Lodish 7E, Select Vocab, Chapter 9

Front 1

bright field light microscopy

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the compound microscope uses several lenses that magnify the image of a specimen to study

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cell line

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a population of cultured cells, of plant or animal origin, that has undergone a genetic change allowing the cells to grow indefinitely

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cell strain

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a population of cultured cells, of plant or animal origin, that has a finite life span and eventually dies, commonly after 25-30 generations

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chimeric proteins

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A hybrid protein encoded by a nucleotide sequence spliced together from 2+ complete or partial genes produced by recombinant DNA technology

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chloroplast

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a specialized organelle in plant cells that is surrounded by a double membrane and contains internal chlorophyll containing membranes (thykaloids) where the light absorbing reactions of photosynthesis occur

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clone

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(1) a population of genetically identical cells, viruses, or organisms descended from a common ancestor; (2) multiple identical copies of a gene or DNA fragment generated and maintained via DNA cloning

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confocal microscopy

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an optical imaging technique used to increase optical resolution and contrast of a micrograph by using point illumination and a spatial pinhole to eliminate out-of-focus light in specimens that are thicker than the focal plane

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cryoelectron microscopy

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a form of transmission electron microscopy (EM) where the sample is studied at cryogenic temperatures (generally liquid nitrogen temperatures)[citation needed]. Cryo-EM is developing popularity in structural biology; The popularity of cryoelectron microscopy stems from the fact that it allows the observation of specimens that have not been stained or fixed in any way, showing them in their native environment, in contrast to X-ray crystallography, which generally requires placing the samples in non-physiological environments, which can occasionally lead to functionally irrelevant conformational changes

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culturing

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complex process by which cells are grown under controlled conditions, generally outside of their natural environment. In practice, the term "cell culture" now refers to the culturing of cells derived from multi-cellular eukaryotes, especially animal cells

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cytoplasm

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viscous contents of a cell that are contained within the plasma membrane but, in eukaryotic cells, outside the nucleus

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differential centrifugation

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a common procedure in microbiology and cytology used to separate certain organelles from whole cells for further analysis of specific parts of cells. In the process, a tissue sample is first homogenised to break the cell membranes and mix up the cell contents. The homogenate is then subjected to repeated centrifugations, each time removing the pellet and increasing the centrifugal force. Finally, purification may be done through equilibrium sedimentation, and the desired layer is extracted for further analysis.

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differential interference contrast (DIC) microscopy

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an optical microscopy illumination technique used to enhance the contrast in unstained, transparent samples. DIC works on the principle of interferometry to gain information about the optical path length of the sample, to see otherwise invisible features. A relatively complex lighting scheme produces an image with the object appearing black to white on a grey background. This image is similar to that obtained by phase contrast microscopy but without the bright diffraction halo.

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endoplasmic reticulum

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network of interconnected membranous structures within the cytoplasm of eukaryotic cells contiguous with the outer nuclear envelope; the rough ER, which is associated with ribosomes, functions in the synthesis and processing of secreted and membrane proteins; the smooth ER, which lacks ribosomes, functions in lipid synthesis

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endosome

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one of two types of membrane bounded compartments: early endosomes (or eukaryotic vesicles), which bud off from the plasma membrane during receptor mediated endocytosis, and late endosomes, which have an acidic internal pH and function in sorting proteins to lysosomes

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fluorescence recovery after photobleaching (frap)

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denotes an optical technique capable of quantifying the two dimensional lateral diffusion of a molecularly thin film containing fluorescently labeled probes, or to examine single cells. This technique is very useful in biological studies of cell membrane diffusion and protein binding. In addition, surface deposition of a fluorescing phospholipid bilayer (or monolayer) allows the characterization of hydrophilic (or hydrophobic) surfaces in terms of surface structure and free energy.

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fluorescent staining

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general technique for visualizing cellular components by treating cells or tissues with a fluorescent dye labeled agent (e.g., antibody) that binds specifically to a component of interest and observing the sample by fluorescent microscopy

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forster resonance energy transfer (fret)

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Fluorescence resonance energy transfer (FRET) is a distance-dependent interaction between the electronic excited states of two dye molecules in which excitation is transferred from a donor molecule to an acceptor molecule without emission of a photon.

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golgi complex

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stacks of flattened, interconnected membrane bounded compartments (cisternae) in eukaryotic cells that function in processing and sorting of proteins and lipids destined for other cellular compartments or for secretion; also called golgi apparatus

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hybridoma

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a clone of hybrid cells that are immortal and produce monoclonal antibody; formed by fusion of a normal antibody producing B cell with a myeloma cell

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immunofluorescence microscopy

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a technique used for light microscopy with a fluorescence microscope and is used primarily on microbiological samples. This technique uses the specificity of antibodies to their antigen to target fluorescent dyes to specific biomolecule targets within a cell, and therefore allows visualisation of the distribution of the target molecule through the sample.

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indirect immunofluorescence microscopy

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Secondary, or indirect, immunofluorescence uses two antibodies; the unlabeled first (primary) antibody specifically binds the target molecule, and the secondary antibody, which carries the fluorophore, recognises the primary antibody and binds to it. Multiple secondary antibodies can bind a single primary antibody. This provides signal amplification by increasing the number of fluorophore molecules per antigen.[3] This protocol is more complex and time consuming than the primary (or direct) protocol above, but it allows more flexibility because a variety of different secondary antibodies and detection techniques can be used for a given primary antibody

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lysosome

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small organelle that has an internal pH of 4-5, contains hydrolytic enzymes, and functions in degradation of materials internalized by endocytosis and of cellular components in autophagy

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membrane transport protein

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collective term for any integral membrane protein that mediates movement of one or more specific ions or small molecules across a cellular membrane regardless of the transport mechanism

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metal shadowing

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a thin layer of evaporated metal, such as platinum, is laid at an angle on a biological sample. An acid bath dissolves the biological material, leaving a metal replica of its surface, which can then be examined in the transmission electron microscope. Variations in the angle and thickness of the deposited metal allow an image to be formed because some incident electrons will be scattered in various directions rather than pass through the preparation. If the metal is deposited mainly on one side of the sample, for instance, the image seems to have “shadows,” where the metal appears dark and the shadows appear light.

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mitochondria

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large organelle that is surrounded by two phospholipid bi-layer membranes, contains DNA, and carries our oxidative phosphorylation, thereby producing most of the ATP in eukaryotic cells

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monoclonal antibody

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antibody produced by the progeny of a single B cell and thus a homogeneous protein that recognizes a single antigen (epitope); it can be produced experimentally by hybridoma

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organelles

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any membrane-limited subcellular structure found in eukaryotic cells

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peroxisome

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small organelle that contains enzymes for degrading fatty acids and amino acids by reactions that generate hydrogen peroxide, which is converted to water and oxygen by catalase

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phase-contrast microscopy

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an optical microscopy technique that converts phase shifts in light passing through a transparent specimen to brightness changes in the image. Phase shifts themselves are invisible, but become visible when shown as brightness variations; It reveals many cellular structures that are not visible with a simpler bright field microscope. These structures were made visible to earlier microscopists by staining. This required additional preparation which killed the cells. The phase contrast microscope made it possible for biologists to study living cells and how they proliferate through cell division

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photoactivated localization microscopy (palm)

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a superresolution technique that dramatically improves the spatial resolution of the optical microscope by at least an order of magnitude (featuring 10 to 20 nanometer resolution), which enables the investigation of biological processes at close to the molecular scale. The technique relies on the controlled activation and sampling of sparse subsets of photoconvertable fluorescent molecules, either synthetic or genetically-encoded

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polyclonal antibody

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are antibodies that are secreted by different B cell lineages within the body. They are a collection of immunoglobulin molecules that react against a specific antigen, each identifying a different epitope.

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resolution

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the minimum distance between two objects that can be distinguished by an optical apparatus; also called resolving power

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scanning electron microscope (sem)

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a type of electron microscope that produces images of a sample by scanning it with a focused beam of electrons. The electrons interact with atoms in the sample, producing various signals that can be detected and that contain information about the sample's surface topography and composition.

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total internal reflection fluorescence (tirf) microscopy

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It allows imaging of fluorescent molecules located close to the glass/water (or glass/specimen) interface. This is achieved by employing an evanescent wave for excitation of the fluorophores instead of direct illumination via light delivered by an arc lamp, LEDs or lasers. The evanescent field occurs if incident light is totally reflected at the interface of two transparent media with different refractive indices.

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transmission electron microscopy (tem)

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a microscopy technique whereby a beam of electrons is transmitted through an ultra-thin specimen, interacting with the specimen as it passes through. An image is formed from the interaction of the electrons transmitted through the specimen; the image is magnified and focused onto an imaging device, such as a fluorescent screen, on a layer of photographic film, or to be detected by a sensor such as a CCD camera.