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Biochemistry > Nitrogen Metabolism > Flashcards

Nitrogen Metabolism Flashcards

1
Q

What are proteases?

A

They cleave specific sites on peptides:

  1. internal cleavage
  2. cleavage at termini (amino and carboxypeptidase)
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2
Q

What does pepsin digest

A

Proteins to form large polypeptides

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3
Q

Where is pepsin synthesised and where does it act

A

Stomach chief cells; stomach

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4
Q

What do trypsin, chymotrypsin, carboxypeptidase and elastase digest?

A

Large polypeptides to form small polypeptides

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5
Q

Where are trypsin, chymotrypsin, carboxypeptidase and elastase synthesised?

A

Pancreas

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6
Q

Where do trypsin, chymotrypsin, carboxypeptidase and elastase act?

A

Small intestine

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7
Q

What does aminopeptidase digest?

A

small polypeptides to form amino acids

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8
Q

Where is aminopeptidase synthesised?

A

Brush border cells of small intestine

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9
Q

Where does aminopeptidase act?

A

small intestine

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10
Q

What is a proenzyme

A

A larger inactive enzyme precursor, requires proteolytic cleavage to be activated

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11
Q

Why is pepsinogen formed/ why is pepsin not synthesized in active form?

A

It will degrade intercellular protein

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12
Q

Where is pepsin activated?

A

stomach

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13
Q

How is pepsinogen activated to form pepsin?

A

Catalytic site of pepsinogen blocked by inhibitory domain.
At low pH in stomach, inhibitory domain unfolds, catalytic site activated and cleaves its own inhibitory domain (autolytic activation)-> forms pepsin

Pepsin activates another pepsinogen via cleavage of inhibitory domain (catalytic activation)

Positive feedback activation mechanism

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14
Q

What pH is optimal for pancreatic enzymes

A

pH 9, bicarbonate of pancreaic juic neutralises stomach acid from 2.5 to 9

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15
Q

What cleaves and activates trypsinogen to form trypsin?

A

Enteropeptidase

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16
Q

Which enzymes do trypsin cleave and activate

A

Proelastase-> elastase
Chymotrypsinogen=> chymotrypsin
Procarboxypeptidase-> carboxypeptidase

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17
Q

What are the sources for amino acids?

A

Biosynthesis, breakdown of dietary and body’s proteins

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18
Q

What can amino acids be used for?

A

metabolism for energy, protein synthesis, non-protein body constituents, small loss in urine and sweat

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19
Q

What is nitrogen balance?

A

Dietary N intake vs urinary N output as urea.

Positive nitrogen balance, intake> output
(growth, pregnancy, refeeding, muscle building)

Negative balance (starvation, amino acid/protein deficiency)

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20
Q

What is transamination?

A

The transfer of amino group to keto acid to form a non-essential amino acid

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21
Q

name 2 transaminases

A 
Aspartate aminotransferase (AST)
Alanine aminotransferase (ALT)
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22
Q

Describe the action of ALT

A

transfers amino group from alanine to alpha kg to form glutamate (nonessential amino acid) and pyruvate which can enter TCA cycle

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23
Q

What are pyruvate, OAA and alpha-kg

A

ketoacids

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24
Q

Describe the action of AST

A

Transfers amino group from aspartate to alpha kg to form glutamate (non-essential amino acid) and oxaloacetate which can enter TCA cycle

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25
Q

What is oxidative deamination?

A

Carried out by Glutamate dehydrogenase (GDH). GDH accepts wither NAD+ or NADP+ as redox coenzyme.

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26
Q

What is the forward reaction for oxidative deamination with GDH?

A

Ammonia liberated when glutamate is reacted to form alpha kg. Ammonia used to synthesise other amino acids or excreted in urea

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27
Q

What is the reverse reaction for oxidation deamination with GDH?

A

Generation of glutamate collects free NH4+ from amino acid degradation and NH4+ produced by bacteria metabolism in gut

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28
Q

What is non-oxidative deamination?

A

When amino acid catabolism produces free NH4+

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29
Q

What is the action of glutaminase

A

Carries our non-oxidative deamination of glutamine to form glutamate, which can be converted to alpha kg to enter TCA

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30
Q

What is the action of asparaginase

A

Carries out non-oxidative deamination of asparagine to form aspartate with can be converted to OAA to enter TCA

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31
Q

What is the function of the glucose-alanine cycle

A

transport glucose generated by gluconeogenesis from the liver to the muscles, glucose undergoes glycolysis, forms pyruvate, converted into alanine, transported back to liver.

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32
Q

how does glutamine serve as a nitrogen carrier

A

alphakg and NH4+ converted to glutamate by GDH.

Glu and NH4+ converted to Gln by glutamine synthetase

Both NH4+ transported as Gln through circulation to liver.

Gln converted to Glu by gltaminase

Glu converted to alphakg by GDH

2 NH4+ released

NH4+ converted to urea in liver

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33
Q

How is NH4+ excreted in urine

A

Glutamine deaminated to form NH4+ in renal tubule cell

NH4+ dissociates into NH3 and H+

NH3 diffuses into tubular fluid

H+ actively pumped into tubular fluid via Na+/H+ exchanger

NH3 combines with H+, form NH4+, NH3 equilibrium shift, more NH3 diffuses out, more NH4+ formed.

NH4+ cannot go back into renal tubule cell (ion-trapping mechanism)

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34
Q

Rank the relative contribution of the four nitrogenous waste products

A 
highest
Urea
creatinine
NH4+
Uric acid
Lowest
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35
Q

What is the immediate precursor of urea?

A

Arginine

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36
Q

What contributes the 2 N atoms in urea?

A

Aspartate and free NH4+ ions

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37
Q

What contributes the carbon atom in urea?

A

CO2

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38
Q

Where does the urea cycle take place?

A

Partly in mitochondria, partly in cytosol

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39
Q

What is the primary function of the urea cycle?

A

Remove toxic NH4+ from the blood as urea

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40
Q

How is carbamoyl phosphate formed?

A

CO2+H2)-> HCO3-

HCO3-+NH4+—Carbamoyl Phosphate synthetase I (CPSI)—> Carbamoyl Phosphate

2 ATP is used to form 2ADP+Pi

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41
Q

Which enzyme converts ornithine to citrulline

A

Ornithine transcarbamoylase

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42
Q

Which enzyme converts citrulline and aspartate into argininosuccinate

A

Argininosuccinate synthetase

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43
Q

Which enzyme converts argininosuccinate into arginine and fumarate

A

Argininosuccinate lyase

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44
Q

Which enzyme converts arginine into urea and ornithine?

A

arginase

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45
Q

Which reactions occur in the mitochondria

A

Ornithine+carbamoyl phosphate—> citrulline

HCO3-+NH4+—> carbamoyl phosphate

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46
Q

How is the urea cycle connected to the TCA cycle?

A

Fumarate exits urea cycle to enter TCA cycle

Aspartate can be formed by transamination of OAA from the TCA cycle, and it enters the urea cycle to form argininosuccinate

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47
Q

What is the benefit of fumarate entering TCA cycle?

A

Helps to generate NADH in TCA cycle to compensate for loss of ATP in Urea cycle.

Fumarate recycled to form Asp via TCA cycle to assist in transferring more N to urea

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48
Q

How can urea cycle be regulated by substrate availability

A

NH4+ increase, arginine increase, urea increase

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49
Q

How does N-acetylglutamate synthetase (NAGS) regulate urea cycle

A

Arginine is a positive allosteric activator of NAGS, NAG is synthesised, and is a positive allosteric activator of Carbamoyl Phosphate Synthetase I (CPS I)

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50
Q

How can urea cycle be induced by glucagon and glucocorticoids?

A

During prolonged fasting, glucagon and glucocorticoids are secreted.

At the same time, increased proteolysis also results in increased NH4+ produced.

Glucagon and glucocorticoids result in increased flux of the urea cycle to excrete NH4+

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51
Q

How does a high protein elevate urea production?

A

Increased protein digestion and absorption, increased amino acid catabolism, increased NH4+, higher rate of urea cycle due to substrate availability, more arginine, more NAGS activated, more NAG, more CPSI activated, higher rate of urea cycle, more urea

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52
Q

How does starvation elevate urea production?

A

Increase in glucocorticoid secretion, increase in proteolysis, more amino acids catabolised, more NH4+ produced, Ala and glutamine synthesis in skeletal muscle increased and released into circulation as N carriers

Amino acid carbon converted to glucose, N converted to urea, increase in urea production

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53
Q

What does ornithinine transcarbamoylase enzyme defect result in?

A

Low citrulline and elevated urinary orotic acid

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54
Q

What does argininosuccinate synthetase enzyme deficiency result in?

A

High citrulline and low argininosuccinate

Aspartate accumulation results in lesser conversion of glutamate to aspartate (via transamination). less NH4+ and alphakg converted to glutamate. NH4+ accumulates.

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55
Q

What does argininosuccinate lyase enzyme deficiency result in?

A

High citrulline and high argininosuccinate.

Arginine not produced, NAGS not activated, NAG not produced, CPSI not activated

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56
Q

What does arginase enzyme deficiency result in?

A

High citrulline, high argininosuccinate. Ornithine not regenerated, citrulline cannot be exported by antiport.

57
Q

How does a low protein diet help manage urea cycle disorder.

A

minimal protein consumed, equilibrium nitrogen balance, less amino acid degradation, less free NH4+, supplement diet with only essential amino acids

58
Q

Which urea cycle disorders is a low protein diet effective for?

A

All

59
Q

Why is arginine replenishment a favourable treatment method of urea cycle disorder?

A

High arginine intake ensures regeneration of ornithine by arginase.

Ornithine replenishment would result in no Arg, NAGS not activated, no NAG, no CPSI activation.

60
Q

Which urea cycle disorder is arginine replenishment not effective.

A

Arginase deficiency

61
Q

In Argininosuccinate Lyase deficiency, how is N excreted?

A

In the form of argininosuccinate (2 NH4+ incorporated)

62
Q

In Argininosuccinate synthetase deficiency, how is N excreted?

A

In the form of citrulline (1 NH4+ incorporated)

63
Q

How does phenylbutyrate act to treat urea cycle disorder?

A

Phenylbutyrate undergoes beta oxidation to form phenylacetate, which reacts with glutamine (N carrier) to form phenylacetylglutamine which can be excreted

64
Q

What is one possible explanation of hyperammonemia resulting in neurotoxicity?

A

Conversion of NH4+ and alpha-kg into glutamate, and then NH4+ and glutamate into glutamine, glutamine associated with cerebral edema

65
Q

What is an essential amino acid?

A

An amino acid that a human cannot synthesise and must be obtained via diet

66
Q

Name the essential amino acids

A

(only those we need to remember) Leucine, isoleucine, valine, phenyalanine

67
Q

Which amino acid is semi-essential?

A

arginine, because some preterm infants cannot synthesise it

68
Q

Name the non-essential amino acids

A

Alanine (can be generated by ALT with pyruvate)
Asparagine
Aspartate
(asparagine and aspartate can generate each other via non-oxidative deamination/asparagine synthetase)
Glutamine
Glutamate
(Glutaminase non-oxidative deamination/ glutamine synthetase)
Tyrosine

69
Q

What is a non-essential amino acid?

A

An amino acid that a human can synthesise in adequate amount from common intermediates

70
Q

What is a glucogenic amino acid?

A

Degradation of amino acid yields glucogenic precursor

71
Q

What is a ketogenic amino acid?

A

Degradation of amino acid yields compounds that can be converted to KB or FA

72
Q

Which amino acids are strictly ketogenic?

A

Lysine and leucine`

73
Q

Why are lysine and leucine strictly ketogenic?

A

Catabolism of their carbon skeleton does not produce any intermediates that can result in the net synthesis of glucose. Lysine and leucine enter TCA cycle as acetyl CoA

74
Q

What enzyme is key in the reaction of Branched Chain Amino Acids (BCAA) to Branched Chain Keto Acids (BCKA)?

A

BCAA transaminase.

alpha ketoglutarate converted to glutamate.

75
Q

What is the key enzyme that reacts with BCKA to form ketogenic and glucogenic substrates?

A

BCKA dehydrogenase to form succinyl CoA, Acetyl CoA and acetoacetate

76
Q

Describe the basis for maple-syrup urine disease

A

Defective BCKA d/h, cannot decarboxylate BCKA, BCAA and BCKA accumulate in blood.

Presence of BCAA and BCKA in urine gives maple-syrup odour.

77
Q

What is an effect of maple-syrup urine disease?

A

Accumulation of BCKA results in neurological damage, coma and seizures

78
Q

What are the possible treatment options for maple-syrup disease?

A

Diet low in BCAA (leucine, isoleucine and valine) and close monitoring of blood amino acids

Manmade infant formula with low BCAA levels

79
Q

How is phenylalanine catabolised?

A

Phenylalanine—phenylalanine hydroxylase—> tyrosine—> fumarate or acetoacetate

80
Q

What is the coenzyme for conversion of phenylalanine to tyrosine?

A

tetrahydrobiopterin (BH4)—> dihydrobiopterin (BH2)

BH2 regenerated to BH4 by dihydrobiopterin reductase

81
Q

What is phenylketouria (PKU)?

A

Impaired ability to convert phenylalanine to tyrosine, inherited disorder

82
Q

What is classical PKU?

A

Deficiency in phenylalanine hydroxylase

83
Q

What is non-classical PKU?

A

Deficiency in BH4 or dihydrobiopterin reductase, impair pheylalanine hydroxylase activity

84
Q

What happens when phenylalanine cannot be converted to tyrosine?

A

Phenylalanine converted to phenylacetate and phenyllactate.

Phenylalanine buildup can impair the central nervous system and cause brain damage

85
Q

What are possible explanations for phenylalanine neurotoxicity?

A

Phenylalanine—> phenylpyruvate results in the depletion of alphakg to form glutamate. This disrupts the TCA cycle.

Phenylpyruvate—> phenylacetate results in phenylacetate forming phenylacetylglutamine to be excreted

Glutamate is required to form glutamine.

Glutamate (neurotransmitter) depleted

Depletion of glutamine which is a source of glutamate

86
Q

How does PKU cause hypopigmentation?

A

Albinism occurs when tyrosine is not produced and thus melanin production is impaired.

Phenylalanine and L-tyrosine are also very similar in structure, andthe high concentration of phenylalanine in PKU will compete with tyrosine for tyrosinase as a competitive inhibitor

87
Q

What is dopamine?

A

Neurotransmitter

88
Q

What is norepinephrine?

A

A hormone and neurotransmitter

89
Q

What is epinephrine?

A

A hormone

90
Q

How is conversion of tyrosine to DOPA catalysed in melanocytes?

A

tyrosinase

91
Q

How is conversion of tyrosine to DOPA catalysed in neurons and adrenal medulla?

A

tyrosine hydroxylase with BH4 as a coenzyme

92
Q

Describe the production of epinephrine from tyrosine

A

tyrosine—> DOPA—> dopamine—>norepinephrine—>epinephrine

93
Q

What is a cofactor for aromatic acid hydroxylase?

A

Coenzyme BH4 converted to BH2 , regenerated by dihydrobiopterin reductase.

Hydroxylation adds -OH

e. g.
1. Phe->Tyr
2. Tyr->DOPA
3. Trp-> 5-hydroxyTrp

94
Q

What is serotonin?

A

It is a neurotransmitter that regulates emotions, perception of pain, body temperature and basic activities

95
Q

What does low serotonin result in?

A

Depression, anxiety, schizophrenia and increased appetite

96
Q

What is melatonin?

A

It is synthesised in response to light-dark environment, increased secretion in dark environment.

Regulates sleep-wake cycle and seasonal rhythms

97
Q

What is histamine?

A

Stimulates dilation of capillaries and increases blood flow. Allows immune cells to infiltrate site of infection, mediator of inflammatory response in allergies

98
Q

Which reactions are pyridoxal phosphate (PLP) dependent?

A

Tr—> Serotonin

Histidine—>histamine

DOPA—>dopamine

Decarboxylation reations where CO2 leaves

99
Q

What is PLP?

A

key cofactor of amino acid metabolism, covalently binds to amino acid substrate

Synthesised from Vit B6

100
Q

What does Vit B6 deficiency result in?

A

PLP synthesis inhibition, drop in serotonin and dopamine synthesis , symptoms of depression

101
Q

What is a precursor of melatonin?

A

serotonin

102
Q

Which organs participate in the synthesis of creatine?

A

begins in kidney and completed in liver, synthesised from Gly Arg and Met

Transported to brain, heart and skeletal muscles

103
Q

What is the role of creatine?

A

High ATP inhibits glycolysis, so energy is stored in creatine.

Creatine phosphate formed via creatine kinase.

Allows glycolysis to continue as ATP levels are lowered.

ATP released from creatine phosphate when needed

104
Q

How is creatinine formed?

A

Spontaneous cyclisation of creatine and creatine phosphate.

105
Q

What happens when creatinine is formed??

A

Excreted in urine.

If creatinine is formed by creatine phosphate, energy stored is lost

106
Q

What is a nucleoside?

A

It is a base (pyrimidine or purine) and ribose/deoxyribose sugar

107
Q

What is a nucleotide?

A

Nucleoside+phosphate

108
Q

When the base is a purine what does the nucleoside name end with?

A

-osine
adenosine and guanosine

2 ring structure

109
Q

When the base is a pyrimidine what does the nucleoside name end with?

A

-idine
cytidine, thymidine and uridine

1 ring structure

110
Q

Which amino acids are involved in the de novo synthesis of purine and pyrimidine rings?

A

glutamine, aspartate and glycine (only purine)

111
Q

Why is de novo synthesis of purine and pyrimidine bases important?

A

Dietary nucleotides degraded by intestinal bacteria. Too little nucleotides assimilated to meet need for purine and pyrimidine

112
Q

What is 5-phosphoribosyl-pyrophosphate (PRPP)?

A

A critical enzyme at biosynthetic crossroad, a precursor which is required for both purine and pyrimidine nucleotide synthesis

113
Q

What is used to form PRPP?

A

Ribose-5-phosphate from the PPP.
R5P—PRPPsynthetase—> PRPP

ATP is consumed!!

114
Q

Which amino acid contributes nitrogen to purine synthesis?

A

Aspartate. Carbon skeleton leaves pathway as fumarate.

Similar to reaction catalysed by ASS and ASL in urea cycle

115
Q

What is the branch point for AMP and GMP synthesis?

A

IMP

116
Q

How is ATP formed from AMP?

A

AMP is phosphorylated to ADP, and further phosphorylated to ATP.

ATP converted to ADP can be reverted back via glycolysis and oxidative phosphorylation.

117
Q

How doe slow rate of glycolysis/oxidative phosphorylation affect cell division?

A

Low ATP levels, lower DNA synthesis, less cell division

118
Q

How is purine nucleotide synthesis regulated?

A

BY negative feedback mechanisms.

119
Q

How is ATP and GTP synthesis balanced?

A

high ATP concentration results in accumulation of ADP and thus AMP, which inhibits adenylosuccinate synthetase. IMP is not converted to adenylosuccinate and IMP is accumulated. More IMP converted to XMP, resulting in higher GTP.

High GTP results in accumulation in GDP and thus GMP, which inhibits IMP dehydrogenase. IMP accumulates and more IMP converted to adenylosuccinate, resulting in higher ATP.

ATP encourages XMP—> GMP

GTP encourages IMP—> adenylosuccinate

120
Q

What is the purine nucleotide cycle?

A

AMP— AMP deaminase—>IMP—adenylosuccinate synthetase—>adenylosuccinate—adenylosuccinate lyase—>AMP

Produces fumarate from aspartate to enter TCA cycle for skeletal muscle energy production

121
Q

What is the effect of AMP deaminase deficiency?

A

Exercise intolerance

122
Q

Why does AMP deaminase deficiency result in exercise intolerance

A

During exercise, more energy demanded, need higher rate of TCA

AMP deaminase deficiency= less fumarate produced, less fumarate enters TCA cycle to be converted to OAA, to accept glucose/FA-derived acetyl-CoA and produce more energy

123
Q

What is a common manifestation of gout?

A

Painful athritic joint inflammation and kidney stones

124
Q

What is the biochemical basis of gout?

A

Purine catabolism produces urate (uric acid). Abnormal elevation of uric acid in blood results in abnormal deposits of sodium urate crystals around joint cartilage.

125
Q

How can you treat gout?

A

Allopurinol which is a competitive inhibitor of xanthine oxidase.

Allopurinol has a very similar structure to xanthine and hypoxanthine

126
Q

Why is the salvage of purine and pyrimidine bases important?

A

De novo synthesis requires large amounts of nutrients and energy. Conserve nutrients and energy when salvage pathways convert free purines and pyrimidines to corresponding nucleotides

127
Q

What is Lesch-Nyhan syndrome?

A

Severe HGPRT (hypoxanthine-guanine phosphoribosyltransferase). Hypoxanthine and guanine not converted back to IMP and GMP. Both hypoxanthine and guanine converted to xanthine and then uric acid. Excessive urate, gout-like symptoms. Allopurinol can only ameliorate gout symptoms, not neurological abnormalities

128
Q

What are the differences between CPS I and CPS II function?

A

CPS I in urea cycle, CPS II in pyrimidine synthesis

129
Q

What are the differences between CPS I and CPS II location?

A

CPS I in mitochondria, CPS II in cytoplasm

130
Q

What are the differences between CPS I and CPS II source of nitrogen?

A

CPS I NH4+, CPS II Glutamine amide N

131
Q

What are the differences between CPS I and CPS II activators?

A

CPS I NAG, CPS II ATP and PRPP

132
Q

What are the differences between CPS I and CPS II function?

A

CPS I no inhibitor, CPS II UTP, end-product feedback inhibition

133
Q

How is orotate converted to UMP

A

Orotate—UMP synthase—> OMP—UMP synthase—>UMP

134
Q

What is orotic aciduria?

A

Deficiency in UMP synthase. Accumulation of orotate, increased orotic acid in urine

135
Q

How do you treate orotic aciduria?

A

Supplement uridine for cellular function, UTP formed, inhibits CPS II to decrease orotate production

136
Q

How is CTP formed?

A

UMP—> UTP—>CTP

137
Q

What is used for nucleic acid synthesis (RNA)?

A

ATP, GTP, UTP, CTP

138
Q

How are deoxynucleotides synthesised? (dATP, dTTP, dGTP, dCTP)

A

Reduction of ribose moeity. 2’OH replaced by 2’H.
NDP—ribose reductase—>dNDP

dNDP phosphorylated to form dNTP

EXCEPT dUDP dephosphorylated into dUMP and converted to dTMP—> dTDP—> dTTP

139
Q

What is the difference between pyrimidine and purine catabolic end products?

A

pyrimidine catabolic end products can be further metabolised and enter TCA cycle to contribute to energy production, but purine catabolic end products cannot

Biochemistry (3 decks)

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