Term
| Van der Waals Interaction |
|
Definition
| The ___ describes the relation between interatomic distances, electronic charge, solution dielectric and free energies |
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|
Term
| Interatomic Distances, electronic charge, solution dielectric and free energies |
|
Definition
| The Van der Waals Interactions describes the relation between ___, ___, ___, and ___ |
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|
Term
|
Definition
| Protein ___ defines the relation among subunits in a multisubunit lattice |
|
|
Term
| subunits in a multisubunit lattice |
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Definition
| Protein Quaternary Structure defines the relation among ___. |
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Term
|
Definition
| Protein ___ defines the amino acid sequence |
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Term
|
Definition
| Protein primary structure defines the ___ |
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Term
|
Definition
| Protein ___ defines the packing of helices, sheets, turns, etc |
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Term
| Packing of helices, sheets, thurns, etc |
|
Definition
| Protein tertiary structure defines the ___ |
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Term
|
Definition
| Protein __ defines the motifs formed by short-range interactions between amino acids |
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Term
|
Definition
| Protein secondary structure defines the motifs formed by ___ between amino acids |
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Term
|
Definition
| A ___ interaction involves polar O, N or both and the atom for which it is named, and constitutes one of the important protein stabilization elements |
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Term
| Protein stabilization elements |
|
Definition
| A hydrogen bond interaction involves polar O, N or both and the atom for which it is named, and constitutes one of the important ___ |
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Term
|
Definition
| ___ is used to determine the sequence of protein based on sequential chemical reactivity |
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Term
|
Definition
| Edman degradation is used to determine the ___ of a protein based on sequential chemical reactivity. |
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|
Term
| sequential chemical reactivity |
|
Definition
| Edman degredation is used to determine the sequence of a protein based on ___ |
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Term
|
Definition
| A ___ induces denaturation of proteins by disturbing the hydrophobic effect |
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Term
|
Definition
| A chaotrophic agent induces ___ by disturbing the hydrophobic effect |
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|
Term
|
Definition
| A chaotrophic agent induces denaturation of proteins by disturbing the ___ |
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Term
|
Definition
| A ___ is a graph of the conformational torsion angles for the residues in a protein or peptide, a map of the structure of polypeptide backbone |
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Term
| Conformational torsion angles |
|
Definition
| A ramachandran plot is a graph of ___ for residues in a protein or peptide, a map of the structure of the polypeptide backbone |
|
|
Term
| structure of polypeptide backbone |
|
Definition
| A ramachandran plot is a graph of the conformational torsion angles for the residues in a protein or peptide, a map to the ____ |
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Term
|
Definition
| A ___ has two charges which neutralize each other |
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Term
|
Definition
| A zwitter ion has two charges which ___ each other |
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|
Term
|
Definition
| The ___ is the primary force of protein structural stabilization |
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|
Term
|
Definition
| The hydrophobic effect is the primary force of protein ___ |
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|
Term
|
Definition
| The ___ is the characteristic speed of an enzyme's kinetics extrapolated to the time when a defined amount of substrate is added to the enzyme solution. |
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Term
| amount of substrate is added to the enzyme solution |
|
Definition
| The initial rate is the characteristic speed of an enzyme's kinetics extrapolated to the time when a defined ___. |
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Term
|
Definition
| An act of ___ does not change an enzyme and lowers the transition state free energy of the associated reaction |
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Term
| Enzyme, Transition state free energy |
|
Definition
| An act of catalysis does not change an ___ and lowers the ___ of the associated reaction |
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Term
|
Definition
| The ___ of an enzymatic catalysis reaction is achieved when it is saturated with substrate. |
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|
Term
|
Definition
| The maximum velocity of an enzymatic catalysis reaction is achieved when it is ___. |
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|
Term
|
Definition
| The ___ equation defines parameters that are used to characterize the kinetics of an enzyme |
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|
Term
|
Definition
| The Lineweaver-Burk equation defines parameters that are used to characterize the ___. |
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Term
|
Definition
| ___ is the substrate concentration when vo = vmax/2, or michaelis-menten constant |
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|
Term
|
Definition
| Km is the ___ when vo = vmax/2, or michaelis-menten constant |
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|
Term
| Michaelis-Menten constant |
|
Definition
| Km is the substrate concentration when vo = vmax/2, or ___ |
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|
Term
|
Definition
| A ___ is the enzyme-substrate combination formed during an enzyme catalysis event. |
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|
Term
|
Definition
| A Michaelis complex is the enzyme-substrate combination formed during an ___. |
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|
Term
|
Definition
| The ___ of an enzyme is abbreviated as kcat. |
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|
Term
|
Definition
| The catalytic rate constant of an enzyme is abbreviated as ___. |
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|
Term
|
Definition
| ___ of an enzyme catalysis occurs when an inhibitor bonds to the active site of an enzyme |
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|
Term
|
Definition
| ___ of enzyme catalysis occurs when the inhibitor only binds to the enzyme substrate complex |
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|
Term
| binds to the enzyme substrate complex |
|
Definition
| Uncompetitive inhibition of enzyme catalysis occurs when the inhibitor only ___ |
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|
Term
| steady state approximation |
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Definition
| The ___ postulates that a constant input feed of substrate is supplied whose rate equals that of product formation |
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|
Term
| Hydrophobic effect, H-Bonding, disulfide bonds, van der Waals forces, ionic bonds or dipole-dipole intractions |
|
Definition
| Two internal factors that limit velocity of an enzymatic reaction are ___ and ___. |
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|
Term
| pH, solvent polarity, temperature, salt concentration, presence of chaotrophs |
|
Definition
| Two external factors that limit the velocity of an enzymatic reaction are ___ and ___. |
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|
Term
|
Definition
| What amino acid and functional group in the esterase site of acetylcholine esterase reacts with the substrate? |
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|
Term
|
Definition
| Pyrimidine aldoximine methiodine (PAM) reactivates acetylcholine esterase, functioning as a ___ |
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|
Term
| Pyrimidine aldoximine methiodine |
|
Definition
| ___(PAM) reactivates acetylcholine esterase, functioning as a Nerve gas anticdote |
|
|
Term
| Nulceophilic substitution |
|
Definition
| What kind of reaction produces the reactivated enzyme? |
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|
Term
|
Definition
| The bisubstrate enzyme ___reaction is used by transaminases in the exchange of amino group for a carbonyl group between two progressively binding substrates |
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|
Term
|
Definition
| The bisubstrate enzyme ping-pong reaction is used by ___ in the exchange of amino group for a carbonyl group between two progressively binding substrates |
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|
Term
|
Definition
| An ___ works by amplifying an initial signal via several linked protease cleavage reaction stages |
|
|
Term
| amplifying an initial signal |
|
Definition
| An Enzyme cascade works by ___ via several linked protease cleavage reaction stages |
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|
Term
|
Definition
| A ___ is a protein that is converted from inactive to active forms by a covalent modification typically protease clevage. |
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|
Term
|
Definition
| A Zymogen is a protein that is converted from inactive to active forms by a ___ typically protease clevage. |
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|
Term
| typically protease clevage |
|
Definition
| A Zymogen is a protein that is converted from inactive to active forms by a covalent modification; ___. |
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|
Term
|
Definition
| A ___ of an enzyme as a result of binding of a product from the reaction in question or subsequent reactions is referred to as feedback inhibition. |
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|
Term
|
Definition
| A decrease in the activity of an enzyme as a result of binding of a product from the reaction in question or subsequent reactions is referred to as ___. |
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|
Term
|
Definition
| ____ involves binding of a regulatory molecule at a site other than the active site |
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|
Term
|
Definition
| Allosterism involves binding of a ___ at a site other than the active site |
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|
Term
|
Definition
| ___ and ___ reactions, involving phosphate addition and removal respectively, regulate both glycolysis and the Krebs cycle. |
|
|
Term
| phosphate addition, removal |
|
Definition
| Kinase and phoaphatase reactions, involving ___ and ___ respectively, regulate both glycolysis and the Krebs cycle. |
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|
Term
|
Definition
| ___ regulates entry and exit from mitosis by catalyzing a covalent modification reaction |
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|
Term
| Entry and exit from mitosis |
|
Definition
| Cyclin Kinase regulates ___ by catalyzing a covalent modification reaction |
|
|
Term
| catalyzing a covalent modification reaction |
|
Definition
| Cyclin Kinase regulates entry and exit from mitosis by ____. |
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|
Term
|
Definition
| What two amino aids are modified in the reactions catalyzed by cyclin kinase? |
|
|
Term
| noncovalent modifications, pH changes, salt concentration changes |
|
Definition
| Two examples of reversible factors that control the catalytic capability of an enzyme are: |
|
|
Term
| covalent modification, proteolysis, irreversible inhibitors |
|
Definition
| Two examples of irreversible factors that control the catalytic capability of an enzyme are: |
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|
Term
|
Definition
| The ___ accounts for the temperature dependence of the rate of a reaction. |
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|
Term
|
Definition
| The Arrhenius equation accounts for the ___ of the rate of a reaction. |
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|
Term
|
Definition
| Two chemical modes of catalysis |
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|
Term
|
Definition
| Acid base and covalent catalysis are two types of ___ modes of catalysis |
|
|
Term
| Proximity effect, transition-state stabilization |
|
Definition
| Two binding modes of catalysis |
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|
Term
|
Definition
| Proximity effect and transition state stabilization are two ___ modes of catalysis |
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|
Term
|
Definition
| A ___attacks an electropositive site in its role in a chemical (enzymatic) reaction. |
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|
Term
|
Definition
| A nucleophile attacks an ___ site in its role in a chemical (enzymatic) reaction. |
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|
Term
|
Definition
| A common process used to produce a nucleophile is |
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|
Term
|
Definition
| The most common amino acid used by enzymes to carry out acid-base catalysis is |
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|
Term
|
Definition
| A "catalytic triad" of amino acids is typically present in (enzyme class name) |
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|
Term
|
Definition
| A ___ of amino acids is typically present in serine proteases |
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|
Term
|
Definition
| The amino acids "collaborate" to accomplish ___ |
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|
Term
|
Definition
| The most typically cited currency of energy in metabolism is |
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|
Term
|
Definition
| ___ is typically required to achieve optimal activity with ATP cosubstrate enzyme reactions |
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|
Term
|
Definition
| A coenzyme is loosely bound cosubstrate or tightly bound ___. |
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|
Term
|
Definition
| A coenzyme is loosely bound ___ or tightly bound prosthetic group |
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|
Term
|
Definition
| The heavy metal molybdenum is used to facilitate the biochemical reaction in ___, a key enzyme in purine catabolism. |
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|
Term
|
Definition
| The heavy metal molybdenum is used to facilitate the biochemical reaction in Xanthine oxidase, a key enzyme in ___. |
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|
Term
|
Definition
| When ATP is used in some biochemical applications it yields ___ and ___. |
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|
Term
|
Definition
| The (vitamin) ___ is required to synthesize a coenzyme NAD+ for use in metabolic redox reactions. |
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|
Term
|
Definition
| The (vitamin) nicotinamide is required to synthesize a coenzyme ___ for use in metabolic redox reactions. |
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|
Term
|
Definition
| The (vitamin) nicotinamide is required to synthesize a coenzyme NAD+ for use in ___ reactions. |
|
|
Term
|
Definition
|
|
Term
|
Definition
| The coenzyme ___ often forms a Schiff base with the E-amino group of a lysine residue in the enzyme |
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|
Term
|
Definition
| The coenzyme pyridoxal phosphate often forms a ___ with the E-amino group of a lysine residue in the enzyme |
|
|
Term
|
Definition
| The coenzyme pyridoxal phosphate often forms a Schiff base with the E-amino group of a ___ in the enzyme |
|
|
Term
|
Definition
| What chemical group does coenzyme A typically carry in the course of its biochemical function? |
|
|
Term
|
Definition
| The ___-avidin noncovalent binding interaction is used to capture ligand-binding entities in the "affinity capture" technique. |
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|
Term
|
Definition
| The Biotin-avidin noncovalent binding interaction is used to capture ligand-binding entities in the ___ technique. |
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|
Term
|
Definition
| The Biotin-avidin noncovalent binding interaction is used to capture ___ in the "affinity capture" technique. |
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|
Term
|
Definition
| The coenzyme ___ is required to incorporate the methyl group into thymidine, a necessary prerequisite for the production of DNA |
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|
Term
|
Definition
| The coenzyme N5, N10 tetrahydrofolate is required to incorporate the methyl group into ___, a necessary prerequisite for the production of DNA |
|
|
Term
|
Definition
| The coenzyme N5, N10 tetrahydrofolate is required to incorporate the methyl group into thymidine, a necessary prerequisite for the ___ |
|
|
Term
|
Definition
| Our understanding of the N5, N10 tetrahydrofolate coenzyme in DNA production is used in a strategy for ___ |
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|
Term
|
Definition
| The coenzyme bound carbohydrate ___ and ___ are required to synthesize lactose. |
|
|
Term
|
Definition
| The coenzyme bound carbohydrate UDP-galactose and glucose are required to synthesize ___. |
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|
Term
|
Definition
| ___ functions in transducing the signal of a photon of light into a chemically recognizable form |
|
|
Term
|
Definition
| Cis-retinal functions in ___ the signal of a photon of light into a chemically recognizable form |
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|
Term
|
Definition
| Two important straight chain forms of carbohydrate structure are ___ and ___ |
|
|
Term
|
Definition
| Two important ring conformations of Beta-D-glucopyranose are the ___ and ___. |
|
|
Term
|
Definition
| The ___ containing compound inositol triphosphate is released by phospholipidase C in the phospholipid signal transduction mechanism. |
|
|
Term
|
Definition
| The cyclohexane ring containing compound ___ is released by phospholipidase C in the phospholipid signal transduction mechanism. |
|
|
Term
|
Definition
| The cyclohexane ring containing compound inositol triphosphate is released by ___ in the phospholipid signal transduction mechanism. |
|
|
Term
| phospholipid signal transduction |
|
Definition
| The cyclohexane ring containing compound inositol triphosphate is released by phospholipidase C in the ___ mechanism. |
|
|
Term
|
Definition
| The acronym NAG is an abbreviation for |
|
|
Term
|
Definition
| The key polysaccharide in starch is |
|
|
Term
|
Definition
| The key polysaccharide in the liver is |
|
|
Term
|
Definition
| Then antibiotic ___ selectively inhibits cell wall peptidoglycan synthesis in bacteria. |
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|
Term
|
Definition
| Then antibiotic penicillin selectively inhibits cell wall ___ in bacteria. |
|
|
Term
|
Definition
| Extra-cellular surface ___ regulate the osmotic pressure around cells. |
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|
Term
|
Definition
| Extra-cellular surface carbohydrates regulate the ___ around cells. |
|
|
Term
|
Definition
| Phospholipidase C produces two different second messengers in the phospholipid signal transduction pathway. The lipid containing second messenger is |
|
|
Term
|
Definition
| The compound chondroitin sulfate ___ cartilage and skeletal joints. |
|
|
Term
|
Definition
| The compound ___ lubricates cartilage and skeletal joints. |
|
|
Term
|
Definition
| ___ fatty aids of the same length have lower melting temperature. |
|
|
Term
|
Definition
| Lipid Tm values monitor the transformation from ___ to dispersed form |
|
|
Term
|
Definition
| Lipid Tm values monitor the transformation from liquid crystal to ___ form |
|
|
Term
|
Definition
| Lipid ___ values monitor the transformation from liquid crystal to dispersed form |
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|
Term
|
Definition
| Lipid ___ are composed of two face-to-face monolayers while lipid ___ form a biphasic sphere |
|
|
Term
| monolayers, biphasic sphere |
|
Definition
| Lipid bilayers are composed of two face-to-face ___ while lipid micells form a ___. |
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|
Term
|
Definition
| The post popular model for biological membrane is called the ___ |
|
|
Term
| adenine, guanine, cytosine, uracil |
|
Definition
| The 4 nucleid acid bases in RNA are |
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|
Term
|
Definition
| The two normal base pairs in DNA and RNA are called ___ base pairs |
|
|
Term
|
Definition
| The ___ bond in a nucleoside connects the base to sugar |
|
|
Term
|
Definition
| The glycosidic bond in a ___ connects the base to sugar |
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|
Term
|
Definition
| The ___ can be used to determine if a double helix forms from 2 single strands of DNA or RNA |
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|
Term
|
Definition
| The absorbance at 260 nm can be used to determine if a ___ forms from 2 single strands of DNA or RNA |
|
|
Term
|
Definition
| The face-to-face interaction between nucleic acid bases is called ___ |
|
|
Term
| phosphodiester phosphates. |
|
Definition
| Counterions bind all nucleic acids are are required to neutralize the ___. |
|
|
Term
|
Definition
| ___ bind all nucleic acids are are required to neutralize the phosphodiester phosphates. |
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|
Term
|
Definition
| The proteins called ___ serve the counterion (where phosphodiester phosphates are neutralized) function in the case of most chromosomal DNA. |
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|
Term
|
Definition
| The ___ catalyzes alkaline hydrolysis of RNA, a good example of anchiomeric assistance in a non-protein bimolecular mechanism |
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|
Term
|
Definition
| The 2'-hydroxyl group catalyzes alkaline hydrolysis of RNA, a good example of ___ in a non-protein bimolecular mechanism |
|
|
Term
| non-protein bimolecular mechanism |
|
Definition
| The 2'-hydroxyl group catalyzes alkaline hydrolysis of RNA, a good example of anchiomeric assistance in a ___ |
|
|
Term
| antisense oligonucleotide |
|
Definition
| An ___ functionally inactivate a mRNA for use in translation by a ribosome by forming a double helix with it and precluding tRNA anticodon binding. |
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|
Term
|
Definition
| An antisense oligonucleotide functionally inactivate a mRNA for use in translation by a ribosome by forming a double helix with it and precluding ___ binding. |
|
|
Term
|
Definition
| An antisense oligonucleotide functionally inactivate a mRNA for use in translation by a ribosome by forming a ___ with it and precluding tRNA anticodon binding. |
|
|
Term
| ribosomal RNA and transfer RNA |
|
Definition
| The two most prevalent of the 4 classes of DNA |
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|
Term
| Monocistronic, containing introns and exons, poly A tail |
|
Definition
| Two distinctive features of most eukaryotic mRNA are: |
|
|
Term
|
Definition
| A ___ is used to detect the presence of a specific complementary nucleic acid sequence |
|
|
Term
| Restriction endonucleases |
|
Definition
| ___ are required to produce, manipulate, and clone specific pieces of DNA |
|
|
Term
| Anticodon and amino acid acceptor |
|
Definition
| Two functional ends of transfer RNA |
|
|
Term
| glycolysis, Krebs cycle, electron transport/oxidative phosphorylation |
|
Definition
| The three most catabolic pathways of intermediary metabolism are |
|
|
Term
| ATP, NADH, FADH2, Coenzyme Q |
|
Definition
| 4 major compounds in which energy is captured in a chemically usable form by metabolic reaction pathways are |
|
|
Term
|
Definition
| The ___ (Q) corrects for deviations from standard state concentrations (1M) |
|
|
Term
| standard state concentrations |
|
Definition
| The mass action ratio (Q) corrects for deviations from ___(1M) |
|
|
Term
|
Definition
| Number of steps in glycolysis control most of the flux through the pathway under actual cellular conditions |
|
|
Term
| Metabolically irreversible, near equilibrium |
|
Definition
| The 3 reactions in glycolysis that control the flux through the pathway are ___ while the others are ___. |
|
|
Term
| actual concentration of the reactant |
|
Definition
| The kinetics of an enzyme reaction are most easily controlled when Km is approximately equal to the ___. |
|
|
Term
|
Definition
| The kinetics of an enzyme reaction are most easily controlled when Km is ___ to the actual concentration of the reactant. |
|
|
Term
|
Definition
| The kinetics of an enzyme reaction are most easily controlled when ___ is approximately equal to the actual concentration of the reactant. |
|
|
Term
| triose phosphate isomerase |
|
Definition
| The enzyme ___converts dihydroxyacetone phosphate into glyceraldehyde-3-phosphate. |
|
|
Term
| dihydroxyacetone phosphate glyceraldehyde-3-phosphate |
|
Definition
| The enzyme triose phosphate isomerase converts ___ into ___. |
|
|
Term
|
Definition
| When citrate negatively regulates the phosphofructokinase-1 reaction, the general name for this reaction is |
|
|
Term
|
Definition
| When fructose-1,6-bissphosphate stimulates teh pyruvate kinase reaction, the general name for this is |
|
|
Term
| Acetyl CoA, ethanol, lactate |
|
Definition
| 3 possible catabolic fates of pyruvate are |
|
|
Term
|
Definition
| The enzyme alcohol dehydrogenase converts ___ to ethanol |
|
|
Term
|
Definition
| The enzyme alcohol dehydrogenase converts acetaldehyde to ___ |
|
|
Term
| Dihydrolipoamide acetyl transferase |
|
Definition
| ___ used the coenzyme lipoic acid in "fueling" the Krebs cycle? |
|
|
Term
|
Definition
| What "symport" reaction accompanies import of pyruvate into the mitochondrion and what enzyme catalyzes the reaction? |
|
|
Term
isocitrate dehydrogenase
alpha-ketogluterate dehydrogenase |
|
Definition
| The two "oxidative decarboxylation" reactions of the Krebs cycle are catalyzed by ___ and ___. |
|
|
Term
|
Definition
| list the reactions, coenzymes, cofactors, and enzymes involved with "substrate-level phosphorylation" reaction of the Krebs cycle |
|
|
Term
fumerase
malate dehydrogenase |
|
Definition
| The enzymes ___ and ___ "fix" a carbonyl group on succinate in the production of oxaloacetate. |
|
|
Term
|
Definition
| The enzymes fumerase and malate dehydrogenase "fix" a carbonyl group on succinate in the production of ___. |
|
|
Term
|
Definition
| What 2C compound is fixed to OAA after the fumerase and malate dehydrogenase step? |
|
|
Term
|
Definition
| What amino acid and what product of pyruvate metabolism are the principle substrates for gluconeogenesis in mammals? |
|
|
Term
|
Definition
| What energy sources are used to produce the "protomotive force"? |
|
|
Term
|
Definition
| What enzyme complex uses the proton gradient phenomenon as the driving energy for ATP synthesis in oxidative phosphorylation? |
|
|
Term
| exports H+ from mitochondrion |
|
Definition
| How does electron transport drive production of the protomotive force? |
|
|
Term
| 4 - oxidation 1, hydration, oxidation 2, thiolysis |
|
Definition
| How many reactions does each round of Beta-oxidation of fatty acid require? |
|
|
Term
| 1 CoQH2, 1NADH, H+, 1 acetyl CoA, 1 Fatty acid (minus 2 C's) |
|
Definition
| What are the products of one round of Beta-oxidation and how many ATP equivalents of energy conserving products? |
|
|
Term
| CoA, FAD/FADH2, Fe-S2+/3+, CoQ/CoQH2 |
|
Definition
| A set of coupled cofactor regeneration cycles siphon off reducing equivalents then fix them into coQ in reactions that are coupled to the first oxidative step of fatty acid beta-oxidation. Write names of cofactors |
|
|
Term
| succinate dehydrogenase, fumerase, malate dehydrogenase |
|
Definition
| Which 3 steps of the Krebs Cycle do the first three steps of the fatty acid Beta-oxidation cycle resemble |
|
|
