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Biochemistry Metabolism
TCA Cycle et al.
48
Biology
Undergraduate 3
10/28/2009

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Term
Classify organisms based on their ENERGY sources:
Definition
Phototrophs: get energy from photons,
Chemotrophs: get energy from oxidizing chemical sources.
Term
Classify organisms based on their CARBON sources:
Definition
Autotrophs: Use CO2 as their carbon source.
Heterotrophs: use more complex organic compounds as carbon sources.
Term
Why is the hydrolysis of a phosphoanhydride bond energetically favorable?
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.
Term
Name the electron carriers in oxidative reactions:
Definition
Nicotinamide adenine dinucleotide
Flavin adenine dinucleotide
Term
What is the role of electron carriers in metabolism?
Definition
They transport electrons to the mitochondrial membrane where the electrons they transport are used to pump protons outside of the matrix.
Term
How can thermodynamically unfavorable reactions be overcome?
Definition
Reduce the relative amounts of products, raise the relative amounts of reactants, or couple an unfavorable reaction with a favorable one.
Term
What is the semiquinone state?
Definition
FAD+ accepts one proton and one electron to be partially reduced.
Term
Phosphorylation of electron carriers does what?
Definition
It distinguishes NADH from NADPH and keeps anabolic processes distinct from anabolic processes. Anabolism is generally performed by the phosphorylated form.
Term
Why does Coenzyme A have a thioester linkage rather than an oxygen ester?
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.
Term
What are the ways in which metabolic pathways are controlled?
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
Term
Name the six basic reactions in metabolism and briefly describe each:
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)
Term
What Rxn does hexokinase facilitate?
Definition
Group transfer reaction of a phosphate from ATP to Glucose
Term
What is a priming reaction?
Definition
Requires energy initially to yield energy later.
Term
Why does glucose need to be "primed" before glycolysis can begin?
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.
Term
What is the importance of ASP 205 in Hexokinase?
Definition
The ASP helps deprotonate the hydroxyl on the glucose molecule so that it can perform nucleophilic attack on the phosphate of ATP.
Term
Which enzymes demonstrate the induced fit phenomina?
Definition
hexokinase, phosphofructokinase, phosphoglycerate kinase, pyruvate kinase
Term
What does phosphofructokinase do?
Definition
Group transfer reaction of a phosphate from ATP to fructose-6-phosphate to make fructose-1,6-biphosphate (2nd priming reaction)
Term
What are the respective charges on the matrix side and cytoplasmic side of the inner mitochondrial membrane?
Definition
Inside is negatively charged and the outside is positively charged.
Term
Where does the citric acid cycle take place?
Definition
Mitochondrial Matrix
Term
Where does oxidative phosphorylation take place?
Definition
The inner mitochondrial membrane
Term
Where does glycolysis occur?
Definition
The cytosol
Term
Glucose can be synthesized from what starting molecules?
Definition
Pyruvate, oxaloacetate, DHAP, lactate, Glycerol, amino acids
Term
Where does gluconeogenesis occur? Where does it occur inside the cell?
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.
Term
What is the main purpose of gluconeogenesis?
Definition
To maintain blood glucose to brain and muscle tissue.
Term
What are the different enzymes in gluconeogenesis vs. glycolysis?
Definition
hexokinase/ glucose-6-phosphate, phosphofructokinase/fructose-1,6-bisphosphate, pyruvate kinase/phosphoenol pyruvate carboxylase and pyruvate carboxylase
Term
Why isnt gluconeogenesis the reverse of the respective reactions in glycolysis?
Definition
Some of the steps have too large of activation energies and need new enzymes.
Term
Where does gluconeogenesis start?
Definition
mitochondrial matrix
Term
How does gluconeogenesis leave the mitochondrial matrix?
Definition
The oxaloacetate must be converted into malate in order to be pumped out by the malate/phosphate antiporter
Term
What is the purpose of a decarboxylation in gluconeogenesis? Why might it be required to accomplish a step?
Definition
Decarboxylation is the driving force for reactions that are highly endergonic.
Term
Why are essentially irreversible reactions important in gluconeogenesis?
Definition
They are important sites for control (allosterically controlled).
Term
What is the main difference between gluconeogenesis in the muscle tissue and in the liver?
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.
Term
Name the ways in which phosphofructo kinase is allosterically inhibited:
Definition
Fructose-2,6-Bisphosphate, and AMP both increase the enzyme's activity. ATP, Citrate and H+ ions all downregulate the enzyme's activity.
Term
Name the ways that Fructose-1,6-bisphosphate is regulated.
Definition
Fructose-2,6-Bisphosphate, and AMP downregulate the enzyme. Citrate up regulates the enzyme.
Term
How is pyruvate kinase regulated.
Definition
Fructose-1,6-Bisphosphate up regulates the enzyme. ATP and alanine both downregulate the enzyme.
Term
How is phosphoenol pyruvate carboxylkinase regulated?
Definition
ADP downregulates the enzyme.
Term
How is pyruvate carboxylase regulated?
Definition
Acetyl CoA upregulates the enzyme. ADP downregulates the enzyme.
Term
What are the key reciprocal regulated enzymes in glycolysis?
Definition
Phosphofructokinase vs. fructose-1,6-bisphosphate and pyruvate kinase vs. phosphoenolpyruvate carboxylkinase and pyruvate carboxylase
Term
Why do the concentrations of ATP, AMP and ADP affect the regulation of glycolysis and gluconeogenesis?
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.
Term
Why does high concentrations of H+ ions slow down the activity of phosphofructokinase?
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.
Term
Why does citrate affect the activity of phosphofructokinase and fructose-1,6-bisphosphate?
Definition
Excess buildup of citrate is a sign to the liver that the system is backing up.
Term
What is citrate?
Definition
Citrate is a product of the TCA cycle. (more to come later)
Term
What is the purpose of phosphofructokinase2?
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.
Term
When the brain needs glucose, how does the liver shift from a glucose consuming mode to a glucose producing mode?
Definition
Pyruvate kinase can be phosphorylated and that will ultimately inhibit that enzyme so that it stops the production of pyruvate.
Term
What is the normal serum glucose concentration? If the Km is lower than this number, what does that mean?
Definition
Normal serum glucose concentration is 4-8mM. If the Km is lower than the serum concentration, then the organ will soak up glucose.
Term
What is the purpose of the Na+/glucose symporter in an intestinal epithelial cell?
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.
Term
Why is the Km of the liver and pancreas so high?
Definition
After eating, the liver and pancreas can soak up excess glucose from the bloodstream.
Term
Glycolysis is often limited by what and how is it overcome?
Definition
It is limited by a low concentration of NAD+ and is overcome by lactate accumulation and the Cori cycle.
Term
What is the purpose of the Cori cycle?
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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