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SPM > Week 4 > Flashcards

Week 4 Flashcards

1
Q

Describe the necessity for protein in our diet.

What are the three pathways of use in the body?

A
  • Protein → free AA → →
    • Essential nitrogenous compounds (trivial)
    • Participate in the equilibrium of cell and plasma proteins/nucleic acids/hormone turnover (major)
    • Degradation to provide energy from carbon skeleton (10-15%)
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2
Q

Describe the maintenance of the pools of amino acids required for protein synthesis. (in terms of KM)

A
  • KM of aminoacyltransferases is low and therefore prefers to charge tRNA to attract AAs
    • Degradation has high KM, or low affinity
    • tRNA formation has low KM, or high affinity, favoring protein synthesis
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3
Q

What is nitrogen balance?

A
  • For normal individuals: intake of nitrogen = urea excretion of nitrogen
  • Nitrogen balance depends on three things
    • N only comes from other AAs (N is never fixed to AAs from outside sources)
    • Most waste N excreted as urea
    • No dedicated N storage
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4
Q

What is negative nitrogen balance?

Why does it happen?

A
  • Description: nitrogen intake < nitrogen excretion
  • Why: individuals are degrading proteins for energy
    • Surgery
    • Disease
    • Trauma (i.e. burns or fractures)
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5
Q

What is positive nitrogen balance?

Why does it happen?

A
  • Description: nitrogen intake > nitrogen excretion
  • Why: individuals are in period of growth
    • Childhood growth
    • Pregnancy
    • Post-traumatic event
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6
Q

Describe why some AAs are essential while others are nonessential.

A
  • Essential AAs cannot be synthesized or the body cannot make them in sufficient quantities
    • R MLK had HIV WTF
  • Nonessential are synthesized in appropriate quantities by the body
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7
Q

What is the relationship of most nonessential AAs to common intermediary metabolites.

A
  • The carbon skeletons of the nonessential amino acids are largely related to common intermediates of metabolism [consider alanine and pyruvate. The reason that the essential amino acids are essential is that we cannot make their carbon skeletons]
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8
Q

What is the general equation for creating different metabolites from AAs?

What is the cofactor?

Name some specific examples?

A
  • General: AA1 + alpha-keto acid2 = alpha-keto acid1 + AA2 (PLP or vitamin B6 as cofactor)
    • The Keq of reactions using aminotransferases is ~1, meaning the reaction is dependent on concentrations
  • Alpha-ketoglutarate + aspartate = glutamate + oxaloacetate (using aspartate aminotransferase and PLP as cofactor)
  • Alpha-ketoglutarate + alanine = glutamate + pyruvate (using alanine aminotransferase and PLP as cofactor)
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9
Q

What does high ALT and AST indicate?

A

High levels of serum aminotransferases indicate tissue/organ damage (i.e. MI)

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10
Q

How is PLP affected by certian TB treatments?

A

Isoniazid – used to treat TB – competitively binds to PLP, inducing a B6 deficiency

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11
Q

Describe the importance of the AA composition in the diet.

A

Any AAs that are not made endogenously are considered essential AAs, and those essential AAs need to be consumed through diet

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12
Q

Describe the inadequacy of certain diets based on vegetable protein.

A

Vegetarians – have an inadequate consumption of essential AAs

Cereal is low in lysine

Beans low in methionine

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13
Q

Describe Kwashiorkor?

A
  • Inadequate protein intake
  • “the disease of the deposed baby when the next baby is born” so no nutrients through breast milk
  • Characterized by retention of water in the stomach, failure to thrive, composition of gut bacteria
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14
Q

Describe Marasmus?

A
  • Inadequate energy intake
  • Characterized by failure to thrive and delayed mental development
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15
Q

Describe Marasmic Kwashiorkor?

A

Inadequate energy and protein intake

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16
Q

Describe the occurrence of protein energy malnutrition in anorexia nervosa, bulimia, severe illness, aging.

A

Occurs in more advanced societies due to inadequate energy and protein intake

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17
Q

Describe the diversity of AA derivatives including post-translational modifications and metabolic products. Give 6 examples.

A
  • 20 AAs are produced through translation into proteins, but lots of AAs are transformed by post-translational modification OR are produced through metabolic processes
  • Examples
    • Hydroxyproline and hydroxyproline: collagen stability
    • Trimethyl-lysine: epigenetic regulation and carnitine synthesis
    • Acetyl-lysine: epigenetic regulation
    • 3-methylhistidine: modicication on actin and myosine
    • Phosphoserine: enzyme regulation
    • Gla: binding Ca++
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18
Q

What are proteases?

A

Proteases hydrolyze the peptide bond

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19
Q

Name some example of extracellular proteases.

A
  • Pepsin in stomach
  • Trypsin and chymotrypsin in intestine
  • Proteases can be given via oral therapeutics
    • CF treated with pancreatic proteases
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20
Q

Name some examples of intracellular proteases?

A
  • Ubiquitin-proteasome pathway: intracellular proteins
    • Multiple ubiquitin units must be added to a protein before recognized for degradation to proteasome
  • Lysosomes (cathespins): endocytosed proteins and membrane proteins
  • Mitochondrial proteases: mitochondrial proteins
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21
Q

What is the urea cycle?

Explian the cycle. (Intermedates and major enzymes)

A
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22
Q

Describe the role of glutamine in movement of nitrogen.

A
  • Glutamate + NH3 + ATP = Glutamine + ADP+ Pi via Glutamine Synthetase in periphery
  • Glutamine + H2O → glutamate + NH3 via Glutaminase in liver and kidney tissue
  • Therefore, glutamate acts as a shuttle carrier for NH3
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23
Q

Describe the glucose-alanine cycle and its roles.

A
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24
Q

What is the difference between NH4+ detoxification in normal people and those with liver cirrhossis? (Describe the pathways)

A
  • Normal: portal vein is high in NH4 → liver detoxifies NH4 → detoxed blood in inferior vena cava
  • Liver Cirrhosis: portal vein is high in NH4 → liver cirrhosis → new vasculature forms from portal vein to inferior vena → increased NH4 → blood toxicity
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25
Q

What are some consequences of hyperammonemia?

A
  • Episodic ataxia—muscle weakness
  • Dysmetria—uncoordinated movement
  • Stupor
  • Hepatic coma (encephalopathy)
  • Liver Cirrhosis
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26
Q

Describe glucogenic AAs.

A

Glucogenic: breakdown of glucogenic AAs provide carbon skeletons that enter into pathways making net glucose

  • AAs that breakdown to pyruvate or oxaloacetate
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27
Q

Describe ketogenic AAs.

A
  • Ketogenic: breakdown of ketogenic AAs provide carbon skeletons that enter into pathways giving rise to ketone bodies
    • AAs that breakdown to acetyl-CoA and acetoacetyl-CoA
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28
Q

Describe the degradation and use of AAs as energy sources.

A
  • Glucogenic: pyruvate or oxaloacetate create a net gain of glucose
  • Ketogenic: acetyl-CoA and acetoacetyl-CoA enter into citric acid cycle with no net gain of glucose
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29
Q

What is the source of NO and pathway?

A

Source: arginine

Arginine + O2 + NADPH → citrulline + nitric oxide + NADP+

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30
Q

Function of NO (4)

A

Vasodilation (nitroglycerin)

Vascular tone

Inhibition of platelet aggregation

Cytotoxic agent in immune system

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31
Q

What is the importance of Vitamin K?

What does deficiency lead to?

A
  • Vitamin K is a cofactor for post-translational modification of glutamate to Gla
    • Vitamin is oxidized, and in order to be used as a cofactor again, it must be reduced through 2 enzymatic steps
    • Gla is used in clotting and in osteocalcin (Ca++ binding protein in bone)
  • VKDB (Vitamin K Deficiency Bleeding): internal bleeding due to lack of blood clotting (can be mistaken for child abuse)
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32
Q

What are Vitamin K inhibitors?

A

Dicumerol

Warfarin

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33
Q

Describe translational research.

A

Bench-to-bedside (i.e. warfarin)

ARSH SAYS – remember the story about the dead cow blood. :)

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34
Q

What are the five metabolites that trypotphan breaks down into?

A
  1. seretonin
  2. melatonin
  3. xanthuenote
  4. NAD+
  5. acetoacetyl CoA
35
Q

How tryptophan broken down?

A
  • Tryptophan is broken down into alanine (glucogenic) and acetoacetyl CoA (ketogenic)
    • Degradation:
      • Urine color via xanthurenate
      • Feces odor
      • Halitosis (bad breath)
36
Q

How is Nicotinate created?

How is it regulated?

A
  • Tryptophan → kynurenine + formate → → nicotinate mononucleotide → NAD+
    • Regulation: 1st step - via Tryptophan oxygenase
      • Substrate activation
      • Enzyme stabilization (increasing [enzyme])
      • Nicotinamide nucleotides
37
Q

What is serotonin? and how is created?

A

Neurotransmitter and vasoconstrictor (released by platelets)

  • Tryptophan → 5-hydroxytryptophan → serotonin
    • 1st step: tryptophan hydroxylase with BH4 as a cofactor
    • 2nd step: PLP with a decarboxylase
38
Q

How does Sumatriptan work?

A

5-HT1 agonist. Treatment for migraines.

39
Q

How does Prozac work?

A

serotonin specific reuptake inhibitor

40
Q

What is melatonin and how is it created?

A
  • Regulates sleep/wake cycles
  • Tryptophan → serotonin → N-acetylserotonin → melatonin
    • Regulation: via SAM
      • Inhibited by light
41
Q

Describe the nutritional disease pellagra.

A
  • Diet deficient in niacin and tryptophan can cause pellagra
  • Nicotinate and nicotinamide, which are precursors to NAD+, protect against pellagra
  • Starving people do not develop pellagra because their body is breaking down proteins into AAs (aka: tryptophan)
  • Symptoms
    • Dermatitis
    • Diarrhea
    • Dementia
    • Death
42
Q

Describe the relationship of phenylalanine and tyrosine?

A
  • Phenylalanine (essential) synthesizes tyrosine (non-essential as long as there is enough F)
    • F → Y via phenylalanine hydroxylase and BH4 oxidation
    • BH2 must be reduced back to BH4 in order to act as a cofactor in future reactions
43
Q

PKU causes?

A
  • Phenylketonuria
    • Malignant: mutation in the dihydrobiopterine reductase (BH2 to BH4)
    • Mutation in phenylalanine hydroxylase, so there is an accumulation of its alpha-ketoacid, phenylpyruvate
44
Q

Describe alkaptonuria and the first concept of inborn errors of metabolism.

A
  • First concept of inborn errors of metabolism – it is genetically based
  • Alkaptonuria: benign disease resulting from a defect in tyrosine degradation
    • Deficiency in homogentisate oxidase → buildup up of homogentisate → black urine and pigment accumulation in sclera
45
Q

What is the pathway of catecholamines?

A
  • Tyrosine → L-Dopa → Dopamine → Norepinephrine → Epinephrine
  • 1st Step: tyrosine hydroxylase uses BH4 as cofactor
    • Negative feedback by all catecholamines
  • 3rd Step: vitamin C is a cofactor
  • 4th Step: SAM methylates norepinephrine
  • Lack of dopamine causes Parkinson’s, which can be treated with L-Dopa because it can cross the blood brain barrier
46
Q

Pathway for melanin?

A

Tyrosine → → → Melanin using tyrosinase by adding 2O2

47
Q

How are thryroid hormones created?

A
  • Derived from post-translationally modified tyrosines
  • Thyroglobulin degrades into T4
48
Q

Describe the symptoms and basis of oculocutaneous albinism.

A
  • Deficiency in tyrosinase
  • Symptoms
    • Sensitivity to sunlight
    • Decreased visual acuity
49
Q

How are catecholamines inactivated?

A
  • Monoamine oxidase inhibitors (MAOIs)
    • Catecholamines must be degraded to become inactive
    • MAO and COMT AND COMT and MAO act together to inactivate these compounds
    • MAOIs are used to treat depression
      • May interfere with metabolism of monoamines
50
Q

Describe the sources and uses of C1 units

A

Cofactors/Sources

  • THF
  • SAM
  • Vitamin B12

Uses

  • Methylated compounds (proteins, nucleic acids, lipids, hormones)
  • Thymine
  • Purine rings
51
Q

Describe how tetrahydrofolate (THF) carries C1 units at (3) different oxidation levels.

A
  • C1 level at methanol
    • C1 unit is passed from N5-methyl-THF to another cofactor, S-adenosylmethionine (SAM)
    • B12 deficiency creates a “folate trap” that prevents 5-methyl-THF from making dTMP and methionine
  • C1 level at formaldehyde
    • Glycine/serine interconversion
  • C1 level at formate
    • Two reactions in purine biosynthesis
52
Q

Describe why sulfanilamide inhibits bacterial folic acid synthesis
.

A
  • Bacteria treated with sulfanilamide mis-incorporate this compound in place of PABA during synthesis of folic acid
  • Humans do not have this enzyme to synthesize folic acid, so unaffected
53
Q

Describe the transfer of C1 units from THF to SAM.

A
  • Homocysteine + 5-methyl-THF → methionine via homocysteine methyltransferase (with B12)
  • Methionine + ATP → SAM + PP + Pi via methionine adenosyl transferase
54
Q

Describe the critical role of vitamin B12.

A
  • Used as a cofactor in only two reactions in the body
    • Homocysteine methionine (for DNA synthesis)
    • L-methylmalonyl-CoA → succinyl-CoA (oxidation of some AAs or beta-oxidation of odd-numbered fatty acids)
      • B12 deficiency leads to build up of methylmalonyl-CoA, which can go on to degrade myelin sheaths
55
Q

Describe effects of deficiencies in vitamin B12 and folic acid and their roles in spina bifida

A

Spina bifida: an incomplete closure of the neural tube, which can result in paralysis

Each deficiency presents as independent risk factors

56
Q

Describe the use of creatinine levels to measure kidney function

A

Creatinine is neither absorbed or secreted, so it is filtered out of the blood and is a good measure of the glomerular filtration rate (GFR)

57
Q

Describe the synthesis of pyrimidine bases and nucleotides

58
Q

Describe the synthesis of purine nucleotides

59
Q

Formation of deoxyribonucleotides by ribonucleotide reductase

A
  • Ribonucleotide reductase converts NDPs (ribose) to dNDPs (deoxyribose)
    • 3 different classes of RNRs
    • Reaction proceeds via free radical mechanism of action
60
Q

Describe thymidine (as TMP) synthesis

61
Q

The biochemical basis of pernicious anemia and megaloblastic anemia

A
  • Pernicious anemia – anemia associated with neurological problems (assoc. with B12)
  • Megaloblastic anemia – cells that are unable to divide but produce proteins (assoc. with B9 and B12)
62
Q

How does Trimethoprim work

and

what does in inhibit?

A
  • Trimethoprim
    • Antibiotic
    • Binds to bacterial DHF reductase strongly, inhibiting it in bacteria
    • Binds weakly to human version
    • Selectively inhibits bacterial growth
63
Q

How does Hydroxyurea work

and

what does in inhibit?

A
  • Hydroxyurea
    • Free radical scavenger
    • Inhibits ribonucleotide reductase → decreasing dNTP pool (especially in proliferating cells)
64
Q

How does Methotrexate work

and

what does in inhibit?

A
  • Methotrexate
    • DHF reductase inhibitor
      • Competes with DHF for binding DHF reductase
        • Can’t convert to THF
    • Recovery and reversal by giving high levels of nucleosides and folate
    • Anti-cancer (inhibits DNA synthesis, stopping cell division)
65
Q

How does 5-fluorouracil work

and

what does in inhibit?

A
  • 5-fluorouracil
    • FdUMP a derivative of 5-fluorouracil
    • “suicide inhibitor” for thymidylate synthase (UMP → TMP)
66
Q

How does 5-azacytidine work

and

what does in inhibit?

A
  • 5-azacytidine
    • Prodrug
    • Pyrimidine biosynthesis inhibitor
67
Q

How does 6-mercaptopurine work

and

what does in inhibit?

A
  • 6-mercaptopurine
    • Inhibits purine synthesis at multiple steps
    • Cells starve of purines and die​
68
Q

How are purines catabolized in the body?

69
Q

Factors effecting onset on gout?

A
  • Onset
    • Men over 30yo and post-menopausal women
    • Hyperuricemia
70
Q

Factors effecting presentation of gout?

A
  • Presentation
    • Present at physiological pH as sodium urate
    • Alcohol consumption – beer has yeast, which produces high levels of purines
    • Dehydration
    • High purine diet (meat, seafood, asparagus, spinach)
    • “Tophi” – monosodium urate tissue aggregates that eat through bone
    • Sodium urate precipitate in joints and kidney stones
71
Q

Describe the salvage pathway for purines.

72
Q

Describe the salvage pathway for pyrimidines.

73
Q

Describe the essential role of salvage pathways in achieving pool balance.

A
  • Pool balance is important because there needs to be a level of concentration of nucleotides for DNA and RNA synthesis
  • Salvage pathways recycle bases
74
Q

Treatments for chronic gout?

A

Chronic Gout

  • Xanthine oxidase inhibitor – inhibits purine degradation
    • Allopurinol
    • Febuxostat
  • Uricosuric agent – increase excretion of uric acid in urine
    • Pegloticase
75
Q

Treatments for acute gout?

A

Acute Gout

  • NSAIDs – COX1 & COX2 inhibitor – reduce pain and inflammation
    • Indomethacin
  • Colchicine – Reduces gout symptoms
  • Intra-articular Corticosteroids – Reduce inflammation
76
Q

What is Azanthioprine (AZA)?

Whats the mechanism?

and effect?

How is it affected by Xanthione oxidase inhibitors?

A

Azathioprine (AZA)

  • Prodrug
  • Immunosuppressant
  • Cyclosporin is often used in conjunction with AZA
    • Decreases uric acid excretion, leading to higher prevalence of gout in transplant recipients
  • Xanthine oxidase inhibitors (allopurinol) are used then to decrease uric acid production
    • Can lead to AZA toxicity because some AZA metabolites use xanthine oxidase
77
Q

What is Cytosine Arabinoside (AraC) and Alanine Arabinose (AraA)?

Whats the mechanism?

and effect?

A

Cytosine Arabinoside (AraC) and Alanine Arabinose (AraA)

  • Arabinose is substituted in place of ribose
  • Results in cell death in leukemia tumors
  • Must be phosphorylated to nucleoside triphosphates to be incorporated into DNA
78
Q

What is 2-cholorodeoxyadenosine?

Whats the mechanism?

and effect?

A

2-cholorodeoxyadenosine

  • Used in treatment of hairy cell leukemia
  • Cytotoxic, especially in inhibition of DNA repair of double-strand breaks
  • As resists breakdown by adenosine deaminase as a chemotherapeutic drug
79
Q

What is 5-Iodouridine?

Whats the mechanism?

and effect?

A

5-Iodouridine

  • Functional analogue of thymidine (not uridine!) that must be metabolized to a dNTP before it is incorporated into DNA
  • Pairs with G instead of A due to aberrant hydrogen bonding properties
    • Mispairs in DNA and RNA
  • Treats herpesvirus infections
80
Q

What is Acyclovir?

Whats the mechanism?

and effect?

A

Acyclovir

  • Analogue of guanosine that lacks most of ribose ring
  • Missing 3’-OH group causes chain termination of DNA strand once incorporated
  • Treats herpesvirus infections
    • Must be in monophosphorylated form
    • Only virally-encoded thymidine kinase phosphorylates acyclovir (human thymidine kinase does not)
81
Q

What is Azidothymidine (AZT)?

Whats the mechanism?

and effect?

A

Azidothymidine (AZT)

  • Analogue of thymidine and has no 3’-OH group on ribose ring
  • DNA elongation is terminated
  • Treats HIV
    • Anti-viral because the HIV DNA reverse transcriptase has 100x increase in affinity for AZT triphosphate than normal DNA polymerases
82
Q

What is Hydroxyurea?

Whats the mechanism?

and effect?

A

Hydroxyurea

  • Inhibits ribonucleotide reductase, decreases dNTP pool, especially in proliferating cells
  • Helps drugs like AZT, which competes with endogenous TTP supply
83
Q

Connect elevated uric acid levels to Lesch-Nyhan Syndrome.

A

HGPRT deficiency → increased [hypoxanthine] → increased [uric acid]

SPM (17 decks)

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