L1-5: Cells- Function, Transport, Growth & Division Flashcards
What can all life forms be traced back to?
Last Universal Common Ancestor (LUCA)
How did eukaryotes develop a mitochondria and chloroplasts?
Through endosymbiosis with bacteria, meaning eukaryotes are chimeras
What is a phylogenetic tree and what does it show?
It is an evolutionary history of a group of organisms
Inferred indirectly from nucleotide or AA sequence
Certain genes/proteins are globally distributed which allows global investigations of phylogenies
What is the most widely used phylogenetic marker?
small subunit ribosomal RNA (SSU rRNA) gene (SSU rDNA)
What are the 3 domains of an early phylogenetic tree?
Bacteria, Archaea and Eukarya
What are the 2 different origins of eukaryotic compartments and membranes?
Endogenous which lead to development of the nucleus and RER
Exogenous which lead to development of the mitochondria
What is the archezoa hypothesis?
That the nucleus was first developed through endogenous origin using endomembranes
What was phase 2 of the archezoa hypothesis?
That the mitochondria was developed using endomembranes of exogenous origin
How are mitochondrial proteins encoded?
By the nuclear genome (>1000 proteins)
What were the first eukaryotes according to the archezoa hypothesis?
Anaerobes
What discoveries would make The Archeoza Hypothesis fall?
-Archeozoans branch among aerobic species with mitochondria
-Mitochondrial genes on archezoan genomes
-Mitochondrion-derived organelles are present in archezoans
Where do Archexoa contain mitochondrial proteins?
In double membrane bounded organelles called hydrogenosomes or mitosomes
How were chloroplasts developed in eukaryotes?
Through endomembranes of exogenous origins, which evolved after the eukaryotic cell
How was phagocytosis discovered?
Using the unicellular eukaryote Paramecium caudatum
What were chloroplasts and mitochondria derived from?
C: cyanobacteria
M: alpha-proteobacteria
Which membrane systems are related?
Gram negative bacteria, mitochondria and plastids
What are properties of the plasma membrane?
-Lipids and proteins are major components
-Enclose cell content separate from external environment
-Allow different concentrations of substances to be maintained
How are eukaryotic internal membranes (endomembranes) complex?
They allow separate compartments to have different constituents and functions
What are biological membranes made of?
Lipid bilayers and proteins
What are the functions of the plasma membrane and proteins associated?
-Communication with the environment + other cells
-Barrier functions of molecules in & out the cell
-Cell growth, shape change, movement, division
What type of genetic impacts are there on phenotype?
Deterministic and probabilistic
What does amphiphilic mean and which biological molecule relates the most to it?
A chemical compound is both hydrophilic and hydrophobic, lipids relate the most
What are the most common lipids in eukaryotes?
-Phospholipids (main type phosphoglycerides)
-Cholesterol (impacts membrane fluidity)
-Glycolipids
What are the 4 major phospholipids in the PM?
-Phosphatidylethanolamine
-Phosphatidylserine
-Phosphatidylcholine
-Sphingomyelin
-Sphingosine
What are glycolipids?
Sugar containing lipids
Where are glycolipids located?
Embedded into the PM facing away from the cytosol (to the apical side of epithelial cells)
What is the function of glycolipids?
Cell recognition process
Entry point for some bacterial toxins and viruses
What are 2 examples of glycolipids?
Galactocerebroside and GM1 ganglioside
What are features of membrane fluidity and lipid composition?
Fluidity modulates transporter and enzyme activity
Fluidity is precisely regulated ensuring survival
Lipid composition and temperature contribute to fluidity
Organisms can adjust composition of membrane
How are the membranes specific functions carried out?
Using membrane proteins
How is protein composition in membranes variable?
As protein composition determines functional repertoire
What are the different types of membrane-associated proteins?
Integral membrane proteins
Lipid attached proteins
Peripheral, membrane associated proteins (released by agents that disrupt protein-protein interactions)
What are the different functions of membrane proteins?
Transporters, linkers, receptors and enzymes that catalyse reactions at membrane surfaces
What is the use of membrane transport proteins?
Move nutrients, metabolites or ions across membranes
What is the use of membrane linkers?
They join membranes to intra or extracellular macromolecules (generate structures)
What is the use of membrane receptors?
They transduce signals from environment
Transport of ligand - plgR, transferring receptor (collect iron to import to cell)
How are hydrophobicity plots used?
They are used to identify the hydrophobic amino acids contained in the membrane
What is the most and the least hydrophobic amino acids?
Most: Isoleucine
Least: Arginine
How is the glycocalyx formed?
From glycoproteins and glycolipids
What is the function of the glycocalyx?
It protects cells against chemical, physical and biological damage
What are N-linked glycans?
Asparagine liked glycans
What are O-glycans?
Serine/Threonine linked
What are proteoglycans?
Glycoproteins with GAGs (glycosaminoglycan)
What are properties of glycosylation in humans?
Some glycoproteins have more than one type of glycan
Some rare genetic diseases relate to disruption of glycans formation
Glycans affect health and disease in numerous ways
What are the functions of the glycocalyx?
Protect (unwanted interactions distanced)
Allow adhesion (carbs binding proteins on other cell surfaces)
Recognise (cell type specific glycosylation patterns)
Store (bind and release growth factors)
What are the three domains of guinea pig sperm?
Anterior head, posterior head and tail
What are the 3 different energy driven transporters?
Coupled transporter
ATP-driven pump
Light-driven pump
What is FRAP?
Fluorescent recovery after photobleaching
What are the 2 different ways the protein membranes can diffuse?
Cell fusion and FRAP
Where can proteins be restricted to?
A polarised distribution (apical, lateral and basal parts of membrane)
By cell-cell interaction
What are the properties of the 3 domains in guinea pig sperm?
The domains are completely separated and do not leave their domain
What is an example of cell-cell interaction when proteins are restricted?
Spectrin-based cytoskeleton in the red blood cell
What is an example of polarised distribution of membrane proteins?
In epithelial cells:
Apical - cotransporter
Basal - carrier protein, Na+/K+ pump
How do membrane bending proteins help shape membranes?
Using:
Protein wedges
Curved proteins
Protein binding to large heads of lipids
How is membrane bending beneficial?
Membrane shape regulated dynamically
Cellular processes require elaborate transient membrane deformations (vesicle budding, cell movements and division)
Which organelles are membrane-enclosed organelles with an interior/lumen?
ER, golgi apparatus, endosomes, lysosomes and peroxisomes
What are the 3 major types of transport?
Gated transport (nucleus)
Transmembrane transport (mitochondria)
Vesicular transport (golgi + ER)
Where does gated transport take place?
Through nuclear pores
How are proteins sorted and targeted?
By signal sequences using nuclear location signals, mitochondrial signal sequences and signals on N-terminal of proteins made by RER
What organelles does vesicular transport take place between?
Golgi, endosomes, lysosomes and plasma membrane
Where are most proteins made?
In cytosol
What is a main property of the nuclear membrane?
Both membranes are connected (differs to other membrane bound organelles)
How are proteins made in the mitochondria?
Mitochondria have 70s ribosomes so they are made via protein synthesis
Which proteins are made by ribosomes on RER?
-Plasma membrane
-ER
-Golgi and secreted proteins
What are characteristics of nuclear pores?
-Small molecules can diffuse through
-Larger molecules need specific transport mechanisms
-Continuous and dynamic in and out movements
Why is it important that proteins are transported to the nucleus?
For structure, gene transcription (enzymes) and regulation
What are the components of the nuclear membrane?
Inner and outer nuclear membrane containing nuclear pores all
How was protein signaling identified?
Due to SV40 virus as when AA sequence changed to a uncharged AA the protein was unable to travel through the membrane
What is the process of regulated nuclear localisation?
Nuclear factor of activated shuttling protein, inactivated T-cells gene transcription is activated by NF-AT
Some immunosuppressive drugs target calcineurin blocking T-cell activation
How are proteins transported into the mitochondria?
Via post-translational import:
Precursor protein binds which unfolds and translocates binding to TOM and TIM23 allows translocation in matrix then peptidase cleaves signal which leaves the mature mitochondrial protein
What other cell has similar transport of proteins into cell?
Bacteria
How are proteins transported into RER?
Co-transport translocation
What is the process of protein being transported to the ER?
Protein synthesis starts in cytosol
Protein contains N-terminal signal sequence
Signal seq binds to receptor on RER ribosome associates
Polypeptide synthesis completed on RER
Protein translocates into RER memb/lumen during
Signal peptide cleaved
What happens to proteins when they enter the RER?
They are glycosylated:
N-glycosylated (Asn)
O-glycosylated (Ser/Thr)
What happens to proteins once they enter the RER?
They can remain in RER, travel to other organelles or export to cell surface, they become vesicular transport dependent
What fate do different proteins have once they enter the RER?
Water-soluble: remain in organelles or are secreted
Membrane-associated: remain with organelle membranes or move to plasma membrane
Which organelles use vesicular transport of proteins?
Peroxisomes, ER, golgi, late endosome, lysosome, early endosome, cell exterior, secretory vesicles
What is a key example of vesicular transport?
Eating- phagocytosis
Communication with other cells
Quick response to environmental changes
What types of vesicular transport are there?
Secretory, endocytic and retrieval
What are the 3 different types of protein coats used in vesicle traffic?
Clathrin, COPI and COPII
Where do the protein coats travel?
Clathrin - Golgi vesicles
COPI & COPII - ER and Golgi
What are the components of the golgi apparatus?
-Located near nucleus
-Cisternae
-Polarised:
Cis face - vesicles from RER enter golgi
Trans face - export vesicles to organelles/plasma memb to bud off from there
What are the functions of the golgi apparatus?
-Core oligosaccharides trimmed
-Further sugars added/removed
-Enzymes in specific regions (cis or trans)
-Proteins leave golgi in membrane vesicles (memb or lumen, sorted specifically to final destination)
How does endocytosis contribute to protein transportation?
Engulfed by early endosomes that can leave to the PM or recycling endosome or can mature to late endosome where fusion leads to endolysosome to lysosome
What happens to endocytosed material?
Transport vesicles are recycled
Endolysosomes degraded
Transport vesicle is moved to extracellular fluid in transcytosis
What is an example of transcytosis?
Transport of antibodies (IgG) to foetus inside the mother then secretion of SIgA at mucosal surfaces (breast milk)
What cells phagocytose antibody coated bacteria?
Macrophages and neutrophils
How was phagocytosis discovered?
Using unicellular eukaryote Paramecium
How do lysosomes work?
They contain acid hydrolases that can degrade entire cellsH
How do lysosomes maintain their acidic nature?
A H+ pump uses ATP to pump H+ making it more acidic than the cytosol
What are the 4 different degradation pathways?
Endocytosis
Macropincytosis
Phagocytosis
Autophagy
How does autophagy occur?
Nucleation and extension, closure, fusion with lysosomes then digestion
Why is autophagy important?
During normal cell growth and differentiation
Adaptive response to stress
Dysfunctional autophagy is associated with infectious disorders, neurodegenerative diseases and cancer
What are the 2 different secretory pathways?
Constitutive and regulated
What is the pathway for constitutive secretion?
Plasma membrane lipids and proteins fuse with membrane secreting soluble proteins
What is the pathway for regulated secretion?
Secretory vesicles store secretory proteins that are fused with the membrane using an intracellular signaling pathway using hormone/NT which secretes the vesicles into extracellular space
What 3 sorting pathways are used in the trans golgi network (TGN)
-Signal-mediated diversion to lysosomes
-Constitutive secretory pathway
-Signal-mediated diversion to secretory vesicles
What are the major cytoskeletal filaments?
Intermediate filament
Microtubule
Actin
Spectrin
What are the internal compartments of a typical cell?
Nucleus, PM, ER (with poly-ribosomes), mitochondrion, golgi apparatus, lysosome, cytosol, free polyribosomes, peroxisome and endosome
What is the function of the cytoskeleton?
To dynamically organise distinct membrane bound compartments to maintain cell shape and facilitate intracellular movement
What are the properties of intermediate filaments?
Found in cytoplasm and nucleus
10nm wide
Polymers
Strong
Flexible
Prevent excessive stretching
Distribute tensile force
What is the structure of intermediate filaments?
Alpha helical region of monomer
In a coiled-coil dimer
Then staggered tetramer of 2 coiled-coil dimers
What type of intermediate filaments are there and where are they found?
Cytoplasmic:
Keratins (epithelia)
Vimentin (connective tissue, muscle cells & neuroglial cells)
Neurofilaments (nerve cells)
Nuclear:
Nuclear Lamins (all animal cells)
What are lamins?
Protein subunits
Where are lamins located?
They line the inner face of the nuclear envelope in a fibrous meshwork
What are characteristics of lamins?
Provide structural support
Provides attachment sites for proteins & chromosomes
Breaks down during cell division (phosphorylated during mitosis)
What are neurofilament protein domains?
NFL, NFM, NFH
How does keratin work as an intermediate filament protein domain?
It forms a barrier to allow adhesion between other cells via desmosomes
What are the properties of microtubules?
25nm diameter
Tube
Polymers (globular monomers-tubulins using GTP)
Cytoplasm only
Rigid
Dynamic
What are the functions of microtubules?
Organelle and vesicle shuttling
Segregation of chromosomes during mitosis
Facilitate movement
Where are microtubules used?
Cytoplasmic microtubules
Mitotic spindle (bipolar architecture)
Basal body (cilia/flagella to facilitate movement)
What is the structure of microtubules?
Assemble from dimers of alpha and beta tubulin (13 protofilaments using GTP)
Polar structures (+ end beta, - end alpha)
Dynamic instability
What are the microtubule motor proteins and how do they work?
Kinesins and dyneins, head and tail regions
Globular heads bind ATP
Heads bind to microtubule, ATP hydrolysis drives movement, kinesins + dyneins -
Which motor protein drives cilia and flagella?
Dyneins
How does dynein movement effect structure?
Produces microtubule sliding and causes microtubule to bend
What are properties if cilia and flagella?
Cilia:
Numerous and short
Stick out of cell surface
Flip back and forth
Locomotion of cell
Flagella:
Few and long
Locomotion of entire cell
How are microvilli different to cilia?
Non-motile
Increase surface area
Contain actin filament
What are the properties of actin filaments?
6-8nm diameter
Polymers (actin, use ATP, regulated by binding proteins)
Cytoplasm (cortex, bundles, 2D networks, 3D gels)
Flexible
Polar filaments & quick growth
Dynamic polarisation
What are the functions of actin filaments?
Cell motility and contraction
Adhesion and mechanosensing
How are actin filaments formed?
G-actin added at either end (more rapid at +)
Forms polarised filaments (F-actin)
Polymerisation associated with ATP hydrolysis
Assembly and organisation regulated with binding proteins
Where are actin filaments used?
Microvilli in intestine
Contractile bundles in cytoplasm
Sheetlike and fingerlike protrusions
Contractile ring during cell division
What are examples of actin binding proteins?
Severing
Cross-linking
Capping
Side binding
Motor
Bundling
How are actin filaments used for movement?
Protrusion in membrane due to polymerisation which attaches (focal adhesion- integrins) and traction takes place (due to myosin)
What are the actin filament motor proteins?
Myosins
Globular heads bind ATP
ATP hydrolysis drives movement
Tails bind structures
Move cell or cellular components
What are the properties of Myosin I?
All cells
One head & tail
Intracellular organisation
Moves cargo along actin filament
What are the properties of Myosin II?
Muscle cells
Dimer
Forms filaments
Contractile structures
What is spectrin?
Cytoskeletal protein that lines the inner plasma membrane
What are the properties of spectrin?
Crucial mechanical strength, stability and shape
Links membranes to motor proteins and all major filament systems
First isolated as major component of RBCs
What are the differences between mitosis and meiosis?
Mitosis:
2 genetically identical daughter cells
Meiosis:
4 genetically different daughter cells
How to prokaryotes divide?
Binary fission - replication and division
DNA replication through interphase
How do eukaryotes divide?
4 distinct phases:
M (mitosis&cytokinesis)
S (synthesis)
Gap phases (G1&G2)
Interphase (G1, S & G2)
What are the phases of mitosis?
Prophase
Prometaphase
Metaphase
Anaphase
Telophase
Cytokinesis
What takes place during prometaphase?
Break down of nuclear envelope, chromosomes attach to spindle microtubules via kinetochores and undergo active movement
What happens during G1 of interphase?
Recovery from previous division
Preparation for DNA synthesis
Doubles organelles
Sythetase proteins for DNA rep
What happens during S phase?
Sythesis of proteins associated with DNA
Replication of DNA
What happens during G2 phase?
Preparation for mitosis - synthesis of proteins required for division
Where are the checkpoints for the cell cycle and why are they important?
G1, G2 and M
Regulated by internal and external factors
G1 cell is committed to DNA synthesis and replication
How are checkpoints controlled during the cell cycle?
By specific kinases (cyclin-dependent kinases)
They add Pi group from ATP to AA
Phosphorylation signals cell to proceed with cycle
Cdk alone are inactive and require other proteins (cyclins) to bind
What is quiescence?
A pause meaning cells cannot proliferate unless they receive signals, absence means cells enter G0 or programmed cell death
What is the G0 phase?
No growth takes place
Can re-enter G1
Can last any amount of time (reversible - skin cells)
Can be indefinite (irreversible - neurons, muscle)
What are growth factors?
Stimulate cell growth, division and differentiation
Continuation of cells through G1 requires specific GFs
When GFs deprived of cell it enters G0
Low concentrations required
Many have receptors in cell membrane
What is apoptosis?
Programmed cell death
Regulated and programmed process
Regulated by distinct processes
Variation of cell cycle control
What are the characteristics of apoptosis?
-Cell shrinks
-Nuclear condensation and fragmentation
-Membrane changes triggering phagocytosis
(Is the digested and recycled)
When is apoptosis triggered?
Physiologically:
Crucial for embryonic development
Removes/remodels tissues
Maintains homeostasis
Pathogenically:
Viral infection
Heat shock, toxins, cytotoxic T cells
Removal of stresses/damaged cells
How is apoptosis regulated?
Cells are alone
External signals
Hormonal signals
Signals from contacting cell
How is apoptosis supressed?
Survival factors
Contact with extracellular matrix
What are the key events in apoptosis?
Activation of gene p53- TF increase apoptosis genes (tumour suppressor)
Leaky mitochondria
Activation of protein degrading enzymes (capsases)
What is p53?
Transcription factor
Tumour suppressor
Maintains genomic integrity and tumour surveillance
Most commonly mutated gene
What is the sequence that leads to apoptosis?
DNA damage activates p53
Blocks cell cycle progression
Mitochondrial membrane ruptures
Cytochrome c in cytosol activates capsases
Capsase cascade leads to activation of DNAse and cleavage of lamins and cytoskeleton
How do activated capsases work?
Cleave nuclear lamins - lead to nuclear fragmentation
Activate DNase - cuts cell DNA into fragments
Cleaves cytoskeleton - detaches from neighbours, cell loses contact with extracellular matrix and cell rounds up
What is necrosis?
Accidental cell death due to injury
How does necrosis work?
Nuclear swelling
Cell swelling membrane damaged becomes leaky
Cell bursts
Cell contents into tissues
Triggers inflammatory response (messy)
