Category - Definitions

Query - What definition best describes the term below?

Reversal

Category - Term Recognition

Query - What term does the description below refer to?

(Terms are shown on left, descriptions in middle, figures on right)

5-Adenosylcobalamin | An enzymatically active form of vitamin B 12 responsible for isomerization of glutamate to methylaspartate. | Figure 20.19 | Adenylylation/deadenylylation | Covalent modification mechanism that regulates glutamine synthetase. In it, a specific tyrosine residue (close to the active site) reacts with ATP to form an ester between the phenolic hydroxyl group and the phosphate of the resultant AMP. Twleve sites in glutamine synthetase can be adenylylated. The effect is cumulative. Inhibition is correlated with the amount of adenylylation. The enzyme catalyzing the reaction is a complex of adenylyl transferase and a regulatory protein called PII. | Figure 20.9 | Anaerobic | Refers to the absence of oxygen or the absence of a need for it. |  | Antimetabolite | A synthetic compound, usually a structural analog of a normal metabolite, that interferes with the utilization of the metabolite to which it is structurally related. |  | Autolysis | The digestion of the cell by lysosomes as a normal morphogenetic process in development. |  | Biological Nitrogen Fixation | A term used to describe reduction of N2 to NH3. | Figure 20.2 | Calpains | Two calcium activated proteases in the cytosol |  | Cathepsins | A group of lysosomal proteases designed to work under acidic conditions |  | Cobamides | Term for a compound containing B 12. This arises from the fact that such molecules have many amide nitrogens and cobalt. |  | Corrin Ring | Tetrapyrrole ring that coordinates cobalt in vitamin B12. | Figure 20.18 | Cumulative feedback Inhibition | A regulatory mechanism that controls the activity of glutamine synthetase. It involves the action of eight specific feedback inhibitors. Six of the inhibitors are metabolic endproducts of glutamine metabolism (tryptophan, histidine, glucosamine-6-phosphate, carbamoylphosphate, CTP and AMP). Two of the inhibitors are indicators of the general status of amino acid metabolism (alanine, glycine). | Figure 20.9 | Cytochrome 557 | Name of the cytochrome bound by nitrate reductase. It accepts electrons from the FAD cofactor and passes them on to the molybdenum cofactor. |  | Denitrifying Bacteria | Bacteria which catabolize NH3 to N2 | Figure 20.2 | Dihydrofolate (DHF) | A reduced form of folic acid produced by dihydrofolate reductase-catalyzed reduction of folate using NADPH |  | Essential Amino Acids | Amino acids that must be provided in the diet to meet an animal's metabolic needs. |  | Ferredoxin | A low potential electron carrier in Rhizobium, which donates electrons for the reduction of atmospheric nitrogen. | Figure 20.4 | Flavodoxin | A low potential electron carrier in Klebsiella, which donates electrons for the reduction of atmospheric nitrogen. | Figure 20.4 | Glucogenic | Substances (such as some amino acids) that can be used as substrates for glucose synthesis. |  | Glucose-Alanine Cycle | Muscle cycle for handling ammonia in which pyruvate from glycolysis is converted to alanine, which carries the amine nitrogen to the liver, where it is converted back to pyruvate for gluconeogenesis. | Figure 20.14 | Glycine Cleavage System | A multienzyme complex in mitochondria catalyzing the reaction: Glycine + Tetrahydrofolate + NAD+ <=> 5,10-methylenetetrahydrofolate + CO2 + NH3 + NADH + H+ |  | Intrinsic Factor | A glycoprotein secreted by gastric tissue that complexes with ingested B12 in the digestive tract and promotes its absorption through the small intestine into the blood. |  | Ketogenic | Substances (such as some amino acids) that can be used as substrates for ketone body synthesis. |  | Lysosomes | Eukaryotic cell organelle which forms by budding of the Golgi complex. It contains many digestive enzymes, including proteases, nucleases, lipases, and enzymes that break down carbohydrates |  | Methionine Synthase | Homocysteine + Methylcobalamin <=> Methionine + Vitamin B12 |  | Methylcobalamin | An enzymatically active form of vitamin B 12 that transfers a methyl group to homocysteine, converting it to methionine. |  | Negative Nitrogen Balance | A condition of nitrogen metabolism that exists in senescence, starvation, and certain disease states in which the daily intake of nitrogen is less than the daily loss of nitrogen. |  | nif | A gene cluster of about 24,000 bases in Klebsiella involved in nitrogen fixation. |  | Nitrobacter | A genus of bacteria that oxidizes NO2- to NO 3- for energy. | Figure 20.2 | Nitrogen Equilibrium (Normal Nitrogen Balance) | A condition of nitrogen metabolism that exists in a well-nourished adult in which the daily intake of nitrogen equals daily loss of nitrogen. |  | Nitrogenase Complex | The enzyme system responsible for N2 reduction. |  | Nitrosomonas | A genus of bacteria that oxidizes NH3 to NO2- for energy | Figure 20.2 | Nonessential Amino Acids | Amino acids that need not be provided in an animal's diet because they can be biosynthesized in adequate amounts. |  | Pernicious Anemia | Stomach disease arising from insufficient secretion of intrinsic factor. |  | Positive Nitrogen Balance | A condition of nitrogen metabolism that exists during pregnancy, in juveniles, or in recovery from starvation, in which the daily intake of nitrogen equals or exceeds daily loss of nitrogen. |  | Proteasome | A large ATP-dependent protease found in the eukaryotic cytosol. |  | Pyridoxal Phosphate | A coenzyme in aminotransferases derived from vitamin B 6. Catalysis begins with condensation of the aldehyde of this group with the amino group of an amino acid, to give a Schiff base or aldimine, intermediate. |  | Siroheme | A partially reduced iron porphyrin found in nitrite reductase. |  | Transamination | A reaction involving transfer of the amino group (usually of glutamate) to an -keto acid, with formation of the corresponding amino acid plus the -keto derivative of glutamate (- ketoglutarate). Catalyzed by aminotransferases (transaminases) |  | Ubiquitin | A 76-residue, heat-stable protein found in all eukaryotic cells that is covalently attached to another protein to target it for degradation. | Figure 20.11 | Ubiquitination | An ATP-dependent reaction which attaches the C-terminal glycine residue of ubiquitin to lysine amino acid groups on a target protein. Such modified proteins are degraded soon afterward by a large protease complex that requires ATP and recognizes the ubiquitin marker. | Figure 20.11 | Urea | Chemical form in which most mammals excrete the bulk of their nitrogen. |  | Uric Acid | Chemical form in which birds, terrestrial reptiles, and insects convert most of their excess ammonia to for excretion. |

Oreotelic Organisms | Orgnaisms that excrete most of their nitrogen in the form of urea. |

Leghemoglobin | An abundant protein found in the root nodules of plants infected with Rhizobium. It assists in nitrogen fixation by binding any O2 that makes its into the nodule. This helps to maintain the strict anaerobic environment required for nitrogen fixation to occur. |

Urea Cycle | Cyclic, synthetic pathway discovered by Hans Krebs and Kurt Henseleit in 1932. The cycle is a major pathway of nitrogen metabolism. | Figure 20.13

Category - General

Query - What description best fits this enzyme from Chapter 20?

Reversal

Category - Enzymes

Query - What enzyme best fits the description below?

(Enzyme on left, description in middle, figures on right)

Nitrogenase reductase (iron protein) | Also called component II of the nitogenase complex. It transfers electrons from ferredoxin of flavodoxin to component I. It contains an iron sulfur cluster fe4S4. | Figure 20.4 | Adenylyl Transferase | An enzyme in complex with a protein called PII that catalyzes either adenylylation or deadenylylation of glutamine synthetase, depending on the state of PII. If PII is deuridylylated, it catalyzes adenylylation. If it is uridylylated, it catalyzes deadenylylation. | Figure 20.9 | Uridylyl Transferase | Catalyzes transfer of a UMP residue to a specific site on the PII protein that regulates adenylyl transferase. The enzyme is stimulated by ATP and -ketoglutarate and inhibited by glutamine. | Figure 20.9 | Nitrogenase (molybdenum-iron protein) | Also called component I of the nitrogenase complex. It catalyzes the reduction of N2. It contains an iron sulfur cluster fe4S4 and a tightly bound iron-molybdenum cofactor. | Figure 20.4, Figure 20.5

L-Amino acid oxidase | A flavoprotein enzyme catalyzing conversion of an amino acid to an -keto acid with reduction of a flavin, FMN, to FMNH2. |

Nitrate Reductase | An enzyme which catalyzes reduction of nitrate to nitrite using electrons from NADH or NADPH. It contains bound FAD, molybdenum, and cytochrome 557 (which contains an Fe4S4 complex). The reaction is as follows: NO 3- + NAD(P)H + H+ <=> NO2- + NAD(P) + H2O |  | Nitrite Reductase | Enzyme which carries out the three steps of reduction of nitrite to ammonia: NO2- -> NO- -> NH2OH -> NH3 It contains one Fe2S2 center and one molecule of siroheme, a partially reduced iron porphyrin. The electron donor is ferredoxin. |  | Glutamate dehydrogenase | Enzyme that catalyzes the reductive amination of -ketoglutarate: -ketoglutarate + NH3 + NAD(P)H + 2H+ <=> Glutamate + H2O + NAD(P) It is activated by ADP or GDP and inhibited by ATP or GTP. The enzyme is used primarily for assimilation of ammonia in bacteria, but is probably used primarily for energy generation in animal cells. |

Glutamine Synthetase | The enzyme contains 12 identical subunits that form two facing hexagonal arrays. It is regulated by cumulative feedback inhibition and covalent modification of the enzyme brought about by a regulatory cascade. | Figure 20.8

Category - General

Query - Describe the function of the molecule below

Reversal

Category - Molecules

Query - What molecule fits this description?

(molecule on left, function in center, figures on right)

Uric Acid | Chemical form to which birds, terrestrial reptiles, and insects convert most of their excess ammonia for excretion. |

Dihydrofolate (DHF) | A reduced form of folic acid produced by dihydrofolate reductase-catalyzed reduction of folate using NADPH |

Pyridoxal Phosphate | A cofactor used in transamination and other reactions of amino acid metabolism. A derivative of pyridoxine, also known as vitamin B6. |  | Molybdopterin | A common molybdenum containing structure found in all molbdenum-requiring enzymes, except nitrogenase. |  | Tetrahydrofolate (THF) | A fully reduced form of folic acid, produced by dihydrofolate reductase-catalyzed reduction of dihydrofolate, using NADPH. |  | Fumarate | Amino acid formed by action of argininosuccinase on argininosuccinate. Another product of the reaction is arginine. | Figure 20.13 | Arginine | Amino acid formed by action of argininosuccinase on argininosuccinate. Another product of the reaction is fumarate. | Figure 20.13 | Folic Acid | Coenzyme important in one-carbon metabolism |  | Ornithine | Formed by hydrolyzing arginine (catalyzed by arginase). Urea is a product of the reaction. | Figure 20.13 | Citrulline | Urea cycle intermediate formed by combination of ornithine and carbamoyl phosphate. The enzyme catalyzing the reaction is ornithine transcarbamoylase. | Figure 20.13 | Aspartate | Urea cycle intermediate formed in a reaction catalyzed by transaminase action on oxaloacetate. | Figure 20.13 | Argininosuccinate | Urea cycle intermediate formed in an ATP requiring reaction by linkage of aspartate to citrulline. The enzyme catalyzing the reaction is argininosuccinate synthetase. | Figure 20.13 | Urea | Chemical form in which most mammals excrete the bulk of their nitrogen. |

Category - Structures

Query - What is the structure of the molecule below?

Reversal

Category - Molecules

Query - What is the name of the molecule with the structure below?

(molecule on left, structure in middle, figure on right)

Pyridoxal Phosphate | Structure |  | Fumarate | Structure |  | Arginine | Structure |  | Folic Acid | Structure |  | Ornithine | Structure |  | Citrulline | Structure |  | Aspartate | Structure |  | Argininosuccinate | Structure |  | Urea | Structure |  | Malate | Structure |  | Oxaloacetate | Structure |  | Aminopterin | Structure |  | Amethopterin (methotrexate) | Structure |  | Uric Acid | Structure |  | Pyridoxine | Structure |

Category - General

Query - Is contained in the left column below, solution in middle, figure on right

Reversal - there is no reversal

What are the eight inhibitors of glutamine synthetase? | Tryptophan, histidine, glucosamine-6-phosphate, carbamoylphosphate, CTP, alanine, glycine, and AMP |

What four structural features affect the turnover rate of a protein? | 1. Ubiquitination 2. Metal-catalyzed oxidation of particular residues 3. PEST sequences 4. Particular N-terminal residues |

What are the two proteins of the nitrogenase complex? | Component I - Nitrogenase (molybdenum-iron protein) Component II - Nitrogenase reductase (iron protein) | Figure 20.4

What is unusual about the nitrogenase complexes of Azotobacter? | It has three such systems, one of which uses vanadium instead of molybdenum and one that has iron as the sole bound material. |  | Which amino acids in proteins are most sensitive to oxidation by fe2+ or hydroxyl radical? | Lysine, arginine, and proline. |

Which organisms mentioned in Chapter 20 can reduce atmospheric nitrogen to ammonia? | The soil bacteria, Klebsiella and Azotobacter; cyanobacteria (blue-green algae); and Rhizobium, which lives symbiotically in the roots of leguminous plants, such as beans or alfalfa. |  |  |  |  | What function is performed by leghemoglobin in root nodules of plant infected with Rhizobium? | It helps to maintain the strict anaerobic environment required for nitrogen fixation to occur by tightly binding any oxygen that gets into the nodule. |  | What are electron sources for reduction of atmospheric nitrogen? | Low potential electron carriers, either ferredoxin or flavodoxin |  | What is a byproduct of nitrogen reduction? | Hydrogen |  | What is the first step in reduction of nitrate to ammonia? | Reduction of nitrate to nitrite |  | How is the molybdenum bound in nitrate reductase? | In a pteridine ring-containing structure called molybdopterin. |  | What is the electron donor for reduction of nitrite to ammonia? | Ferredoxin |  | How is ammonia assimilated in all organisms? | Via reactions leading to glutamate, glutamine, asparagine, and carbamoyl phosphate. | Figure 20.7 | Which two amino acids are involved in assimilation of most of the ammonia? | Glutamate and glutamine |  | Ammonia assimilated through glutamine is passed on to what biological molecules? | Purine nucleotides, cytidine nucleotides, amino sugars, tryptophan, and histidine. | Figure 20.7 | Ammonia assimilated through carbamoyl phosphate is passed on to which biological molecules? | Arginine, pyrimidines, urea | Figure 20.7 | Where is glutamate dehydrogenase located in animal cells? | Mitochondria |  | Why is it thought that glutamate synthase has a larger role in glutamate synthesis than glutamate dehydrogenase? | Because glutamate dehydrogenase has a relatively high KM for ammonia |  | Which enzyme exhibits cumulative feedback inhibition and covalent modification of the enzyme? | Glutamine synthetase |  | What amino acids are often deficient in plant proteins? | Lysine, methionine, and tryptophan |  | Which two amino acids in animal cells do not have aminotransferases for their synthesis from corresponding -keto acids? | Threonine and lysine |  | What amino acid is most commonly involved in aminotransferase reactions? | Glutamate |  | Which two transaminase enzymatic activities are monitored to measure damage to heart and liver? | Serum Glutamate-Oxaloacetate Transaminase (SGOT) and Serum Glutamate-Pyruvate Transaminase (SGPT) |  | What are four cytosolic proteases found in eukaryotic cells? | Calpains (2), a neutral protease, and a large ATP-dependent protease called the proteasome. |  | What are functions performed by lysosomes? | Secretion of digestive enzymes, digestion of organelles destined for destruction, digestion of food particles or bacteria, and intracellular release of enzymes followed by autolysis - the digestion of the cell as a normal developmental process. |  | What are PEST sequences | The presence of proline, glutamate, serine, and threonine residues (P,E,S, and T in the one letter code) in regions of proteins 12-60 residues long that appear to give rise to short-lived proteins. |  | Which N-terminal acid residues are correlated with shorter metabolic half-lives of proteins in bacteria? | Phe, Leu, Tyr, Trp, Lys, or Arg |  | Name one mammal that excretes most of its excess ammonia as uric acid. | Dalmation dog. |  | How is urea formed in the urea cycle? | Hydrolysis of arginine, catalyzed by arginase | Figure 20.13 | Which enzymes of the urea cycle are located in the mitochondrion? | Ornithine transcarbamoylase, transaminase, fumarase, malate dehydrogenase, (glutamate dehydrogenase, carbamoyl phosphate synthetase) | Figure 20.13 | How many high energy phosphates are required for each turn of the urea cycle? | Four (includes two necessary to regenerate ATP from AMP) | Figure 20.13 | In what animal organ does the urea cycle occur? | Liver |  | In what form is ammonia transported in animal's bodies? | Most tissues generate glutamine for transport. Muscle cells generate alanine, which is part of the glucose-alanine cycle. | Figure 20.14 | In what animals is urea reutilized for amino acid synthesis? | Hibernating animals. |  | What drug, used in treating tuberculosis, reduces vitamin B6 levels by reacting with pyridoxal? | Isoniazid (isonicotinic acid hydrazide) |  | What types of reactions does pyridoxal phosphate participate in? | Transminations, amino acid decarboxylations, racemizations, and numerous modifications of amino acid side chains. |  | All pyridoxal phosphate-requiring enzymes act via the formation of what chemical structure? | Schiff's base | Figure 20.15 | What moieties compose folic acid? | 6-methylpterin, p-Aminobenzoic acid, and glutamate. |  | What are two antimetabolites of dihydrofolate | Aminopterin and amethopterin (methotrexate). |  | What enzyme does trimethoprim inhibit? | Dihydrofolate reductase of bacteria. |  | What enzyme does pyrimethamine inhibit? | Dihydrofolate reductase of protozoa. |  | What part of folate does sulfanilamide resemble and mimic in its antibiotic action? | p-Aminobenzoic acid |  | What enzyme catalyzes NADPH reduction of 5,10-Methenyl-THF to 5,10-Methylene-THF? | Methylenetetrahydrofolate dehydrogenase. | Figure 20.17 | Which form of folate is important in purine nucleotide synthesis? | 10-Formyl-THF | Figure 20.17 | Which form of folate is important for converting dUMP to dTMP? | 5,10-Methylene-THF | Figure 20.17 | Which form of folate is important in converting homocysteine to methionine? | 5-methyl-THF | Figure 20.17 | Which form of folate is important in accepting a carbon from serine to make glycine? | THF | Figure 20.17 | What metal is found in vitamin B12? | Cobalt | Figure 20.18 | What is the methyl group donor that converts vitamin B12 to methylcobalamin? | 5-methyltetrahydrofolate. |  | What two types of reactions are catalyzed by B12-containing enzymes? | 1) Methyl groups transfer, 2) adenosylcobalamin-dependent isomerizations involving exchange of a carbon-bound hydrogen with another carbon-bound functional group. | Figure 20.20

What are the activators and inhibitors of glutamate dehydrogenase? | Activators - GDP or ADP Inhibitors - GTP or ATP |

What are the differences between the two forms of carbamoyl phosphate synthetase found in eukaryotic cells? | Form I - Found in mitochondria. Prefers ammonia as a substrate and is used in arginine biosynthesis. Form II - Found in cytosol. Has a strong preference for glutamine. Inhibited by UTP. |

Category - Enzymes

Query - What enzyme catalyzes this reaction?

Reversal

Category - Reactions

Query - What catalytic activity does the enzyme below have?

(enzyme on left, reaction in middle, figures on right)

Asparagine Synthetase | Aspartate + ATP + NH3 (Gln) <=> Asparagine + AMP + PPi + (Glu) |  | Argininosuccinase | Argininosuccinate <=> Arginine + Fumarate | Figure 20.13 | Argininosuccinate synthetase | Aspartate + ATP + Citrulline <=> Argininosuccinate + AMP + Ppi | Figure 20.13 | Ornithine Transcarbamoylase | Ornithine + Carbamoyl phosphate <=> Citrulline + Pi | Figure 20.13 | Carbamoyl Phosphate Synthetase | Ammonium + CO2 + 2 ATP <=> Carbamoyl phosphate + 2ADP + Pi | Figure 20.13 | Argininase | Arginine + H2O <=> Urea + Ornithine | Figure 20.13 | Glutaminase | Gutamine + H2O <=> Glutamate + NH3 |  | Serine Transhydroxymethylase | Serine + Tetrahydrofolate <=> Glycine + 5,10-Methylenetetrahydrofolate + H2O | Figure 20.17 | Transaminase | Oxaloacetate + Glutamate <=> -ketoglutarate + Aspartate | Figure 20.13

Carbamoyl Phosphate Synthetase | Catalyzes either of the reactions below: 1. NH3 + HCO 3- + 2ATP <=> Carbamoyl phosphate + 2ADP + Pi 2. Glutamine + HCO 3- + 2ATP <=> Carbamoyl phosphate + 2ADP + Pi + glutamate |

Glutamate Synthase | -Ketoglutarate + Glutamine + NADPH + H+ <=> 2 Glutamate + NADP+ |  | Glutamine Synthetase | Glutamate + NH3 + ATP <=> Glutamine + ADP + Pi | Figure 20.8

Category - General

Query - Under the following condition, predict the activity of adenylyl transferase

Reversal - there is no reversal

(condition on left, activity in middle, figure on right)

High ATP | Deadenylylation |  | High -Ketoglutarate | Deadenylylation |  | High Glutamine | Adenylylation |

Category - General

Query - Under the following condition, predict the adenylation status of glutamine synthetase

Reversal - there is no reversal

(condition on left, adenylation status in middle, figure on right)

High ATP | Mostly deadenylylated |  | High -Ketoglutarate | Mostly deadenylylated |  | High Glutamine | Mostly adenylylated |

Category - General

Query - Under the following conditions, predict the activity of glutamine synthetase

Reversal - there is no reversal

(condition on left, activity in middle, figure on right)

High ATP | High activity |  | High -Ketoglutarate | High activity |  | High Glutamine | Low activity |

Category - General

Query - Under the following conditions, predict the uridylylation status of PII

Reversal - there is no reversal

(condition on left, uridylylation status in middle, figure on right)

High ATP | Uridylylated |  | High -Ketoglutarate | Uridylylated |  | High Glutamine | Deuridylylated |

Category - General

Query - Classify the amino acid below as 1) strictly ketogenic, 2) strictly glucogenic, or 3) glucogenic and/or ketogenic

Reversal - there is no reversal

(amino acid on left, glucogenic/ketogenic in middle, figure on right)

Alanine | Glucogenic and/or Ketogenic |  | Glycine | Glucogenic and/or Ketogenic |  | Cysteine | Glucogenic and/or Ketogenic |  | Serine | Glucogenic and/or Ketogenic |  | Asparagine | Glucogenic |  | Aspartate | Glucogenic |  | Tyrosine | Glucogenic and/or Ketogenic |  | Phenylalanine | Glucogenic and/or Ketogenic |  | Valine | Glucogenic |  | Methionine | Glucogenic |  | Threonine | Glucogenic and/or Ketogenic |  | Isoleucine | Glucogenic and/or Ketogenic |  | Glutamate | Glucogenic |  | Glutamine | Glucogenic |  | Histidine | Glucogenic |  | Proline | Glucogenic |  | Arginine | Glucogenic |  | Tryptophan | Ketogenic |  | Leucine | Ketogenic |  | Lysine | Ketogenic |