacts of older imaging or experimental techniques rather than true organelles.

Give an example of when a cell might use a clathrin- and caveolin-independent pathway.

A cell might use clathrin- and caveolin-independent pathways to internalize glycosylphosphatidylinositol (GPI)-anchored proteins or certain toxins (like Shiga or cholera toxin). These pathways may function in specific lipid raft domains and are less understood mechanistically.

Which of the following molecules is MOST likely to freely diffuse across a biological membrane without the aid of a protein?

A. Sodium ion (Na⁺)
B. Glucose
C. Carbon dioxide (CO₂)
D. Lysine

C. Carbon dioxide (CO₂)

Why can't fatty acids freely cross the membrane even though they are lipids?

A. They are too large
B. Their carboxylic acid group is charged at physiological pH
C. They are hydrophobic
D. Membranes are impermeable to all lipids

B. Their carboxylic acid group is charged at physiological pH

Which of the following statements best distinguishes a chemical gradient from an electrical gradient?

A. Chemical gradients depend on charge; electrical gradients depend on size
B. Chemical gradients involve concentration differences; electrical gradients involve ion charge distribution
C. Electrical gradients only exist when channels are closed
D. Chemical gradients only apply to ions

B. Chemical gradients involve concentration differences; electrical gradients involve ion charge distribution.

What defines a uniporter?

A. It transports two molecules in opposite directions
B. It hydrolyzes ATP to move solutes
C. It passively facilitates the transport of a single type of molecule along its concentration gradient
D. It allows the bidirectional movement of water

C. It passively facilitates the transport of a single type of molecule along its concentration gradient

What type of membrane protein is always open and allows passive movement along an electrochemical gradient?

A. Ligand-gated channel
B. Voltage-gated channel
C. Constitutively open channel
D. Primary active transporter

C. Constitutively open channel

Give two examples of molecules that can cross the lipid bilayer without a transporter and two that cannot.

• Can cross: O₂ (oxygen), CO₂ (carbon dioxide)

• Cannot cross: Na⁺ (sodium ion), glucose (large polar molecule)

Explain the difference between a chemical gradient and an electrical gradient using an example.

• A chemical gradient exists when there is a difference in concentration of a substance across a membrane (e.g., more glucose outside than inside a cell).

• An electrical gradient exists when there is a difference in charge (e.g., side A has 7⁺ and 2⁻; side B has 2⁺ and 7⁻ → same number of ions, but different charges)

Why is facilitated transport via a uniporter slower than diffusion through a channel?

Uniporters undergo conformational changes to transport molecules across the membrane, making the process slower than ion channels, which allow rapid passive diffusion without shape change.

Which of the following is an example of secondary active transport?

A. Na⁺/K⁺ ATPase pumping ions
B. Glucose uniporter facilitating sugar uptake
C. Na⁺/lysine co-transporter moving lysine against its gradient using Na⁺
D. K⁺ channel creating electric potential by passive flow of K⁺

C. Na⁺/lysine co-transporter moving lysine against its gradient using Na⁺

What is the net effect of the Na⁺/K⁺ ATPase pump?

A. 2 Na⁺ in, 3 K⁺ out → depolarizes the cell
B. 3 Na⁺ out, 2 K⁺ in → creates high Na⁺ outside and high K⁺ inside
C. Equal exchange of Na⁺ and K⁺ across the membrane
D. Passive movement of both ions to balance charges

B. 3 Na⁺ out, 2 K⁺ in → creates high Na⁺ outside and high K⁺ inside

Which of the following best describes the difference between primary and secondary active transport?

A. Primary active transport uses ATP directly; secondary does not use energy at all
B. Primary uses facilitated diffusion; secondary is simple diffusion
C. Primary uses ATP directly; secondary uses ion gradients as energy
D. Secondary active transport is always faster than primary

C. Primary uses ATP directly; secondary uses ion gradients as energy

What would happen in the systemic capillaries in red blood cells during CO₂ transport?

A. HCO₃⁻ converts into CO₂ and diffuses into the blood
B. CO₂ diffuses into the erythrocyte and is converted to HCO₃⁻
C. O₂ displaces H⁺, which promotes more HCO₃⁻ formation
D. AE1 transports Cl⁻ out of the cell in exchange for Na⁺

B. CO₂ diffuses into the erythrocyte and is converted to HCO₃⁻

What factor determines the Vmax of a uniporter-mediated transport?

A. Thickness of the lipid bilayer
B. Number of ion channels present
C. Concentration of ATP
D. Number of transporter proteins in the membrane

D. Number of transporter proteins in the membrane

Explain how the Na⁺/K⁺ ATPase contributes to the resting membrane potential.

The Na⁺/K⁺ ATPase pumps 3 Na⁺ out and 2 K⁺ in per ATP hydrolyzed. This creates a net negative charge inside the cell and maintains high Na⁺ outside and high K⁺ inside, contributing to a negative resting membrane potential.

Describe how the Cl⁻/HCO₃⁻ antiporter (AE1) works differently in systemic vs pulmonary capillaries.

• n systemic capillaries (high CO₂), CO₂ enters erythrocytes, is converted to HCO₃⁻ by carbonic anhydrase, and AE1 exchanges HCO₃⁻ out for Cl⁻ in.

• In pulmonary capillaries (low CO₂), the process reverses: AE1 brings HCO₃⁻ in, which is converted back to CO₂ and exhaled.

How does the Na⁺/lysine symporter work? What type of transport is this?

he Na⁺/lysine symporter uses the energy of Na⁺ moving down its electrochemical gradient to move lysine into the cell against its concentration gradient. This is an example of secondary active transport.

What feature of aquaporins ensures their selectivity for water?

A. Wide pore diameter and hydrophobic walls
B. Positive charge in the pore that repels ions
C. Narrow pore diameter and arrangement of hydrophilic residues forming H-bonds
D. ATP-dependent gating mechanism

C. Narrow pore diameter and arrangement of hydrophilic residues forming H-bonds

Which of the following statements about GLUT1 is TRUE?

A. GLUT1 requires ATP to function
B. GLUT1 transports glucose against its concentration gradient
C. GLUT1 undergoes conformational changes to transport glucose
D. GLUT1 is gated by voltage

C. GLUT1 undergoes conformational changes to transport glucose

What does Km represent in GLUT1-mediated glucose transport?

A. The maximal rate of glucose transport
B. The concentration of ATP required for half-maximal activity
C. The concentration of glucose at which the transport rate is half-maximal
D. The amount of glucose inside the cell after equilibrium

C. The concentration of glucose at which the transport rate is half-maximal

Which of the following best describes a key difference in affinity switching in the Na⁺/K⁺ ATPase?

A. Na⁺ affinity stays high regardless of conformation
B. K⁺ binds first, then Na⁺
C. Binding site affinity for Na⁺ is high in cytosolic-facing conformation but drops after phosphorylation
D. ATP is used only after K⁺ binds

C. Binding site affinity for Na⁺ is high in cytosolic-facing conformation but drops after phosphorylation

How many sodium and potassium ions are exchanged per cycle of the Na⁺/K⁺ ATPase?

A. 2 Na⁺ in / 3 K⁺ out
B. 3 Na⁺ in / 2 K⁺ out
C. 3 Na⁺ out / 2 K⁺ in
D. 1 Na⁺ out / 1 K⁺ in

C. 3 Na⁺ out / 2 K⁺ in

Describe the full conformational cycle of the GLUT1 glucose transporter.

1. Outward-open conformation binds extracellular glucose.

2. Conformational change to ligand-bound occluded state.

3. Transition to inward-open conformation, releasing glucose inside.

4. Ligand-free occluded state reforms and then resets to outward-open for another cycle.

• The cycle is reversible and does not require ATP.

Why are aquaporins necessary in biological membranes, even though water is small and uncharged?

While water can diffuse slowly through the membrane, aquaporins significantly increase water permeability, allowing for rapid and regulated movement. Their selectivity prevents ions or charged solutes from passing, maintaining osmotic balance.

Outline the key steps of the Na⁺/K⁺ ATPase cycle.

• 3 Na⁺ bind inside the cell (high affinity sites).

• ATP binds and phosphorylates the pump on an Asp residue.

• Conformational change exposes Na⁺ to outside; Na⁺ affinity drops, Na⁺ released.

• 2 K⁺ bind (now high-affinity extracellular sites).

• Dephosphorylation occurs → returns to cytosolic-facing conformation.

• K⁺ released, and Na⁺ affinity restored for next cycle.

What is a defining feature of P-class pumps?

A. They rotate to transport protons into lysosomes
B. They are phosphorylated on a conserved aspartate during the transport cycle
C. They generate ATP from a proton gradient
D. They use a single ATP per transport cycle and are only found in mitochondria

B. They are phosphorylated on a conserved aspartate during the transport cycle

Which of the following pumps lowers the pH of lysosomes by moving H⁺ into the lumen?

A. F-class pump
B. Na⁺/K⁺ ATPase
C. V-class pump
D. ABC transporter

C. V-class pump

Which type of pump uses proton gradients to drive ATP synthesis instead of hydrolyzing ATP?

A. V-class
B. F-class
C. ABC superfamily
D. P-class

B. F-class

Which of the following is TRUE about ABC transporters?

A. They are specific for ions and always use phosphorylation intermediates
B. They function through rotational movement of the V0 complex
C. They use ATP hydrolysis to transport a wide range of substrates including drugs
D. They are primarily found in mitochondria and use H⁺ gradients to synthesize ATP

C. They use ATP hydrolysis to transport a wide range of substrates including drugs

Which pump type was first discovered in drug-resistant cancer cells and is involved in multidrug resistance?

A. P-class pump
B. V-class proton pump
C. ABC superfamily transporter
D. F-class ATP synthase

C. ABC superfamily transporter

Compare and contrast V-class and F-class ATPases.

• V-class ATPases use ATP hydrolysis to pump H⁺ into organelles, lowering internal pH (e.g., lysosomes, vacuoles). They do not become phosphorylated and use rotational catalysis (V1 rotates and drives proton flow through V0).

• F-class ATPases work in reverse: they use a proton gradient to power ATP synthesis (e.g., in mitochondria and bacteria). Also no phosphorylation intermediate.

What structural features are found in ABC transporters and what do they transport?

ABC transporters contain:

• Two transmembrane domains (T domains)

• Two cytosolic ATP-binding domains
  They use ATP hydrolysis (2 ATPs) to power solute export, including toxins, drugs, lipids, and small molecules. Each transporter is substrate-specific, and they are important in multidrug resistance.

Describe the rotation-based mechanism of V-class ATPases.

• ATP hydrolysis occurs in the V1 domain

• This causes a 120º rotation of the rotor

• The V0 domain uses this mechanical motion to move H⁺ ions from the cytosol into the lumen

• This involves protonation and deprotonation of glutamate/aspartate residues, driving proton translocation without direct phosphorylation

Which of the following correctly matches a signaling type with its description?

A. Endocrine – local communication between adjacent cells
B. Paracrine – hormone travels through bloodstream to distant targets
C. Autocrine – the same cell both secretes and responds to the signal
D. Juxtacrine (cell-cell contact) – signal diffuses to multiple distant cells

C. Autocrine – the same cell both secretes and responds to the signal

Which is an example of endocrine signaling?

A. Acetylcholine released at a synapse
B. Insulin secreted by the pancreas affecting liver cells
C. A cancer cell secreting growth factors that it responds to
D. A membrane protein binding a receptor on an adjacent cell

B. Insulin secreted by the pancreas affecting liver cells

Which of the following statements about hydrophobic signaling molecules is TRUE?

A. They cannot diffuse through the plasma membrane
B. They activate G-protein coupled receptors on the cell surface
C. They bind cytosolic receptors and directly regulate transcription
D. They require second messengers to activate nuclear targets

C. They bind cytosolic receptors and directly regulate transcription

What best describes the amplification step in signal transduction?

A. Ligand binding causes dimerization of receptors
B. A second messenger is released and binds a membrane protein
C. One receptor activates many downstream signaling proteins in a cascade
D. Ion channels open to allow rapid depolarization of the cell

C. One receptor activates many downstream signaling proteins in a cascade

Which of the following can act as an effector protein in a signaling cascade?

A. GTP
B. DNA
C. A transcription factor
D. A receptor tyrosine kinase

C. A transcription factor

Define the four types of extracellular signaling and give an example of each

• Endocrine: Signal travels through bloodstream to distant cells (e.g., insulin, epinephrine)

• Paracrine: Signal acts on nearby cells (e.g., neurotransmitters, growth factors)

• Autocrine: Signal is secreted and acts on same cell (e.g., tumor growth factors)

• Cell-cell contact (juxtacrine): Signal passed via membrane protein to adjacent cell (e.g., Notch signaling)

Compare how hydrophilic and hydrophobic signaling molecules transmit information into the cell.

• Hydrophobic signals (e.g., steroids) diffuse through the membrane, bind intracellular receptors, and often enter the nucleus to regulate transcription.

• Hydrophilic signals (e.g., peptides, neurotransmitters) bind to cell surface receptors, initiating a signal transduction cascade involving second messengers and effector activation.

Outline the general steps of a signal transduction cascade starting from ligand binding to effector activation.

1. Ligand (H) binds to receptor (R)

2. Receptor undergoes conformational change

3. Receptor activates first signaling protein (S1)

4. Amplification: S1 activates multiple S2 proteins, which then activate S3–S5

5. Signaling proteins activate an effector (E) → can be a transcription factor, enzyme, ion channel, etc.

6. Feedback regulation may occur to inhibit upstream components

Which of the following correctly matches a second messenger with its enzyme and downstream effector?

A. cAMP – generated by guanylyl cyclase – activates protein kinase C
B. cGMP – generated by adenylyl cyclase – opens calcium channels in the ER
C. IP₃ – generated by phospholipase C – opens Ca²⁺ channels in the ER
D. DAG – generated by phospholipase A – activates protein kinase A

C. IP₃ – generated by phospholipase C – opens Ca²⁺ channels in the ER

What does adenylyl cyclase do in a signaling pathway?

A. Converts GTP to GDP
B. Converts ATP to cyclic AMP (cAMP)
C. Converts PIP₂ to DAG
D. Phosphorylates protein kinase A

B. Converts ATP to cyclic AMP (cAMP)

Which of the following correctly describes the role of diacylglycerol (DAG)?

A. Activates protein kinase G in mitochondria
B. Opens calcium channels in the nucleus
C. Stays in the membrane and activates protein kinase C with Ca²⁺
D. Is a nucleotide that activates transcription factors

C. Stays in the membrane and activates protein kinase C with Ca²⁺

Which second messenger is soluble and diffuses through the cytosol to bind ER calcium channels?

A. cAMP
B. DAG
C. IP₃
D. PIP₂

C. IP₃

What is the role of cyclic GMP (cGMP) in signaling?

A. Activates voltage-gated calcium channels
B. Activates guanylyl cyclase
C. Activates protein kinase G and cation channels
D. Activates protein kinase A

C. Activates protein kinase G and cation channels

What are the two second messengers generated by phospholipase C, and what are their roles?

• DAG (diacylglycerol): Stays in the plasma membrane and, with Ca²⁺, activates protein kinase C (PKC).

• IP₃ (inositol 1,4,5-trisphosphate): Diffuses through the cytosol, binds IP₃ receptors on the ER, and triggers Ca²⁺ release.

Explain the sequence of molecular events starting from ATP and ending in the activation of PKA.

• A ligand binds a G protein-coupled receptor (GPCR).

• This activates adenylyl cyclase via a G protein.

• Adenylyl cyclase converts ATP to cAMP.

• cAMP binds and activates protein kinase A (PKA) by releasing its regulatory subunits.

• PKA then phosphorylates target proteins in the cell.

How does Ca²⁺ act as a second messenger in conjunction with other molecules?

Ca²⁺ is released from the ER after IP₃ binds to ER receptors. The cytosolic Ca²⁺ can then work with DAG to activate PKC, or it can bind other calcium-binding proteins (e.g., calmodulin) to regulate downstream enzymes and processes.

What structural feature is shared by all GPCRs?

A. Phosphorylation domains that dimerize with ligand binding
B. 12 transmembrane domains and intracellular N-terminus
C. 7 transmembrane domains and extracellular N-terminus
D. Alpha-helical domains that span the nuclear envelope

C. 7 transmembrane domains and extracellular N-terminus

Which of the following is a correct match between a GPCR family and its features?

A. Family A – VFD domain, senses Ca²⁺ and glutamate
B. Family B – long extracellular domain (ECD), binds peptides
C. Family C – shortest GPCRs, respond to light and odorants
D. Family A – only found in lower organisms

B. Family B – long extracellular domain (ECD), binds peptides

What is the function of GPCRs as GEFs?

A. They phosphorylate downstream enzymes
B. They open ion channels directly
C. They promote exchange of GDP for GTP on the Gα subunit
D. They hydrolyze GTP to stop signaling

C. They promote exchange of GDP for GTP on the Gα subunit

Which enzyme is often activated by Gαs to produce the second messenger cAMP?

A. Phospholipase C
B. Adenylyl cyclase
C. Protein kinase A
D. Guanylyl cyclase

B. Adenylyl cyclase

What are orphan GPCRs?

A. GPCRs that function without G proteins
B. GPCRs that lack a transmembrane domain
C. GPCRs whose ligands are currently unknown
D. GPCRs that only exist in bacteria

C. GPCRs whose ligands are currently unknown

Outline the general steps in GPCR signal transduction involving a trimeric G protein and adenylyl cyclase.

• Ligand binds to the GPCR → conformational change

• Activated GPCR binds Gα subunit of trimeric G protein

• GPCR acts as a GEF, promoting GDP → GTP exchange on Gα

• Gα-GTP dissociates from βγ subunits and activates adenylyl cyclase

• Adenylyl cyclase converts ATP → cAMP

• cAMP activates PKA, triggering downstream signaling

• Gα hydrolyzes GTP → GDP (with intrinsic GTPase activity), re-associates with βγ

• Signal terminates

Describe the differences between the three families of GPCRs in terms of structure and ligands.

• Family A: Short extracellular domain; responds to biogenic amines, light, odorants, lipids, purines

• Family B: Long extracellular domain (ECD); binds peptides (e.g., peptide hormones)

• Family C: Contain Venus flytrap domain (VFD); bind glutamate, Ca²⁺, and amino acids

What role does the trimeric G protein play in GPCR signaling, and how is it regulated?

The trimeric G protein (α, β, γ subunits) is activated when the GPCR acts as a GEF, allowing Gα to exchange GDP for GTP.

• Gα-GTP activates enzymes like adenylyl cyclase.

• βγ subunits can also activate ion channels or kinases.

• The signal is terminated when Gα hydrolyzes GTP → GDP and reassociates with βγ.

What is the first intracellular event after a ligand binds to a GPCR?

A. Gα hydrolyzes GTP to GDP
B. The GPCR activates its intrinsic kinase activity
C. The GPCR undergoes a conformational change and binds the G protein
D. The βγ subunit binds to the effector protein

C. The GPCR undergoes a conformational change and binds the G protein

What activates the Gα subunit of a trimeric G protein?

A. Phosphorylation by PKA
B. Binding of ATP
C. Exchange of GDP for GTP, catalyzed by the GPCR
D. Hydrolysis of cAMP

C. Exchange of GDP for GTP, catalyzed by the GPCR

Which of the following correctly describes cAMP signaling?

A. Activated Gαq directly produces cAMP
B. cAMP is converted into ATP by phosphodiesterase (PDE)
C. Activated Gαs stimulates adenylyl cyclase to convert ATP to cAMP
D. Gβγ directly opens calcium channels that generate cAMP

C. Activated Gαs stimulates adenylyl cyclase to convert ATP to cAMP

What is the role of Gαi in GPCR signaling?

A. Inhibits phosphodiesterase activity
B. Activates phospholipase C
C. Inhibits adenylyl cyclase, reducing cAMP production
D. Promotes phosphorylation of Gβγ

C. Inhibits adenylyl cyclase, reducing cAMP production

Which effector enzyme is activated by Gαq or Gαo and leads to production of IP₃ and DAG?

A. Adenylyl cyclase
B. Phosphodiesterase
C. Protein kinase A
D. Phospholipase C

D. Phospholipase C

Summarize the general steps of GPCR signal transduction from ligand binding to effector activation

• Ligand binds GPCR → causes conformational change

• GPCR binds trimeric G protein (anchored to membrane)

• GPCR acts as GEF → promotes GDP → GTP exchange on Gα

• Gα-GTP separates from βγ subunits

• Gα-GTP activates an effector enzyme (e.g., adenylyl cyclase or phospholipase C)

• Signal proceeds via second messengers

• Gα hydrolyzes GTP → GDP (intrinsic GTPase activity), reassociates with βγ, turning signal off

How do Gαs and Gαi differ in their effects on adenylyl cyclase and cAMP levels?

• Gαs: Stimulates adenylyl cyclase → increases cAMP production

• Gαi: Inhibits adenylyl cyclase → decreases cAMP production
  This regulation allows for hormone-induced control of metabolism and signaling, as seen in adipose cells.

Describe how PIP₂ is cleaved and what two second messengers are produced. What do they do?

Phospholipase C cleaves PIP₂ into:

• IP₃: Soluble; diffuses to ER and triggers Ca²⁺ release

• DAG: Stays in membrane; activates protein kinase C (PKC) in presence of Ca²⁺
  These second messengers amplify the signal and regulate various cellular responses

How does cAMP activate protein kinase A (PKA)?

A. By phosphorylating the catalytic subunits
B. By binding to and activating DAG
C. By releasing the catalytic subunits from regulatory subunits
D. By hydrolyzing GTP to GDP

C. By releasing the catalytic subunits from regulatory subunits

What protein localizes inactive PKA to specific regions of the cell?

A. CREB
B. Arrestin
C. AKAP
D. GRB2

C. AKAP

What is the co-activator that binds phosphorylated CREB to initiate transcription?

A. SOS
B. MAPK
C. CBP/P300
D. SRF

C. CBP/P300

What activates protein kinase C (PKC) in the phosphoinositide pathway?

A. Phosphorylation by Raf
B. cAMP and PKA
C. Ca²⁺ release from ER and DAG in the membrane
D. GTP-bound Ras

C. Ca²⁺ release from ER and DAG in the membrane

What is the function of SOS in RTK signaling?

A. Activates adenylyl cyclase
B. Opens calcium channels
C. Acts as a GEF for Ras
D. Degrades phosphorylated RTKs

C. Acts as a GEF for Ras

Which of the following is the correct order of the MAPK cascade downstream of Ras?

A. MEK → Raf → MAPK
B. Ras → MAPK → Raf
C. Ras → Raf → MEK → MAPK
D. Raf → MAPK → MEK

C. Ras → Raf → MEK → MAPK

Describe how PKA is activated and how it leads to gene transcription via CREB.

• cAMP binds to PKA’s regulatory subunits, releasing the catalytic subunits.

• These translocate into the nucleus and phosphorylate CREB (cAMP response element-binding protein).

• Phosphorylated CREB recruits CBP/P300 (a transcriptional co-activator).

• This complex binds CRE sequences in DNA and initiates transcription of target genes.

Explain how GPCR signaling via PLC leads to PKC activation.

• GPCR-Gαq/o activates phospholipase C (PLC)

• PLC cleaves PIP₂ into IP₃ and DAG

• IP₃ diffuses through the cytosol and binds ER Ca²⁺ channels, releasing Ca²⁺

• Ca²⁺ and DAG together activate PKC, which dissociates from the membrane and phosphorylates target proteins

Detail the steps from RTK activation to MAPK activation in the Ras signaling pathway.

• Ligand binds RTK, causing dimerization and autophosphorylation on Tyr residues

• GRB2 binds to phosphorylated Tyr via its SH2 domain

• GRB2’s SH3 domain binds SOS

• SOS (a GEF) promotes GDP → GTP exchange on Ras, activating it

• Ras-GTP activates Raf by releasing 14-3-3 and an autoinhibitory domain

• Raf phosphorylates MEK (dual-specificity kinase)

• MEK phosphorylates MAPK (ERK) on Tyr and Ser/Thr residues

• MAPK enters the nucleus and phosphorylates transcription factors like TCF and SRF, activating transcription

How does arrestin regulate GPCR signaling and receptor internalization?

• Arrestin binds phosphorylated GPCRs, preventing further G protein coupling

• It also mediates receptor internalization via endocytosis

• Prolonged PKA activation can lead to receptor desensitization, triggering arrestin recruitment

• Internalized receptors are either recycled or degraded, depending on context

What is the correct order of biological organization from smallest to largest?

A. Protein → Cell → Organelle → Tissue → Organism → Organ
B. Protein → Organelle → Cell → Tissue → Organ → Organism
C. Organelle → Protein → Cell → Tissue → Organ → Organism
D. Protein → Organelle → Tissue → Cell → Organ → Organism

B. Protein → Organelle → Cell → Tissue → Organ → Organism

What distinguishes membraneless compartments in cells?

A. They are surrounded by lipid bilayers
B. They have long-range crystal order
C. They form coherent, round assemblies without membranes and carry out functions
D. They are protein aggregates with rigid structures

C. They form coherent, round assemblies without membranes and carry out functions

Which of the following best describes the material state of protein condensates?

A. Solid—proteins form crystals with long-range order
B. Liquid—proteins can rearrange and diffuse rapidly within the compartment
C. Gas—proteins are scattered and do not interact
D. Supercritical fluid—proteins partially interact in two phases

B. Liquid—proteins can rearrange and diffuse rapidly within the compartment

Which physical technique demonstrates protein mobility within a condensate?

A. Electron microscopy
B. Mass spectrometry
C. FRAP (fluorescence recovery after photobleaching)
D. X-ray crystallography

C. FRAP (fluorescence recovery after photobleaching)