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BIOL 302 Part 1 > Amino Acid Catabolism > Flashcards

Amino Acid Catabolism Flashcards

1
Q

describe the reaction between amino and keto acids (2)

A
  • reversible reaction

- direction of reaction determined by concentration of each within a cell

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2
Q

which keto acid is the catalytic component in the TCA cycle and why? (2)

A
  • alpha-ketoglutarate

- it is not regenerated

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3
Q

what are the main ketoacid - amino acid pairs? (3)

A
  • alpha-ketoglutarate and glutamate
  • oxaloacetate and aspartate
  • pyruvate and alanine
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4
Q

what are the sources of amino acids for catabolism? (3)

A
  • ingested amino acids in excess of the body’s need for protein synthesis
  • normal protein turnover
  • during starvation (or uncontrolled diabetes) when carbohydrates are not available or can not be properly utilized
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5
Q

nitrogen balance equation and its possible values (4)

A

nitrogen balance = nitrogen ingested - nitrogen excreted

  • zero: ideal, protein synthesis = protein degradation
  • positive: protein synthesis > protein degradation
  • negative: protein synthesis < protein degradation
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6
Q

in what situations are nitrogen balance positive or negative? (2)

A
  • positive: during immune response, pregnancy, exercise, injury repair
  • negative: starvation
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7
Q

what happens when dietary protein enters the stomach? (2)

A
  • stimulates production of gastrin hormone

- gastrin hormone causes secretion of HCl (lowers pH) and pepsinogen (a zymogen)

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8
Q

what is a zymogen?

A
  • the storage form of a protease
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9
Q

how does pepsinogen contribute to the digestion of protein? (2)

A
  • pepsinogen turns into pepsin, a protease, at low pH

- pepsin starts degrading proteins at amino terminal side of aromatic amino acids

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10
Q

what happens to proteins as they leave the stomach and enter the small intestine? (2)

A
  • the pancreas secretes secretin which induces release of bicarbonate
  • bicarbonate neutralizes HCl in the low pH contents
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11
Q
  • what is the pancreas’ role in protein digestion (3)
A
  • secretion of secretin to neutralize HCl
  • releases zymogens which are converted to active proteases by enteropeptidase, a proteolytic enzyme secreted by intestinal cells
  • these and other proteases degrade most proteins to their component amino acids (proteases have different specificities to target different functional groups)
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12
Q

how are digested proteins absorbed by the body? (2)

A
  • they enter intestinal cells through a transporter as they are polar and cannot diffuse freely, but not much energy is required for transport
  • they exit intestinal cells through a transporter and enter the blood
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13
Q

where do dietary nitrogen and carbon skeletons go after they are absorbed? (2)

A
  • nitrogen goes toward the urea cycle

- carbon skeletons go toward the citic acid cycle

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14
Q

NH4+

A
  • ammonium
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15
Q

NH3

A
  • ammonia
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16
Q

how is NH4+ produced in the body?

A
  • amino acid degradation, which occurs in all cells of the body
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17
Q

how is NH4+ carried in the bloodstream?

A
  • NH4+ is carried in the form of glutamine or alanine in the blood stream to the liver and kidney
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18
Q
  • where is urea produced?
A
  • liver
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19
Q

what is the fate of NH4+ and why?

A
  • NH4+ is toxic

- it is converted to NH3 (urea) in the liver via the urea cycle

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20
Q

aminotransferases/transaminases role (2)

A
  • equilibrate amino acids among available alpha-keto acids
  • permits synthesis of non-essential amino acids, using amino groups from other amino acids and carbon skeletons synthesized in a cell
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21
Q

how is nitrogen obtained in humans and what can it be used for? (3)

A
  • N must be obtained in the diet as amino acids (proteins)
  • we get them from pants/bacteria that can obtain N themselves
  • amino N of one amino acid can be used to synthesize another amino acid
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22
Q

aminotransferases

A
  • catalyze transfer of an alpha-amino group from an alpha-amino acid to an apha-ketoacid
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23
Q

aminotransferase reactions (2)

A
  • reaction is reversible as there is very little chance in free energy (close to chemical equilibrium)
  • direction of rxn controlled by concentration of reactants/products
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24
Q

what mechanism does the Ping-Pong use?

A
  • Ping-Pong catalytic mechanism: two reactions occurs sequentially, with two sequential substrates taking turns accessing the enzyme active site
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25
Q

what are the two sequential aminotransferase reactions?

A
  1. removal of NH3+ created alpha-keto acid

2. addition of NH3+ to keto acid creates amino acid

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26
Q

why is glutamine, and not glutamate, the main carrier of amino groups on the blood? (2)

A
  • glutamine does not alter pH of the blood due to the lack of negative charge
  • negatively charged glutamate will cause blood pH to change
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27
Q

describe the glucose-alanine cycle (4)

A
  1. muscles degrade protein into amino acids and amino groups are collected into glutamate by aminotransferase
  2. amino group can be transferred to pyruvate to generate alanine and regenerate alpha-ketoglutarate
  3. alanine carries amino group to the liver
  4. in the liver, alanine is converted back to pyruvate, liberated NH4+ enters the urea cycle
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28
Q

what does alanine do for the urea cycle? (2)

A
  • carries NH4+ to the liver

- 2nd most abundant amino acid in the blood

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29
Q

describe the first step of the glucose-alanine cycle (2)

A
  • during strenuous exercise, muscles degrade protein into amino acids for fuel
  • this liberates amino groups which are collected into glutamate by aminotransferases
30
Q

describe the second step of the glucose-alanine cycle (2)

A
  • glutamate is converted to glutamine
  • amino group can also be transferred to pyruvate to generate alanine (alanine transferase) and regenerate alpha-ketoglutarate
31
Q

describe the fourth step of the glucose-alanine cycle (3)

A
  • in the liver, alanine is converted back to pyruvate
  • pyruvate is used to synthesize new glucose and the net effect is to shift the energetic cost of gluconeogenesis to the liver
  • liberated NH4+ enters the urea cycle
32
Q

what are the sources of glutamate in the liver? (3)

A
  • glutamine from the blood
  • alanine from the blood
  • glutamate from intracellular protein catabolism
33
Q

how is glutamates alpha-amino released in the liver?

A
  • oxidative deamination catalyzed by glutamate dehydrogenase to liberate NH4+ and alpha-ketoglutarate
34
Q

oxidative deamination of glutamate (4)

A
  • occurs within the mitochondrial matrix of the liver
  • enzyme: glutamate dehydrogenase, only enzyme that ->
  • can use either NAD+ or NADP+ as electron acceptor
  • ammonia is processed onto urea for excretion
35
Q

how is oxidative deamination regulated? (3)

A
  • controlled by energy balance of the cell
  • positively regulated by ADP
  • negatively regulated by ATP
36
Q

what can happen to arginine in the urea cycle?

A
  • it can be liberated outside of cycle for other protein needs if necessary
  • of this occurs, urea cycle does not go to completion
37
Q

how is the urea cycle regulated? (2)

A
  • allosterically

- transcriptionally

38
Q

how is the urea cycle regulated transcriptionally?

A
  • carbamoyl phosphate synthetase I (CPS-1) and 4 urea cycle enzymes are up-regulated during starvation (break down of protein occurs) and when there is excess protein
39
Q

how is the urea cycle regulated allosterically? (2)

A
  • CPS-1 is activated by glutamate via N-acetylglutamate

- N-acetylglutamate is only made when there is enough arginine, glutamate and acetyl-CoA in the cell

40
Q

what are the consequences of deficiencies in the urea cycle enzymes? (2)

A
  • lead to elevated NH4 in blood (hyperammonemia)

- can not tolerate protein rich diets

41
Q

what is the treatment for urea cycle enzyme deficiences? (2)

A
  • treatment by liver transplantation (usually from parents, but baby will have to take immunosuppressants for the rest of their life)
  • dialysis (filter substances out of the blood)
  • prodrugs: benzoate or phenylbutyrate is ingested and converted to benzoyl-CoA (removes glycine) or phenylacetyl-CoA (removes glutamine) in body
42
Q

what processes usually occurs in the mitochondria

A
  • energy producing or energy using reactions
43
Q

the administration of these molecules can help treat those with urea cycle enzyme deficiencies (3)

A
  • administration of phenylbutyrate to lower levels of ammonia in blood
  • administration of N-acetylglutamate to patients deficient in CPS-1
  • administration of arginine to patients deficient in ornithine transcarbamoylase, arginiosuccinate synthetase, or argininosuccinase
44
Q

what other enzymes is PLP used in for amino acid metabolism? (2)

A
  • decarboxylation

- racemization

45
Q

functions of the TCA cycle (3)

A
  • oxidize acetate to CO2, releasing reducing (NADH/FADH2) equivalents
  • intermediates can be drawn out to be used as precursors in various biosynthetic pathways
  • 4-5 carbon end products of catabolic pathways (ie. amino acid catabolism) feed into the cycle and serve as fuel
46
Q

ketogenic (2)

A
  • degraded to acetyl-CoA ->-> ketone bodies

- lysine and leucine are purely ketogenic

47
Q

glucogenic

A
  • degraded to pyruvate ->-> glucose
48
Q

which amino acids are both ketogenic and glucogenic and why? (6)

A
  • tryptophan
  • phenylalanine
  • tyrosine
  • threonine
  • isoleucine
  • complex skeletons get broken down and enter cycles as different pieces
49
Q

ketone bodies (2)

A
  • acetoacetate, acetone, and beta-hydroxybutyrate

- synthesized by liver when there is excess of acetyl-CoA and depletion of oxaloacetate

50
Q

what happens when there is an overproduction of ketone bodies?

A
  • acidosis (drop in blood pH)
51
Q

what scenario might cause an excess of acetyl-CoA and depletion of OAA?

A
  • high protein, low carb diet
52
Q

which of the TCA cycle enzymes is membrane bound?

A
  • succinate dehydrogenase (produced FADH2)
53
Q

where does pyruvate enter the TCA cycle and what is generated/consumed? (2)

A
  • oxidized to acetyl-CoA by pyruvate dehydrogenase, generating NADH
  • carboxylated to oxaloacetate by pyruvate carboxylase, consuming an ATP
54
Q

how is pyruvate dehydrogenase regulated? (3)

A
  • allosterically inhibited by ATP, acetyl-CoA, NADH, and long-chain FAs
  • stimulated by AMP, CoA and NAD+ (which accumulate when too little acetate flows into the TCA cycle)
  • activity is regulated by ATP/ADP and NADH/NAD levels
55
Q

how is pyruvate carboxylase regulated? (3)

A
  • inactive in absence of its allosteric activator, acetyl-CoA
  • in excess acetyl-CoA, activity is stimulated to produce more oxaloacatate to enable the TCA cycle to use more acetyl-CoA, an anaplerotic reaction
  • can be a major reaction in the OAA deficiency situations
56
Q

anaplerotic reaction

A
  • reactions that form intermediates of a metabolic pathway
57
Q

characteristics of enzymes involved in carbon skeleton breakdown (2)

A
  • catalyze chemical rearrangements

- contain co-factors at their active site

58
Q

what are the main reactions of carbon skeleton breakdown and their co-factors? (3)

A
  • transamination: pyridoxal phosphate (PLP)
  • racemization: PLP
  • one carbon transfers (most oxidized carbon, intermediate oxidized C, least oxidized C): biotin, tetrahydrofolate, S-adenosylmethionine (SAM)
59
Q

phenylketonuria (PKU) (2)

A
  • accumulation of phenylalanine or derivatives impair normal development of brain
  • 8/100,000
60
Q

phenylketonuria treatment

A
  • treated by rigid dietary control (beware of aspartame = dipeptide of Phe and Asp)
61
Q

what causes phenylketonuria?

A
  • defect in the first step of Phe breakdown due to malfunctioning phenylalanine hydroxylase enzyme that catalyzes phenylalanine -> tyrosine
62
Q

what are the ways that an enzyme can be malfunctioning/defected? (3)

A
  • completely missing enzyme
  • under-expressed levels of perfectly functional enzyme
  • normal expression of complete/partial loss of function enzyme, due to a mutation in the catalytic or allosteric site
63
Q

what is the minor phenylalanine catabolic pathway that is activated in patients with phenylketonuria?

A
  • aminotransferase reaction between phenylalanine and pyruvate to generate phenylpyruvate and alanine
64
Q

what are the compounds that build up in patients with PKU and why is it harmful? (4)

A
  • compounds are toxic and can cause damage to brain cells if left untreated
  • phenylpyruvate (ketoacid of phenylalanine)
  • phenylacetate
  • phenyllactate
65
Q

how is phenylacetate produced from phenylpryruvate?

A
  • addition of H20 and CO2 leaving group
66
Q

alkaptonuria (3)

A
  • 0.4/100,000
  • build-up of homogentisate
  • homogentisate appears in urine and is deposited in cartilage and elsewhere, making substances appear black (polymerization is black)
67
Q

why does alkaptonuria occur?

A
  • defect in homogentisate 1,2-dioxygenase enzyme that prevents complete breakdown of phenyalanine by inability to convert homogentisate
68
Q

cachexia (3)

A
  • wasting syndrome: weight loss and muscle wasting due to cancer
  • tumours produce factors which are secreted and stimulate protein breakdown/autophagy in host cells (in muscle tissue)
  • use protein breakdown products to feed the tumours
69
Q

treatment of cachexia

A
  • new drug therapy being developed: normal hormone that stimulates protein anabolism in the muscle
70
Q

what does the breakdown of phenylalanine produce? (2)

A
  • phenylalanine is first broken down to tyrosine

- tyrosine breakdown produces fumarate and acetoacetyl-CoA (which is broken down into 2 acetyl-CoA)

BIOL 302 Part 1 (4 decks)

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