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Biochem 2 (CHEM 441B) > Ch. 17 > Flashcards

Ch. 17 Flashcards

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1
Q

What is ammonia assimilation?

A

Process of incorporating NH4+ into glutamine and glutamate

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2
Q

What 3 enzymes mediate ammonia assimilation?

A
  1. Glutamine synthetase
  2. Glutamate synthase
  3. Glutamate dehydrogenase
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3
Q

What reaction does glutamine synthetase catalyze?

A

Conversion of glutamate to glutamine (2-step reaction)
1. Requires ATP and involves the formation of a phosphoryl intermediate, γ-glutamyl phosphate
2. NH4+ replaces the phosphate group to form glutamine

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4
Q

What reaction does glutamate dehydrogenase catalyze?

A

Interconversion of α-ketoglutarate and glutamate in the presence of NH4+

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5
Q

What type of reactions do aminotransferases catalyze?

A

Reversible reactions that transfer the amino group of amino acids to α-keto acids

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6
Q

What happens in the 2-stage reactions of aminotransferases?

A
  1. α amino group of the amino acid is transferred to an enzyme-linked PLP group
    - Results in formation of pyridoxamine phosphate and release of the corresponding α-keto acid
  2. Amino group from pyridoxamine phosphate is transferred to an incoming α-keto acid (α-ketoglutarate or oxaloacetate) to generate the amino acid product

TL;DR - alpha amino group to PLP to alpha-keto acid

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7
Q

What is the mechanism of the aminotransferase reaction?

A

Ping pong mechanism

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8
Q

What is the ping pong mechanism?

A

First product leaves the active site before the second substrate enters

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9
Q

What is nitrogen balance?

A

When an organism’s daily intake of nitrogen equals the amount of nitrogen it excretes

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10
Q

A normal healthy adult needs about ___ g of protein per day to maintain nitrogen balance

A

60 g

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11
Q

What type of nitrogen balance (positive or negative) do young children and pregnant women have? Why?

A

Positive nitrogen balance because they accumulate nitrogen in the form of new protein (needed to support tissue growth)

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12
Q

In what case would someone have a negative nitrogen balance?

A
  • Sign of disease or starvation
  • Occurs in individuals with elevated rates of protein breakdown (loss of muscle tissue) or an inability to obtain sufficient amounts of amino acids in their diets
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13
Q

Where does protein digestion in humans take place?

A

Stomach and small intestine

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14
Q

When food enters the stomach, it stimulates the release of ___.

A

Gastrin

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15
Q

What is gastrin?

A

Peptide hormone secreted by mucosal cells in the stomach lining

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16
Q

What does gastrin do?

A

Triggers the release of gastric juices containing hydrochloric acid from parietal cells and the secretion of pepsinogen from chief cells
- Increases acidity of stomach (pH ~2)

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17
Q

What is the inactive state (zymogen) of pepsin?

A

Pepsinogen

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18
Q

What does the increased acidity in the stomach do?

A
  • Denatures dietary proteins, resulting in greater exposure of peptide bonds for hydrolysis
  • Kills most bacteria contained in the food
  • Activation of the protease by autocatalytic cleavage of pepsinogen to expose the protease active site (now in the active form: pepsin)
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19
Q

At what pH is pepsin maximally active?

A

pH ~2

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20
Q

What does the esophagus do?

A

Delivers food to the stomach

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21
Q

What does the esophageal sphincter do?

A

Prevents acid reflux

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22
Q

What does the stomach do?

A

Has a low pH that denatures proteins and activates pepsin

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23
Q

What does the pyloric sphincter do?

A

Functions as a valve and closes off the stomach

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24
Q

What does the duodenum do?

A

Secretes the hormones secretin and cholecystokinin, as well as enteropeptidase

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25
Q

What is enteropeptidase?

A

Intestinal protease released into the duodenum that activates several pancreatic proteases

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26
Q

What is the role of secretin?

A

Stimulates the pancreas to secrete HCO3- to neutralize chyme

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27
Q

What does the activated trypsin enzyme do?

A

Cleaves pancreatic zymogens chymotrypsinogen, proelastase, and procarboxypeptidase, as well as trypsinogen itself to amplify the proteolytic cascade

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28
Q

Small intestine contains ___ and ___ that degrade peptides into amino acids.

A

Aminopeptidases and dipeptidases

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29
Q

What are aminopeptidases?

A

Group of enzymes that remove amino acids from the amino terminus of proteins and peptides

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30
Q

What are dipeptidases?

A

Group of intestinal enzymes that hydrolyze dipeptides into individual amino acids

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31
Q

What does the pancreas do?

A

Secretes HCO3- to neutralize chyme and stimulate enteropeptidase to cleave trypsinogen to generate trypsin

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32
Q

What are the two pathways for protein degradation?

A
  1. ATP-independent process that degrades proteins inside lysosomes, which are intracellular vesicles derived from Golgi membranes
  2. ATP-dependent process that degrades proteins containing a polymer of ubiquitin protein
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33
Q

What is ubiquitin?

A

Small protein that tags the proteins for destruction in a proteasome

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34
Q

What is a proteasome?

A

Large protein complex in cells consisting of an inner chamber lined with proteases that degrade ubiquitinated proteins targeted to it

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35
Q

What are lysozomes?

A

Low-pH (∼5) compartment filled with digestive enzymes that function nonselectively

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36
Q

What does a proteasome consist of?

A
  • 20S core particle
  • Two 19S regulatory particles
    • Serve as caps to regulate protein entry into and exit from the proteolytic core
    • Contain binding sites for ubiquitinated proteins and also encode ATP hydrolyzing enzymes that function in protein unfolding
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37
Q

What are the three classes of proteins involved in uqbiquitination?

A
  1. E1 enzymes: attach ubiquitin to E2 enzymes
  2. E2 enzymes: attach ubiquitin to target proteins
  3. E3 enzymes: facilitate ubiquitination of target proteins by forming heterotrimeric complexes with E2 enzymes and target proteins
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38
Q

What is another name for the E3 enzymes?

A

Ubiquitin ligases

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39
Q

What are the steps of ubiquitination?

A
  1. Ubiquitin is covalently attached to a cysteine residue in the E1 active site through an ATP-dependent reaction
  2. E1 associates with an E2 enzyme and transfers the ubiquitin to a cysteine residue in the E2 active site
  3. Each E2–ubiquitin complex then binds to an E3 enzyme to form an E2–ubiquitin–E3 complex
  4. Complex attaches ubiquitin to target proteins recognized by the complex
  5. Ubiquitin is either first transferred from E2 to E3 before the target protein is ubiquitinated or the target protein is ubiquitinated directly by the E2 subunit in the complex
  6. Minimum of 3 more ubiquitins must be attached by Gly76–Lys48 linkages before the protein is recognized by the 19S complex of the proteasome
  7. Sequential attachment of ubiquitin subunits occurs within the same E3–target protein complex through continual of E2-ubiquitin moieties
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40
Q

How is protein ubiquitination regulated? (2 most common mechanisms)

A
  1. Biochemical changes in target proteins
  2. Biochemical changes in E3 ligases
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41
Q

Target proteins that have a Phe/Leu/Asp/Lys/Arg residue at the N terminus are __ and ___ by ___.

A

Recognized and ubiquitinated by certain E2-E3 complexes, which follow the N-end rule of protein degradation

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42
Q

What is the N-end rule?

A

Half-life of a protein in the cytosol is greatly determined its N terminal amino acid residue

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43
Q

What does the deamination of amino acids generate?

A

NH4+
- Used for synthesis of other nitrogen-containing compounds or excreted as urea
- Remaining carbon skeletons are used as metabolites in energy conversion pathways

44
Q

What amino acids are the primary nitrogen carriers?

A

Glutamate and glutamine

45
Q

What are the nitrogens in urea derived from?

A
  1. NH4+ released when Glu and Gln are deaminated
  2. Asp (formed when oxaloacetate is transaminated by aspartate aminotransferase
46
Q

What are the 3 sources of the amino acids that are transported to the liver, where the nitrogen is removed and used for urea synthesis?

A
  1. Amino acids derived from the digestion of dietary proteins
  2. Gln, which is generated from Glu and NH4+ in peripheral tissues by glutamine synthase
  3. Ala, which is formed by the alanine aminotransferase reaction
47
Q

idk man i guess just know this figure (17.27)

A
48
Q

What is carbamoyl phosphate?

A

Small molecule that transfers NH4+ into the urea cycle by transferring a carbamoyl group to ornithine to form citrulline

49
Q

What is the alanine-glucose cycle?

A

Mechanism for transporting amino groups from muscle to liver in the nontoxic form, alanine

50
Q

What problem does the alanine-glucose cycle solve?

A

Muscle protein is degraded during exercise –> excess nitrogen from amino acid catabolism must be removed to avoid cell toxicity

51
Q

Where does the urea cycle occur?

A

Almost exclusively in the liver

52
Q

What does the urea cycle accomplish for the organism?

A

Provides an efficient mechanism to remove excess nitrogen from the body

53
Q

What is the key regulated enzyme in urea synthesis?

A

Carbamoyl phosphate synthetase I

54
Q

What is the net reaction of the urea cycle?

A

NH4+ + HCO3- + Aspartate + 3 ATP –> Urea + Fumarate + 2 ADP + 2 Pi + AMP + PPi

55
Q

What is carbamoyl phosphate synthetase I?

A

ATP-dependent urea cycle enzyme that forms carbamoyl phosphate from ammonia and bicarbonate

56
Q

What is an example of the urea cycle in everyday biochemistry?

A

Deficiency in the enzyme argininosuccinase inhibits flux through the urea cycle, causing hyperammonemia and neurologic symptoms
- Treated with a low-protein diet supplemented with Arg

57
Q

What are the 5 enzymatic reactions of the urea cycle?

A
  1. Carbamoyl phosphate synthetase I
  2. Ornithine transcarbamoylase
  3. Arginosuccinate synthetase
  4. Arginosuccinase
  5. Arginase
58
Q

Which urea cycle reactions occur in the mitochondria?

A
  • Carbamoyl phosphate synthetase
  • Ornithine transcarbamoylase
59
Q

Which urea cycle reactions occur in the cytosol?

A
  • Pyrophosphatase
  • Arginosuccinase
  • Arginase
60
Q

Which urea cycle reactions are ATP-dependent?

A

Carbamoyl phosphate synthetase and arginosuccinase
- Use a total of 4 high-energy phosphate bonds for every molecule of urea produced

61
Q

What is the first step of the urea cycle?

A
  1. Carbamoyl phosphate synthetase I forms carbamoyl phosphate in the mitochondrial matrix using HCO3- and NH4+
62
Q

What is the second step of the urea cycle?

A
  1. Ornithine transcarbamoylase combines carbamoyl phosphate with ornithine to form citrulline
63
Q

What is the third step of the urea cycle?

A
  1. Citrulline is then exported to the cytosol, where it is activated by AMP before being converted to argininosuccinate by arginosuccinate synthetase when aspartate displaces the AMP
    - Results in the incorporation of a 2nd nitrogen atom into the product
    - Reaction consumes 2 high-energy phosphate bonds
64
Q

What is the fourth step of the urea cycle?

A
  1. Ariginosuccinase cleaves arginosuccinate to yield fumarate and arginine, the latter containing both nitrogens
65
Q

What is the fifth step of the urea cycle?

A
  1. Arginase converts arginine to urea and ornithine
66
Q

Urea cycle net reaction including the pyrophosphatase reaction

A

NH4+ + CO2 + Aspartate + 3 ATP –> Urea + Fumarate + 2 ADP + AMP + 4 Pi

67
Q

How are the urea cycle and citric acid cycle linked?

A

Through fumarate (shared intermediate)

68
Q

What is the Krebs bicycle?

A

AKA aspartate-arginosuccinate shunt connecting the urea cycle to the citric acid cycle

69
Q

What happens in the Krebs bicycle?

A

Fumarate is converted to malate in the cytosol by an isozyme of fumarase

70
Q

At what 2 points does nitrogen enter the Krebs bicycle?

A
  1. Deamination of Gln and Glu
  2. Transfer of the amino group from Glu to oxaloacetate to generate Asp
71
Q

Why is the recycling of fumarate to generate oxaloacetate a good thing?

A

It produces NADH in the malate dehydrogenase reaction, which can be used by the electron transport system to generate 2.5 ATP (helps offset energy cost of urea cycle)

72
Q

What is hyperammonemia?

A

Physiologic condition where ammonia levels are elevated in the blood
- Can be caused by a deficiency in urea cycle enzymes

73
Q

What happens if a patient has an arginosuccinase deficiency?

A

No arginine is produced –> no ornithine is produced –> ammonia build-up

74
Q

What are glucogenic amino acids?

A

Their carbon chains can be used to from glucose and glycogen
- Give rise to CAC intermediates

75
Q

What are ketogenic amino acids?

A

Their carbon chains can be used to form ketone bodies

76
Q

List the glucogenic amino acids.

A

Everything EXCEPT leucine and lysine

77
Q

List the ketogenic amino acids.

A
  • Isoleucine
  • Leucine
  • Threonine
  • Lysine
  • Phenylalanine
  • Tryptophan
  • Tyrosine
78
Q

What are the Group 1 amino acid degradation pathways?

A

Degrades Ala, Cys, Gly, Ser (to pyruvate) and, Thr and Trp (to acetyl-CoA and acetoacetyl-CoA)

79
Q

What is the 3rd pathway for glycine degradation? Draw the structures and reactions.

A

D-amino acid oxidase (present in high levels in kidney)
- Primary function is detoxification of ingested D-amino acids

80
Q

What is tetrahydrofolate (THF)?

A

Intermediate in the pathway that regnerates N5,N10-methylenetetrahydrofolate
- Biologically active form of folate (vitamin B9)
- Involved in the transfer of one carbon units

81
Q

What are the Group 2 amino acid degradation pathways?

A

Degrades Arg, His, Gln, and Pro (to Glu and then α-ketoglutarate)
Know that Arg, His, Gln, and Pro are converted to Glu

82
Q

What are the Group 3 amino acid degradation pathways?

A

Degrades Phe (to Tyr and then to acetoacetyl-CoA)

83
Q

What is alkaptonuria?

A

Black urine disease
- Defective homogentisate-1,2-dioxygenase causes homogentisate to accumulate

84
Q

What is phenylketonuria (PKU)?

A

Defective phenylalanine hydroxylase causes Phe and its metabolites to build up and cause neurologic damage

85
Q

Amino acids are derived from intermediates of what 3 metabolic pathways?

A
  • Glycolysis
  • PPP
  • Citrate cycle
86
Q

What glycolysis intermediates are used in amino acid biosynthesis?

A
  • 3-Phosphoglycerate
  • Phosphoenolpyruvate
  • Pyruvate
87
Q

What PPP intermediates are used in amino acid biosynthesis?

A
  • Ribose-5-phosphate
  • Erythrose-4-phosphate
88
Q

What citrate cycle intermediates are used in amino acid biosynthesis?

A
  • α-Ketoglutarate
  • Oxaloacetate
89
Q

What are the essential amino acids?

A

Must be obtained from diet:
Arginine
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine

90
Q

What are the nonessential amino acids?

A

We can synthesize:
Alanine
Asparagine
Aspartate
Cysteine
Glutamate
Glutamine
Glycine
Proline
Serine
Tyrosine

91
Q

Which requires more reactions: nonessential or essential amino acid biosynthesis?

A

Essential

92
Q

Draw out the steps of alanine synthesis.

A
93
Q

Draw out the steps of aspartate and asparagine synthesis.

A
94
Q

Draw out the steps of glutamate and glutamine synthesis.

A
95
Q

How is amino acid synthesis regulated?

A
  • Allosteric regulation (contributes to minute-to-minute adjustment of pathway activities)
  • Presence of isozymes or enzyme multiplicity (prevents one end product from shutting down key steps in pathway when other products of same pathway are required)
  • Sequential feedback inhibition
  • Glutamine synthetase regulation
96
Q

Explain glutamate synthetase regulation.

A
  • Major regulation point
  • Allosteric and covalent modification in bacteria
  • Quick response to changes in cell metabolites
  • Glycine and alanine act as sensors for amino acid abundance
  • 6 direct end products of glutamine metabolism
  • Each of the inhibitors work partially
  • All inhibitors action simultaneously will shut down enzyme completely
97
Q

What is heme nitrogen derived from? (What is the precursor of porphorins?)

A

Glycine

98
Q

Where in the cell are the heme biosynthetic pathway enzymes located?

A

Mitochondria and cytosol

99
Q

Summarize heme biosynthesis.

A

δ-aminolevulinate is derived from glycine in the mitochondria and then transported to the cytosol

100
Q

What is heme essential to?

A

Cytochromes, hemoglobin, and myoglobin

101
Q

What enzyme completes heme synthesis in the mitochondria?

A

Ferrochelatase

102
Q

Where does heme biosynthesis occur?

A
  • Erythrocytes precursors in bone marrow to produce hemoglobin
  • Liver cells to provide heme for enyzmes
103
Q

What are porphyrias?

A

Group of diseases characterized by the accumulation of heme precursors in the blood due to deficiencies in the enzymes responsible for heme biosynthesis

104
Q

What is acute intermittent porphyria?

A
  • Due to dominant mutations in the porphobilinogen deaminase gene
  • Causes build up of δ-aminolevilunate or porphobilinogen
  • Asymptomatic or mild symptoms
  • Dietary changes, hormonal fluctuations, certain drugs can cause acute abdominal pain, neurological dysfunction
105
Q

What is variegate porphyria?

A
  • Rare form due to defect in PPOX
  • Accumulation of uroporphyrinogen I, a protoporphyrin precursor
106
Q

How much hemoglobin is degraded by liver macrophages and excreted daily?

A

~6 g

107
Q

How is heme degraded?

A
  • Excess heme is converted by liver enzymes first to biliverdin and then to bilirubin in a two-step process
  • 1st reaction: heme oxygenase removes the Fe2+ and releases carbon monoxide to form biliverdin
  • 2nd reaction: biliverdin reductase reduces biliverdin to form bilirubin, of which a portion is bound to the protein serum albumin and secreted directly into the bile duct.

Biochem 2 (CHEM 441B) (23 decks)

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