Lecture 5 Flashcards
What are microtubules?
Microtubules are polymers of tubulin that form part of the cytoskeleton. They are found in all eukaryotic cells, and they are involved in mitosis, cell motility, intracellular transport, and maintenance of cell shape.
Motor proteins carrying a vesicle?
Motor proteins are a class of molecular motors that can move along the cytoskeleton of cells. They convert chemical energy into mechanical work by the hydrolysis of ATP.
An example of a motor protein is kinesin which transports a vesicle* by using a microtubule track (an example is found in digital notes)
Note that the kinesin undergoes unidirectional movement
- Vesicle is a small sac formed by a membrane and filled with liquid
What is ATP synthase
i feel this gives a bit more in-depth background about card 2:
Okay, so ATP synthase is a high-tech micromolecular power generated inside your body’s cells.
It works like a rotary engine:
The barrel-shaped rotator is composed of 10-15 subunits of proteins, the rotator spins around converting mechanical energy into the drive shaft of the machine which helps make ATP, This drive shaft has a specifically placed bump that opens and closes paths as the drive shaft spins around. This bump opens special protein subunits at the bottom of the machine.
When the bottom subunits open a spent energy molecule called ADP enters the machine. The mechanical motion causes ADP to bind with an extra phosphate group creating an ATP energy molecule. Then the ATP drifts into the cell ready to power some biomechanical reactions.
microtubules vs actin filaments
Microtubules determine the positions of membrane-enclosed organelles and direct intracellular transport. Actin filaments determine the shape of the cell’s surface and are necessary for whole-cell locomotion
Graphite and graphene: Differences and definitions
Graphite:
* naturally occurring allotrope of carbon
* electrical conductor
* anisotropic
* used in pencils, electrodes
Graphene:
* allotrope of carbon (isolated in 2004)
* strong, light, nearly transparent
* excellent conductor of heat and electricity
* potential applications: lightweight, thin,
flexible, durable display screens, electric
circuits, solar cells, transistors, nanodevices
etc.
Structures are shown in digital notes
Unzipping of carbon nanotubes
Carbon nanotubes (CNTs) are made of graphene sheets seamlessly rolled into a concentric tube. The unzipping of carbon nanotube (CNT) is a promising approach to obtaining high-quality graphene nanoribbon or graphene nano-strips. Several methods, including chemical oxidation, electron beam, steam and plasma etching, hydrothermal, electrochemical, intercalation, etc., have been documented in the literature for the unzipping of CNTs.
In the chemical oxidation method, the overoxidation of edges generates defects and a large number of oxygen-containing functionalities. The nature of the oxidizing agent actually controls the unzipping of CNT as well as the defects in the graphene sheet
This is shown in digital notes
SEM
Scanning electron microscopy, or SEM, produces detailed, magnified images of an object by scanning its surface to create a high-resolution image.
SEM works by scanning a sample with electron beams. An electron gun fires these beams, which then accelerate down the column of the scanning electron microscope. During this action, the electron beams pass through a series of lenses and apertures, which act to focus them.
This occurs under vacuum conditions, which prevents any molecules or atoms already present in the microscope column from interacting with the electron beam. This ensures a high-quality of imaging. The vacuum also protects the electron source from vibrations and noise.
The electron beams scan the sample in a raster pattern, scanning the surface area in lines from side to side, top to bottom. The electrons interact with atoms on the surface of the sample. This interaction creates signals in the form of secondary electrons, backscattered electrons and rays that are characteristic of the sample. Detectors in the microscope pick up these signals and create high-resolution images displayed on a computer screen.
The resulting images show information about what the object is made of and its physical features.
SEM is used at the nano to atomic level!
A schematic is shown in the digital notes!
STM
STM is a remarkable and rare example of harnessing a quantum mechanical process (electron tunneling) in a real-world practical application. The term “tunneling” refers to the situation where electrons traverse a barrier (in this case, a tiny gap between the tip and surface) that initially seems like it should be impenetrable—like throwing a ball against a wall. The physics that describes this ball-wall interaction is called the “classical paradigm,” and the ball will never tunnel through the wall. Electrons, by contrast, have a quirky wave-like character that makes them a “fuzzy” cloud (unlike a ball), so they can actually exist on both sides of the barrier simultaneously and therefore have a non-zero probability of moving across the barrier even if the barrier energy is higher than the total energy of the electron.
STM works by scanning a sharp conductive probe very close to the surface of a conductive specimen and forcing electrons to traverse the gap between them. When the tip is sufficiently near the surface (usually <1 nm away), the fuzzy electron cloud of the first atom of the tip and surface begin to overlap. Applying a bias voltage between the tip and the surface in this configuration produces a current because electrons are driven to tunnel through the potential barrier from the tip to the surface via the overlapping electron cloud. This tunneling current is highly sensitive to the gap between the probe tip and surface, varying exponentially with the tip-sample distance. As the tip scans line by line across the surface of the sample, the intensity of the tunnelling current maps the sample’s electronic density of states.
STM is produced at low temps to prevent the molecules from ‘jumping’ and interacting with each other
A schematic of this and different microscopies are shown in digital notes (and should inshallah be annotated)
AFM
AFM microscopes operate on the principle of surface sensing using an extremely sharp tip on a micromachined silicon probe. This tip is used to image a sample by raster scanning across the surface line by line, although the method varies dramatically between distinct operating modes. The two primary groups of operating modes are widely defined as contact mode and dynamic, or tapping, mode.
The underlying principle of AFM is that this nanoscale tip is attached to a small cantilever which forms a spring. As the tip contacts the surface, the cantilever bends, and the bending is detected using a laser diode and a split photodetector. This bending is indicative of the tip-sample interaction force. In contact mode, the tip is pressed into the surface and an electronic feedback loop monitors the tip-sample interaction force to keep the deflection constant throughout raster scanning.
Tapping mode limits the contact between the sample surface and the tip to protect both from damage. In this mode, the cantilever is caused to vibrate near its resonance frequency. The tip subsequently moves up and down in what is described as a sinusoidal motion. This motion is reduced by attractive or repulsive interactions as it comes near the sample. A feedback loop is used in a similar fashion to contact mode, except it keeps the amplitude of this tapping motion constant rather than the quasistatic deflection. By doing so, the topography of the sample is traced line by line.
A schematic of this and different microscopies are shown in digital notes (and should inshallah be annotated)
Trapping and moving metal atoms with a six-leg molecule
In this process, a six-leg molecule is used to trap and move metal atoms, such as copper, on a surface. Here’s a simplified explanation:
Trapping Metal Atoms: The molecule, with six “legs” extending from its center, is placed on a metal surface. The molecule is moved around using a tool called an STM (Scanning Tunneling Microscope) until its legs grab onto metal atoms (adatoms) on the surface.
Moving the Trapped Atoms: Once the metal atoms are trapped, the STM moves the entire molecule, carrying the trapped atoms to a new location on the surface.
Creating Atom Clusters: As the molecule traps more atoms, they start to form a small cluster at the center of the molecule. After collecting enough atoms, the molecule is lifted off the surface with the STM tip.
Checking the Results: Sometimes, not all metal atoms are picked up successfully, and some may stay behind. Scientists compare the leftover atoms with those moved atom-by-atom to see how many were successfully trapped.
With is depicted in notes
What is the most common six-leg molecule? (at least the one we use)
The HB-HPB (C66H78) molecule (Fig. 1a) consists of a central benzene ring connected to six phenyl groups by σ-bonds, and of six t-butyl lateral groups, each attached to a phenyl ring. In our design, the lateral phenyls can rotate whereas steric hindrance between the phenyl groups forbids a full planar conformation of the molecule. The t-butyl end groups have the function of elevating the central HPB, creating a sizable cage for the Cu adatoms to be trapped between the central HPB group and the metal surface underneath.
The structure is depicted in the notes
Rotating a microscale object
this is done by dopping LCs with a molecule motor and placing a microscopic rod on it! Once light is shown the molecule’s helicity will change causing the rod to rotate
Light-driven plastic motor
So this basically builds off the concept of switchable molecules on surfaces, where as we already know when light is shown on the trans isomer the size will almost half and the dipole will change to form a cis isomer.
This can be used to make the tap move via rapping it with a film made of the discussed molecule. The film will have different UV wavelengths shone at it at different places causing a series of contraction and expansions (since changing between trans and cis). this then effectively allows the tape to move
Stereotunable catalyst
It is basically where a catalyst can catalyze different reactants depending on its helicity
This concept basically allows for ONE catalyst to be able to catalyze many reactions so it will be very efficient in the industry
Photopharmacological Chemotherapy
- external and local activation of chemotherapeutic agents by light
- photoswitchable histone deacetylase (HDAC) inhibitors as potential antitumor agents
- analogues of the clinically used chemotherapeutic agents now designed with a photoswitchable azobenzene moiety
(molecules that can act locally at a certain point by which light acts as a doormat and activates it for it to result in a healing treatment)
