Cellular Signaling and Protein Phosphorylation
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Questions and Answers

What is one of the main roles of protein phosphorylation in cellular signaling?

  • It stabilizes protein structures.
  • It transduces information along protein cascades. (correct)
  • It prevents protein degradation.
  • It enhances the binding affinity of all proteins.
  • Which residues are involved in the process of protein phosphorylation?

  • Glycine, proline, and asparagine
  • Cysteine, methionine, and phenylalanine
  • Alanine, valine, and leucine
  • Tyrosine, threonine, or serine (correct)
  • Which statement about structural domains is correct?

  • All structural domains perform the same functions.
  • There are typically no more than two structural domains in proteins.
  • Domains can have the same structure but differ in function. (correct)
  • Structural domains cannot be modular.
  • What is the significance of chemical modification in proteins?

    <p>It serves as a signal for regulating downstream signaling events. (A)</p> Signup and view all the answers

    What does it mean for a structural domain to be described as modular?

    <p>It can form repeated regions within the same polypeptide or across different proteins. (B)</p> Signup and view all the answers

    What is the primary function of receptor tyrosine kinases (RTKs)?

    <p>To catalyze phosphorylation of protein substrates (B)</p> Signup and view all the answers

    Which domains are specifically involved in binding oligopeptide motifs?

    <p>SH2, SH3, and PTB domains (C)</p> Signup and view all the answers

    What role does PTEN play in cellular signaling?

    <p>It functions as a dual-specificity protein phosphatase (B)</p> Signup and view all the answers

    Which statement about Grb2 is true?

    <p>It interacts with the phospho tyrosine of RTKs through its SH2 domain. (B)</p> Signup and view all the answers

    Which of the following motifs is involved in binding to phosphoinositides?

    <p>PH domains (C)</p> Signup and view all the answers

    What is the characteristic feature of SH2 domains?

    <p>They bind specifically to motifs containing a phosphotyrosine. (A)</p> Signup and view all the answers

    Which domains provide sites for interaction with other proteins but do not have enzymatic activity?

    <p>Structural interaction domains (C)</p> Signup and view all the answers

    Which proteins are examples of those containing SH2 domains?

    <p>Receptor tyrosine kinases and non-RTKs (A)</p> Signup and view all the answers

    What is the main function of PDZ domains?

    <p>Anchor transmembrane proteins to the cytoskeleton (B)</p> Signup and view all the answers

    Which of the following motifs is involved in calcium binding?

    <p>EF-hand motif (D)</p> Signup and view all the answers

    What do the first letters of the acronym PDZ stand for?

    <p>Post synaptic density protein (C)</p> Signup and view all the answers

    Which type of domains are considered to have intrinsic catalytic activity?

    <p>Protein kinase domains (C)</p> Signup and view all the answers

    What happens in the signaling pathway activated by light in Drosophila photoreceptors?

    <p>Coupling of receptor to Gq (B)</p> Signup and view all the answers

    What does a loss of the InaD scaffold result in?

    <p>Retardation of visual resolution (B)</p> Signup and view all the answers

    Which of the following is an example of a phosphoinositide-binding domain?

    <p>C2 domain (D)</p> Signup and view all the answers

    What is the purpose of the coupling of PKC to PLCβ via the InaD scaffold?

    <p>To facilitate calcium release (A)</p> Signup and view all the answers

    What is the primary role of a PDZ binding motif?

    <p>To recognize and bind a PDZ domain on other signaling molecules (C)</p> Signup and view all the answers

    Which of the following statements is true about scaffold proteins?

    <p>They enhance the efficiency and/or specificity of cellular pathways (D)</p> Signup and view all the answers

    Which of the following is NOT a characteristic of MAGUK proteins?

    <p>Contain an active guanylate kinase domain (A)</p> Signup and view all the answers

    What type of proteins does the InaD protein function primarily with in fruit flies?

    <p>Phototransduction cascade proteins (B)</p> Signup and view all the answers

    How does the PDZ domain interact within PDZ-based scaffold proteins?

    <p>Through peptide interactions recognizing specific sequences (D)</p> Signup and view all the answers

    Which of the following correctly describes the domains found in MAGUK proteins?

    <p>PDZ domain, SH3 domain, and GUK domain (C)</p> Signup and view all the answers

    Which of the following proteins is a PDZ-based scaffold protein?

    <p>NHERF (C)</p> Signup and view all the answers

    What is a key characteristic of proline-rich sequences recognized by SH3 domains?

    <p>They generally consist of 8–10 residues of Pro. (A)</p> Signup and view all the answers

    Which of the following statements best describes PDZ- and nonPDZ-based scaffold proteins?

    <p>PDZ-based scaffold proteins can interact with a diverse range of signaling partners. (A)</p> Signup and view all the answers

    Which proteins are examples of those that contain SH3 domains?

    <p>Adaptor proteins such as Grb2 and Nck. (C)</p> Signup and view all the answers

    Which domain is known for binding phosphotyrosine residues?

    <p>PTB domain. (D)</p> Signup and view all the answers

    What is the physiological significance of PH domains?

    <p>They play a role in protein–protein interactions. (A)</p> Signup and view all the answers

    Which of the following statements is true regarding Src family kinases?

    <p>They are involved in regulating cellular processes. (B)</p> Signup and view all the answers

    What ability do PTB domains have that is not shared with SH2 domains?

    <p>To recognize sequences distinctly from phoshotyrosine motifs. (B)</p> Signup and view all the answers

    PH domains primarily bind to which type of ligands?

    <p>Phosphoinositides. (A)</p> Signup and view all the answers

    Which of the following best describes the structural characteristic of SH3 domains?

    <p>They possess a hydrophobic binding surface. (C)</p> Signup and view all the answers

    What type of structural motif is the EF-hand motif primarily associated with?

    <p>Calcium binding (B)</p> Signup and view all the answers

    Which domain is characterized by its ability to bind phosphoinositides?

    <p>PH domain (D)</p> Signup and view all the answers

    Which of the following domains is specifically recognized for binding oligopeptide motifs?

    <p>SH2 and SH3 domains (A)</p> Signup and view all the answers

    What is the structural arrangement of the GRK2 PH domain?

    <p>Beta-sandwich structure (A)</p> Signup and view all the answers

    What type of ion do C2 domains primarily bind?

    <p>Calcium (A)</p> Signup and view all the answers

    Which of the following correctly describes the coordination of the Ca2+ ion in calmodulin's EF-hand region?

    <p>Involves a helix-loop-helix structure (A)</p> Signup and view all the answers

    The C2H2 zinc finger domain is named due to the presence of which amino acids coordinating zinc?

    <p>Two cysteines and two histidines (C)</p> Signup and view all the answers

    What characterizes the structure of PH domains?

    <p>Antiparallel beta strands (C)</p> Signup and view all the answers

    Flashcards

    Protein Modules

    Specific regions within proteins that actively participate in recognition processes.

    Protein Phosphorylation

    A common way for cells to transmit information by adding a phosphate group to a protein.

    Protein Kinase

    An enzyme that adds a phosphate group to a protein.

    Structural Domains

    Regions within proteins with a specific 3D structure and function.

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    PTB and SH2 Domains

    Domains that bind to phosphorylated tyrosine residues.

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    Receptor Tyrosine Kinases (RTKs)

    Transmembrane proteins with intrinsic tyrosine kinase activity. They play a crucial role in signal transduction by phosphorylating tyrosine residues on target proteins, including themselves.

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    Tyrosine Kinase Domain

    The catalytic domain of RTKs located in the cytoplasm. It is responsible for phosphorylating tyrosine residues on target proteins, initiating signal transduction pathways.

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    PTEN

    A dual-specificity protein phosphatase that removes phosphate groups from tyrosine, serine, and threonine residues on proteins. It plays a crucial role in regulating cell growth and survival.

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    PIP2

    Phosphatidyl inositol (4,5) biphosphate, a lipid molecule present in cell membranes. It serves as a substrate for enzymes like phospholipase C and PI3K.

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    PIP3

    Phosphatidyl inositol (3,4,5) triphosphate, a lipid molecule generated from PIP2 by PI3K. It acts as a second messenger in various signaling pathways.

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    Protein Interaction Domains

    Specialized regions within proteins that facilitate interactions with other proteins. They bind to specific peptide motifs or structural elements, enabling protein-protein interactions.

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    SH2 Domain

    A protein interaction domain that binds to phosphorylated tyrosine residues (pTyr) on proteins. It plays a crucial role in mediating protein-protein interactions in signaling pathways.

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    SH3 Domain

    A protein interaction domain that recognizes and binds to proline-rich motifs on proteins. It plays a key role in scaffolding proteins and signaling complexes.

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    Proline-Rich Sequences

    Short sequences of amino acids within proteins that are rich in proline residues. They are often recognized by SH3 domains.

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    PhosphoTyrosine Binding Domains

    Domains that bind to phosphotyrosine residues (N-P-X-pY) but recognize distinct sequences compared to SH2 domains. They can also bind to acidic phospholipid head groups.

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    What are seven main phosphoinositides?

    Seven main phosphoinositides are found in membranes of organelles and plasma membrane.

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    What are the major protein domains that bind to oligopeptide motifs?

    The major protein domains that bind to oligopeptide motifs are SH2, SH3, and PTB domains.

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    What are important factors that regulate protein localization to membranes?

    Phosphoinositide-binding motifs and domains, such as PH domains, help regulate protein localization to membranes.

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    EF-hand Motif

    A helix-loop-helix structure that binds calcium ions. Two EF-hand motifs often pair together to form a functional unit.

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    Calmodulin

    A calcium-binding protein with multiple EF-hand motifs. It acts as a calcium sensor, triggering downstream signaling pathways.

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    Zinc Finger Domain (C2H2)

    A protein domain containing a zinc ion coordinated by two cysteines and two histidines. This structure aids in DNA binding and recognition.

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    What binds to IP3?

    The PH domain of some proteins, such as GRK2, can bind to IP3 (inositol triphosphate).

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    How does PLCγ1 attach to the membrane?

    PLCγ1 uses its PH domain to bind to PIP3, which is a lipid found in the cell membrane.

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    What are the major protein domain families?

    Major families include domains that bind oligopeptide motifs (SH2, SH3, PTB), phosphoinositide-binding motifs (PH), calcium-binding domains (EF-hand, C2), zinc finger domains (C2H2), protein kinase domains, and PDZ domains.

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    PDZ Binding Motif

    A short sequence of amino acids within a protein that specifically binds to a PDZ domain on another protein.

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    What does a PDZ binding motif interact with?

    A PDZ binding motif interacts with a PDZ domain on another protein.

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    Scaffold Proteins

    Proteins that act as organizing centres by binding to multiple other proteins, bringing them together to enhance signaling pathways.

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    What are the two main types of scaffold proteins?

    Scaffold proteins can be PDZ-based or non-PDZ-based.

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    MAGUK Proteins

    Scaffold proteins that have PDZ, SH3, and guanylate kinase (GUK) domains, involved in membrane-associated signaling pathways.

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    What are the three domains found in MAGUK proteins?

    MAGUK proteins contain PDZ, SH3, and guanylate kinase (GUK) domains.

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    InaD

    A scaffold protein involved in the fly phototransduction cascade, helps organize the signaling proteins.

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    Visual Transduction Pathway (Drosophila)

    A series of steps involving light, rhodopsin, Gq, PLCβ, DAG, Ca2+, TRP channels, and phosphorylation by PKC, leading to membrane depolarization and visual signal transduction in Drosophila photoreceptor cells.

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    Rhodopsin

    A light-sensitive receptor protein in photoreceptor cells, which initiates the visual transduction pathway by activating Gq upon light absorption.

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    Gq

    A G protein that couples to rhodopsin and activates PLCβ in the visual transduction pathway.

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    PLCβ

    An enzyme that hydrolyzes PIP2 into DAG and IP3, generating signaling molecules that trigger Ca2+ release and further downstream events in the visual transduction pathway.

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    TRP Channels

    Transient receptor potential (TRP) channels are ion channels in photoreceptor cells that open in response to Ca2+ release, leading to membrane depolarization and signal transduction.

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    Study Notes

    Bioc 325: Lecture 2

    • Learning Objectives:
      • Introduce the structure, function, and different types of signaling structural domains.
      • Understand the roles of structural domains in signal propagation between signaling proteins.
      • Introduce scaffold proteins and their role in signal propagation.
    • Signaling Proteins:
      • Serve as building blocks.
      • Have special structural domains aiding cross-recognition, binding, and signal propagation.
    • Signal Initiation:
      • Begins with ligand interaction with its cognate receptor,
      • Inducing stoichiometric and conformational changes.
    • Signal Transduction Cascades:
      • Involve protein-protein interactions and protein phosphorylation.

    Protein-Protein Interactions

    • Essential for Signal Propagation:
      • Signal transfer across the intracellular space relies on proteins interacting with each other.
      • Interactions maintain signal specificity until the target is achieved (e.g., gene promoters).
      • These interactions are tightly controlled and not random, limited to specific authorized partners.
      • Protein modules (interaction motifs) are crucial for these processes.

    Protein Phosphorylation

    • Mechanism for Information Transduction:
      • A key mechanism in protein cascade information transfer.
      • Phosphorylation occurs when a protein kinase interacts with tyrosine, threonine, or serine residues.
      • Considered a signal to either activate or deactivate downstream signaling events.

    Part 1: Structural Domains

    • Definition:

      • Regions within proteins with similar architecture, specific spatial arrangements, and functional roles.
      • Modular structures, forming repeating modules or recurring structures throughout proteins.
      • Some domains have different structures yet identical functions, for instance, PTB and SH2 domains in binding pTyr.
    • Variations:

      • Other domains have similar structures but different functions (ex: PTB and PH domains).
      • Most signaling molecules contain multiple domains.
    • Functional Considerations:

      • A specific structural domain may confer a function but may not guarantee it due to mutations or exon shuffling within the gene encoding the domain.
    • Classification:

      • Catalytic Domains: Have enzymatic activity(ex: protein kinases, protein phosphatases).
      • Protein Interaction Domains: Do not have enzymatic activity, primarily provide interaction sites for other proteins (ex: SH2 and SH3 domains).

    Part 2: PDZ- and nonPDZ-based Scaffold Proteins

    • Definition: Proteins associating with two or more other proteins to enhance efficiency and specificity of a cellular pathway.
    • Types:
      • PDZ-based: Include InaD, PSD-95, NHERF, MAGUK.
      • Non-PDZ-based: Include AKAP, JAK-STAT, and β-arrestin.

    PDZ Domains

    • Function: Binding to C-terminal residues of some ion channels and receptors, as well as phosphoinositides.
      • Function in anchoring transmembrane proteins to the cytoskeleton.
      • Aid in holding together signaling complexes.

    MAGUK Proteins

    • Description: A specific type of PDZ-based scaffold protein characterized by specific domains ( PDZ, SH3, and GUK).
      • MAGUK proteins are characterized by having a PDZ domain, an SH3 domain, and a GUK (guanylate kinase) domain.
      • Serve as scaffolds for organizing signaling pathways.

    NonPDZ-based Proteins

    • Examples:

      • AKAP (A-kinase anchoring protein)
      • JAK-STAT (Janus kinases and STATs).
      • β-arrestin
    • Function:

      • AKAPs anchor protein kinases,
      • JAK proteins facilitate signaling cascades.
      • β-arrestins are involved in GPCR regulation.

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