Atomic Force Microscopy and Amino Acids Quiz

A technique that uses fluorescent probes to identify specific DNA sequences on chromosomes. These probes bind to complementary sequences, allowing researchers to pinpoint their location.

A technique that uses fluorescently labeled probes to identify and locate specific RNA sequences, such as mRNA, lncRNA, and miRNA, within cells, tissue samples, or circulating tumor cells. It utilizes the principles of base pairing to target and visualize specific RNA transcripts.

A method used to label DNA probes in molecular biology. It employs the enzyme DNA polymerase I to replace some nucleotides in a DNA sequence with their labeled counterparts.

A protein that strongly binds to biotin. It is frequently used in conjunction with biotin-labeled molecules for detection and purification purposes.

An early stage of cell death where the cell membrane remains intact, but phosphatidylserine (PS) is exposed on the outer membrane leaflet.

A late stage of cell death where the cell membrane is compromised, allowing propidium iodide (PI) to enter the cell and stain the nucleus.

A chemical compound used as a fluorescent dye. It is commonly used to stain DNA and is unable to cross intact cell membranes, but can enter cells with damaged membranes.

A phospholipid that is normally found on the inner leaflet of the cell membrane. During early apoptosis, it becomes exposed on the outer leaflet, acting as a signal for phagocytosis by other cells.

Atomic Force Microscopy (AFM) is a high-resolution imaging technique that allows scientists to visualize surfaces at the atomic level.

AFM uses a sharp tip attached to a cantilever, which vibrates at a specific frequency. As the tip scans the surface, it interacts with the sample, causing the cantilever to bend or deflect. The changes in cantilever motion are measured, providing information about the surface topography.

AFM has a resolution on the order of fractions of a nanometer, which is significantly better than the optical diffraction limit. This allows it to resolve features that are too small to be seen with traditional microscopes.

In Tapping mode, the tip oscillates at a certain frequency and gently taps the surface. This mode is ideal for imaging soft and delicate samples, such as biological cells.

In Scanning mode, the tip is dragged across the surface, similar to a stylus on a record player. This mode is suitable for imaging harder materials, like metals or semiconductors.

Electron diffraction uses electrons to create an image of a specimen. It offers benefits over X-ray crystallography because it doesn't require a single crystal or powder, and the image reconstruction happens physically, eliminating the phase problem.

The main drawback of TEM is the requirement for extremely thin sections of the specimen, typically around 100 nanometers.

Biological specimens, due to their delicate nature, need preserving before viewing under TEM. This involves chemical fixation, dehydration, and embedding in a polymer resin for stability.

Heavy metal ion stains are used to enhance contrast in TEM images of biological specimens, making them visible.

STEM uses a focused electron beam that scans across a thinned specimen, similar to TEM, providing high resolution imaging.

In STEM, the focusing lens and any aberrations occur before the electrons hit the specimen, unlike in TEM where they occur after.

STEM's use of beam rastering simplifies techniques like annular dark-field imaging, but data acquisition occurs in a serial, rather than parallel, manner.

The rapid freezing of specimens in cryoelectronic microscopy is crucial, forming vitreous ice. This allows direct viewing without fixation, staining, or drying, preserving the specimen's natural state.

A laboratory technique that separates cellular components based on their size and density using centrifugal force.

A type of centrifuge rotor where tubes are fixed at an angle, allowing particles to sediment quickly.

A type of centrifuge rotor where tubes are suspended and swing outward during rotation.

A method of separating cellular components using a gradient of increasing density, allowing components to settle at their respective densities.

A technique that separates cellular components based on their sedimentation rate through a solution.

A phenomenon where a denser solution overlies a lighter solution, causing mixing and disrupting separation.

A solution with a gradual increase in density from top to bottom, preventing convective mixing during centrifugation.

A common molecule used in a density gradient to prevent convective mixing during centrifugation. Creates a stable gradient for better separation.

A technique used in biochemistry and molecular biology to study cellular processes. It involves exposing cells to a labeled compound (pulse) followed by an unlabeled compound (chase) to track the movement of the compound over time.

A short period where cells are exposed to a radioactive tracer. This tracer is usually a molecule involved in a specific pathway of interest.

A period where cells are exposed to an excess of the same compound as the pulse, but now unlabeled. This helps to dilute the radioactive tracer.

The radioactive tracer used in pulse-chase experiments. It is incorporated into DNA (but not RNA) and its movement is tracked through the cell.

Using a photographic emulsion to detect the location of the radioactive tracer. Developed silver grains appear as dark precipitates on the image.

The radioactive tracer used in pulse-chase experiments. It is incorporated into DNA (but not RNA) and its movement is tracked through the cell.

A substance with added radioactivity. It is used to follow the movement of something like a molecule within the cell.

A photographic emulsion containing silver bromide (AgBr) that reacts with radioactivity, leading to the development of dark precipitates on the image.

A unique amino acid with a cyclic structure formed by the amino group and a side chain. It disrupts alpha-helices due to its rigid structure, creating a 'kink' in protein chains.

A non-polar amino acid with a sulfur-containing side chain (thiol group). It can form disulfide bonds, crucial for protein structure and stability.

A group of amino acids with a hydroxyl (OH) group in their side chains making them polar. They can form hydrogen bonds, contributing to protein structure and interactions.

These amino acids have a polar amine group in their side chains. They play a crucial role in forming hydrogen bonds, influencing protein structure and interactions.

Non-polar amino acids often cluster together in the interior of folded proteins. This contributes to the 3D shape of the protein and helps maintain its function.

Non-polar amino acids can interact with the lipid environment of cell membranes, leading to their localization as intrinsic membrane proteins.

The amino acids with non-polar side chains are sometimes called 'hydrophobic' because they tend to avoid water and prefer to associate with other non-polar molecules.

The location of non-polar amino acids influences the protein's final shape (conformation), function, and where it resides within the cell, such as inside membranes.