Week 1 Flashcards
What are stem cells and the different types?
- Stem Cells: have unique to differentiate into other cell types
- Pluripotent (embryonic stem cell): can differentiate into any cell line
- Multipotent: can differentiate into limited cell lines (ex: bone marrow)
What are terminally differentiated cells?
- Terminally Differentiated: adult cell that enters into non-dividing state (ex: skeletal cells, neurons)
- Specialized stem cells can be present for repair mechanisms
List the steps of the interphase, their main functions and how it is regulated.
- Interphase
- Gap1 Phase: growth phase where cells can enter into G0 (no division)
- S Phase: replication
- Gap2 Phase: growth phase
- Checkpoints are regulated by [Cdk]
List the steps of the mitosis, their main functions and how it is regulated.
- Mitosis
- Prophase: duplicated centrosomes; mitotic spindles form (microtubules)
- Metaphase: nuclear envelope breakdown; chromosomes align
- Anaphase: chromatids separate
- Telophase: nuclear envelope reforms
- Cytokinesis: cells divide using actin mechanism
- Checkpoints are regulated by [Cdk]
What is cell signaling and how does the process work?
- Change in external environment → Change in receptor binding → Secondary messengers → amplify response → adapts gene expression
What are the types of intracellular signaling and how do they work?
- Intercellular Signaling
- Contact-dependent: membrane-bound receptor interaction
- Paracrine: mediator molecule secreted to local environment
- Synaptic: neurotransmitters (think ACh!)
- Endocrine: hormones through bloodstream
What are the differences between Eukaryotic and Prokaryotic cells?
- Eukaryotic has membrane-bound organelles for specialized functions, nucleus, and mitochondria while prokaryotic utilizes cytosol for all functions. Both have PMs.
What is the function of cytoskeleton and what are the types?
- Provides cell stability and movement
- Types
- Actin
- Intermediate filaments
- Microtubules
What are the three phases of polymerization for cytoskeleton?
What is dynamic instability?
How do kinesin and dynein play a role?
Name a disease associated with cytoskeleton.
- 3 phases of polymerization
- Nucleation: assembly of monomers
- Elongation: rapid growth at (+) end
- Steady-state: equal rate of polymerization and de-polymerization
- Dynamic instability: rapid de-polymerization to cause separation of mitotic spindle.
- Polymerization and de-polymerization occurs at (+) end and nucleation occurs at (-) end
- Kinesin moves things to (+) end {cell surface is +}
- Dynesin walks things back to (-) end {centrosome is -}
- Disease: Hereditary Spherocytosis
Describe the function and properties of the cell membrane.
- Expands with budding and fusion events
- Impermeable to most ions and water molecules
- Contains pumps and channels which allow movement of ions, molecules, and proteins
- Glycoproteins on ECM interact with EC environment
Describe the properties and function of the nucleus. Name a disease associated with the nucleus.
- Description: made up of nuclear envelope and nuclear pores
- Function: storage of DNA
- Disease: Hutchinson Gilford Progeria
Describe the properties and function of ribosomes.
What is the SRP’s role in ribosome function?
- Description: cytosol and ER-bound organelles
- Function: protein synthesis
- SRP: signal recognition particle targets synthesized protein to ER
Describe the properties and function of the endoplasmic reticulum (ER).
- Description: network of tubules that acts as the outer bilayer of the nuclear envelope
- Function: processes proteins and lipid biosynthesis
- Ca++ storage and detoxification
Describe the properties and function of the golgi apparatus. Name diseases often associated with the golgi.
- Description: structure is dependent on microtubules with bi-directional transport from cis to trans-face
- Function: supplies membrane and is site of glycosylation
- Disease: congenital diseases associated with glycosylation such as seizures
Describe the properties and function of the lysosome. Name a disease associated with the lysosome.
- Description: contains hydrolytic enzymes
- Function: utilizes endocytosis (foreign macromolecules), macropinocytosis (fluid near PM), autophagy (cell components), and phagocytosis (foreign large particles/microorganisms)
- Disease: Lysosomal Storage Disease
Describe the properties and function of the mitochondria. Name two types of diseases associated with the mitochondria.
- Description: contains inner and outer membrane layers with own DNA
- Function: generates ATP
- Diseases
- Lufts
- Age-Related Degenerative Diseases (Parkinson’s and Alzheimer’s)
Describe the properties and function of the peroxisome. Name a disease associated with the peroxisome.
- Description: single membrane with dense matrix
- Function: oxidative reactions with hydrogen peroxide and FAs
- Disease: Zellweger Syndrome Spectrum
Describe the properties and function of the cilia/flagella. Name a disease associated with the cilia/flagella.
- Description: structural arrangement (9+2) of microtubules that extend from basal body
- Function: lines tracts to move mucus and cause movement (sperm)
- Disease: Dyskinesia (Kartagener’s Syndrome)
What is the general mechanism of direct transport between membrane enclosed organelles?
How are compartments in the cell diverse?
- Vesicles bud from marked specific sites contain cargo proteins that are delivered to another membrane compartment by fusion.
- Compartment diversity
- Some require cytoskeletal elements to maintain shape
- Small vesicles – diffusion, large vesicles – cytoskeleton tract
What are the types of trafficking pathways?
- Types of trafficking pathways
- Biosynthetic: secretory pathway from ER to golgi to PM
- Endocytosis: PM to early/late endosomes to lysosomes
- Retrieval: backflow of selected components is maintained
Where do clathrin coats, COP I coats, and COP II coats transport to and from?
Clathrin
- Transport: PM to early endosomes and Golgi to lysosomes
COP I
- Transport: Golgi to PM and Golgi to ER
COP II:
- Transport: From ER to Golgi
What is the structure of clathrin coats?
made of triskelion (3 light, 3 heavy chains) that self assembles to a hexagonal structure
What is the assembly process of clathrin coats?
- Arf-GEF recruits Arf-ADP → Arf-ATP → inserts into membrane → fatty acid tail exposure → clathrin recruitment → dynamin pinches off vesicle using accessory proteins and PIP2
- Phorsphorylation of PIPs to PIP2s are also involved in recruitment
What is the disassembly process of clathrin coats?
- Heat shock protein (Hsp70) is an ATPase stimulated by Auxilin → ATP hydrolyzes into ADP → Hsp70 uses energy from ATP hydrolysis to peel off coat
- PIP2s are dephosphorylated to PIPs weakening coat-membrane interactions
What is the COP I assembly process?
- Arf-GEF recruits Arf-ADP → Arf-ATP → inserts into membrane → fatty acid tail exposure → COPI recruitment → dynamin pinches off vesicle using accessory proteins and PIP2
- Phorsphorylation of PIPs to PIP2s are also involved in recruitment
What is the COP I disassembly process?
- Heat shock protein (Hsp70) is an ATPase stimulated by Auxilin → ATP hydrolyzes into ADP → Hsp70 uses energy from ATP hydrolysis to peel off coat
- PIP2s are dephosphorylated to PIPs weakening coat-membrane interactions
What is the COP II assembly process?
- Sar1-GEF recruits Sar1-GDP → Sar1-GTP → inserts into membrane → fatty acid tail exposure → COPII recruitment → dynamin pinches off vesicle using accessory proteins and PIP2
What is the COP II dissassebly process?
- Heat shock protein (Hsp70) is an ATPase stimulated by Auxilin →ATP hydrolyzes into ADP →Hsp70 uses energy from ATP hydrolysis to peel off coat
- PIP2s are dephosphorylated to PIPs weakening coat-membrane interactions
What is the function, structure of SNARE proteins, and the fusion process?
- Function: acts as tethers to bring membranes together for fusion; this is a Ca++ dependent process
- Structure
- V-SNARE (transport vesicle made up of one polypeptide chain)
- T-SNARE (target membrane made up of three polypeptide chains)
- Fusion Process
- T-SNARE traps V-SNARE
- Energy from four helix bundle drives membrane fusion
What is the disassembly process of SNAREs?
- NSF (i.e. NEM sensitive factor) and accessory proteins react with two cysteine residue to block activity
- Hydrolyzes ATP to destabilize four-helix bundle
What is the function of RAB GTPases?
- Function: molecular switches that control protein-protein interactions to allow for specific vesicle targeting
What is the process of RAB GTPases?
- Rab-GEF (could be a SNARE or tether) recruits Rab-GDP on donor membrane → Rab-GTP → Rab-GTP inserts into donor membrane → transport vesicle/budding forms/occurs → Rab effector binds Rab-GTP → fusion → Rab-GDP
What are the effectors of Rab GTPases?
What is the idea of cooperative action for Rab GTPases?
- Effectors
- Motors, SNAREs, Tethers
- Cooperative Activation
- When subunits (ex: SNAREs and Rabs) work together
What is the process of protein exit from the ER and transport to and from the Golgi?
How does membrane thickness play a role?
- ER exit sites to Golgi are with COPII; Golgi exit sites to ER are with COPI
- Budding exit sites contain cargo receptors that bind to exit signals on cargo proteins (but are not necessary)
- Membrane thickness (i.e. cholesterol) plays role in sorting transmembrane proteins
- TM proteins in thick membranes goes to PM and TM proteins in thin membranes stays in ER and Golgi
What are ER resident proteins and how do they work?
- ER Resident Proteins: marked by signal sequences on protein (i.e. KDEL or KKXX)
- Return to ER through retrieval pathway
- Affinity in ER Resident Receptors
- More acidic pH in Golgi increases affinity of receptor for ER resident proteins
How do chaperone proteins work and provide an example?
- Chaperone Proteins: fold proteins and keep misfolded proteins from leaving ER
- Example: BiP act as chaperones for ABs (but also think of CFTR protein)
Where does glycosylation occur and what are the two main types?
- Glycosylation occurs in Golgi
- Golgi more prominent in cells that secrete large amounts of glycoproteins (i.e. goblet cells in small intestine)
- Features
- N-linked glycosylation: sugar attached to asparagine reside
- O-linked glycosylation: sugar attached to serine or threonine residue
What is the importance of glycosylation?
- Importance
- Prevents approach of proteases
- Prevent aggregation
- Promotes cell signaling
- Transport – M6P is linked to lysosomal hydrolases to target to lysosome
What is the transport mechanism for lysosomal hydrolase?
- Acid hydrolases are only active at low pH
- Vacuole ATPase pumps H+ against gradient into lysosome
- M6P is used to tag lysosomal hydrolase precursors from ER in the Golgi
- M6P binds to M6P receptor in Golgi → early endosome → lysosome through Clathrin
- Addition of GlcNAc-P to M6P in the early endosome to release hydrolase precursor
- M6P receptor is recycled back to Golgi
What are the features of phagocytes?
What types of professional phagocytes?
What is the ingestion process of phagocytes?
Phagocytosis
- Greater than 250nm diameter
- Professional phagocytes (components of WBCs)
- Macrophages: apoptotic cells
- Neutrophils: foreign organisms
- Ingestion Process
- Attachment (through tagging) → Engulfment (formation of phagocytotic cup through the use of GTPase-dependent actin protrusions) → Fusion with Lysosome (degradation)
What is pinocytosis?
- Ingestion of fluids
- Less than 100nm diameter
What is receptor-mediated endocytosis and give the process using LDL particles?
- Clathrin mediated
- Example: LDL particles
- LDL receptors on ECM of PM recognize LDL particle
- LDL receptor binds adaptor protein and clathrin coat assembles
- Transported to early endosomes then lysosomes
- LDL receptor dissociates from LDL particle in early endosome and receptor is recycled back to PM
- Free cholesterol enters cytoplasm
- Promotes homeostasis by inhibiting LDL receptors and shutting down cholesterol synthesis when [LDL]cell is high
What is transcytosis used for and provide an example of where it would be used?
- Used in polarized epithelial cells to transfer macromolecules from one extracellular space to another (apical to basolateral)
- Example: transferring of ABs from mother’s blood to baby’s blood
What are the two types or regulated pathways and provide examples of where each would be used?
- Signal Mediated Diversion to Lysosomes
- M6P receptor example
- Signal Mediated Diversion to Secretory Vesicles
- Occurs in specialized cells for the release of neurotransmitters and hormones