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BZ 310 Exam 1
| Question | Answer |
|---|---|
| outside a cell a virus is called a | virion |
| inside a cell a virus is called a | virus |
| what comprises the endo-membrane system? | nucleus, ER, golgi, vesicles, and lysosome |
| the lysosome is the ___ in plant cells | vacuole |
| what is the chemical/physical barrier of cells? | plasma membrane, cell wall |
| peroxisome function | special breakdown reactions, special enzyme (1 membrane) |
| endoplasmic reticulum functions (4) | barrier for nucleus, detoxification, lipid synthesis, secretory protein synthesis |
| definition of cytoplasm | organelles (-nucleus), cytosol |
| hydrolysis | releases energy (broken down w/ water) |
| condensation | activated w/ ATP, releases energy (and water) |
| more entropy in free... | P (rather than bound as ATP) |
| what is the ATP/ADP ratio in cells? | between 10 and 1000 |
| direction of synthesis for nucleic acid and proteins | 5'-3' and amino to hydroxy |
| which stereoisomer of AAs is used in protein synthesis? | L (CH3 and NH2 on the left) |
| 3 types of media | solid, liquid, defined |
| defined media | growth requirements |
| 4 components of media | salts, carbon source, light, "goodies" (AAs etc) |
| suitable medium for multicellular organisms | many ingredients and growth factors |
| animal vs plant cells laboratory | animal cells have a limited number of divisions vs plant cells can re-grow |
| plant cells re-growth | cell-> callus -> plant regeneration |
| how to make cells immortal? | fuse w/ cancer cell line (each missing capability to make something like a nucleotide so they fuse) |
| how are x-ray crystallography and NMR different? | static/complex molecules vs dynamic/simple (small) molecules |
| depth of field | area of the specimen in focus at one time |
| bright field: contrast by | light absorption |
| bright field: limitations | must be thin and stained |
| bright field: advantage | simple optics |
| phase contrast: contrast by | interference (difference in refractive index) |
| phase contrast: advantage | visualize living cells |
| phase contrast: limitation | single cell layer |
| phase contrast variant | Nomarski/DIC (thicker tissues) |
| dark field use | to view motility |
| dark field contrast by: | light scattering |
| fluorescence microscopy | emission wavelength always > than emission wavelength (lower energy) |
| 2 fluorescence microscopy probes | indicator dyes, antibodies bound to fluorophoresin |
| green fluorescent protein | insert gene for GFP into target gene, express mRNA-> protein (make sure it doesn't affect function) |
| other version of fluorescence microscopy | confocal scanning-> eliminates depth of field limitation |
| basic structure of TEM | source, magnets, obj lens, condenser lens, ocular lens |
| why must you stain electron microscope stuff w/ metals? | few electrons in organic matter, much more in a heavy metal |
| drawbacks of electron microscopy (3) | must be fixed and in a vacuum, heavy metal staining, samples must be thin (TEM) |
| why must samples in electron microscope be in a vacuum? | electrons would collide with air molecules and scope would melt |
| what is the primary image in TEM? | the primary electrons that pass through the specimen (darker) |
| 3 main kinds of TEM samples | thin sections, negative staining, shadowing |
| shadowing contrast TEM | samples appear like a landscape in 'black snow' |
| what is the best preservation of structure for electron microscopy? | freeze fracture |
| where does breakage occur in freeze fracture? | through the bilayer |
| who is Francis Collins? | Head of NIH |
| PCR cycle | heating, annealing, elongation |
| 4 requirements for PCR | template DNA, dNTPs, primer, Taq polymerase |
| what does phoresis mean | "to carry" |
| chain termination method | dideoxynucleotide (stops without the 3' OH) |
| southern blot | DNA sequences in a genome can be ID'd by a hybridization with a labeled DNA probe |
| northern blot | separated RNA by size and hybridized w/ RNA label to detect specific mRNA species |
| what are microarrays used for? | analyze mRNA expression levels in the genome |
| microarray: red | high expression on ethanol |
| microarray: yellow | high expression on ethanol and glucose |
| microarray: green | high expression on glucose |
| recombinant expression | DNA expressed in bacteria and protein can be purified |
| how to study function of a protein? | expressed in a host cell & study function of gene product |
| the word collagen is derived from | glue (in French) |
| EGF-R | epidermal growth factor receptor |
| secondary structure | local hydrogen bonding in the backbone |
| tertiary structure | overall shape b/c of R groups (may consist of domains) |
| protein domains | functional elements of proteins with a specific tertiary structure |
| motif | (secondary structure) defined by short sequence stretches (only one polypeptide chain) |
| tertiary structure is stabilized by | Van der Waals, H-bonds, ionic bonds |
| proteins evolved for optimal functionality which requires | flexibility (proteins are dynamic and flexibility is crucial) |
| protein domain example | Ca2+ binding domain in various species |
| proteins w/ __% sequence ID ___ | 25%, share the same shape |
| disulfide bonds are found between | cysteine residues |
| 3 'special' ways to stabilize protein structure | disulfide bonds, covalent modifications, cofactor binding sites |
| 3 types of cofactors | coenzymes, prosthetic groups, metal ions |
| what is a protein with no cofactor called? | apoprotein |
| 3 examples of coenzymes | ATP (transfers Pi), NADH (transfers H), Co-A (transfers acetyl) |
| IgG | main blood antibody; binds phagocytic cells and complement activation |
| epitope | a specific part of an antigen to which an antibody binds |
| antibodies are produced by | B cells |
| IgG can be used as a tool for what? (4) | immunogold labeling (TEM), immune fluorescence, detection of proteins, and affinity purification of protein/complexes |
| heat shock proteins | short periods of moderate heat help express them; rescue vulnerable proteins |
| Western Blot | uses SDS and polyacrylamide gel, protein binds to corresponding antibody |
| 4 mechanisms of enzyme action | alignment, substrates "stressed", attacks on bonds, charge in active site |
| non-competitive inhibitors | lower Vmax (artificial?) |
| competitive inhibitors | increase Km |
| 3 types of allosteric control | (regulated somewhere other than active site); negative modulation, positive modulation, cooperativity |
| Kinases and Phosphatases | add PO4, remove PO4 |
| blod clotting | factor X activated, this converts prothrombin to thrombin, which converts fibrinogen to fibrin |
| why is centrifugation necessary? | things would not separate naturally b/c of centrifugation |
| 2 types of centrifugation | differential centrifugation and density gradient centrifugation |
| density gradient centrifugation | separation based on buoyant density |
| 5 functions of cell membranes | selective barrier (transport), order, enzymatic activity, signaling, energy conversion |
| what average shape to PPLs make? | cylinder w/ the polar and nonpolar regions b/c of rotation |
| 3 lipid movements | rotation, lateral diffusion, flip flop (rare) |
| purpose of sterols in the membrane? | maintain membrane fluidity and barrier function over a wider temperature range |
| 3 ways proteins associated w/ membrane | integral, anchored, peripheral |
| study that found that proteins move | fuse human and mouse cells; all proteins mixed |
| cytosolic faces | cytosol, nucleus, mitochondrial matrix, stroma (plastids) |
| one exception to the 2 faces rule | outer membrane of gram negative bacteria has 2 exoplasmic solutions |
| what ions more common outside? (what kind of environment?) | Na, Ca, Cl, H **oxidizing environment |
| what ions more common inside? (what kind of environment?) | K **reducing environment |
| proteins/etc outside of cell | tightly folded, single-subunit; aggressive chemistry, no nucleic acids |
| proteins/etc inside cell | multi-subunits w/ regulation, nucleic acids |
| fick's law | Flux= C x (Δconc) (simple diffusion) |
| animal cells like it ____ | isotonic |
| plant cells like it ____ | hypotonic (more salt inside so water flows in) |
| what transporter does not saturate? | pores/open channels |
| channels: transport is always __ __ | down gradient |
| oocyte experiment | inject mRNA for aquaporins (control= random mRNA); put in hypotonic solution; cell bursts |
| carriers are (3) | saturable, dependent on conc gradient, follow M.M kinetics |
| 3 classes of ATP driven pumps | P-type, V-type, ABC |
| ABC pumps | ATP binding cassette over-expressed in tumor cells (aka multidrug resistance) |
| P-type pumps | phosphorylated intermediate |
| V-type pumps | use pyrophosphate |
| Na/K pump | 1 ATP= 3 sodium out, 2 K in |
| Ouabain | inhibits Na/K pump; blocks K+ binding |
| Digitalis | inhibits Na/K pump; stabilizes E2 state |
| Donnan effect | charged macromolecules attract counter ions from outside the cell, would cause cell to burst if not dealt w/ |
| how to plants/fungi/bacteria deal w/ donnan effect? | rigid cell wall; pressure counteracts and specific proteins regulate solute composition |
| how animal cells deal w/ donnan effect | pump excess ions out |
| how protozoa deal w/ donnan effect | contractile vacuole squeezes water out |
| what gradient in plant/fungi? | protons (pumped out) |
| why don't K+ leak out more? | held inside by the negative charge |
| membrane potential of most cells | 60-200mV |
| membrane potential exceptions | plastid outer membrane, mitochondrial OM, bacterial OM (because of porins) |
| 4 significant things about electrochemical gradients | energy-requiring transport, signaling, motility, energy conversion |
| acidic amino acids | glutamate and aspartate |
| basic amino acids | lysine, histidine, arginine |
Created by:
melaniebeale
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