EXAM 2 - Session 12: Atypical Organelles and Functional Condensates Flashcards
Explain membrane-less organelle structure/compartment seperation.
liquid within another liquid situation
* doesn’t have cell membrane
* ex. like oil and water seperation
What are the function MLOs are associated with?
- cell divison
- chromatin remodeling
- gene transcription
- synapse function
- virus assembly
Name the “classic” structures in MLOs.
P-body - concetrates of RNA and proteins without a supporting membrane
* function: RNA breakdown
Nucleolus - domain that is responsible for cell divison (disassembly/reassembly)
Contents within MLO are very dynamic
Explain some characteristics of MLOs.
- Generate new compartments - form/fusion of cytoplasmic granules and create subnuclear compartments.
- Reorganize existing compartments - nucleoli fusion
- Vary in time, location, and size
What are the similarities of membrane-bound organelles and MLOs?
- Organization –> optimized function
lysosome (MB) - acid hydrolases efficiency
mitochondria (MB) - e- transport, H+ gradients
p-body (MLO) - RNA decay - Vary in size and shape
nucleus (MB) - 5-10 um diameter
nucleolus (MLO) - 0.5-2.5 um diameter
*other MLO (MLO) - <0.5 (frequent) – ~20um (rare)
Describe the membrane-bound “organizer”.
Phospholipid bilayer(s) - boundary from aqueous cytoplasm
Explain the MLO “organizer”.
Protein biochemistry - dependent on characteristics that are more likely to interact with themselves than interact with aqueous cytoplasm
* similar or partnered proteins that are more likely to associate with specific partners (compatibility) and form membrane-less seperation from cytoplasm.
Describe liquid-liquid phase seperation (LLPS).
Dissolved proteins interact with each other (possibly RNA) to “de-mix” from surrounding homogeneous mixtures in the cytoplasm.
* can be reversible depending on the stimulus
* variable in time
Give two examples of MLO diversity.
Most MLOs have varied content –> varied functions
Cajal nuclear bodies –> varied content & function
* partially regulate transcription
* process RNA for spliceosome assembly
PML nuclear bodies (green dots in image)
* PML protein - replication suppressor
* ~100 possible partner proteins in different PML bodies for varied function
* apoptosis, telomere elongation
What does protein condensation (LLPS) lead to?
- Reaction crucible
- Sequestration
- Organizational hub
Explain the reaction crucible after protein condensation (LLPS).
Reaction crucible leads to more efficient processing of reactions
* ex. post-translational modifications –> concentrated subset of molecules enhances reactions
* by increasing the concentration of the processor (red triangle in image) the cell increases the efficiency of the reaction
“liquid” organization allows for easier entry and exit
Explain sequestration that occurs after protein condensation.
Proteins are condensed and stored for later processing or secretion
* reduces response time to extracellular signals
* builds a reservoir/deposit
Explain the organizational hub that forms after protein condensation.
Normal condensation of proteins (e.g., tau) focuses interaction/polymerization of partner proteins (microtubules)
Explain scaffold proteins versus client proteins.
Scaffold proteins - drive LLPS on their own
* enriched for domain repeats (multivalent)
* little 3D structure (disordered)
Client proteins - interact w/ scaffold proteins
* compatible with LLPS of partner proteins
* insufficient for LLPS on their own
What does it mean by multivalent?
Multivalent = repeated subdomains –> repeated site for interactions
What does it mean by disordered?
- NOT the same as denatured
- no rigid 3D “lock & key-type” conformation
- bc of flexibility –> proteins can interact with many partners
- high content of polar/charged amino acids –> keeps proteins in extended shape
- low content of hydrophobic AA –> less likely to fold up to reduce interaction with water
List other extracellular and intracellular conditions that drive phase seperation.
Extracellular: (outside conditions can change intracellular organization)
* pH
* osmolarity
* stressors (toxins)
Intracellular:
* protein concentration
* ion concentration
* partners (other proteins, RNA or DNA)
* ATP (as charged molecule)
* post-translational modifications (e.g, phosphorylation)
Explain phase transition.
- occurs abruptly after LLPS
- excessive interactions among components
- uncertain reversibility, uncertain concequences
Explain aggregation.
- may occur independently or following LLPT
- disrupts normal cell function
- abnormal, often disease-associated and typically irreversible
How does further interaction of proteins beyond LLPS result in dysfunction?
Disperse –> LLPS –> LLPT –> aggregation
* condensation from excess interactions –> generates “solid” structures, insoluble, fibrous amyloids
* nucleation - aggregated proteins are the focal point of condensation for proteins that would otherwise remain in LLPT or return to LLPS (formation of deterimental clumps)
Name the conditions that are associated with dysfunctional MLOs.
- Amyotrophic lateral sclerosis (ALS, Lou Gehrig’s disease)
- Alzheimer’s disease
- Parkinson’s disease
LLPS/T are located in the nucleus and cytoplasm –> has possible impact on many cell functions –> related to many diseases
* result: diverse pathologies
What is the desired outcome of therapeutic interventions for MLOs.
- Facilitate LLPS for reaction crucible, sequestration, and organizational hub.
- Reduce LLPS that might be precursor of LLPT or aggregate.
- Regulate post-translational modification for desired effect.
