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Nanochemistry

Nanochemistry

by amperka9, Dec. 2012

Subjects: Nanotechnology

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	How can you regulate /protect protein activity?	Placeing an molecule close to active site, which can block/release active site.
	What is very important requirement modulating an molecule activity?	-effectiveness of the reaction -selectivity of the reaction
	Which three types of chemistry there are?	-covalent enzymatic -covalent chemical -non-covalent attachment.
	What are the nucleophiles?	They have free electronpaires that they can donate and can be used to attach the species that have lack of electrons ( electrophiles ).
	Which avalaible conjugation handles there are?	Acid, hydroxy, thiol, amine
	Which of the two nucleophiles are the most important?	Amine , thiol (strong nucleophiles) Lysines and the N terminus of cysteines are that nucleophilic places.
	What are the problems of alkylation reaction?	nucleophiles can react with other electrophiles cysteines are not so abundant as lysines are thiol reaction is 100x efficient than amine reaction.
	Why is N-hydroxysuccinimide (NHS) popular?	Mechanism acylaiton: NHS ester selective towards amines Reasonably stable and easy to make Negative: Susceptible to hydrolysis Multiple lysines result in multiple modifications and loss of function
	How can we Protect the active site/biological activity?	bracnhed PEG molecule - biotin into avidin + PEG-NHS. This binds on all NH2 groups on avidin. This is called pegylation: -reduces immunogenicity -reduces renal clearance
	How can we destinguish between lysine amine and N term amine?	Reductive alkylation: By changing the pH, or by looking at pH. Lower pH prevents the addition of lysine due to protonation.
	Why is Thiol chemistry very popular?	Thiol is a strong nucleophile Cysteines are much less abundant than lysines Only few cysteines are not locked in cystine bridges and therefore reactive Cysteines can be easily introduced via site-directed mutagenesis Thiols are highly versatile and selective chemical handles
	What do thio esthers ?	react with cysteines.
	What do native chemical reaction?	creates natural peptide bond; works only with cysteines only at N terminus.
	How to fool Amynoacyl tRNA synthetase?	deplete all the amino acids with the bacterium so only the aa of interest will be incorporated Necessary: auxotroph strain (cannot produce amino acid itself) Mutation of tRNA-synthetase also possible Multisite replacement
	Azide: most popular moiety to introduce	tine modification does not reacts with any functionalities inside the system ( its stable ) its only reacts with very specific reaction particles azides are involved in staudinger reaction. Azides can specifically and selectively react with phosphines and alkynes
	Which reaction is possible between azides and alkynes?	click reaction, beneficial effect of Cu(I) on the reaction rate The reaction readily proceeds at room temperature The reaction is completely regioselective, favoring the 1,4-adduct
	Which enzymatic methods there are?	Human O6-alkylguanine-DNA alkyl transferase (hAGT) -DNA repair enzyme (19 kDa) - Forms covalent alkyl bond with O6-alkylguanine -Irreversible reaction -Broad substrate tolerance
	What is sortase A and in which reactions it can be involved?	Sortase A: transpeptidase from staphylococcus aureus Natural function: linking proteins to the cell wall Target sequence in proteins: LPXTG Target sequence in cell wall: Tetra- or penta-glycine
	Which non-covalent strategies there are?	Biotin-streptavidin binding: 4 binding pockets on streptavidin (2 on each site) Kd = 10−14 mol/L Almost covalent attachment Biotin can effectively be conjugated via carboxylic acid Extensively used in bio-assays Ni-NTA(Nitrilo Triacelic acid) His(Oligohistidine) tag interaction Extensively used for protein purification Easily introduced in proteins Relatively weak interaction: Kd = 10−6 mol/L Useful for reversible conjugation
	How can you improve S:N ratio?	Various techniques exist to improve the S:N ratio by decreasing the detection volume
	What can you do with none/modified molecules?	non modified: procedures, adsorption, entrapment modified: covalent chemical bond, via receptor ligand interaction, enzyme catalyzed.
	How to characterize a procedure?	covalent / non-covalent > stability of established bond random / site-specific > controlability selective / non-selective > purity of biomolecule used monolayer / multilayer / network >surface density/accessibility biocompatibility - non specific binding / activity
	Name 3 frequent problems by immobilization?	• stability of the modification • inaccessibility of the binding site • inactivation of the binding site
	What is adsorbtion?	Adsorption is the adhesion of atoms, ions, or molecules from a gas, liquid, or dissolved solid to a surface. (by ionic interactions!) non-covalent random non-selective low biocompatibility
	Give the examples of crosslinkers?	heterobifunctional, „short“ (SMCC) homobifunctional, cleavable (DSP) heterobifunctional, long hydrophilic spacer (NHS-PEG-maleimide)
	How the molecules can be labeled? ( covalent attachment of small molecules)	NHS-LC-fluorescein attachment maleimide-xxx-biotin
	Which covalent immobilization methods there are?	modification of silicon oxide surfaces with silanes silane with one hydrolyzable group silane with three hydrolyzable groups
	How does covalent immunobilization with silanes works?	hydrolysis > crosslinking > hydrogen bonding to the surface > bond formation .
	How can we improve biocompatibility of silanization with mono - reactive silanes?	with PEG spacers (PEG: poly (ethylene glycol) long, hydrophilic & biocompatible spacer
	Covalent assembly of self assmbled monolayers on gold?	R-SH thiol containing molecule binds on gold surface.
	Which interactions there are in receptor ligand recognition?	hydrogen bonds ionic interactions van der Waals interactions hydrophobic interactions reversible & specific
	What is strongest covalent bond known and how does it work?	(strept)avidin-biotin attachment of the tag at N- or C-terminus (site-specific!!!) coexpression of biotin ligase *addition of biotin to the expression medium
	Which other receptor ligand interactions there are, describe briefly.	Ni2+ - NTA - his tag Antibody antigen surface binding peptides genetically engineered proteins for inorganics (GEPI) 7 – 20 amino acid long peptides selected from libraries attached to protein of interest as N- or C-terminal tag bind to gold, semiconductor materials, metal oxides, glass,... different surfaces require different peptide sequences
	What is the summary of receptor-ligand interactions?	non-covalent bond might be relatively weak normally site-specific (multivalent binding partners?) highly selective for the binding partner multilayer formation with multivalent binding partners high biocompatibility interaction can also be used for detection and purification *often require the previous immobilization of the receptor
	Immobilization via enzyme-substrate (inhibitor) reactions and enzyme catalyzed coupling?	* a biomolecule binds to a surface bound inhibitor. This binding is covalent) *Two parts of the biomolecule ( one covalently attached to the surface other is not) bind togather. With the help of an enzyme the fully assembled molecule loses its covalent attachement.
	How does formation of covalent adducts hAGT works?	hAGT ( DNA repair enzyme ) forms covalent adduct with alkyl chain upon reaction reaction is irreversible => every hAGT performs only one reaction low substrate specificity => accepts artificial substrates cutinase can also form covalent adducts.
	How does enzyme-catalyzed coupling with sortase A works?	Sortase A: transpeptidase from Staphylococcus aureus Links proteins covalently to the cell wall... ... by recognizing LPXTG peptide sequences in target proteins followed by covalent attachment to pentaglycine in the cell wall
	What is the summary of enzymatic methods?	covalent bond ensures high stability site-specific and highly selective multilayer formation depending on surface chemistry high biocompatibility (size of the fusion partner?) require the previous immobilization of the substrate! flexible: one fusion protein – many reactions (different dyes, labels, surfaces, polymers,...)
	What are the PLL-PEG-Copolymers?	PLL for adsorption to the surface PEG for “passivation” PEG also introduces functionality
	How can glucose oxidase be encapsulated?	in a liposome
	Which biosensors there are?	electronic detection of blood glucose levels using glucose oxidase
	How could you improve on the methods of immobilization?	Of all the problems mentioned and discussed, the main issue remains the reversibility of the Michael reaction. The simplest option to circumvent this problem is by using irreversible coupling strategies. For this the more recently developed click chemistries could be useful, e.g. the coupling of azides to (strained) alkynes will lead to a permanent fixation of the analytes on the surface
	What are the principles of fluorescent microscopy?	Excited filter, selects light which excites molecule from low state to excited state. ( excited filter is required when we use white light or several wavelenghts for excitation.
	Which popular fluorophores there are?	Oregon green, Bodipy maleimide Alexa488
	Which important spectral characteristics there are?	Extitation spectrum Emission spectrum Stokes shift Quantum yield Molar extintion coefficient Enviromental dependence of all these above mentioned characteristics.
	How can enviroment have an impact on fluorophore?	Quenching/increase of fluorescence by DNA binding.
	Which wavelenghts penetrate tissue the best?	red. So hemoglobine absorbs a lot of red, but also water, because there is a lot of water in our body.
	What are the advantages of nanoparticles probe design?	protective matrix • tuning of molecular environment • increase of signal intensity • focal signal Unlimited degrees of freedom in the generation of nanoparticle. linkage chemistry polymer matrix *size of particle.
	Where do quantum dots consist of?	coat ( organic polymer ) Shell (ZnS) Core ( e.g CdSe) quantum dot is a semi conductor vary the diameter of the qd, the larger qd, the larger wavelengts it will emmit.
	What is the major challenges of quantum dots?	to put an organic shell around a qd to help to interact of qd with the enviroment. overlap ex. vs emm. spectrum problem in fluorophores.
	How the macromolecules come into tumor from the bloodstream? How does this phenomen called?	Tumor endothelium is not well structured. This is called EPR - enhanced permeation and retention. Furthermore tumor tissues can be targeted due to receptor internalization in tumor enviroment. *tumor tissues are slightly more acidic, they use a lot of glycolisis.
	What are liposomal doxoribucine?	It works by intercalating DNA, with the most serious adverse effect being life-threatening heart damage. It is commonly used in the treatment of a wide range of cancers. there is a short window of having doxoribucine it the bloodstream ( its toxic ) so giving a small pulses of doxoribucine injections
	Which quantum dots modifications there are?	QD capping ligand TOPO (coating) polymer coating ( coating) PEG (surface) affinity ligands (surface)( antibody, peptide, small molecule drug, inhibitors) *
	What is major advantage of QD t.o.v other fluorophores?	QD are not bleacheble.
	How non covalent coupling of protein to QD works?	coupling through nitrilo-triacetic acid.
	What are the chimeric designs of QD with other proteins?	Qdot-GFP conjugates. coupling of the FP by standard amino-group to carboxy-group coupling FRET change is not the result of a conformaJonal change but of the absorpJon characterisJcs of the FP
	Why is GFP signal reduced in cells after some time and QD not reduced?	*GFPs are go to late endosomes ( low pH) >>> less signals.
	Which ways of loading of molecules into cells theare are?	Direct transfer -microinjection Carrier mediated transfer -protein transduction -Liposome mediated treansfer -microprojectile bombardement Transfer by pm permeabelization *SLO permeabelization Transient masking of charged drugs. Prodrugs. ( when the drug reaches the target it will activate itself)
	How is PEGilated QD particle will enter the tumor?	MMP( matrix metalo proteases) of tumors cleave the PEG and only then QD can enter the cell.
	How is resolution limited? How is the best resolution achieved?	Interference of light waves does not allow us to go to max resolution. The smaller the size of light path, the larger the angle of constructive interference. For good resolution we need to capture the light on the much big angle as possible. Because then you can detect the interference maxima of small objects. In optics, the numerical aperture (NA) of an optical system is a dimensionless number that characterizes the range of angles over which the system can accept or emit light. N.A = n*sin(a) n= diffractive index of the medium in between. a = de hoek van inval. Larger N.A > wider angle.
	What is total internal reflection? How can we avoid TIR?	Total internal reflection is an phenomenon that happens when a propagating wave strikes a medium boundary at an angle larger than a particular critical angle with respect to the normal to the surface. If the refractive index is lower on the other side of the boundary and the incident angle is greater than the critical angle, the wave cannot pass through and is entirely reflected. Medium between the front and cover slip should be similar to medium from which the lens is made. ( glass) The critical angle is the angle of incidence above which the total internal reflectance occurs.
	By what is resolution determined?	by the numerical apperture of the lens.
	What is the principle of working of confocal microscope?	Light coming from focal plane falls on pinhole. This light will be detected by detector. The overall light does not pass a pinhole. (200 nm resolution)
	What is deconvultion?	calculate how much signal in one plane comes from neighbouring planes.
	How can we really improve resolution?	play tricks on light ( TIRF,SNOM) exploit photophysics
	What is TIRF?	Fluorescence decreases with penetration depth. So we have very restricted layer on the surface of water, where we excite fluorophores. BUt you can not see internal fluorescence inside cell. The evanescent wave is generated only when the incident light is totally internally reflected at the glass-water interface. The evanescent electromagnetic field decays exponentially from the interface, and thus penetrates to a depth of only approximately 100 nm into the sample medium. Thus the TIRFM enables a selective visualization of surface regions such as the basal plasma membrane (which are about 7.5 nm thick) of cells as shown in the figure above.
	What is near field scanning optical microscopy?	OPtical fiber has tiny window in the tip. This window is smaller than a light wave. Light can not exit it in conventional wave, only in evanescent wave.
	What is 2-photon microscopy? what is the main challenge of 2 photon microscopy?	-two photons are used to excite an electron -these photons need to arrive with very narrow time interval ( main challenge of this technique) -each photon has half the energy, so full energy difference is reached in 2 steps. -the excitation efficiency depends quadratically on light intensity. - 2 photon microscopy can penetrate deeper into tissues ( low resolution- low wavelenghts) -reduced photobleaching ( confined excitation volume)
	Which superresolution methods ( nanoscopy methods) there are?	Ensemble switching methods. -RESOLFT ( Reversible saturable optical fluorescence microscopy) -STED (Stimulated emission depletion) Single emitted switching -STORM ( Stochastic optical reconstruction microscopy) -PALM ( Photoactivation localization microscopy)
	How do STED work?	If we have a fluorophore its excited from ground state to excited electronic states. Which after relaxing back to the ground state emmits photon. ( nanoseconds) . Avoid the excitation of photon by STED excitation 100 picoseconds later. This excitation exactly fits the emission energy of flurophore STED kick out photon from the excited state to the ground state. STED interrupts this process before the photon is released. The excited electron is forced to relax into a higher vibration state than the fluorescence transition would enter, causing the photon to be released to be red shifted. Because the electron is going to a higher vibrational state, the energy difference of the two states is lower than the normal fluorescence difference. This lowering of energy raises the wavelength, and causes the photon to be shifted farther into the red end of the spectrum. This shift differentiates the two types of photons, and allows the stimulated photon to be ignored. -Photobleaching can occur either from excitation into an even higher excited state, or from excitation in the triplet state. - we need to detect multiple fluorophores, find their position, then activate another fluorophores and find their position. -for fixed samples only, -use CCD camera.
	What is PALM?	rapid detection of whole image simultaneous imaging of several molecules. *CCD camera
	What is the conceptually new idea of BaLM in comparison to STORM and PALM?	In STORM and PALM only few individual molecules are switched on at a time and then the position of these molecules is recorded. In BaLM fluorescence from a large number is recorded and the fluorescence from single fluorophore is identified by subtraction of subsequent images.
	What is BALM?	- bleaching/blinking assisted localization microscopy -To detect single fluorophores, we simply acquire a stream of fluorescence images. Fluorophore bleach or blink-off events are detected by subtracting from each image of the series the subsequent image. Similarly, blink-on events are detected by subtracting from each frame the previous one. After image subtractions, "uorescence emission signals from single fluorophores are identified and the localizations are determined by fitting the fluorescence intensity distribution with a theoretical Gaussian. We also show that BaLM works with a spectrum of fluorescent molecules in the same sample. Thus, BaLM extends single molecule-based superresolution localization to samples labeled with multiple conventional fluorescent probes.
	In which way does image acquisition for BaLM need to be different from the one in STORM and PALM?	In STORM and PALM it is sufficient to acquire the image with a resolution equal to the size of the point-spread-function. In BaLM smaller pixel sizes are needed to obtain sufficient signal-to-noise. Furthermore, this helps to avoid saturation of individual pixels. BaLM can tolerate high backgrounds while PALM detects individual molecules in a background-free context.
	What is the advantage of BaLM over STORM and PALM?	BaLM can be done with any fluorophore that bleaches or shows blinking behaviour. There is no need for switching off of all fluorophores before recording of a few.
	Where do you see a potential disadvantage of BaLM over STORM and PALM?	The authors stress that bleaching between subsequent images is used to create the differences. With bleaching, the observation time will be limited.
	Why is BaLM easier to apply for multichannel imaging than PALM?	For each fluorophore, BaLM uses only one wavelength, while depending on the fluorophore PALM needs two wavelength per fluorphore for switching on and off.
	Which reactions with amines there are? (amine/N-terminus)	-Alkylation -Acetylation -Urea formation
	Which reactions with thiols there are?	-Maleimide chemistry -Disulfide exchange -Native chemical reaction
	What is disulfide exchange?	Thiol-disulfide exchange is a chemical reaction in which a thiolate group -S− attacks a sulfur atom of a disulfide bond -S-S-. The original disulfide bond is broken, and its other sulfur atom is released as a new thiolate, carrying away the negative charge
	What is michael addition?	The 1,4-addition (or conjugate addition) of resonance-stabilized carbanions.
	What is native chemical reaction?	Based on a natural protein (intein) splicing process Works only for N-terminal cysteines *Necessary: thioester Advantages: highly selective and specific Disadvantages: thioesther is labile.
	Why do we do conjugation with unnatural functionalities?	* to improve on selectivity * Thiols can lead to undisired disulfide formation.
	How to introduce conjugation with unnatural functionalities?	In proteins: - by chemistry - by replacement of natural amino acids - by extending the ribosomal production with additional amino acids In glycans and lipids: -by metabolism in living cells -by chemical synthesis In oligonucleotides: -by chemical synthesis
	Which aminoacids are introduced in the proteins?	Lysines and cysteines
	Which enzymatic covalent methods there are for formation of covalent adducts?	cutinase hAGT (O6 - alkylguanine DNA alkyltransferase *Enzyme catalyzed coupling with sortase A
	Which directed and oriented immobilizations there are?	DNA directed immobilization Immobilization using BSA foot
	Describe microarrays.	sample miniaturization (about 400/cm2) parallel handling of many samples identity is identified via position ( a key feature of microarrays) very efficient probing of a cell‘s response to different environments *no dimensions smaller than those of a cell
	What are the examples of microarrays?	Protein microarray :application identification of antigens. Proteins bind on the antigens on microarray. Then only phosphorylated proteins are bound by second antibody with a fluorescent label. Cellular microarray: 1) testing of different stimuly in cellular microarrays. 2) siRNA screening : needle array. A needle is doped in the water ( to release a compoud). Little flexibility in spacing , volume. But they are still high parallel.
	What is the compound to make soft lytography?	PDMS: organosilicone inert non-toxic non-flammable * controlled polymerization crosslinker and curing agent determine the stifness of PDMS PDMS creates microchannels when you put it on top of other material. Creation of microgradient: (BSA + laminin) ( design a structure with computer use PDMS to use microfluidic of certain geometry, GeneraIon"of"microchannels by linking"PDMS"to"glass) PDMS can attach biomolecules in quite dry fashion ( put it on glass, press lytography). These biomolecules attract very well. Problems: PDMS structure is to soft > structure collapse Limitations of signals of photoresist >>> changing characterization of PDMS to avoid this problem. Introduction of silanon groups to PDMS. Silanon groups can condense. So you can bind PDMS strong to surfaces.
	What is the model of TCR-MHC binding?	Clustering changes the kinase-phosphatase equilibrium
	What is the experimental design of studying the TCR-MHC interactions?	Surface is covered with barriers. Lipid films can form inbetween the barriers. Integrins can move free in the bilayer but not between the barriers. The cell can bind on this surface on MHC, ICAM by TCR. GPI anchors are also present in the layer. Furthermore there is an fluorescent molecule ( FAB fragment + fluorescent molecule) bind on one site of the AB, so AB can not crosslink. Outcome:tyrosine phosphorylation occurs before receptor clustering
	What did this study revealed?	There is a driving force of signaling clusters towards the center of the contact zone (independent of the APC) Clustering down-regulates signaling Clusters are not preformed Signaling intensity within a cluster is position-dependent
	A photolithographic strategy to achieve equal immobilization in contact and periphery	1) Photomask is degraded with UV 2)Deposit biotinilated antibodyes, they will be deposited on different layers 3)If you wash the surface with a certain pH, then the highest layers will be removed, so only AB bound to lower layers remain. 4) Now you can deposite the AB of interest on the lowest level, so you have bound different antibodyes in a certain ration,position fasion on a plate.
	What is negative photoresist?	Those structures that are exposed to light are insoluble.
	What are the bifunctialized surfaces?	Features: -transfer to homogenous monolayers -99% of the molecules are adhered to the stamp are being transferred to the substrate -usually no denaturation of proteins -hardly any drying effects problem: different maintance of functionality of printed and coated protein.
	What is the application of silanon with PDMS?	Silanon groups attached to PDMS. Silanon groups can condence. So you can bind strong PDMS to surfaces.
	Which self-assembled monolayers there are?	-alkanthiols on gold -silanes on glass
	What is geometric model of integrin crosslinking?	The distance between the integrin binding proteins should be less than 70nm, otherwise integrin will not attach. Ordered positioning of complexes gives less clustered integrin that disordered positioning.
	What do single molecule measurmenets allow us to do?	do not avarage over whole population require no synchronization to measure time dependent phenomena allow observation of spatial / temporal heterogenities. provide oportunity to directly manipulate molecule of interest
	What is the intensity of Raman scattering?	scattering of other molecules interacts with your measurments. Thats why small volume is better to use when making a measurment.
	What are the free energies of unfolded vs folded proteins?	unfolded - large free energy folded - small free energy
	How to estimate folded or unfolded state?	Fluorescence of tryptophane, where is it inside or outside the cell?
	How to describe free energy and stability of a protein?	free energy: delta G = RT ln(Keq) stability: stability= - RT ln(Keq)
	What are the stopped flow kinetics?	you mix 2 solutions relative quickly, so they can be measured very fast by the spectrometer. requires large volumes requires high concentrations *dead time in ms range
	What is FRET?	forster resonance energy transfer: one fluorophore should have emission spectrum which overlaps with absorbtion spectrum of fluorophore. FRET is very sensitive to distance changes it is ideal tool for measuring distances in nm scale donor-acceptor-emission occurs at distances between 2 and 10 nanometers. non radiative energy transfer
	Single molecule protein folding measured with FRET? what are the outcomes?	folded protein- high FRET , narrow distribution unfolded protein - low FRET , wide distribution unfolded protein > flexible chain that can move around so more wide distribution of fluorescence signal by FRET. Lower FRET efficiency.
	What are the microfluidic mixing?	fast, efficient. Need high protein concentration to achieve more stability of the protein, low concentration - protein starts to unfolding.
	Describe Michaelis MEnten kinetiks?	Km - stability of the enzyme substrate complex Kcat - rate for the chemical step ( accurate enzyme conc. is needed to measure Kcat) v = (Kmax * [Substrate]) / (Km + [substrate] ) with V max = K cat * [enzyme] Km= k(-1) / k1
	What is single turnover detection?	enzyme is covalent coupled to a surface, which can process substrates. volume 0.1 fl - determine which of the spikes are ternovers and which are the noice.
	How is dataanalysis for turnover works?	waiting time t(off) distribution stretched exponential P(t(off))=e^(-t/pi)^a a = stretched exponential term, if a gets smaller , the curve get exponential. data analysis is done by 2D correlation graphs. long/short turnover is subsequently followed by long/short turnover
	What are the explanation of existent turnover kinetiks?	enzymes are ensembles of different conformers. factor modifying the energy landscape of the enzyme
	How do you electronically detect enzyme activity with carbon nanotube? Describe carbon nanotube biosensor? (ofwel CNT-based field effect transistors (CNT-FETs).	Current flows from source to drain. This makes the switch. Electrode in the liquid solution. Charging potential in the liquid gate, changes current in nanotubes. Replace the semiconductor by carbon nanotube. Its sensitiy to gate potential and also changes in enviroment. Small detection volume. Apply current with AFM to destroy the carbon nanotube you do not need. Enzymes immobilized on nanotube. Addition of substrate gives some current.
	How can we know that carbon nanotube is modified?	Oxidize one ring of CNT, it will introduce a point defect in nanotube. Carboxilic acid will be introduced which reacts with ADC, which later hydrolyzed and you get carboxilic acid again. This switching does not happen without ADC. DNA also can be dybridized to the point defect. Measure DNA kinetics. DNA is charged so it changes the conductance of nanotube.
	When een enzyme processes an substrate on a nanotube, why does it lead to conductance change?	enzyme undergoes a conformational change, changed aa's on the surface are rearranged so it leads to conductance change.
	What is sanger sequencing?	The Sanger (chain-termination) method for DNA sequencing. (1) A primer is annealed to a sequence, (2) Reagents are added to the primer and template, including: DNA polymerase, dNTPs, and a small amount of all four dideoxynucleotides (ddNTPs) labeled with fluorophores. During primer elongation, the random insertion of a ddNTP instead of a dNTP terminates synthesis of the chain because DNA polymerase cannot react with the missing hydroxyl. This produces all possible lengths of chains. (3) The products are separated on a single lane capillary gel, where the resulting bands are read by a imaging system. (4) This produces several hundred thousand nucleotides a day, data which require storage and subsequent computational analysis.
	What is pyrosequencing?	read the sequence by polymerase. Release of phosphate which can be converted in ATP, which can be detected by luciferase. You should delete all previous nucleotides after they were detected. This is done by an enzyme.
	What is shut gun sequencing?	sequence small pieces of genomic DNA, then assemble overlapping pieces.
	How do sequencing in zero mode waveguides work?	Fluorescence molecules are buld in by polymerase. Optical detection from the side where the enzyme is attached to the surface. ( van de onderkant) Increased noice to signal ratio: The holes in ZMW are small, so you get evanescent field > smaller detection volume, higher fluorophore concentration. Important for sequencing reaction. detection volume: attoliter fluorophore concentrations: micromollar even less bright fluorophores can be used.
	What is the experimetal setup in ZWM?	fluorescently labelled nucleotides polymerase immobilized at the bottom of ZWM polymerase molecules are statistically distributed in the holes ( Poison distribution) template is ssDNA sequencing by synthesis detection of many holes in parallel with CCD camera.
	What is the basic principle of sequencing through nanopores?	An exonuclease is attached to the nanopore The exonuclease cleaves off individual bases sequentially The cleaved base is released into the nanopore A hairpin at the end of the DNA strand allows sequencing of both the forward and the reverse strand *a nucleotide falls into the pore, where the current is measured so it can be estimated which nucleotide it is.
	What are the parameters used in nanopore? ( sequencing by hydrolysis) = exonuclease sequencing	sigma I: dwell current amplitude t(d): dwell time in pore delta t: waiting time between events the thickness of nanopore is the most crucial parameter. The thinner the pore, the better the signal to noice ratio. But also the diameter is important.
	Which enzyme used by the sequencing in nanopores?	pfi-29 polymerase. Highly processive enzyme, is attached to nanopore, DNA is directly inserted into nanopore. A hairpin at the end of the DNA strand, allows sequence of both forward and reverse strand.
	What are the basic principes of scanning tunneling microscopy?	A conducting tip and surface are separated by a finite distance (typically 0.2 - 0.5 nm). This distance forms uniform potential barrier. The electron wave function can tunnel through the barrier leading to a finite current which is called tunneling current. *The tunneling current flows between the tip and the sample when a DC bias voltage is applied (exponential distance dependence).
	How does tunneling in STM exactly works?	Electron with A(1)=amplitude1 passes a barrier of width (d). After the electron has passed the barrier, its amplitude has decreased, that means that the probability of finding the electron in this "place" is lower. The transmission coefficient (i.e. the probability of an electron penetrating the barrier), is found to decrease exponentially with the barrier width (d)
	What is error signal calculation in STM?	The distance between the tip and the surface will change, the current changes as well. The tip is always adjusted so the current stays constant.
	What does the signal tells you in STM?	shape of the atom, electron density of the atom.
	What are the applications of STM?	imaging surfaces with atomic resolution - Si111 imaging organic monolayers on conductive surfaces *moving & positioning atoms
	What is the set up of AFM?	The AFM detects vertical and lateral forces acting between a small tip (attached to a cantilever) and the sample/surface. These forces are detected by the altered deflection of a laser beam when the cantilever is bent or twisted. *As with the STM atomic resolution is possible for stiff samples.
	What determines the lateral resolution of AFM?	The shape of the very end of the tip determines the lateral resolution!
	Does the tip of AFM resonate?	-yes -In liquid the resonance frequency shifts to lower values (viscous damping) and the peak becomes broader (Brownian motion).
	Which forces acting between the tip and surface in AFM?	repulsive component: Pauli exclision principle attractive component: van der waals interactions. -There are strong attractive capillary forces ( resulting from water meniscus, several nN). -Attractive and repulsive interactions affect images, use both imaging modes, to get a good idea of how the sample on the surface looks like.
	Which AFM scanning modes there are?	contact mode tapping mode *true non-contact mode
	Describe contact mode?	the tip is in contact with sample the cantiliver is operated below its resonance frequence the feedback is used to keep the deflection/force on the sample constant The spring constant k of the cantilever is smaller than k of the sample. + high resolution - friction forces lead to damage of the sample and the tip
	Describe the tapping mode?	The tip is touching the sample with a certain frequency. The cantilever oscillates close to its resonance frequency The feedback is used to keep the oscillation amplitude constant In air k needs to be high (liquid meniscus), in liquid low k is desired. -*Contact with the sample leads to a change in the resonance frequency and the amplitude and phase of the oscillation. - we need to use different paramets to estimate how surface looks like. + no lateral forces on the sample (less damage) -- sample is hit with a few nN (energy transfer onto the sample)
	Describe the non-contact mode of the AFM imaging?	The tip is not touching the sample at all The cantilever oscillates close to its resonance frequency The feedback is used to keep the oscillation amplitude constant The spring constant k should be low as the forces are very small + no lateral and normal forces on the sample (no damage) - difficult to set up, slow - possible artefacts from water on the surface
	What can be visualized with AFM contact mode?	F0 F1 -ATPase from spinach chloroplasts degradation of a mica supported phospholipid membrane by phospholipase A2 ( enzymes at work) beating cardiocites*
	What are the technical requirements for high speed AFM?	objective-based detection system to focus the laser beam on small cantilevers very small cantilevers with low spring constant and very high resonance frequency *very fast feedback system with high frequency bandwidth, narrow resonance peak and minimized vibrations
	What can we visualize with high speed AFM?	*real-time imaging of myosin on an actin fiber
	What is nanopatterning with AFM?	*surface functionalization on small length scales -nanoshaving (removing molecules from the surface) -deep pen litography (placing molecules on the surface)
	What can we learn from ubiquitin unbinding kinetics?	You get force (Y-as) with loading rate(x-as) diagram. Loading rate - natural logaritm of increase in force. From the sloop the width of the potential "b" can be calculated. Knowing x the intercept with the x-axis “a” yields k(off) (unbinding rate under zero force) deltaX says something about how big the binding pocket is of a protein. delta x is big when the binding pocket is also big. under zero force.
	What is the basic set up of the optical tweezer?	Laser beam goes through two microscope objectives, with a polysterene bead inbetween. Another bead is attached to it and is manipulated with a glass micropitpette. Inbetween 2 beads a DNA molecule is spanned.
	What is the set up of a magnetic tweezer?	the beads are attached by the magnet. There is a camera. The advantage is that you can pull on both magnets. The magnets can be rotated, repulsive forces can also be applied. ( you can rotate ATPase in different directions)
	Unfolding and refolding kinetiks of RNA hairpin?	Keq= % unfolded / % folded
	What is summary of AFM? ( force range, type experiment)	works with forces 20nm> hunderds of Nm. mostly used for unbinding/unfolding experiments (constant velocity mode)
	What is summary of optical tweezers? ( force range, type experiment)	work well in the low force range (0.1 pN to 150 pN) perfect for experiments where constant force is required (constant force mode; force clamp)
	What is summary of optical tweezers? ( force range, type experiment)	force range depends on the magnet perfect for experiments where constant force is required *parallel measurements of many molecules feasible
	Why is it desirable not to have a rectangular cross section in microchannels?	Because cells can sense shape and curvature is an important characteristic of, for example, blood vessels.
	Which shortcomings of PDMS are mentioned and how are they overcome?	- difficult to introduce surface functionalization – incorporation of gold particles into the PEG hydrogel - release of unpolymerized monomers – use of a PEG-(diacrylate) hydrogel-forming polymer.
	Describe the types of nanoparticles?	Metal nanoparticles, Semiconductor nanoparticles Metaloxide / Metalsalt nanoparticles
	Describe metal nanoparticles?	Nanoparticles made by metal: the surface of these particles are very catalitically active. example Pt nanoparticles
	Describe semiconductor nanoparticles:	CdSe is toxic. Fluorescence is long lasting than by all fluorescent dyes.
	Which procedures to make a nanoparticles there are?	precipetation from supersaturated solution (super saturate a solution of salt >>> cristalization chemical reaction (reduction of metal salts) templating: precipitating inside micelles ( organic/hydrophilic solvents are brought togather in a particle) pyrolysis
	How do you stabilize a particle when its growing? How can you control size, shape?	capping agents which bind with one side to growing particle, with the other side they create a stable layer to avoid aggreagtion of particles. You also need to control a size of nanoparticles. (uniformity) Smaller particles start to grow faster than big particles. Different shape of a particle by varing concentrations. Fast growth prevents rearrangement of metal ion.
	What are the multipod metal nanoparticles?	Reduction of metal salts: Pt multipods via high kinetic growth. ( fast growth prevent rearrangement of metal atom)
	Which nanoparticles there are?	synthetic organic (liposome) micelles and vesicles polymer nanoparticles polymer nanoparticles with host guest interactions natural organic ( protein cages, ferritin) protein clusters ( ribosome 50S subunit) virus Metabolon
	Which non covalent interactions play rol within the nanostructures?	• Van der Waals forces few kJ/ mole • Hydrophobic forces few kJ/mole • dipole-dipole interactions 8 kJ/mole • π-π interactions • Hydrogen bonds 10-40 kJ/mole • Electrostatic interactions 50-200 kJ/mole *Direct forces ( H bridges) can control the kind of structure you can make.
	How is self assembly via hydrophobic interactions works?	Increase the concetration of surfactants ( compound which is active on the surface) in water, by increasing the T(kraft). So all hydrophilic heads come togather to form a micelle. If you do not increase the temperature, the entopy loss of oriented water molecules around hydrophobic molecules takes place. H2O molecules form a mantel around a hydrophobic tale of the micelle. So no micelles forming takes place. The concentration at which micelles start to form is called critical micelle concentration (CMC)
	How do Amphiphilic Self-Assembled Structures depend on critical packing parameter? What is CPP?	N=V/a(c) * I V= volume of hydrophobic part a= optimized head group area I = length of hydrophobic part I (hydrophobic) < I ( hydrophilic ) >>> curve bilayer I ( hydrophobic ) > I ( hydrophilic ) >>> inverted micelles
	How do liposomes made?	* lipids dissolving in organic solvent * deposit lipids in film around bottle * add water, resolubolize > get bilayer structure some of them will close in vesicles ( also in multilamelar structures, many bilayers). Sonicate to get only monolamella structures or you push your vesicle solution through a small holes in the membrane. So they lose their shell so you get monolamella.
	What is the difference between liposome and polymerosome?	p: 15 nm membrane thickness l: 3 nm membrane thickness l: the thicker the membrane the stable the surface would be. If you increase the size of particle, lipids will be more dynamic. p: polymerosome is less mobile, polymers chain do not move easy inside bilayer.
	Which ways to form polymerosome there are?	Polymer solution in organic solvent is dried in on glass substrate; film is hydrated by addition of water @Works with flexible polymer@ • Polymer solution in organic solvent added to water, followed by washing step/filtration step: @Kinetic trapping, less organic solvent exposure of biomolecules@ Water added to an organic solvent containing polymer, followed by quenching: @Thermodynamic procedure, more solvent exposure@
	What is microcapsulle formation by precipitation?	Emulsification of surfactant in water + polymer in dichloromethane + dodecane oil. Evaporation of dichloromethane. Get polymer with inside dodecane oil.
	Ho wdo microcapsule by precipitation work?	polymer dissolved in aquaus core with excess volatile (fast evaporating) solvent. evaporation makes small polymers polymer migrates to the interface complete evaporation results in microcapsule formation. *Different polymer concentrations give different shell thickness
	Block copolymer stabilized nanoparticles?	easy upscale high reproducibility *encapsulation of certain compounds ( drug delivery)
	What is CDP?	CDP can easy complex with RNA(-). Connect adamantine unit with PEG, make adamantine watersoluble. Bind this adamantine-PEG to a surface of polymer(?) , so many of A-PEG can be bound to the surface. Inbetween the PEG on the surface negative charged RNA can bind.
	Host-guest Nanoparticles through hydrophobic interactions there are?	CD: cyclodextrin AD: adamantane Tf: transferrin PEG: poly (ethylene glycol)
	What do Host-guest nanoparticles in clinical trials?	Increase in tumor loading via the Enhanced Permeability and Retention (EPR)* effect (pores ca 100 nm).
	What are the advantages / disadvantages of nanoparticles in medicine?	Adv. - Carrier and reservoir system - Protection against degradation/immune system - Controlled delivery and release Dis: -Size -Cellular uptake -Release mechanisms necessary Spleen and liver filter out nanoparticles. Liver takes out particles from the blood stream. Particles need to be <100nm to escape spleen and liver. Stealth particles with PEG escape clearance by macrophages.
	How do particles are taken up by the cell?	clathrin mediated endocytosis. Clathrin proteins coat a molecule, then these proteins are recycled. TAT derived peptide. Poly aa tail which binds on protein of cell and internalizes a molecule of interest. TAT molecule will stack to cell with electrostatic interactio and then is taken up by marcopinocytosis. Phagocytosis Macropinocytosis ( close a large amount of volume outside the cell. ( not often happens, can take up big particles)
	Which particles are most preferable for cellular uptake?	Small particles of about 25nm, preferable spheres, are most efficient for cellular uptake
	How is self assembly of flat peptide rings work?	Based on H bonding Alternating D and L amino acids *Side chains poin outward These peptide rings form tubes. So these tubes can stick and interact with the memrbane of bacteria. You can create a pore in a lipid bilayer. It stops the bacterial growth.
	How do directed assembly of peptides work?	cysteines crosslinks the structure Gly: make spacers between structures domain and hydrophobic domain. phosphate: water solubility there is also a chemical group that helps for molecule to enter the cell,
	What can promote vascularization in rat chorea?	peptide fiber, with heparin and GF adding into eyes induces vascularization.
	How does TMV assembly works?	1)formation of disks 20S aggregate: 2 times 17 proteins 2)binding to initiation tract, specific sequence on single stranded viral RNA 3)Dislocation of the nucleation disk to a helical structure Ss RNA binds into the disc , the shape of the disc is changed, RNA becomes a little bit screuwd ( there occurs a site where other proteins can nucleate) . The proteins wrap around the RNA. If there is no RNA, the disc becomes aggregated, so they will have uncontrolled size.
	How is CMV assembled? ( footbal shaped virus)	This system can be assembled without RNA. IT all starts with a dimer, under the right conditions ( pH,salt) the structure begins to assemble ( dimers, tetramets). It has two sites finally to bind Ca2+ and RNA. When protein wrap around the RNA, the proteins change their shape, they are bending.
	DNA assembly Interplay between H bonds and π-π interactions.	• Helical stack • 36º conformation space • 10 pairs per turn • right-handed helix • vertical distance 3.4 Å • pitch is 34 Å
	DNA blocks copolymer micelles?	the length of DNA determines which structure are formed. short chains - micelles shaped. MOlecule of interest in the middle, DNA on the surface like needles. Long chains - parallel DNA molecules with a molecule of interest spanned between it.
	What are the leucine zippers?	Leucine zippers regulate DNA transcription. Lysines (+) interact with DNA backbone. 2 helixes - hydrophobic interactions inbetween. There are also aa's in helix, which have + charge, they stick to each other, so leucine zipper come togather. Using these electrostatic interactions they form dimers , trimers, tetramers. Homo-, heterodimers, parallel, antiparallel.
	Where you can apply leucine zippers, beside its natural role in transcription regulation?	Gold nanoparticles covered with leucine zipper. Particles will cluster and form aggregates. leucine mediated assembly of particles.
	What is layer by layer technique?	Glass (+) charge coated with polymer which has (-) charge. YOu can put (+) layer on this layer. Since you compensate charges you build up layer by layer polymer structure. When you use a particle instead of glass layer, you can dissolve this particle after getting a certain amounts of layers. So you get an layer capsule.
	Which nanoreactors there are?	Micelles Virus capsids LbL capsules Polymersomes
	Describe polyion-complex micelles entrapping enzyme molecules in the core? How can you release an enzyme from these particles?	* has ionic domain, hydrophobic and hydrophilic domain. * if you add a cationic enzyme the ionic and hydrophilic part become hydrophobic As result of enzyme binding you get a particle-micelle. You can stabilize micelle and free an enzyme. You can release enzyme by high salt concentration > enzyme becomes active.
	Describe a virus based nanoreactor? (CCMV virus)	-RNA is positioned inside. -particles falls apart at pH 7.5 -reassembly at pH 5 in presence of enzyme. -if you do the assembly in presence of molecule of interest, it can be incapsulated.
	How can we increase the loading efficiency of virus based nanoreactors?	Add leucine zipper between the dimers of enzyme. There will be more encapsulation.
	Double LbL enzyme nanoreactors are .....?	intrinsically porous
	What are the polyekectrolyte vesicles?	+ and - charged polymers , these will make a cinokex ad thus will make them less watersoluble. PEG stick to H2O fase, in the middle the internal structure is formed by PIC. If you do the assembly process in the presence of enzymes they will be incapsulated. This molecule is made by electrostatic interactions. The layer consist of PEG-PIC-PEG
	How do polymerosomes made permeable?	with membrane proteins. Use the bacterial pore protein, put it in the polymerosome membrane. Membrane adopts itself to the size of the pore. So the overall polymer thickness decreases in place where the membrane protein is inserted. ( so this MP will not be covered with hydrophobic tales)
	How does artificial organelle work?	Bacterial rhodopsin pomps protons into complex, where as ATP synthase uses these protons to make ATP.
	How do encapsulation of enzyme inside the polymerosome work?	THF + enzyme solution in water, but you can also take water directly out, no to let polymerosomes to be formed, then you add a mixture of enzyme. Then you encapsulate enzymes in bilayer ( but the enzyme needs to be small enough).
	Positional assembly of 2 Enzymes in 1 Polymersome, how does it work?	THF + solution + enzyme . Freeze (take out water?) + second enzyme. Freeze. So you get 1 enzyme in bilayer, other in the middle of the polymerosome.
	What are the clickable polymerosomes?	Enzymes attached on the surface of polymerosome. Functionalization with dansyl probe ( fluorescent probe).
	How can you immobilize an enzyme on the polymerosome?	PS-PIAT PS-PEG with acetylene
	Polymersomes with controlled porosity? Selective Dissolution of a Minor Component. How does it work?	Poplymerosomes are made of amphiphilic molecules. Een amphiphilic part becomes hydrophobic upon the enviroment and makes holes. But the polymerosome is made of other materials that make holes, PEG-PS (polystirene)
	What is kinetically trapped polymer assemblies?	Polystirene become glass when organic solvent is taken out. 50% H2O / 50% THF > remove THF slowly. THF is also removed from particles, but water can not get in the polymerosome. The sfeer shrinks, the bilayer is formed inside. The stomatocytes are formed. This phenomenon is observed for red blood cells and liposomes. The more THF is in the polymerosome, the more change in the opening of new structure ( stomatocyte) will occur You can trap in some molecules in these stomatocytes.
	How do stomatocyte nanorockets work?	2 H2O2 → 2 H2O + O2 fuel is waterstofperoxide
	How is the movement of stomatocytes rockets is detected?	Dynamic light scattering - particles move around, speed is random movement, speed is inversally proportional to size of particle. Nanopaterning scattering analysis - nanoparticles scattering light.
	What are the advantages of polymersomes as drug delivery vehicles according to the authors?	Polymersomes have a thicker shell, making them more stable, and giving them more stealth characteristics. This would improve circulation times. They don’t fall apart that easily upon dilution, which is important when they are introduced in e.g the blood stream. This also prevents the presence of free polymers, which could possibly induce cytoxic responses.
	What is the role of the PMPC and PDPA block copolymer segments?	PMPC is a phospholipid mimetic polymer, which therefore resembles a natural membrane. As a result, its biological properties are very good, i.e. its biocompatibility and antifouling behaviour, which means that proteins will not easily stick to the polymersome. PMPC forms the outer structure of the vesicle. PDPA contains a secondary amine in the side chain. This amine is pH sensitive. At physiological conditions it is not charged and as a result this polymer will be hydrophobic (due to the isopropyl side chains). When the pH is lowered (as in the lysosome), the cationic charge will disrupt the vesicle. This behavior can be used for both efficient encapsulation as release.
	Explain the morphology change of the polymer-DNA complexes when going from pH 7 to pH 6	At pH 7 PDPA is not charged and the interactions with DNA are negligible. Therefore vesicle formation is not interrupted. At low pH, the PDPA block becomes positively charged which results in strong interaction with DNA. Now a DNA-polymer complex is formed which is visible as aggregates in fig 3d and f.
	What is the mechanism of endosomal release for this system?	When inside an endosome, the vesicles will experience a pH change when the endosome turns into a lysosome. The vesicles fall apart and many ne DNA-polymer complexes are formed. The increase in number of particles inside the lysosome results in an increase in osmotic pressure. Influx of water will swell the lysosome and rupture them. The DNA-polymer complex can then reach the cytosol and the nucleus
	How could you improve the DNA delivery system further, and what are possible bottlenecks of this approach?	It is not really known what the fate is of the DNA-polymer complex. The polymer is furthermore not biodegradable, which could hamper prolonged administration. The size of the vesicles (200-400 nm) is large when blood circulation is taken into account. Loading could be improved and targeted uptake is ot introduced.
	. Name three different reactions that can be performed with amines in proteins. How can you make the reaction specific for the N-terminal amine of the protein? (2 points)	- alkylation with cyanuric chloride or epoxides (0.5 points) - acylation with NHS-esters (0.5 points) - reductive alkylation (aldehydes) (0.5 points) Amines need to be deprotonated for all these reactions. As the N-terminal amine has a lower pKa than the amines of the lysine side chains the pH can be adjusted such that the N-term reacts with a much higher probability. (0.5 points)
	2. You want to do an AFM force spectroscopy experiment. For this experiment you need to immobilize the following protein: • 1 disulfide bond on the surface, • 12 lysines, one of these lysines is close to the active site • his tagged (The protein expresses very well in E. coli.) Which strategy would you choose to immobilize the protein and why? (1 point)	Good options are for example (yielding a stable covalent bond!!!): a) reduction of the disulfide bond and coupling to a maleimide-functionalized surface b) using a low pH and trying to couple specifically to the N-term (e.g. NHS- or aldehyde functionalized surface) c) introduction of an additional Cysteine at the genetic level at a position that does not interfere with activity (e.g. at the C-term) and coupling to a maleimide-functionalized surface d) introduction of non-natural amino acids, e.g. having an azide or acetylene functionality and coupling to an acetylene- or azide-functionalized surface, respectively Bad options are for example: a) using the his tag as this does not yield a covalent bond (the his tag bond might be the weakest interaction in the system so that the process of interest cant be probed) b) using NHS-chemistry at a pH where the lysines are reactive (most likely inactivation of the protein + multi-site attachment possible)
	3b. Which physical rules limit (1.5 points) • its lateral resolution in imaging mode? • the scanning speed in imaging mode? • its force resolution in force spectroscopy mode?	- the curvature/shape of the tip (0.5 points) - the feedback loop (0.5 points); (0.25 points given for resonance frequency as this plays a role as well) - external (e.g. acoustic) and internal (thermal) noise. The latter depends on the spring constant of the cantilever. (0.5 points; spring constant only is enough)
	Discuss the advantages and disadvantages of quantum dots over GFP as a fluorophore to study the cellular dynamics of a protein	• resistant to photobleaching, therefore extended observation times are possible • a broad range of quantum dots with different spectral characteristics is available Disadvantages: • larger than GFP, therefore a bigger chance that the function of the protein will be influenced • chemical coupling required • difficult to use for intracellular applications. Import into the cells is required.
	7. You want to create 200 micrometer large spots of stimulatory antibodies. Which method would you chose if you want to generate	micro contact printing , PDMS
	Crosslinked polydimethylsiloxane (PDMS) is the ideal material for microcontact printing. Explain why a rubbery material is required for successful printing and give two disadvantage of using elastomers. (1 point)	Vereist: om over een groot oppervlak te printen is ‘conformal’ contact nodig. Twee harde oppervlakken kunnen niet met elkaar in contact komen vanwege kleine oneffenheden of stofdeeltjes. Daarom is een zacht materiaal vereist. Nadelen: i) geen nanostructuren mogelijk omdat de zachte rubbers door oopervlakte spanning vervormen en ii) over een groot oppervlak zal altijd vervorming optreden omdat de stempel zacht is en de mechanische druk niet overal precies hetzelfde zal zijn.
	Micelles and vesicles are self-assembled structures from small molecule amphiphiles. Describe what property is responsible for a molecule to organize itself in a micelle or a vesicle, and give an example of a micelle- and a vesicle-forming amphiphile. (1.5 points)	Het type assemblage is bepaald door de Israelachvili packing parameter, die de ratio geeft tussen het hydrofiele kopgroep oppervlak en de hydrofobe keten (N = V/ac • l). Wanneer deze parameter zich bevindt tussen 0.5-1, worden vesicles gevormd, kleiner dan 0.33 geeft micellen. Een voorbeeld van een micel-vormend amfifiel is een vetzuur of alkylsulfaat zoals natrium dodecyl sulfaat (SDS), een voorbeeld van een vesicle-vormend amfifiel is een fosfolipide.
	Describe three methods how to create a permeable polymer capsule which can be used as nanoreactor.	Permeable polymer capsules can be made via the introduction of channel proteins, via the removal of sacrificial block copolymers which occupy part of the polymer shell, or by the use of polyelectrolytes, which result in an intrinsically porous structure (this can also be achieved by certain block copolymers with imperfect packing in the polymer shell)

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