Term
| Classify organisms based on their ENERGY sources: |
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Definition
Phototrophs: get energy from photons,
Chemotrophs: get energy from oxidizing chemical sources. |
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Term
| Classify organisms based on their CARBON sources: |
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Definition
Autotrophs: Use CO2 as their carbon source.
Heterotrophs: use more complex organic compounds as carbon sources. |
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Term
| Why is the hydrolysis of a phosphoanhydride bond energetically favorable? |
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Definition
1. Resonance of the products creates a higher disordered state thereby increasing entropy.
2. Electrostatic repulsion of the terminal phosphate (-2) with the (-1) of the beta phosphate is unfavorable.
3. Stabilization by hydration allows ADP to be better stabilized than ATP structure allows. |
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Term
| Name the electron carriers in oxidative reactions: |
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Definition
Nicotinamide adenine dinucleotide
Flavin adenine dinucleotide |
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Term
| What is the role of electron carriers in metabolism? |
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Definition
| They transport electrons to the mitochondrial membrane where the electrons they transport are used to pump protons outside of the matrix. |
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Term
| How can thermodynamically unfavorable reactions be overcome? |
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Definition
| Reduce the relative amounts of products, raise the relative amounts of reactants, or couple an unfavorable reaction with a favorable one. |
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Term
| What is the semiquinone state? |
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Definition
| FAD+ accepts one proton and one electron to be partially reduced. |
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Term
| Phosphorylation of electron carriers does what? |
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Definition
| It distinguishes NADH from NADPH and keeps anabolic processes distinct from anabolic processes. Anabolism is generally performed by the phosphorylated form. |
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Term
| Why does Coenzyme A have a thioester linkage rather than an oxygen ester? |
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Definition
| The linkage must be easily reversible without dumping a whole lot of energy into the reaction. Thioesters don't have the resonance contribution that oxygen esters do. |
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Term
| What are the ways in which metabolic pathways are controlled? |
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Definition
| 1. Controlling the amount of enzyme, 2. Controlling the activity of the enzymes (allosteric control, reversible covalent modification, grouping enzymes into complexes), 3. Controlling the availability of substrates, 4. Separation of reactions through compartmentalization |
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Term
| Name the six basic reactions in metabolism and briefly describe each: |
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Definition
| 1. Oxidation/Reduction, 2. Ligation (free energy from ATP cleavage is used to form bonds), 3. Isomerization, 4. Group Transfer, 5. Hydrolytic Reactions, 6. Lyase Rxns (addition of functional groups to double bonds or removal of groups to form double bonds) |
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Term
| What Rxn does hexokinase facilitate? |
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Definition
| Group transfer reaction of a phosphate from ATP to Glucose |
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Term
| What is a priming reaction? |
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Definition
| Requires energy initially to yield energy later. |
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Term
| Why does glucose need to be "primed" before glycolysis can begin? |
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Definition
| The phosphorylation helps maintain intracellular glucose concentrations since the molecule is poorly recognized by membrane transporters after phosphorylation and the negative charge creates a larger barrier to passing directly through the membrane. |
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Term
| What is the importance of ASP 205 in Hexokinase? |
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Definition
| The ASP helps deprotonate the hydroxyl on the glucose molecule so that it can perform nucleophilic attack on the phosphate of ATP. |
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Term
| Which enzymes demonstrate the induced fit phenomina? |
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Definition
| hexokinase, phosphofructokinase, phosphoglycerate kinase, pyruvate kinase |
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Term
| What does phosphofructokinase do? |
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Definition
| Group transfer reaction of a phosphate from ATP to fructose-6-phosphate to make fructose-1,6-biphosphate (2nd priming reaction) |
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Term
| What are the respective charges on the matrix side and cytoplasmic side of the inner mitochondrial membrane? |
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Definition
| Inside is negatively charged and the outside is positively charged. |
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Term
| Where does the citric acid cycle take place? |
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Definition
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Term
| Where does oxidative phosphorylation take place? |
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Definition
| The inner mitochondrial membrane |
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Term
| Where does glycolysis occur? |
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Definition
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Term
| Glucose can be synthesized from what starting molecules? |
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Definition
| Pyruvate, oxaloacetate, DHAP, lactate, Glycerol, amino acids |
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Term
| Where does gluconeogenesis occur? Where does it occur inside the cell? |
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Definition
| liver and some in kidneys. None in brain, heart, skeletal muscle. It occurs in the ER lumen of the cells of the liver and kidneys to make glucose for export. |
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Term
| What is the main purpose of gluconeogenesis? |
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Definition
| To maintain blood glucose to brain and muscle tissue. |
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Term
| What are the different enzymes in gluconeogenesis vs. glycolysis? |
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Definition
| hexokinase/ glucose-6-phosphate, phosphofructokinase/fructose-1,6-bisphosphate, pyruvate kinase/phosphoenol pyruvate carboxylase and pyruvate carboxylase |
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Term
| Why isnt gluconeogenesis the reverse of the respective reactions in glycolysis? |
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Definition
| Some of the steps have too large of activation energies and need new enzymes. |
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Term
| Where does gluconeogenesis start? |
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Definition
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Term
| How does gluconeogenesis leave the mitochondrial matrix? |
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Definition
| The oxaloacetate must be converted into malate in order to be pumped out by the malate/phosphate antiporter |
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Term
| What is the purpose of a decarboxylation in gluconeogenesis? Why might it be required to accomplish a step? |
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Definition
| Decarboxylation is the driving force for reactions that are highly endergonic. |
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Term
| Why are essentially irreversible reactions important in gluconeogenesis? |
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Definition
| They are important sites for control (allosterically controlled). |
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Term
| What is the main difference between gluconeogenesis in the muscle tissue and in the liver? |
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Definition
| In the liver, a phosphate is removed from glucose-6-phosphate so that it can be transported into the blood stream. In the muscle, we don't want this to happen, so the phosphate remains so that the glucose doesn't simply seep out of the cell. |
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Term
| Name the ways in which phosphofructo kinase is allosterically inhibited: |
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Definition
| Fructose-2,6-Bisphosphate, and AMP both increase the enzyme's activity. ATP, Citrate and H+ ions all downregulate the enzyme's activity. |
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Term
| Name the ways that Fructose-1,6-bisphosphate is regulated. |
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Definition
| Fructose-2,6-Bisphosphate, and AMP downregulate the enzyme. Citrate up regulates the enzyme. |
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Term
| How is pyruvate kinase regulated. |
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Definition
| Fructose-1,6-Bisphosphate up regulates the enzyme. ATP and alanine both downregulate the enzyme. |
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Term
| How is phosphoenol pyruvate carboxylkinase regulated? |
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Definition
| ADP downregulates the enzyme. |
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Term
| How is pyruvate carboxylase regulated? |
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Definition
| Acetyl CoA upregulates the enzyme. ADP downregulates the enzyme. |
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Term
| What are the key reciprocal regulated enzymes in glycolysis? |
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Definition
| Phosphofructokinase vs. fructose-1,6-bisphosphate and pyruvate kinase vs. phosphoenolpyruvate carboxylkinase and pyruvate carboxylase |
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Term
| Why do the concentrations of ATP, AMP and ADP affect the regulation of glycolysis and gluconeogenesis? |
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Definition
| If there is high reserves available of ATP available, then there is no need to perform more glycolysis and it is smarter to begin gluconeogenesis. On the other hand, if there are high concentrations of ADP and AMP around, then there isn't sufficient energy around and glycolysis must be pushed forward. |
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Term
| Why does high concentrations of H+ ions slow down the activity of phosphofructokinase? |
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Definition
| High concentrations of H+ ions shut down phosphofructokinase since too high of levels can cause muscle damage. High H+ concentrations are due to the accumulation of lactic acid formation. |
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Term
| Why does citrate affect the activity of phosphofructokinase and fructose-1,6-bisphosphate? |
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Definition
| Excess buildup of citrate is a sign to the liver that the system is backing up. |
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Term
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Definition
| Citrate is a product of the TCA cycle. (more to come later) |
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Term
| What is the purpose of phosphofructokinase2? |
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Definition
| Phosphofructokinase2 is in the liver and when concentrations of fructose-6-phosphate are high, it converts it into fructose-2,6-bisphosphate which in turn allosterically activates phosphofructokinase. This activation signals to the enzyme that there is plenty of glucose available for glycolysis. It also reduces the inhibitory affect of ATP since there are some situations in which energy may be high but glycolysis must still occur. |
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Term
| When the brain needs glucose, how does the liver shift from a glucose consuming mode to a glucose producing mode? |
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Definition
| Pyruvate kinase can be phosphorylated and that will ultimately inhibit that enzyme so that it stops the production of pyruvate. |
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Term
| What is the normal serum glucose concentration? If the Km is lower than this number, what does that mean? |
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Definition
| Normal serum glucose concentration is 4-8mM. If the Km is lower than the serum concentration, then the organ will soak up glucose. |
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Term
| What is the purpose of the Na+/glucose symporter in an intestinal epithelial cell? |
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Definition
| The concentration of sodium inside the cell is low, so the concentration gradient helps bring glucose into the cell. There the glucose concentration is high, so glucose runs down its concentration out of the cell and into the blood stream through a GLUT2 receptor. The Na+/K+ ATPase maintains a low concentration of Na+ in the cell so that this process can work. |
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Term
| Why is the Km of the liver and pancreas so high? |
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Definition
| After eating, the liver and pancreas can soak up excess glucose from the bloodstream. |
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Term
| Glycolysis is often limited by what and how is it overcome? |
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Definition
| It is limited by a low concentration of NAD+ and is overcome by lactate accumulation and the Cori cycle. |
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Term
| What is the purpose of the Cori cycle? |
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Definition
| The cori cycle accepts lactate generated in the muscles and performs gluconeogenesis to remake glucose. The lactate is originally formed because of a lack of NAD+ to perform glycolysis. |
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