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BIO 3153 > Protein Sorting > Flashcards

Protein Sorting Flashcards

1
Q

define protein sorting

A

refers to the movement of proteins to their appropriate destinations within eukaryotic cells, ensuring each organelle has the necessary components for its function

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2
Q

list the types of sorting

A

gated transport to the nucleus
transmembrane transport into mitochondria and the ER
vesicular transport within the secretory pathway

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3
Q

what do signal sequences do?

A

direct proteins to specific destinations with amino acid sequences at the protein’s terminal end

signal patch means internal amino acid that functions as a sorting signal

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4
Q

how does nuclear transport take place?

A

through nuclear pore complexes that permit passage of proteins in folded form (import/export is driven by Ran GTPase), import receptors bind to NLSs to mediate import

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5
Q

explain mitochondrial transport

A

posttranslational translocation is where proteins are imported from cytosol into mitochondria; signal sequences direct proteins into the matrix and inner membrane, often assisted by translocator complexes (TOM, TIM)

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6
Q

explain the mechanisms of import and mitochondrial import

A

import of proteins into nucleus facilitated by Ran GTPase to maintain direct transport gradient

mitochondrial import involves signal recognition, unfolding of proteins Hsp70 and translocation through mitochondrial membranes by chaperones and ATP hydrolysis

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7
Q

explain crossbridge ratchet model

A

mechanism by which hsp70 facilitiates protein translocation into mitochondria (hsp70 uses energy from ATP hydrolysis to maintain protein in unfolded state, while conformational changes “ratchet” the protein through translocase of the inner membrane channel into the mitochondrial matrix

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8
Q

what is the ER?

A

endoplasmic reticulum is a network of branching tubules responsible for protein and lipid biosynthesis

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9
Q

describe the movement of proteins between compartments

A

gated transport: nucleus
transmembrane transport: mitochondria and ER
vasicular transport: secretory pathway

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10
Q

describe transmembrane vs watersoluble proteins

A

transmembrane: insert into ER membrane and span across with alpha helical segments, transferred into membrane with stop-transfer signals that prevent further translocation
water-soluble: translocated into ER lumen completely and remain soluble, do not integrate into membrane but are enclosed in lumen

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11
Q

describe cotranslation translocation

A

primarily how proteins are transported into the ER.

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12
Q

explain what signal sequences do

A

direct ribosomes to the ER membrane; if the signal sequence is present, the ribosome directs the growing polypeptide to the ER.

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13
Q

what are Signal Recognition Particles (SRP)

A

binds to the signal sequence and directs the ribosome to the SRP receptor on the ER membrane.

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14
Q

explain Sec61 complex’s function

A

forms an aqueous pore in the ER membrane through which proteins are translocated

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15
Q

what is the function of soluble proteins? explain some characteristics

A

Soluble proteins enter the ER lumen directly; single-pass transmembrane proteins are released into the membrane as alpha helices due to a stop-transfer signal.

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16
Q

explain and describe double-pass and multipass membrane proteins

A

involve multiple start and stop transfer signals.

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17
Q

describe Posttranslational translocation

A

Posttranslational translocation involves proteins translated by free ribosomes being transported into the ER lumen.

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18
Q

describe Glycosylation

A

Glycosylation occurs in the ER, aiding in protein folding.

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19
Q

explain misfolded proteins

A

Misfolded proteins are dislocated from the ER, ubiquitinated, and degraded

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20
Q

what are the types of coated vesicles

A

COPII-coated, SNARE, Rab

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21
Q

describe COPII-coated vesicles

A

Involve Sar1-GTP initiating membrane curvature and recruiting coat proteins like Sec23/24. These vesicles concentrate cargo proteins for transport from the ER to the Golgi.

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22
Q

describe SNARE proteins

A

v-SNAREs on vesicles and t-SNAREs on target membranes facilitate vesicle targeting and fusion, crucial for membrane fusion during anterograde transport.

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23
Q

describe Rab proteins

A

Help in recognizing vesicles at the Golgi, ensuring specific targeting and fusion with appropriate membranes.

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24
Q

explain vesicular tube clusters

A

Formed by COPII vesicles, they move along microtubules to deliver proteins to the cis-Golgi.

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25
Q

explain transport through the golgi

A

Glycosylation and chemical modifications occur as proteins pass through Golgi cisternae, sorting them for final destinations.

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26
Q

explain transport from the golgi

A

Involves two secretory pathways: constitutive (continuous) and regulated (signal-induced), leading to exocytosis upon receiving extracellular signals.

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27
Q

explain formation and release from sensory vesicles

A

Progressive acidification and removal of membrane materials occur within vesicles before they are released to the cell exterior, crucial for maintaining cell signaling and functionality.

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28
Q

describe Plasma Membrane Composition:

A

Consists of lipids and proteins. Lipids provide fluidity and a barrier, while proteins contribute to its functional characteristics.

29
Q

explain construction of the membrane bilayer

A

Hydrophilic heads face the aqueous environment while hydrophobic tails form the core, creating a stable yet flexible barrier.

30
Q

list and describe types of lipids

A
  • Phospholipids: Most abundant; amphipathic with hydrophilic heads and hydrophobic tails, influencing membrane fluidity.
  • Cholesterol: Regulates membrane fluidity and deformability.
  • Lipid Rafts: Specialized domains within the membrane for signaling, enriched with sphingolipids and cholesterol.
31
Q

list and describe membrane the types of proteins

A
  • Integral Proteins: Embedded within the lipid bilayer, often as alpha helices or beta barrels.
  • Peripheral Proteins: Attached to the inner surface, providing structural support and linking the cytoskeleton to the membrane.
  • Lipid-Anchored Proteins: Attached to lipids in the bilayer, playing roles in signaling and cell adhesion.
32
Q

describe 2 molecules that work with cell signalling and how they work

A

Phosphoinositides: Involved in intracellular signaling pathways.
Proteins like PI 3-kinase: Recruit signaling proteins to specific membrane sites.

33
Q

describe secondary structures

A
  • Alpha Helices: Flexible structures predominant in transmembrane proteins.
  • Beta Sheets: Rigid, found in porins and transporters in bacteria and mitochondria.
34
Q

explain transport mechanisms

A
  • Simple Diffusion: Movement of gases and water directly through the lipid bilayer.
  • Passive Transport: Movement driven by concentration gradients facilitated by membrane proteins like channels and carriers.
  • Active Transport: Requires energy (usually ATP) to move substances against their concentration gradients.
35
Q

explain and describe carrier-mediated transport

A
  • Carrier Proteins: Bind specific solutes and undergo conformational changes to move them across the membrane.
  • Active Transport Types:
    = Primary Active Transport: Direct use of ATP to move ions like Na+ and K+ across the membrane.
    = Secondary Active Transport: Uses the energy from one ion’s gradient (e.g., Na+) to transport another solute like glucose.
36
Q

describe and explain transport ATPase

A
  • Na+-K+ ATPase: Maintains Na+ and K+ gradients across the cell membrane using ATP.
  • Ca2+ ATPase: Regulates intracellular Ca2+ levels by pumping it out of the cytosol.
  • H+-ATPases: Found in vacuoles, vesicles, and mitochondria, these pumps use ATP to transport H+ ions to maintain acidic environments for processes like ATP synthesis in mitochondria.
37
Q

describe and explain ion gradients

A

Na+-K+ pump generates significant Na+ and K+ gradients.
Ca2+ pumps are crucial for maintaining low intracellular calcium levels, which is essential for signaling.

38
Q

describe and explain aquaporins

A

Channel proteins that facilitate the movement of water across the membrane, crucial for kidney function and other physiological processes.

39
Q

describe and explain ATP-binding cassette (ABC) transporters

A

These transporters use ATP hydrolysis to move molecules across membranes, playing roles in nutrient uptake and drug resistance.

40
Q

explain the simiarities and differences between ion channels and transporters

A
  • ion channels (not using ATP) and some transporters (using ATP) allow passive passage of ions down an electrochemical gradient
  • many ion channels are highly selective for specific ions
  • ion channels exhibit hydrophillic pores and are often gated
41
Q

list and explain the function of common ion channels

A

K+ channels: regulate membrane potential and AP recovery
Na+ channels: underlie action poetntials
Ca2+ channels: increases cytosolic and induces secretion
Cl- channels: reguallte ionic balanced
H+ channels: rapidly increase intracellular pH
Non-selective ion channels: many functions

42
Q

what are some general properties of ion channels

A

pore lined by polar regions of protein, making it hydrophilic
- hydrophobic amino acids interact with lipid bilayer
- conformational change -> ability to buy

43
Q

describe voltage-gated channels

A

Opening Mechanism: Occurs following a change in membrane potential (depolarization or hyperpolarization).
Examples: K+, Na+, Ca2+ channels.
Function: These channels open or close in response to changes in membrane potential, allowing rapid movement of ions across the membrane.

44
Q

describe ligand-gated (extracellular) channels

A

Opening Mechanism: Binding of an extracellular ligand (neurotransmitters such as glutamate, acetylcholine (ACh)).
Examples: Glutamate or ACh receptors.
Function: Open in response to the binding of specific ligands, leading to the opening of the channel and allowing ions to flow through.

45
Q

describe ligand gated (intracellular) channels

A

Opening Mechanism: Regulated by the binding of an intracellular factor (such as ATP, cAMP).
Examples: K+ channels, cyclic nucleotide-gated (CNG) channels.
Function: Involve intracellular signaling molecules binding to the channel protein to open it, controlling ion flux based on intracellular conditions.

46
Q

describe mechanically-gated channels

A

Opening Mechanism: A mechanical stress or force opens the channel.
Example: Cation channels in stereocilia of hair cells.
Function: Open in response to mechanical stimuli, which is critical for sensory functions like hearing.

47
Q

explain kcsa k+ channels and their characteristics

A

KcsA K+ Channel:
Structure: Composed of 4 subunits, each with 2 transmembrane helices (M2 controls gating) and a pore-forming segment with a selectivity filter.
Selectivity: High selectivity for K+ due to its size and the presence of oxygen atoms in the filter, which match the size and charge of K+ ions but exclude Na+.
Function: The channel allows rapid passage of K+ ions while excluding Na+ due to size and electrostatic considerations.

48
Q

describe types of voltage sensitivity

A

S4 Segment: In voltage-gated K+ channels, the S4 transmembrane segment is crucial for voltage sensitivity. At resting membrane potential, S4 is positioned near the cytosol, keeping the channel closed.
Depolarization: Upon depolarization (more positive inside the cell), the S4 segment is displaced across the membrane, opening the channel.

49
Q

describeat kinds of ion channels aren’t voltage-gated

A

Background/Leak K+ Channels: These are always open and do not respond to changes in membrane potential. They help maintain the resting membrane potential of the cell.
Na+ Channels: Exhibit three states: closed, open, and inactivated, which is crucial for the propagation of action potentials along neurons.

50
Q

list forms of intercellular signalling and their characteristics

A

Contact-dependent signaling:
-Signal molecule remains bound to the cell surface. Example: Developmental processes, immune responses.

Paracrine signaling:
- Signal molecules are secreted and diffuse over short distances to nearby target cells. Example: Local growth factors.

Synaptic signaling:
- Signal molecules (neurotransmitters) are delivered via cell extensions (axons) and across synapses. Example: Neuronal communication.

Endocrine signaling:
Hormones are secreted into the bloodstream, allowing long-distance signaling. Example: Hormonal regulation.

51
Q

Explain cell-surface receptors

A

Signal transduction begins when a receptor protein on the cell surface transforms an extracellular signal into an intracellular response.

52
Q

list and describe the types of cell surface receptors

A

Ion-channel-linked receptors (Ionotropic):
- Function: Neurotransmitter binding induces a conformational change, directly opening ion channels for ion flow. Example: Acetylcholine receptor.

G-protein-coupled receptors (Metabotropic):
- Function: Activate intracellular signaling cascades through G-proteins. Example: Receptors for hormones like adrenaline.

Enzyme-linked receptors:
- Function: Ligand binding activates intrinsic enzyme activity or associates with an enzyme. Example: Growth factor receptors.

53
Q

list and describe different neurotransmitters for synaptic signaling

A

Neurotransmitter Production:
- Synthesized in the presynaptic terminal.
Stored in vesicles for rapid release upon stimulation.

Synaptic Communication:
- Presynaptic neurons release neurotransmitters into the synaptic cleft.
Neurotransmitters bind to postsynaptic receptors, triggering an excitatory or inhibitory response.

Excitatory vs. Inhibitory Synapses:
- Excitatory: Net positive charge gain increases excitability (e.g., glutamate, acetylcholine).
Inhibitory: Net positive charge loss decreases excitability (e.g., GABA, glycine).

54
Q

explain how Acetylcholine (ACh) Receptor work and what kind of receptor they are

A

ionotropic,
Structure:
Comprised of 5 subunits (α, α, β, γ, δ), forming a water-filled pore.
Negatively charged amino acids near the pore promote the passage of positively charged ions (Na+, K+).
Activation:
Requires binding of 2 ACh molecules to α subunits.
Leads to Na+ influx, causing depolarization and initiating downstream events.

55
Q

describe the neuromuscular junction and muscle contraction

A
  1. A nerve impulse causes Ca²⁺ influx and ACh release.
  2. ACh binds to receptors on the postsynaptic membrane, opening Na+ channels and depolarizing the membrane.
  3. Depolarization activates voltage-gated Na+ and Ca²⁺ channels, leading to increased cytosolic Ca²⁺.
  4. Increased Ca²⁺ triggers muscle contraction.
56
Q

list and describe the types of glutamate receptors

A

non-NMDA receptors:
Activated by AMPA and kainate; allow Na+ and K+ flow.

NMDA recptors:
Require both glutamate and glycine; allow Na+, K+, and Ca²⁺ flow. Blocked by Mg²⁺ unless depolarized.

57
Q

explain how glutamate affects learning and memory with its role in LTP

A

Glutamate binds non-NMDA and NMDA receptors, causing Na+ influx and depolarization.
Depolarization removes Mg²⁺ from NMDA receptor pores, allowing Ca²⁺ influx.
Increased Ca²⁺ triggers pathways that enhance receptor sensitivity, strengthening the synapse.

58
Q

list and describe the effects of PKA on gene transcription

A
  • Ca2+/calmodulin: Ca²⁺ influx through NMDA receptors (e.g., during long-term potentiation (LTP)) enhances gene transcription.
    This involves increased expression and incorporation of non-NMDA receptors into the membrane, along with new protein synthesis and sorting through the ER and Golgi.
  • LTP: Short-term: Enhanced receptor activity.
    Long-term: Formation of more dendritic spines, improving synaptic connectivity.
59
Q

explain the Phospholipase C (PLC) Pathway

A

Activated by Gq-coupled G-proteins upon ligand binding.
Steps:
PLC activation: Catalyzes the cleavage of PIP₂ into:
IP₃: Soluble molecule that binds to IP₃ receptors in the ER, releasing Ca²⁺ into the cytosol.
DAG: Stays membrane-bound and, with Ca²⁺, activates protein kinase C (PKC).
Downstream effects:
Ca²⁺ elevation: Impacts various cellular processes (e.g., smooth muscle contraction, neuronal signaling).
PKC activation: Phosphorylates target proteins, altering ion channel activity and cellular responses.

60
Q

what are the Physiological Roles of the PLC Pathway

A

Elevates cytosolic Ca²⁺, which drives processes like:
Neuronal signaling in Purkinje neurons of the cerebellum.
Ion channel modulation (e.g., metabotropic glutamate receptor activity).
Slower signaling compared to ionotropic receptors due to its reliance on phosphorylation.

61
Q

describe and explain Cyclic Nucleotide-Gated (CNG) Ion Channels

A

CNG channels are regulated by GPCRs, essential in sensory transduction mechanisms (e.g., vision, olfaction).
Key regulators:
Gt (transducin): Activates cGMP phosphodiesterase (PDE), reducing cGMP levels.
cGMP degradation: Closes CNG channels, altering ion flow and sensory response.

62
Q

describe and explain Vision: GPCR and CNG Channel Regulation

A
  • Rhodopsin GPCR:
    Contains the retinal chromophore, which absorbs light and triggers signaling.
  • Adaptation:
    Mediated by rhodopsin-specific kinase (a GRK) and arrestin, ensuring sensitivity adjustments during prolonged light exposure.
  • CNG channel closure:
    PDE activity lowers cGMP, leading to channel closure and initiating photoreceptor hyperpolarization.
63
Q

explain Ca²⁺ Signaling

A
  • Mechanisms of Ca²⁺ Release:
    Depolarization-induced Ca²⁺ release:
    E.g., skeletal muscle contraction.
  • IP₃-mediated Ca²⁺ release:
    Triggered by phospholipase C (PLC) pathway.
  • Ca²⁺-induced Ca²⁺ release (CICR):
    Observed in cardiac muscle cells and neurons.
    Initial influx of Ca²⁺ through plasma membrane channels activates ryanodine receptors (RyRs) on the SR or smooth ER.
    RyRs release more Ca²⁺ into the cytosol, amplifying the signal.
64
Q

provide an example of CICR in cardiac cells

A

Low resting cytosolic Ca²⁺ maintained by Ca²⁺ pumps.
Ca²⁺ influx triggers RyR activation, sustaining contraction cycles.

65
Q

list and define the types of Ca2+ signals

A

Local signals: Confined to specific cellular regions.
Global signals: Cytosolic Ca²⁺ elevation affects the entire cell.

66
Q

describe and explain calmodulin (cam) or the Ca2+ sensor

A

Binds up to 4 Ca²⁺ ions (2 per “EF-hand” domain).
Binding induces a conformational change, activating the Ca-CaM complex.
Functions:

Regulates target enzymes and proteins, such as:
Adenylyl cyclase (increases cAMP production).
Plasma membrane Ca²⁺ pumps (feedback regulation of Ca²⁺ levels).
Essential for Ca²⁺ signal transduction by altering the activity of target proteins.

67
Q

describe and explain CaM-Kinase II (CaMKII)

A

multifunctional kinase
Structure and Activation:

A large complex of 12 subunits.
Requires Ca²⁺/CaM for initial activation.
Autophosphorylation maintains activity even after Ca²⁺ levels drop, enabling Ca²⁺-independent signaling.
Deactivation occurs via protein phosphatases.
Roles in Long-Term Potentiation (LTP):

Phosphorylation of non-NMDA receptors enhances their activity.
Mobilizes non-NMDA receptors to the plasma membrane, strengthening synaptic connections.

68
Q

describe and explain gap junctions

A

direct intercellular communication
- Structure:
Formed by two connexons (hemichannels), one from each adjacent cell.
Each connexon consists of 6 connexin protein subunits.
Spans an intercellular gap of 2–4 nm, creating a cytosolic connection.

-Functions:
Allow passage of ions, small molecules (<1 kDa), second messengers (e.g., cAMP), and ATP between cells.
Mediate electrical coupling in cardiac muscle cells and retinal neurons.

-Regulation:
Controlled by Ca²⁺, pH, and signaling molecules like dopamine.

69
Q

summarize the key roles

A
  • Ca²⁺ Signaling:
    Crucial for muscle contraction, neurotransmitter release, and intracellular signaling cascades.
  • Calmodulin and CaMKII:
    Act as transducers of Ca²⁺ signals, mediating processes like LTP and receptor mobilization.
  • Gap Junctions:
    Enable direct cell-cell communication for synchronized activity in tissues like the heart and retina.

BIO 3153 (5 decks)

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