UNIT 7 - Metabolism II Flashcards
What is the purpose of storing glucose in the form of glycogen?
The purpose of storing glucose as glycogen is to have a source of glucose as a backup, and to not rely on simply obtaining glucose from gluconeogenesis.
What is the significance of glucose‑1‑phosphate in glycogen degradation?
Having a phosphate attached charges the glucose and prevents it from crossing the cell membrane
The significance of glucose‑1‑phosphate(G1P) in glycogen degradation is that, when glucose is released from glycogen, it is attached to a phosphate.
The advantage of this is that G1P is charged and glucose is not. This prevents the glucose from crossing the membrane and keeps it in the cell for use.
What is the building block for glycogen synthesis?
The building block for glycogen synthesis is UDP‑glucose, a combination of a high energy compound (UTP) with a low energy compound (G1P).
Glycogen phosphorylase and glycogen synthase are the main enzymes involved in glycogen breakdown and synthesis respectively. How does the phosphorylation cascade regulate these enzymes and the pathways they are involved in?
Epinephrine begins a phosphorylation cascade that phosphorylates them, activating the enzyme for glycogen breakdown while inhibiting glycogen production.
Glycogen phosphorylase is needed for glycogen breakdown, and glycogen synthase is needed for glycogen synthesis. When glucose is released into the system, epinephrine signals a cascade of reactions and these enzymes are both phosphorylated. Phosphorylase‑P is active so glycogen breakdown is enhanced. Glycogen synthase‑P is inactive so glycogen synthesis is halted. The process is switched by the activity of phosphatases, which remove the P groups from these key enzymes. Phosphorylase in now inactive so glycogen breakdown stops, and glycogen synthase is active so glycogen synthesis proceeds.
What advice would you give to a person who has an enzymatic deficiency in either the synthetic or the degradative path of glycogen metabolism?
Eat many small meals to avoid needing to rely on glycogen stores
Such a person should eat many small meals. Glycogen storage diseases are a serious medical problem. Glycogen is the shock absorber of metabolism. Without an efficient metabolism of glycogen, there must be constant, controlled eating to supply metabolic needs without overburdening the system.
What are the three primary functions of the pentose phosphate pathway (PPP)?
to produce:
1. NADPH for use in anabolic reductions,
2. ribose‑5‑phosphate for making nucleotides, and
3. erythrose‑4‑phosphate for making aromatic amino acids.
What are the two main phases of the PPP and what happens overall in each phase?
The two main phases of the PPP are:
oxidative phase:
two molecules of NADPH are produced as well as ribulose‑5‑phosphate.
Non‑oxidative phase:
a number of sugars are synthesized including erythrose‑4‑phosphate.
Explain the allosteric regulation of the PPP. What enzyme is regulated and how is it allosterically regulated?
Regulation of the PPP is through the enzyme glucose‑6‑phosphate dehydrogenase. This enzyme is allosterically regulated by the concentration of NADPH. NADP+ stimulates the enzyme and NADPH inhibits the enzyme.
How is the PPP connected to glycolysis? What does this mean in terms of the metabolic needs of an organism?
The PPP is connected to glycolysis because three glycolytic intermediates, G6P, fructose‑6‑P, and G3P, can be funnelled into the PPP for the synthesis of different sugars depending on the energy needs of the cell. In addition, the PPP can provide a mechanism to metabolize sugars (Xu5P and ribulose‑5‑phosphate). The PPP can provide ribulose‑5‑phosphate for nucleotide and nucleic acid synthesis, and erythrose‑4‑phosphate for aromatic amino acid synthesis. Pentose sugars from digestion of nucleic acids can be utilized through this pathway by being converted to glycolytic and or gluconeogenic intermediates.
What are the overall reactants and products of the Calvin Cycle?
The overall reactants and products for the Calvin Cycle are:
3CO2 + 6 NADPH + 5 H2O + 9 ATP → G3P + 2 H+ + 6 NADP+ + 9 ADP + 8 Pi
What molecule has to be regenerated in the Calvin Cycle and how many G3P molecules are required for this to happen? What does this mean in terms of input of CO2? What happens to the extra G3P produced?
Ribulose‑5‑phosphate or Ru1,5BP (or RuBP) is regenerated in the Calvin Cycle. Five G3P molecules produce three RuBP molecules. Since each CO2 molecule produces two G3P molecules, three CO2 molecules produce six G3P molecules; of these, five are used to regenerate RuBP, leaving a net gain of one G3P molecule per three CO2 molecules, which is converted to a hexose through the PPP.
Why do multicellular organisms require an elaborate mechanism to excrete nitrogen, while unicellular organisms do not?
Geography is the key. In multicellular organisms, excess NH4+ must travel from the liver through the bloodstream to the kidneys before being eliminated. A unicellular organism exists (usually) in water as fish do, so NH4+ can be eliminated directly through the cell membrane into the immediate environment.
What does NH4+ combine with and what product is formed? What molecule is recycled in the urea cycle?
NH4+ combines with bicarbonate to form carbamoyl phosphate. Ornithine is recycled after urea is expelled.
Why is nitrogenase not more widely distributed in nature?
The ultimate source of the high‑energy electrons to reduce nitrogenase is photosynthesis. Therefore, only plants or species symbiotic with plants can reduce nitrogenase. Because the enzyme is so easily oxidized, only species with elaborate means to protect it (e.g., bacteria in a relatively O2‑free soil) will contain this enzyme.
Why is it relatively easy to convert diimine back to elemental nitrogen, while hydrazine is more likely to convert into ammonia?
The octet rule provides the explanation. Nitrogen is stable because it possesses a stable octet of electrons around each nitrogen. Nitrogen is more electronegative than hydrogen, so the N−H bonding electrons in diimine will be closer to nitrogen than to hydrogen. Therefore, diimine has an almost‑but‑not‑quite‑stable octet structure, as elemental nitrogen does, and can be easily reduced to N2. The same arguments can be put forward for hydrazine, but in this case there are two hydrogen atoms on each nitrogen. NH3 is also stable. It is easier for hydrazine to proceed to ammonia than to reconvert to diimine and then to elemental nitrogen.
What is the purpose of transamination?
The purpose of transamination is to recycle nitrogen in the body by transferring the amino group (NH3) between α‑ketoacids (amino acids without their amino group). This allows the body to maintain a dynamic pool of amino acids ready for use as protein building blocks. Transamination can be used both as the first step in the elimination of excess nitrogen and as the final step in biosynthesis of amino acids.
What is the purpose of oxidative deamination?
Oxidative deamination is to eliminate amino acids. This occurs through cleavage of the amino group from the α‑ketoacid (carrier), which produces NH4+. The only amino acid from which the amino group can be cleaved directly is glutamate. For other amino acids transamination must occur first.
Is lysine a ketogenic or glucogenic amino acid? What about serine? What about isoleucine?
Lysine is a ketogenic amino acid. Serine is glucogenic. Isoleucine is both.
Name three compounds that are derived from amino acid precursors
epinephrine, serotonin, nucleotide bases (purines and pyramidines)
The compounds that are derived from amino acid precursors are nucleotide bases (purines and pyrimidines), sphingosine, histamine, (also tetrapyrrole, thyroxine, epinephrine, melanin, serotonin, glutathione, tetrahydrofolate).
How could a person adjust their diet to compensate for a partial deficiency in GDH?
reduce protein intake
To compensate for a partial deficiency in GDH, one could reduce protein consumption so that elimination of nitrogen is held to a minimum. GDH is the first enzyme involved in the elimination of nitrogen in vivo.
What is the difference between a vegetarian diet and an omnivorous diet in terms of transamination and deamination?
Meat proteins more closely resemble human proteins in amino acid composition than do vegetable proteins. Therefore, more transamination activity would be expected on a vegetarian diet.
Deamination involves the elimination of excess nitrogen. A well‑balanced vegetarian diet should not involve any more elimination than a well‑balanced diet that includes meat.
Would a dietary deficiency of glutamate or α‑ketoglutarate cause problems in efficient transamination?
No, glutamate is not an essential amino acid and α‑ketoglutarate is synthesized in the citric acid cycle
Why doesn’t a tyr deficiency necessarily develop in PKU sufferers who are on a phe‑free diet?
Humans can only synthesize Tyr from Phe but we could also just ingest Tyr, so cutting out Phe doesn’t necessarily remove our ability to have Tyr in our bodies.
What is the biochemical basis for the change in the colour of leaves in the fall?
Cold destroys proteins and breaks down the porphyrin ring of chlorophyll
Plant proteins (including those associated with chlorophyll) are destroyed by sub‑zero temperatures. The porphyrin ring of chlorophyll will be degraded, as heme is.
What is the function of ATCase? Do the following molecules inhibit or stimulate this enzyme?
aspartate
ATP
CTP
ATCase synthesizes carbamoyl aspartate
It is stimulated by Aspartate and ATP but inhibited by CTP
How is AMP formed from IMP? Does this process require energy?
IMP is a branch point for the synthesis of adenine and guanosine. AMP is formed from IMP and the addition of an amine from aspartate. Yes, this process requires energy from GTP.
If the amount of GTP is high in the cell, what will be the effect on the enzyme RNR and what nucleotides will be produced?
If GTP is abundant, RNR will stimulate the production of more pyrimidine nucleotides such as TTP, UTP, and CTP. It will inhibit the production of purines such as GTP and ATP.
