Cell Biology Exam 1, Ch 1 UMKC

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How are chloroplasts thought to have originated? As photosynthetic bacterium engulfed by an early eukaryotic cell.
How are specimens fixed for TEM?; Similarly to LM specimens: fixed, embedded, cut into thin sections, but then stained with Uranylacetate or Osmiumtetroxide; (these are electron-dense "stains" for membranes and proteins);
How do objects appear under Fluorescence microscopy? Dyed objects show up in bright color on a dark background.
What do the stains for TEM do? They create contrast and a stable sample for large electron fluxes to create images.
What does the cytoskeleton do for the cell? 1. Gives it mechanical strength; 2. Controls shape; 3. Drives and guides its movements
How do things flow through the golgi?; True or False? Membrane is also carried from the plasma membrane to the golgi (so back the way it came). Things move from compartment to compartment from the cis-golgi to the trans-golgi. ; True, there is retrograde membrane vesicular flow which carries membrane back from the plasma membrane to the golgi and then back to the ER.
How do you "see" the molecules arranged with x-ray crystallography?; How do you visualize this?; How is this transformed into a picture? They are arranged in a very orderly pattern within a crystal lattice. ; By the diffraction of short-wave x-rays detected as interference patterns. ; A massive computer calculations transform this into a 3-D model of the molecule. (highest resolution)
How do you create a stained tissue slide? Embed the tissue in paraffin or plastic; Cut a thin slice (~5um); Fix in acid/alcohol; Stain (red dye for nuclei, purple dye for extracellular matrix); Observe under microscope; (is dead and fixed)
How do you view surfaces using TEM? "Shadow" the specimen's surface with a heavy metal (like platinum); A carbon film is then evaporated above the specimen and coats the metal to strengthen it.; A powerful solvent is used to dissolve away thee specimen. ; Metal shadow replica shows the specimens surface structure (carbon support not visible to electrons)
How do you visualize virusees using a TEM? By using negative staining. ; Embed in an electron-dense plastic matrix. ; The virus capsids exclude the stain making them lighter and visible. ; It gives a good idea of shape even though it is collapsed.
How does a TEM work? Like an inverted LM but it uses a beam of electrons instead of light and magnetic coils to focus the beam instead of glass lenses.
How many leaflets do membranes have?; What part of the membrane will stain with heavy metal? 2; Hydrophilic heads (along with proteins, lipids will not)
How many membranes does the chloroplast have? 2 surrounding membranes (an outer and an inner), but there is also a membrane on the internal stacks. (So 2 total)
How many membranes make up the nuclear envelope?; 2 concentric membranes, the outer one is continuous with the ER;
Is it possible to observe fluorescently labeled subcellular structures in living cells? Yes. Done without need for fixation and the observations are less prone to artifacts. Ex: Change in Ca2+ level when egg is fertilized by sperm.
True or False? Mitochondria contain their own DNA. ; How do mitochondria reproduce?; How are they oriented in the cell? True, but 95-98% of genes have moved to the nucleus. A few essential genes are still present in mitochondria, so DNA and ribosomes are found in the matrix.; They reproduce by dividing in 2. ; They are localized by the cytoskeleton but they are NOT continuous with the ER like many other organelles.
True or False? Prokaryotic cells are the most diverse class of cells.; What don't prokaryotic cells have?; What do they have?; How is their DNA packaged? True; No sub-cellular organelles or nucleus; Do have a plasma membrane, ribosomes in the cytosol, and peptidoglycan-based cell wall; It isn't packaged and is circular. (Genomic DNA = single large circle, Plasmid DNA = many small circles)
What 3 filaments make up the cytoskeleton? 1. Actin filaments; 2. Microtubules; 3. Intermediate filaments
What are acidic pH vesicles, fused with endosomes, that digest endocytosed materials? Secondary lysosomes
What are actin filaments? The thinnest filaments, they occur in large numbers in muscle cells
What are centrioles? Organizing centers of microtubule activity. They become part of the organizing center that pulls chromosomes into daughter cells.
What are intermediate filaments? Intermediate in thickness, serve to strengthen the cell mechanically.
What are microtubules? The thickest filaments, they become reorganized into arrays in dividing cells and help pull apart duplicated chromosomes.
What are specialized secretory vesicles of nerve cells containing signal molecules? Synaptosomes
What is the lowest resolution of an electron microscope?; What can be seen with it? 0.2nm; Large macromolecular complexes and membranes
What are the 2 ways do fluorescent dyes work? 1. Dye can bind specifically to particular molecules in cells and reveal the location of those with a fluorescence microscope; 2. The dye can be coupled to antibody molecules. These are highly specific to small sites. See where things are, not what they are.
What are the 3 types of unstained modes in LM? 1. Bright-field optics: low contrast; 2. Phase contrast optics: thin line of light goes through object, greater refraction around some material, see a lot of detail; 3. Nomarski optics: lower light intensity, allows easier taking of videos (so can see dynamics of cell behavior), also called interference-contrast optics
What are the animal model organisms? 1. Drosophila melanogaster = fruit fly; 2. Caenorhabditis elegans = round worm; 3. Mus muscularis = mouse; 4. Homo sapiens
What are the different shapes of bacteria?; What are the different types of bacteria cell surface features? Spherical (coccus), rod (bacillus), or spiral (spirillus); Flagella (long), fimbriae (short), slime capsule
What are the functions of the Golgi Apparatus? 1. To sort proteins to their intended subcelllular or external destination. ; 2. Site of post-synthetic glycosylation of proteins to keep them from proteolytic destruction; 3. Dimerization;
What are vesicles formed from the plasma membrane in response to membrane receptors to take up extracellular material for destruction? Endosomes
What are vesicles producing hydrogen peroxide and other oxygen radicals for oxidation and destruction in secondary lysosomes? Peroxisomes
What are vesicles with digestive enzymes created by the Golgi? Primary lysosomes
What are vesicles with soluble or membrane-bound proteins that fuse with the plasma membrane? Secretory vesicles
What do chloroplasts do?; Where are they found?; True or False? Chloroplasts are the most complicated organelle. Fix carbon dioxide and generate ATP from light. ; Only in plants, algae, and photosynthetic bacteria. ; True
What do fluorescent dyes do? They absorb light at one wavelength and emit it at another, longer wavelength.;
What does the nucleus do? Stores DNA that encodes the genetic information of the organism in chromosomes;
What does the rough ER do?; On which side are all of the ribosomes? It organizes ribosomes on mRNA to make proteins for export from the cell (ex: secreted enzymes, cell surface receptors, etc). Many of these proteins are inserted into its lumen. ; The cytoplasmic side.
What happens in the Endoplasmic Reticulum (ER)?; True or False? The outer nuclear membrane is contiguous with the ER membrane. It is the site where most cell membrane components and where materials destined for export from the cell are made. ; True
What have we learned from D. melanogaster? We formed the basis for genetics (mutation, how genes inherit/interact, physiological pathways associated with genes, regulation of gene expression, and the correlation between gene action and physical appearance) also human development and disease.
What is DAPI? DNA-intercalating fluorescent dye, used in fluorescence microscopy to show nuclei and condensed chromosomes
What is a fluorescence microscope? Similar to an ordinary LM except that the illuminating light is passed through 2 filters. 1st filters light before it reaches the specimen. It only passes wavelengths that excite the particular fluorescent dye. 2nd bocks out this light and passes only those wavelengths emitted when the dye fluoresces. ;
What is a model organism? Organisms selected for intensive study as a representative of a large group of species.
What is commonly found in the cytosol and what do they do? Ribosomes, they manufacture proteins.
What is contained inside the membranes of the internal stacks of chloroplasts?; True or False? Chloroplasts contain their own DNA and reproduce by dividing in 2. The green pigment, chlorophyll. It is used to trap the energy of sunlight which it uses to drive the manufacture of sugar molecules. ; True
What is distinctive about gram positive bacteria?; What about gram negative bacteria? A thick peptidoglycan cell wall and have only 1 membrane. (Ex: Staphylococcus aureus); A think peptidoglycan cell wall and have 2 membranes (the inner is ion tight like the g+ but the outer membrane is porous) (Ex: E. coli);
What is endocytosis? What is exocytosis? The process of the cell engulfing very large particles. The reverse process where vesicles release their contents into the extracellular matrix.
What is heterochromatin?; What is euchromatin? Dark-staining, compacted, inactive chromatin (packed with histones); Light-staining, loosely packaged, transcriptionally active chromatin
What is the LM suited to study? And what do they just detect?; How small can the naked eye see? Multi-cellular tissues, individual cells (5-20um), and large subcellular organelles. They just detect small organelles. ; 0.2mm (200um)
What is the bacterial model organism for molecular biology? And why?; What information have we gained from E. coli? E. coli because it has 1 chromosome.; Information on DNA replication, recombination, and gene regulation.
What is the cytoskeleton? A system of filaments that are either anchored at one end to the plasma membrane or that radiate out from a central site adjacent to the nucleus.
What is the cytosol?; Can it be visualized directly? Cell - Plasma Membrane - Membrane-enclosed Organelles = Cytosol or; A gel-like concentrated solution of proteins, metabolites, multi-protein organizing fibers and a wide variety of protein and protein-nucleic acid complexes. ; No but purification of individual components can be used to visualize pure complexes or to raise antibodies.
What is the function of the mitochondria?; How many membranes does it have? It is a place of cellular respiration. It consumes oxygen, releases carbon dioxide, and makes ATP by oxidative phosphorylation.; 2
What is the inner membrane like on the mitochondria?; What is the outer membrane like? It is convoluted (invaginated) into cristae that contain ATP synthase complexes (these convert the gradient of protons into ATP); Smooth
What is the magnification of a transmission EM (TEM)?; What is the resolution?; What can you see with it? Mag: million-fold; Res: ~2nm; Thin sections of lumen and cytosol, organelles, membrane thickness, and the surfaces
What is the maximum magnification of a light microscope (LM)? What is the resolution?; 1000-fold, 200 nm;
What is the model organism for plants? Why do we use it?; What have we learned from it? Arabidopsis thaliana because the entire sequence is known and because it reproduces relatively quickly. ; We have gained insights into the development and physiology of crop plants.
What is the model organism for viruses?; Why do we use it?; What have we learned from it? Phage/virus; Because it can inject its DNA into bacteria and has a small genome. ; We learned about early genetics/molecular biology, DNA sequence, how genes work, protein-protein interaction, and genetic inheritance.
What is the nucleolus? A dense area in the nucleus of RNA and proteins where rRNA is transcribed from DNA and packaged by ribosomal proteins
What is the process for SEM specimen? Coat the sample with a very thin layer of a heavy metal (specimen can be unfixed if stable, if not must be fixed).; Scan using an electron beam that is focused to the speciment by an electromagnetic coil acting as the lens. ; The quantity of electrons scattered or emitted is measured, recorded by detector, and used to build up an image on a screen. ;
What is the single-celled eukaryotic model organism?; What have we learned from it? Saccharomyces cerevisiae (aka Brewer's Yeast); We use it to study human disease and gene modules because it has the same proteins which often have the same function.
What is the source of illumination for a confocal microscope?; What type of specimen can be analyzed?; Can video be taken? A laser is usedto scan the field, exciting material, highlighting it, and then can be observed. ; Thick, 3-D specimen can be analyzed. ; Yes, sharp video can be taken becuase virtually no out-of-focus light is recorded.
What kind of view does a SEM give? A 3-D surface view where a very large range of magnification can be effectively used. Given in black and white but artifical color is often added later to help interpret the image.
What three things do plant cells also have that animal cells don't? What does it do? A cell wall. It defines the cell location. ; Large vacuoles. They are full of water and supply osmotic/turgor pressure which helps maintain cell shape.; Chloroplasts. Capture energy from sunlight and uses it to make sugars.
What type of surface does the scanning EM (SEM) see? ; What is the resolution of a SEM?; The specimen surfaces that deflect electrons. (Electrons only give density). ; Somewhere between 3nm and 20nm.
Which side of the Golgi is the cis side relative to the nucleus? The side closer to the nucleus is the cis side. ; The cis side recieves new proteins. ; Proteins leave from the trans side.
Why do we study the mouse?; What have we learned from it? Because it has a short life cycle, can reproduce quickly, and is recently divergent from us. ; We have studied mammalian genetics, development, immunology, and cell biology.
Why do we use C. elegans?; What have we learned from it? Because it is transparent so we can see the developmental pathway of cells and cell movement during development. ; An understanding of programmed cell death