Ivo Flashcards
What were the 3 lenses used in Hooke’s microscope?
Bi-convex objective lens, eyepiece lens, and a tube or field lens
what optical issues did Hooke’s microscope suffer from?
Significant chromatic and spherical aberration
How did Hooke’s microscope correct aberrations?
By placing a small diaphragm into the optical pathway to reduce peripheral light rays and sharpen the image
What was used for illumination in Hooke’s microscope?
An oil lamp with light passed through a water-filled glass flask to diffuse and provide even, intense illumination
How was Leeuwenhoek’s microscope constructed?
It consisted of two flat and thin brass plates riveted together with a bi-convex ground lens sandwiched between
What were the magnification and resolution capabilities of Leeuwenhoek’s microscope?
magnifcation of 70-270x and resolution approaching 1 micron
What discoveries did Leeuwenhoek make using his microscope?
He observed “extremely small animals” in “pepper” water (1676) and studied “cloudy water” from the Berkelsemeer near Delft
What is the resolution limit of optical microscopy?
200nm (1000x magnification, 0.2 microns)
How can objects be tracked with nanometer accuracy despite the resolution limit?
By visualising them using advanced microscopy techniques
What technological advancements have extended resolution in light microscopy?
Development of fluorescent microscopy and confocal microscopy
What technological innovation enabled atomic resolution imaging in electron microscopy (EM)?
The use of complementary metal-oxide-semiconductor (CMOS) chips
Why are CMOS chips superior to film and CCD detectors in EM?
They offer greater resolution and sensitivity with a much faster readout rate
What computational advancements have improved EM?
Advanced computational methods for image analysis and processing
What contributions did Albert Claude make to the discovery of organelles?
He developed fractionation and differential centrifugation techniques
What was George E. Palade’s contribution to cell biology?
He combined EM with differential centrifugation to study ribosomes and secretory vesicle pathways
How did Christian de Duve contribute to organelle disocvery?
He described enzymes in compartments, discovering lysosomes and peroxisomes
What techniques are used to separate viruses and organelles?
Fractionation and centrifugation techniques
How are cell contents released during fractionation?
By removing the outer membrane and applying mechanical force through stirring, osmotic pressure, sonication, or tissue homogenisers
What solutions are typically used to keep organelles intact during separation?
Isotonic solutions, such as sucrose
How are organelles separated in centrifugation?
Based on their size and density
What is primary endosymbiosis?
The internalization of a prokaryote by a host cell to form ancestral eukaryotic cells, such as mitochondria and chloroplasts.
How is the double membrane of mitochondria and chloroplasts formed?
The inner membrane comes from the bacterial ancestor, while the outer membrane originates from the host cell.
What is secondary endosymbiosis?
The internalization of a single-celled eukaryote by another eukaryote.
How many membranes typically surround chloroplast organelles in secondary endosymbiosis?
Four membranes.
What typically happens to the nucleus of the internalized eukaryote in secondary endosymbiosis?
It is either lost or forms a nucleomorph.
How many genomes are combined in secondary endosymbiosis?
Four or five
What is required for protein translocation in secondary endosymbiosis?
Proteins must cross multiple membranes.
What are the two phases of membrane asymmetry in cells?
The non-plasmatic (exoplasmic) phase and the plasmatic (cytosolic) phase.
How is membrane asymmetry organized in single-membrane organelles?
The inside is non-plasmatic.
How is membrane asymmetry organized in double-membrane organelles?
The intermembrane space is non-plasmatic, and the matrix is plasmatic.
Why are innermost membranes thinner than outer membranes?
Likely due to functional and structural differences between the membranes.
How can membrane bilayer thickness affect protein activity?
Membrane proteins may have varying activity levels in membranes of different thicknesses.
How can the effect of bilayer thickness on protein activity be validated?
By determining protein activity in different artificial membranes.
What determines the segregation of membrane proteins into lipid rafts?
Membrane thickness and matching protein dimensions.
How do lipid rafts differ from the rest of the membrane?
They are usually slightly thicker.
What two factors regulate membrane protein activity in lipid rafts?
Membrane thickness (affecting activity) and localisation into rafts (concentration of proteins).
What do bio-membranes separate?
They act as separators with cytoplasmic and non-cytoplasmic faces.
How are lipids distributed in membranes?
They vary in thickness, asymmetry, and composition.
What is the significance of beta-barrel proteins in the endosymbiont hypothesis?
Beta-barrel proteins are found only in outer membranes of gram-negative bacteria, mitochondria, and chloroplasts.
Where are beta-barrel proteins found?
In bacterial outer membranes and organellar outer membranes (e.g., mitochondria and chloroplasts).
Name examples of beta-barrel proteins in E. coli and their strand numbers.
OmpX, OmpW, OmpA (8 strands)
OmpT (10 strands)
OmpLa (12 strands)
FadL (14 strands)
Omp85 (12/16 strands)
OmpF (16 strands).
What is the function of OmpF?
A passive diffusion pore with a 16-stranded beta-barrel that allows molecules ~7Å across to pass.
What functions do Omp proteins serve?
Adhesion, water and nutrient transport, and enzymatic activities (e.g., OmpT as a protease, OmpLa as a phospholipase).
How far apart are amino acids in an extended beta-strand?
0.35nm apart, alternating directions.
How many amino acids are required to cross a 4nm thick membrane?
Approximately 11 amino acids.
What are porins, and where are they found?
Porins are outer membrane proteins in gram-negative bacteria, constituting ~2-3% of the proteome.
What are the two types of porins, and how do they differ?
General porins: Non-specific, uptake hydrophilic, uncharged molecules under ~600 Da.
Specific porins: Passive but selective diffusion channels with aqueous pores.
How abundant are porins in bacterial cells?
Up to 100,000 copies per cell.
What is the typical length of beta-strands in beta-barrel proteins, and what is their amino acid pattern?
Beta-strands are 9-11 amino acids long with alternating hydrophobic and hydrophilic residues.
What is the topology of beta-barrel proteins?
Even number of strands in an antiparallel topology with N- and C-termini in the periplasm.
How do the loops of beta-barrel proteins differ on each side of the membrane?
Long extracellular loops and short periplasmatic loops.
What feature stabilizes beta-barrel proteins, and why is this important?
Often oligomeric, which makes them more stable, important for their transport function.
What type of amino acids are found at the membrane boundary of beta-barrel proteins?
Aromatic amino acids.
Where are beta-barrel porins produced and where do they need to be inserted?
Produced in the bacterial cytosol and need to be inserted into the outer membrane.
Why do beta-barrel porins require special handling during transport?
They need to be kept soluble during transport to the periplasm.
Which translocon is used to move beta-barrel proteins into the periplasm?
The Sec translocon.
Name the two chaperone pathways for beta-barrel protein transport.
The SurA and Skp pathways.
What machinery links folding and insertion of beta-barrel proteins?
The Beta-Barrel Assembly Machinery (BAM) complex.
What is the role of the DegP pathway in beta-barrel protein handling?
It is a degradation pathway.
Which model of beta-barrel insertion was proven incorrect?
The BamA insertion-assist model.
What is the correct model of beta-barrel insertion?
The BamA budding model.
What evidence supports the BamA budding model?
Electron microscopy (EM), nanodisc studies, and consistent structural data.
What assists beta-barrel insertion in vivo?
Chaperones (Skp, LPS, SurA) and the BAM complex insertion machinery.
What mechanism do both BAM and mitochondrial SAM complexes share?
The hybrid barrel mechanism.
Which complexes handle beta-barrel insertion in mitochondria and chloroplasts?
Mitochondria: SAM50, Tom40
Chloroplasts: Toc75
How do beta-barrels support the endosymbiont theory?
Beta-barrels are found in bacterial, mitochondrial, and chloroplast outer membranes.
What is the function of TOM and SAM in mitochondria?
They insert beta-barrel proteins into the outer mitochondrial membrane.
What is the role of the dimeric Sam50 complex?
Its open gate conformation may serve as a placeholder for partially folded beta-barrels.
What is the beta-barrel switching mechanism in mitochondrial SAM complexes?
Tom40 is a substrate for SAM, and matured Tom40 can be replaced by Mdm10.
What conclusions can be drawn about SAM complexes in mitochondria?
They utilize the hybrid barrel mechanism for insertion and beta-barrel switching for maintenance and function.
What are the roles of Tom5 and Tom6 in the TOM complex?
They associate with Tom40 as subunits.
What is required for further subunit association with Tom40?
Dissociation from Sam50.
Approximately how many proteins must be imported into chloroplasts?
Up to 3500
What are examples of proteins imported into chloroplasts?
The small subunit of Rubisco and light harvesting complex II.
What does the Arabidopsis chloroplast genome encode?
87 proteins
4 rRNAs
37 tRNAs
Why do chloroplasts require extensive protein import?
The genome does not encode enough proteins for the chloroplast to function.
What do TOC and TIC stand for in chloroplasts?
TOC: Translocon in the outer chloroplast membrane.
TIC: Translocon in the inner chloroplast membrane.
How is protein transport across the chloroplast double membrane organised?
Via a bridge of proteins crossing the intermembrane space (IMS).
What does the endosymbiont theory explain about bio-membranes?
They have cytoplasmic and non-cytoplasmic faces.
They separate environments with distinct characteristics.
How does lipid composition influence membranes?
Between leaflets: explains membrane asymmetry.
Between membranes: explains changes in thickness (e.g., increase from ER to plasma membrane).
Where are beta-barrel membrane proteins exclusively found?
In bacterial or organellar outer membranes.
What are the building principles of beta-barrel membrane proteins?
Beta-strands are 9-11 amino acids long with alternating hydrophobic and hydrophilic residues.
Even number of strands in antiparallel topology, with N- and C-termini in the periplasm.
Long extracellular loops and short periplasmatic loops.
What similarities exist between BAM, Sam & TOM, and Toc75?
All are large membrane-bound protein translocation and beta-barrel insertion complexes.
Auxiliary chaperones and receptor proteins assist in protein transport.
What mechanisms are recognised for beta-barrel insertion?
Lateral gate, hybrid barrel, and beta-barrel switching.
Where does synthesis of membrane proteins occur?
At the ribosome on the ER membrane.
What mechanism ensures the translocation of membrane proteins during synthesis?
Co-translational translocation mechanism.
What types of proteins are targeted to the ER?
Secreted and membrane proteins, guided by signal sequences.
What role does SRP (Signal Recognition Particle) play in the signal hypothesis?
SRP pauses translation and recognizes the signal sequence.
What happens to the signal sequence after SRP recognition?
It is inserted into the ER membrane.
What is the typical length and structure of signal sequences?
15-60 amino acids long, with a degenerate sequence.
What features are found in a signal sequence?
1-2 positively charged residues on the N-terminus.
A central hydrophobic alpha-helical domain.
A C-terminal cleavage site for signal peptidase (no specific motif).
How does the SRP and signal sequence interact with the translocon?
SRP binds the signal sequence and guides the protein to the receptor.
The signal sequence is inserted sideways into the membrane.
How are hydrophobic segments handled by the translocon?
They remain in the translocon long enough for evaluation of their properties (e.g., hydrophobicity and membrane compatibility).
What happens if a hydrophobic segment is compatible with the membrane?
The translocon opens sideways to release the protein’s transmembrane (TM) helix into the membrane.
How does the translocon select TM segments?
Through the concerted action of the translocon and lipid bilayer, using physiochemical partitioning.
What drives the diversion of membrane segments through the translocon?
Favourable free energies (delta Gs) inside the membrane.
How does the U-shaped structure of the translocon contribute to TM segment insertion?
It diverts membrane segments through an exit by physiochemical partitioning.
How do ribosomes and translocons collaborate in co-translational translocation?
The ribosome synthesizes the protein while the translocon facilitates its translocation into or across the membrane.
What must the translocon distinguish during co-translational translocation?
Soluble proteins and membrane proteins.
What determines the selection of transmembrane (TM) segments by the translocon?
Free energy changes.
What is the role of the translocon in co- and post-translational translocation?
It is a universally conserved structure that works with ribosomes for co-translational translocation in the ER membrane.
How must membrane proteins match the character of membranes?
Hydrophobic segments match the hydrocarbon core.
Membrane thickness complements the protein structure.
How does the ribosome and translocon read hydrophobic signals?
Hydrophobic segments slow down translation, allowing physiochemical partitioning into membranes.
What is the “positive inside rule”?
Positively charged residues (Lys, Arg) are found in cytosolic loops, determining protein topology.
How do signal peptides match membrane characteristics?
Hydrophobic segments match the hydrocarbon core.
Positive charges on signal peptides align with the negatively charged phosphatidylserine (PS) on the cytosolic face of the membrane.
What processes occur in the ER during protein passage?
Folding and assembly
Specific proteolysis
Disulfide bond formation
Glycosylation
Which side of the protein undergoes glycosylation in the ER?
The side not exposed to the cytosol.
What are the main functions of the Golgi during protein processing?
Folding, assembly, and glycosylation.
What percentage of eukaryotic proteins are glycosylated?
~50%
What is the precursor for glycosylation in the ER?
A 14-mer oligosaccharide linked to dolichol.
What sequence is recognized by oligosaccharyl-transferase for N-glycosylation?
The Asn-X-Ser sequence.
Where does N-glycosylation occur, and how does it differ from O-glycosylation?
N-glycosylation occurs in the ER and links to NH₂ groups of Asn.
O-glycosylation occurs in the Golgi and links to OH groups of Thr or Ser.
What are the primary functions of glycosylation?
To protect proteins and assist in protein folding.
How does the prevalence of N-glycosylation compare to O-glycosylation?
N-glycosylation is more common, occurring in 90% of cases compared to 10% for O-glycosylation.
What role does calnexin play in the ER?
Calnexin retains incompletely folded glycosylated proteins in the ER by binding to specific glucose residues.
How are unfolded glycosylated proteins processed in the ER?
Some glucose residues are trimmed to facilitate folding and interaction with chaperones like calnexin.
What determines the A, B, and O blood types?
Glycosyl-transferases add specific monosaccharides to the O-antigen:
A-type: N-acetylglucosamine.
B-type: Galactose.
What are the main protein maturation processes in the ER and Golgi?
Glycosylation, phosphorylation, and complex assembly.
What protein folding processes occur in the ER?
Disulfide (S-S) bridge formation
Specific proteolysis
Glycosylation
What ensures proper folding of hemagglutinin in the ER?
Binding of BiP chaperone
Calreticulin and calnexin
PDI catalyzes the formation of 6 disulfide bonds
How is hemagglutinin processed before becoming mature?
Addition of 7 N-linked oligosaccharide chains and oligomerization.
What is a GPI anchor, and how is it formed?
A GPI anchor is added to proteins by ER enzymes, replacing the TM segment.
It is phospholipase-sensitive and targets proteins to the cell surface.
How do African trypanosomes evade the immune response?
By shedding and replacing their Variant Surface Glycoprotein (VSG) coat, preventing antibody recognition.
What role does GPI anchoring play in antigen switching?
GPI anchors facilitate dense packing of VSGs, hiding conserved regions from immune detection.
What is the function of scramblase in the ER membrane?
Scramblase flips lipids non-specifically, disrupting membrane asymmetry.
How does flippase differ from scramblase?
Flippase flips specific lipids to maintain membrane asymmetry.
It requires energy and functions only in live cells.
How does phosphatidylserine flipping signal cell death?
Scramblase flips phosphatidylserine to the outer membrane leaflet, which macrophages recognize to trigger phagocytosis.
What determines the partitioning of membrane proteins during translocation?
Membrane character/asymmetry and physiochemical partitioning, along with the positive inside rule (for membrane protein topology).
What are the main pathways for protein and lipid maturation in the cell?
The ER and Golgi pathways process secreted and membrane proteins, and lipids, involving modification such as glycosylation.
How do glycosylation processes contribute to blood types?
Glycosyl-transferases add specific monosaccharides (e.g., N-acetylglucosamine for A-type, galactose for B-type) to the O-antigen, determining blood types.
How does the flu virus use glycosylation in its lifecycle?
Hemagglutinin in the flu virus undergoes glycosylation, aiding proper folding and immune evasion.
What role do membrane anchors play in diseases like sleeping sickness?
GPI membrane protein anchors are used by trypanosomes to evade immune detection by continually switching their surface antigens.
How is membrane asymmetry a signal for life?
The flipping of phosphatidylserine to the outer leaflet by scramblase signals cell death, which is recognized by macrophages.
What are the three main types of filaments in the cytoskeleton?
Microtubules
Intermediate filaments
Actin (microfilaments)
How are the three types of filaments in the cytoskeleton organized in cells?
Microtubules: form a spider-like network.
Intermediate filaments: form a disorganized structure.
Actin microfilaments: located around the cell’s edge.
Why does a cell need a cytoskeleton?
To:
Maintain cell structure (e.g., organelle positioning).
Maintain cell shape and asymmetry (e.g., neurons, RBCs).
Maintain cell polarity (e.g., epithelial cells).
Allow for movement (e.g., intracellular transport, cilia, flagella).
How is the cytoskeleton dynamic in cells?
The cytoskeleton is highly dynamic, changing quickly for processes like amoeboid movement and phagocytosis, but also stable to maintain shape and polarity.
How are filaments in the cytoskeleton regulated?
Filaments are made from small protein subunits, organized into polymers, and tightly regulated in time and space to allow dynamic responses and stability.
What does critical concentration (Cc) refer to in filament dynamics?
Critical concentration (Cc) is the point of equilibrium that determines when a filament is being built or broken down in the cell.
What techniques are commonly used to study actin polymerization?
Sedimentation
Fluorescence microscopy
Fluorescence spectroscopy
Viscometry
What toxins can affect actin polymerization and how?
Phalloidin stabilizes filaments.
Cytochalasin D and latrunculin promote depolymerization.
Why is there a 10x growth difference for the two ends of actin filaments?
ATP hydrolysis occurs after addition of actin∙ATP at the (+) end.
Association rates are 10x higher at the ATP (+) end than the ADP (-) end, due to structural differences in actin∙ATP and actin∙ADP.
More actin∙ATP is available in the cell (due to profilin).
Dissociation rates are similar at both ends.
How does ATP hydrolysis power treadmilling in actin filaments?
ATP hydrolysis affects the critical concentration (CC) of actin, driving the dynamic treadmilling process.
Cofilin binds actin filaments between actin∙ADP subunits, destabilizing them and promoting filament breaking, which creates new (-) ends.
Profilin binds G-actin and catalyzes the exchange of ADP to ATP, promoting filament growth at the (+) end.
How does the cell maintain a pool of soluble G-actin?
The cell has a large pool of G-actin (100-400 µM total, 50-200 µM unpolymerized).
The critical concentration for F-actin formation is 200 µM.
Thymosin-β4 sequesters G-actin to inhibit premature polymerization.
How is actin filament growth regulated?
CapZ caps the F-actin (+) end, with high affinity, preventing further assembly.
CapZ is inhibited by PIP signaling, and other proteins can protect the (+) end from capping.
Tropomodulin caps the F-actin (-) end, stabilizing filaments in cells such as RBCs and muscles (with tropomyosin).
What is the rate-limiting step in actin filament formation?
Nucleation is the rate-limiting step.
Which proteins are involved in nucleating actin filaments?
Formin: Nucleates and elongates long actin filaments (e.g., muscle filaments, stress fibers).
Arp2/3 complex: Nucleates branched actin networks and requires activation by a nucleation-promoting factor.
How does Formin promote actin polymerization?
Formin has two subunits, FH1 and FH2.
FH2 dimers bring two G-actin molecules together for nucleation.
FH1 binds the profilin∙actin∙ATP complex, and FH2 adds G-actin to the growing filament.
What are the main Rho family GTPases involved in actin polarization?
Rho
Rac
Cdc42
What role does PIP signaling play in actin polarization?
PIP signaling regulates actin filament formation and dynamics in coordination with Rho GTPases.
What are the roles of GEFs, GAPs, and GDIs in RhoGTP regulation?
GEFs (Guanine nucleotide exchange factors) catalyze nucleotide exchange, activating RhoGTP.
GAPs (GTPase-activating proteins) stimulate GTP hydrolysis, inactivating RhoGTP.
GDIs (Guanine nucleotide exchange inhibitors) extract inactive RhoGTP from membranes.
How does RhoGTP influence contraction?
Rho activates p160Rho kinase, which mediates cell shape changes through actin/myosin interactions.
Smooth muscle contraction regulates blood circulation.
Endothelial cell contraction facilitates extravasation of blood cells into surrounding tissues.
What is the role of RhoGTP in phagocytosis?
RhoGTP regulates actin polymerization for the internalization of particles and microorganisms.
Cdc42 and Rac induce actin polymerization.
Rac associates with p67phox (NADPH oxidase) to stimulate superoxide production, which is bactericidal.
How does RhoGTP affect secretion in cytotoxic T cells?
RhoGTP re-orients the microtubule cytoskeleton, enabling the targeted delivery of perforin-containing granules to the target antigen-presenting cell (APC).
Cdc42 is essential for establishing cell polarity, which is crucial for secretion.
What is the role of RhoGTP in cell division?
During G1 phase, Rho prevents expression of the G1 cyclin/Cdk inhibitor p21.
Rac and Rho promote transcription and translation of cyclin D.
Rho and Cdc42 are required for the assembly of the actin-myosin contractile ring, which is essential for daughter cell separation.
What is the structure and critical concentration (CC) of F-actin?
F-actin has a 10 nm diameter and a repeat length of 72 nm, composed of 14 subunits.
Critical concentration (CC) for F-actin formation:
CC- (minus end) = 0.6 µM
CC+ (plus end) = 0.1 µM
CC+ when capped by CapZ = 0.6 µM
What toxins affect actin polymerization?
Phalloidin stabilizes filaments.
Cytochalasin D and latrunculin promote depolymerization.
How is actin polymerization controlled?
Profilin binds G-actin∙ADP and catalyzes ADP/ATP exchange, promoting polymerization at the (+) end.
Tropomodulin stabilizes the (-) end, especially in RBCs and muscles (with tropomyosin).
Cofilin destabilizes actin filaments by binding F-actin∙ADP, leading to filament breaking and more free (-) ends.
What proteins regulate actin nucleation and growth?
Formin protects from CapZ binding, brings two G-actin molecules together for nucleation, and promotes elongation by binding the profilin∙actin∙ATP complex.
Arp2/3 complex creates branched networks of actin filaments.
Both processes are regulated by Rho family GTPases (Rho, Cdc42, Rac) and PIP signaling.
What is the structure of microtubules and their formation?
Microtubules are composed of α/β-tubulin dimers (55 kDa).
Microtubule-associated proteins (MAPs) assist in their stabilization and function.
Tubulin adds to the + end of the microtubule.
GTP hydrolysis regulates microtubule structure.
13 filaments assemble into a sheet, forming the microtubule structure.
What toxins affect microtubule dynamics?
Taxol inhibits depolymerization of microtubules.
Colchicine and nocodazole inhibit polymerization.
How does dynamic instability of microtubules occur?
Microtubules undergo dynamic instability, where they abruptly transition from growth to shrinking.
This is regulated by GTP hydrolysis in the β-tubulin subunit:
GTP-bound β-tubulin promotes growth.
GDP-bound β-tubulin is associated with shrinking microtubules.
Why is microtubule nucleation energetically unfavorable?
Microtubule nucleation is energetically unfavorable and does not occur spontaneously in cells.
It requires a Microtubule-organizing center (MTOC) to catalyze the process
What role does the MTOC play in microtubule assembly?
The MTOC anchors the (-) end of microtubules and facilitates nucleation.
The centrosome (a type of MTOC) is located near the nucleus and organizes microtubules into a radial array for organelle transport.
During mitosis, the two centrosomes act as spindle poles.
What are the characteristics of microtubules?
Microtubules form long, polar tracks up to 20 µm in length.
They bind motor proteins for organelle transport and can be bundled to form structures like cilia and flagella.
How do kinesin and dynein motors differ in their functions?
Kinesin motors mediate anterograde transport, moving cargo toward the (+) end of microtubules.
Dynein motors mediate retrograde transport, moving cargo toward the (-) end of microtubules.
