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125 Cards in this Set
- Front
- Back
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Central Paradigm
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DNA -> RNA -> Protein
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Nuclear Envelope Features
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1.) Pores
2.) Double Membrane |
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Role of Mitochondria
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Cell powerhouse. Makes ATP.
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Properties of Mitochondria
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1.) Double membrane
2.) Inner membrane where DNA for ATP is organized. 3.) Inside = "Matrix" 4.) Has it's own DNA 5.) Produce ATP |
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Why do mitochondria have a double membrane?
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Evolutionary property. Took in some of cell membrane.
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Endoplasmic Reticulum location
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extends from nucleus
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These line up on the ER
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Ribosomes
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ER folds are called this
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Cisternae
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Role of golgi apparatus
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cellular post office
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What is in the cytosol?
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Everything inside PM minus membrane bound organelles.
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What is inside the cytoplasm?
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Everything inside the PM, minus the nucleus.
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Role of the cytoskeleton
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lattice for cell organization, structural
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Cytoskeleton is made from....
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proteins
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Size resolvable by light microscope....
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0.2 micrometers
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Size resolvable by electron microscope....
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0.2 nanometers
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Refractive index of air
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1
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frequency * wavelength =
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c
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What happens when light hits a cell?
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Slows Down + Phase Change
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Resolution vs. Magnification
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Ability to distinguish to two objects for resolution. Consider empty magnification (enlargement without increased resolution).
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Approx wavelength range for visible light
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400-700 nm (red -> violet)
white = 572nm. |
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Resolution formula
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D (resolution) = (0.61*lambda)/(n*sin(alpha))
lambda = wavelength; n = refractive index of medium a = angular aperature |
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Phase Contrast Microscope distinguished by:
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glowing boundaries (membranes, etc.)
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DIC Microscopy =
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Differential Phase Contrast
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DIC Microscopy distinguished by:
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Rate of change of refractive index. 3d-looking cells. Shadow = slow rate of change.
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Two important wavelengths in fluorescence: (and which is longer?)
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Excitation Wavelength
Emission Wavelength (longer) (lower energy) |
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Important Barrel-shaped fluorescing molecule
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Green Fluorescent Protein
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Immunofluorescence Pitfall
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Requires fixed cells
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Role of two antibodies in Immunofluorescence
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One engineered to bind to a specific protein. Second, labeled protein to bind to other antibody. (often goat to rabbit type second antibody)
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Induced Immunofluorescence
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make fluorescence occur only in presence of other molecules (i.e., to show how growth is influenced by presence of calcium)
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Benefit of Confocal Fluorescence Microscopy
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Users a laser to excite individual planes. 3D reconstructions
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What happens to electrons in electron microscopy?
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They pass through the specimen. Expose the sensor.
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What is the limiting factor in EM?
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Aperture.
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Some unfortunate things about EM.
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1.) Slide preparation takes a long time.
2.) Requires fixing of sample. 3.) Samples require staining with metals. |
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Really 3d-looking images come from which time of EM?
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SEM
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What EM produces flat-looking, lightmicroscope-esque (but better resolution, of course!) images
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Transmission EM
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Bacterial Cell size (Average)
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1-2 micrometers. (length)
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EM equivalent of fluorescent tags
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Gold nanoparticles (dense and blocks electrons)
Size of nanoparticle can be different so that various structures can be specifically imaged at once |
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Weak point of cell (especially during fracturing)
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cell membrane
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SEM uses electrons that........ the sample
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scatter off of
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Imaging that has grey levels
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LM and EM
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If color is presence, what type of microscopy?
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fluorescence
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3d-looking images, what type of microscopy?
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DIC, SEM, or shadowed TEM
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Composition of Cells
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Mostly Water, Ions, Small particles (77%)
Inorganic ions (1%) Small molecules (6%) |
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Type of reaction that occurs when monomer building blocks are formed into polymers.
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Condensation reactions
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Condensation reactions have byproduct of....
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H20
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Opposite of condensation reaction....
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Hydrolysis reaction
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Consumed during Hydrolysis reaction
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water
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Primary energy storage in humans
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Glycogen
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Transcription makes ____ from ____
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RNA from DNA
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Translation makes ____ from ____
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proteins from RNA.
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Amino Acids form together to make _____
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proteins
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Central carbon on Amino Acid is called
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alpha carbon
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Amino Acids are always written from ____ side to ____ side
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Amino to Carboxyl
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Amino group has ____ charge at neutral pH
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positive
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Carboxyl group has ____ charge at neutral pH
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negative
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Methionine (and corresponding group)
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--CH2--CH2--S--CH3 (hydrophobic/nonpolar)
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Cysteine (and corresponding group)
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--CH2--SH
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Lysine (and group)
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--CH2--CH2--CH2--CH2--NH3+
(positive charge/basic) |
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Are polar, positively charged R groups of Amino Acids acidic or basic?
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Basic
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Are polar, negatively charged R groups of Amino Acids acidic or basic?
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Acidic
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Lysine
(and group) |
CH2-CH2-CH2-CH2-NH3+
Polar, positively charged, basic |
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Aspartic Acid (and group)
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--CH2--C (=O) (--O(-))
Polar, negatively charged, Acidic |
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Smallest Amino Acid
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Glycine
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AA that can form disulfide links
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Cysteine
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Disulfide Link allows this
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cysteine to covalently bond with another cysteine
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Glyciene is special because
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its size lets it go where other molecules can not and it is neither hydrophilic or hydrophobic
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AA where the R group cyclically bonds to the Amino group
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Proline
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Proline's special ability
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cause a kink in a polypeptide chain
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This is formed after condensation reaction (not H2O)
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peptide
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What type of bond is a peptide bond?
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covalent
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Peptide bonds usually have cis or trans configuration?
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Trans (spread charges away from each other)
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Rotation is a property allowed by
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single bonds
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Primary Structure/type of bonding
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order of AA/covalent (polypeptide backbone)
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Secondary Structure/type of bonding
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3D Form (alpha helices, beta sheets), local structures, hydrogen bonding, and disulfide bonds (-S-S-)
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Tertiary Structure/type of bonding
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polypeptide chain (multiple a helices, beta sheets), ionic, hydrogen, single polypeptide, hydrogen bonding, ionic bonds, hydrophobic effects
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Quaternary Structure/type of bonding
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Multiple Polypeptides (= single protein), H bonding, ionic bonding, van der waals forces
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Alpha helix bonding type
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Hydrogen (oxygen bonds with Hydrogen)
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# amino acids/turn of alpha helix
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3.5
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Location of R groups on alpha helix
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Sticking Out
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Many alpha helices found here in a cell, and why
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membranes. non polar side groups sit well inside the hydrophobic regions of the membrane
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Beta Sheet bonding occurs between separate or local regions? and what type of bonding?
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hydrogen and separate
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parallel vs. antiparallel beta sheets
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parallel -- no tight bends. all sheets point in same direction (all carboxyl terminuses on same end, etc)
antiparallel -- has tight bends. good for glyceine due to small size and proline because of kinks |
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Single Polypeptides can not form this level of structure?
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Quaternary
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Proteins fold to maximize what?
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The number of hydrophilic R groups exposed to water
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Importance of protein folding
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to allow for appropriate interactions (ligands) folding produces a binding site
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Protein Domain
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Compact and stable region of a polypeptide
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Protein Motif
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Smaller structure than a domain and found in many proteins. (as a substructure) Think helix-turn-helix motif, alpha-beta barrel motif, etc.
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Coiled Coil Motif
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(a-b-c-d-e-f-g)n where a and d are hydrophobic regions that undergo interaction
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Common location for coiled coil motifs to be found
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myosin and kinesin (motor proteins)
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Domains are responsible for....
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specific function in proteins (nucleotide binding domain, hormone binding domain)
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If proteins have the same primary structure, do they have the same function?
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No, Folding can change function. Think kCJD. Change in conformation and now a poison.
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An enzyme is a type of _____.
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protein
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Function of an enzyme (general)
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to speed up chemical reaction rate without altering equilibrium
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Enzymes are/are not used up during a reaction.
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Are not.
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Enzymes are specific/not specific to individual compounds.
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very specific
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Spontaneous reactions have negative/positive delta G.
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negative (all reactions that occur in a cell *must* have a negative G)
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When at equilibrium, delta G =
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0
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Delta G = formula
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Delta H (Enthalpy) - Temperature * (delta S (enthropy))
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A positive delta G indicates a reaction is endergonic or exergonic?
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endergonic
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A negative delta G indicates a reaction is endergonic or exergonic?
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exergonic
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Knowing standard state delta g (nought), how to find delta G for specific reaction
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delta G = delta G nought + RT * ln([conc product1 * conc product 2 etc] / [conc reactant 1 * conc reactant 2 etc] where R is gas constant and T is temperature in Kelvin
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Delta G (nought( =
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-R*T*ln(Keq) where Keq is specific to the reaction. R is gas constant; T is temperature in kelvin
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ATP hydrolysis is (spontaneous/not spontaneous)
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spontaneous in the presence of water. results in ADP + phosphate
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How to encourage an endergonic reaction to go forward?
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couple with exergonic reaction. i.e. for sucrose formation from glucose and fructose; intermediate product is made with more negative delta G than desire reaction. If sum is still negative, now spontaneous.
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What to do if negative delta G is there, but reaction is too slow
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add catalyst
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How do catalysts work?
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Substrates bind to specific sites and interact while bound. Otherwise would not.
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Vmax
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Velocity (of reaction) and saturation point for an enzyme
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Kcat
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=Vmax/[Et] number of substrate molecules that a catalyst can convert to product per unit time. RATE
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Km
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Substrate concentration for which reaction velocity is 1/2 Vmax.
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Michaelis-Menten Equation
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V = (Vmax*[S]) / (Km + [S])
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Lineweaver-Burk Plot
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Slope = Km/Vmax; y int = 1/vmax; y = 1/v; x = 1/[s]; x int = -1/[Km]
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Can effect enzymatic activity
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inhibitors
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Competitive Inhibitor
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binds to an active site
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noncompetitive inhibitor
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bonds to a non-active binding site on enzyme and results in conformation change
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What kind of inhibitors change Km but not Vmax?
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Competitive Inhibitors
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What kind of inhibitors change Vmax but not Km
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Noncompetitive Inhibitor
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Allosteric Regulation
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Active binding to secondary binding site. Prohibits binding at primary binding site.
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Where in a pathway should inhibition take place to be most effective?
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Early.
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Protein Kinase
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Takes a phosphate group from ATP and adds it to an enzyme. Works opposite from phosphatase.
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Phosphatase
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Cleaves phosphate group from an enzyme changing the conformation.
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Negatively charged particles interact with ...... very easily
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enzymes
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Source of phosphates
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ATP
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Sink of phosphates
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ADP
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What can covalently linked to proteins to change their functions? (list)
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Phosphates, Methyls, Acetyls, Sugars, and Lipids
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Uses antibodies to detect and bind proteins
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Western Blot
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