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BZ 310 Exam 1

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