Microphys-Ch.7 part 2

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Microphys-Ch.7 part 2
2011-11-13 14:10:15
microbial physiology catabolism alcohols fatty acids

Chapter 7 part 2 slides
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  1. What needs to happen to an alcohol or a ketone before it can be transported into the cell? What are the enzymes responsible for this?
    • To utilize an alcohol (or ketone) for catobolism (or biosysnthesis) it needs to be converted (oxidized) to a fatty acid (R-CH2-COOH)
  2. How is a primary alcohol oxidized to a fatty acid?
    Two step process: Alcohol (-CH2OH) is oxidized to aldehyde (-CHO) Aldehyde is oxidized to caboxylic acid (-COOH) This works for primary alcohols, meaning the -OH is on a terminal carbon. Thus when it is oxidized it forms the aldehyde
  3. How is a secondary alcohol oxidized to a fatty acid?
    The oxidation of the interior alcohol yields a ketone (R-CO-R) oxygen double bonded to the Carbon before conversion to a fatty acid and a primary alcohol by the action of the monooxygenase.
  4. Are isopropanol and butandiol primary or secondary alcohols? What is a similar step in their oxidation pathways?
    They are secondary alcohols. They are both converted to ketones by a dehydrogenase then converted to a compound that can feed into other pathways.

  5. How is propanediol oxidized to propionyl-CoA?
    • Propanediol is a 3 carbon double alcohol (CH3-CHOH-CH2OH). Removing H2O converts the double alcohol to an aldehyde (propionaldehyde, CH3-CH2-CHO). The aldehyde is oxidized and attached to CoA to form Propionyl-CoA
  6. What is the process of removing the amine of an amino acid prior to it's degradation called? What are three classes of enzymes involved in this process?
    Oxidative deamination. Amino acid oxidases, amino acid dehydrogenases and transaminases.
  7. How do amino acid oxidases differ from amino acid dehydrogenases? What is the most common pathway for amino acid degradation?
    Amino acid oxidases have FAD has a prosthetic group. These enzymes have low specificity and one enzyme can oxidize up to 10 different AAs.

    AA dehydrogenases use NAD(P)+ as the prosthetic group. Although there is less range in the numbers of amino acids that can be oxidized by dehydrogenases, when working in combination with transaminase, all AAs can be deaminated.
  8. Which two enzymes are deaminated by an aa dehydrogenase alone?
  9. How does the transaminase reaction work? What is oxidized and what is reduced?
    • The transaminase reaction transfer the -NH2 from the AA to a 2-keto group. AA is oxidized, NAD+ is reduced.
  10. How do amino acid dehydratases work? (serine/threonine dehydratase) What are the end products?
    AA dehydratases work selectively on serine and threonine removing the amine and the hydroxyl group at the same time.

    It is actually a 2 step reaction, first removing water, then removing the amine. Serine to pyruvate, threonine to 2-ketobutyrate.
  11. How do aspartate and histidine degydratases work? (aspartase/histidase)
    • Aspartate and Histidine dehydratase work similarly to AA dehydratases but produce a double bond between the 2 and 3 carbon.
  12. How are cysteine and methionine deaminated? What must happen to methionine first?
    The desulfhydrase removes both the amino and sulfide groups at the same time. Methionine however must first be converted to homocysteine by a transmethylase.
  13. What needs to happen to hydrocarbons before they can be metabolized? What are the end products. What is the challenge in hydrocarbon degradation and how is it overcome by some organisms?
    Hydrocarbons cannot be metabolized with out initial oxidation. Long chain hydrocarbons are oxidized to alcohols and carboxylic acids (fatty acid) as an initial step to catabolism.

    Hydrocarbons are hydrophobic, microbes attack at the water-oil interface. Some microbes produce a surfactant to disperse the hydrocarbon.
  14. Name the enzymes in hydrocarbon oxidation: Where does the fatty acid produced go from here?
    1. rubredoxin:NADH oxireductase 2. n-alkane monooxygenase 3. alcohol dehydrogenase 4. aldehyde dehydrogenase The fatty acid moves on to B-oxidation
  15. What does the monooxygenase do?
    This enzyme oxidizes a hydrocarbon to a primary alcohol at the cytoplasmic membrane and can oxidize two substrate per one molecule of O2.
  16. How does the oxidation of hydrocarbons by Nocardia petroleophila make a secondary alcohol?
    The monooxygenase of Norcadia petroleophila oxidize the second carbon. This produces a ketone which is oxidized to secondary alcohol. The secondary alcohol is oxidized by second monoxygenase followed by an acetylase producing acetate and a primary alcohol..
  17. What kind of conditions are required for aromatic hydrocarbon degradation? What organisms are well known for being able to do this?
    Aerobic conditions, Psuedomonas spp.
  18. What kind of enzymes are needed here:
    • 1. phenylalanine monooxygenase
    • 2. transaminase
    • 3. p-hydroxyphenylpyruvate oxidase
    • 4. homogentisate oxidase
    • 5. maleylacetoacetate isomerase
    • 6. fumarylacetoacetate hydrolase
  19. What do dioxygenases do? Where are they used?
    Dioxygeneases or (oxidases) incorporate both atoms of molecular oxygen into one substrate.

    They are used to open the benzene rings formed in the first step of aromatic ring degradation.
  20. What are the two steps in breaking down an aromatic ring?
    Step 1. monooxygenase incorporates a hydroxyl group into the ring. Three possible intermediates are formed: protocatechuate, catechol and gentisate.

    Step 2. The benzene ring of the intermediates are opened by a dioxygnease.
  21. What kinds of aromatics are converted to protocatechuate? Catechol? Gentisate?
    Aromatics with a hydroxyl group are mainly converted to Protocatechuate.

    Aromatics with an amino group or derived from lignin (a complex aromatic polymer) are mainly converted to Catechol.

    Some bacteria generate Gentisate from naphthalene, phenol derivatives and other substances.
  22. How are ortho and meta cleavage different?
    Meta cleavage opens the ring adjacent to one of the hydroxyl groups. Ortho cleavage opens the ring between the hydroxyl groups.
  23. How does meta cleavage occur on protocatcheuate and catechol? What are the end products and why are they relevant?
    • Meta cleavage opens the ring adjacent to one of the hydroxyl groups. The dioxygenase converts one hydroxyl to -COOH, and the adjacent carbon converted to an aldehyde.
    • The end product from catechol is pyruvate and and acetaldehyde, the end product from protocatechuate is 2 pyruvates.
    • The end products move on to other metabolic pathways.
  24. How does ortho cleavage occur on protocatcheuate and cataechol? What are the end products?
    Ortho cleavage opens the ring between the hydroxyl groups. Since it is a dioxygenase, the hydroxyls are each converted to -COOH, each hydroxyl picking up an oxygen. The end product from either substrate is succinate
  25. How is gentisate attacked by a dioxygenase and what are the end products?
    Gentisate is also attacked by a dioxygenase producing maleypyruvate. The end products produced by this pathway is pyruvate and fumarate.
  26. What kind of cleavage is this?
    Ortho cleavage
  27. What kind of cleavage is this?
    Meta cleavage
  28. What kind of cleavage is this?
    Gentisate cleavage