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M1 > Biochem - Proteins, AA Catabolism vs Urea Cycle > Flashcards

Biochem - Proteins, AA Catabolism vs Urea Cycle Flashcards

1
Q

Conventionally a peptide chain is written in what direction?

A

The opposite as it is synthesized, starting with the N terminus

Synthesis starts with the C-terminus

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2
Q

Cathode and Anode in electrophoresis

A

Chathode (-)

Anode (+)

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3
Q

Alpha Helix

A

-NH H-bond every four AA’s along the chain

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4
Q

Beta Sheet

A

H-bond between C=O and -NH

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5
Q

Secondary Stx Motifs

A

Helix-turn-helix

Leucine zipper

Zinc finger

Found within transcription factors

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6
Q

Structural subunit of F-actin

A

Oligomer

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7
Q

Enthalpy of protein folding

A

Essentially isothermic (change in enthalpy is very small)

Although many H-bonds are broken during protein formation, the same number are broken from water

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8
Q

What energetically drives protein folding?

A

Entropy - resulting from increased disorder of water molecules as hydrophobic regions associate inside the protein

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9
Q

Molten globules

A

Intermediate between secondary structures and the folded protein

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10
Q

Heat shock proteins

A

Chaperones - prevent the aggregation of newly synthesized proteins by binding to their hydrophobic regions

I.e. HSP10, HSP 60, and HSP70

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11
Q

Myoglobin vs. Hemoglobin

A

Myoglobine - single peptide with one O2 binding site

HbA - tetrameric with two alpha and two beta polypeptide chains each conjugated with a heme group.

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12
Q

R state

Hemoglobin

A

Relaxed state

When one O2 molecule binds to a heme of hemoglobin

Increases affinity of O2 binding

Positive cooperativity

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13
Q

What reduces the O2 affinity of hemoglobin

A

Acidity (increased conc. of CO2)

This is called the Bohr effect

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14
Q

Binding of 2,3-bisphosphoglycerate (BPG)

A

Decreases the affinity of HbA for O2

BPG is by-product of glycolysis, this ensures efficient O2 offloading in tissues that are metabolically active, especially in high altitude or anemia, where intracellular BPG levels might be elevated

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15
Q

Sickle-cell anemia

A

The beta chain of hemoglobin undergoes a point mutation that causes a missense (E6V) mutation in the reading frame

The introduction of hydrophobic valine promotes polymerization of deoxygenated mutant hemoglobin

HbS polymers adopt the classic “sickle” shape - prone to hemolysis leading to anemia

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16
Q

Peptide configuration of collagen

A

Gly - X - Y

Gly - every third amino acid

X - typically proline

Y - typically hydroxyproline or hydroxy lysine

Collagen is a triple helical structure, where three polypeptide chains intertwine around each other

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17
Q

Synthesis of collagen

A

pro-collagen syn. in rER, where the signal sequence (pre) is removed)

In the rER lumen, pro and lys residues undergo hydroxylation (depends on presence of oxygen and Vit C)

Hydroxylysine residues are further glycoslated with galactose and glucose

Modified peptide chains are assembled into the triple helix, forming procollagen, which is secreted outside the cell and processed to form mature collagen

Collagen fibers undergo cross-linking by oxidation of amino acid side chains

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18
Q

EDS

A

Ehlers-Danlos Syndrome

Mutations in collagen synthesis and processing - fragile skin and hyper-elastic

Joint hypermobility

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19
Q

Osteogenesis imperfect

A

Mutations in collagen I genes

Brittle bones which are prone to fracture

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20
Q

Scurvy

A

Impairs the hydroxylation of proline and lysine residues

Results in unstable collagen (mp from 42 C to 24 C) as the result of the loss of interstrand H-bond fomration from lack of pro-OH

sxs - bleeding gums and poor wound healing

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21
Q

Alport syndrome

A

Mutations in collagen IV disrupts the collagen network supporting kidney glomerular cells

Leads to compromised kidneys and failure

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22
Q

Proteopathies

A

Diseases classified by misfolded proteins

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23
Q

CJD

A

Creutzfeldt-Jakob Disease - average onset at 68 y/o

Progresses rapidly - death within year

Rare

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24
Q

vCJD

A

Variant Creutzfeldt-Jakob Disease - younger-onset form, avg. death age of 28 y/o

Linked to consumption of beef from cows affected by bovine spongiform encephalopathy

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25
Q

Kuru

A

Prion disease ID’d among the Fore tribe in Papua New Guinea

Believed to have spread through cannabilistic practices

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26
Q

PrPc

A

Normal prion proteins - are primarily alpha-helical structures in the brain

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27
Q

PrPSC

A

Misfolded, disease-causing conformation of the prion, pirmarily beta-sheet conformation

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28
Q

Propagation of prion disease

A

The misfolded PrPSC acts as a template, causing endogenous PrPC to also misfold

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29
Q

Prion disease transmission

A

After consumption, PrPSC crosses the intestinal lining, gets taken up by immune cells, and is transported to the brain

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30
Q

Affect of prions disease in the brain

A

Accumulation of beta-sheet rich prions leads to the formation of protein plaques in the brain

Hallmark of prion disease

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31
Q

Alzheimer’s

A

Buildup of misfoled Aβ42 protein in the brain

APP undergoes enzymatic cleavages - resulting in Aβ42 fragments that can aggregate and form amyloid or senile plaques outside neurons

Much like prions, Aβ42 plaques adopt a beta-sheet conformation, leading to the formation of insoluble aggregates (resists degradation through normal cellular processes)

Intracellular tangles of tau (Aβ42 causes intracellular phosphorylation of tau protein) forms neurofibrillary tangles - believed to damage neurons from within

Aβ42 originates from amyloid precursor protein (APP) - transmembrane protein believed to play role in neuron growth, survival, and repair post-injury

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32
Q

Genetic factors of Alzheimer’s disease

A

Mutations in the APP gene and componenets of the gamma-secretase enzyme (involved in APP cleavage) have been linked to increased Aβ42 production

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33
Q

A patient with a history of recurrent vaso-occlusive crises is found to have a mutation in the β-chain of hemoglobin. Which of the following amino acid substitutions is most likely responsible for this patient’s condition?

A

Glutamate to valine (E6V)

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34
Q

What sequence of AA residues is most commonly found in collagen?

A

Gly-X-Y

X - typically proline
Y - either pro-OH or Lys-OH

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35
Q

Difference between amyloid plaques and neurofirillary tangles?

A

Aβ42 plaques - outside of neurons

Neurofibrillary tangles - inside of neurons (Aβ42 phosphorylates tau causing it to tangle)

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36
Q

A deficiency in what vitamin impairs the hydroxylation of proline and lysine residues in collagen synthesis?

A

Vitamn C (Scurvy)

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37
Q

Active site

A
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38
Q

Michaelis-Mentin Eq

A
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38
Q

Km

A

Affinity of enzyme to substrate (lower Km = higher affinity)

Mathematically derived as the substrate concentration at which v = 1/2(vmax)

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39
Q

When [S] «< Km

How is v affected?

A

The rate is directly proportional to [S]

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40
Q

When [S]&raquo_space;> Km

A

The rate approaches Vmax and becomes independent of [S]

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41
Q

Cofactors

A

Inorganic ions or organic molecules that bind to enzymes and are essential for activity

Types:

Posthetic groups and loosely bound cofactors

Fx - assist substrate binding, stabilize enzyme stx, or participate directly in reaction by facilitating transfer of chemical groups or electrons

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42
Q

Prosthetic Groups

A

Tightly and permanently bound to the enzyme (i.e. heme is a prosthetic group of hemoglobin)

Type of cofactor

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43
Q

Loosely Bound Cofactor

A

Can associate and dissociate from the enzyme (when bound, activate the enzyme)

44
Q

Coenzymes

A

Subset of cofactors that are organic molecules - often derived from vitamins

Unlike cofactors, coenzymes are not permanently bound to the enzyme

Fx - carriers, transporting specific groups or electrons from one reaction to another (many redox rx’ns)

i.e.

NAD+ and NADP+ (derived from niacin)
CoA (derived from panthenic acid)
FAD (derived from riboflavin)

45
Q

Affect of cofactors/coenzymes on enzyme

A

Catalytic activity
Specificity
Regulation (allosteric)
Diversity of rx’ns

46
Q

Cooperativity

A

The binding of a substrate to one active site can affect the binding of substrates to other active sites

47
Q

Allosteric enzymes often display _____ kinetics when rx’n velocity is plotted against [S]

A

Sigmoidal

48
Q

Affects of allosteric regulation

A
  1. Fine-tuning of metabolic pathways
  2. Feedback inhibition
  3. Rapid response
  4. Integration of mlutiple signals
49
Q

Competitive inhibitors

A

Can be overcome by adding more substrate (increasing [S])

Ex: Statins competitively inhibit HMG-CoA reductase

Vmax remains unchanged
Km increases (a higher [S] is need to achieve half of Vmax)

50
Q

Noncompetitive inhibitors

A

Bind to allosteric site, causing conformational change

Increasing [S] does not overcome inhibition

Ex: heavy metals like lead or mercury

Vmax decreases
Km remains unchanged (affinity is not affected)

51
Q

Lineweaver-Burke

A
52
Q

Enzyme inhibition graphs

A
53
Q

Graphs of V vs [S] for an allosteric enzyme

A

Does not follow MM kinetics, but is hyperbolic and the v vs. [S] is sigmoidal

54
Q

Inborn errors of metabolism

A

PKU, galactosemia, and Tay-Sachs disease

55
Q

Accumulation of toxic substances

A

PKU - deficiency of phenylalanine hydroxylas leads to accumulation of phenylalanine which causes intellectual disability if not managed

56
Q

G6PD deficiency

A

glucose-6-phosphate dehydrogenase deficiency can lead to hemolytic anemia (especially after exposure to certain drugs or infections)

57
Q

Disorder of purine and pyrimidine metabolism

A

Can lead to conditions like Lesch-Hyhan syndrome or orotic aciduria

58
Q

Congeital adrenal hyperplasia

A

An endocrine disorder that can result from deficiencies in enzymes involved in cortisol synthesis

59
Q

Where are AA’s abosrbed

A

Intestinal epithelial cells and taken up into cellular AA pools

60
Q

Essential AA’s

A

Cannot be made and must be obtained through diet

PVT TIM HaLL (Phe, Val, Trp, Thr, Ile, Met, His, Lys, Leu)

a = arginine (conditionally essential during periods of rapid growth)

61
Q

Primary reserve of AA’s

A

Muscle (this includes reserve for essential AA’s)

Diets deficient in essential AA’s can cause muscle wasting (when diet is deficient in essential AA’s, it can take up to six weeks for sxs to manifest due to muscle reserves)

62
Q

Kwashiorkor malnutrition

A

Protein deficiency with adequate calories

Children develop swollen belly (ascitic belly) becuase albumin is 97% of serum protein and is responsible for oncotic pressure

Fluid collects in abdomen due to gravity

63
Q

Marasmus malnutrition

A

Inadequate energy intake in all forms, including protein

64
Q

Cystinuria

A

Autosomal recessive

Impairs the reabsorption of dibasic AA (disulfide linked Cys-Cys, ornithine, arginine, and lysine)

Hexagonal crystals of cystine in urinalyses are diagnostic of cystinuria

Recurrent nephrolithiasis (kidney stones)

Management:

Low cystine diet and increased fluid intake

Potassium citrate and sodium bicarb (make urine less acidic and increases solubility of cystine)

Pencillamine and topronin are cystine-binding thiol drugs that bind and form a water-soluble complex

65
Q

Hartnup Disease

A

Autosomal recessive

Affects renal tubule reabsorption of neutral AA’s, importantly tryptophan

Trp is used to synthesize B3 (niacin) so sxs resemble deficiency of niacin (pellagra)

Management:

Dietary intake of trp-rick foods, trp and niacin supplements

66
Q

3 D’s of Pellagra

A

Dermatitis
Diarrhea
Dementia
(Death)

Other malabsorption disorders and chronic alcoholism can present with pellagra like sxs

Corn-based diets (low in trp and niacin) increase risk of pellagra

67
Q

Hartnup vs. Cystinuria

A
68
Q

Ammonia

A

Toxic, especially to the CNS (causing encephalopathy)

When ammonia levels are high, astroctyes onvert excess into glutamine, which is osmotically active. This draws water into astrocytes leading to cellular swelling and cerebral edema

69
Q

Disposal of ammonia

A

80-90% of ammonia is disposed via formation of urea in the liver and excreted by the kidneys

Carried in blood by alanine (muscle) and glutamine (most tissues)

70
Q

What are the most abundant AA’s in the blood?

A

Alanine (muscle) and glutamine (most tissues)

Transport ammonia to the liver

71
Q

Enzymes of AA catabolism

A

Amino transferases (aka transaminases) - transfer NH2 from an AA to another alpha-keto acid, which is converted to its cognate AA

Requires pyridoxal phosphate (PLP) a B6 derivative, as a cofactor

Reversible to allow interconversion of AA and ketoacids as needed for metabolic need

Specific aminotransferases for each AA (except thr. and lys)
-Most use alpha-ketoglutarate and glutamate

Thus amino groups are funneled i nto glutamate by transamination reactions

72
Q

ALT

A

Crucial in the glucose-analine cycle (allows the body to ransport nitrogen and carbond between muscles and the liver to maintain blood glucose levels during fasting or exercise, providing a way to remove excess nitrogen from muscle tissue.

In muscle, when AA are broken down their amino groups are transferred by aminotransferases to alpha-KG to generate Glu. ALT then transfers the amino from Glu to pyruvate producing Ala.

Ala is released into the blood and travels to the livers

The liver converts Ala back to pyruvate and Glu

The pyruvate can be used to produce glucose

The amino group from glutamate is used to form urea

73
Q

AST

A

Aspartate transaminase

74
Q

Where are ALT and AST highly expressed?

A

Liver

Also expressed in heart, muscle, and kidneys

75
Q

Glutamine Synthetase

A

Glu + NH3 +ATP -> Gln + ADP + Pi

GS fixes free NH3 to glutamate (produced by transaminases) to make glutaminewhich is released into the bloodstream for transport to liver

Kidneys and brain also take up Gln for metabolic use

76
Q

Glutaminase

A

Releases NH3 from glutamine to regenerate glutamate

In the liver, the released NH3 enters the urea cycle

Glutamate is deaminated again by glutamate DH which regenerates alpha-ketoglutarate

77
Q

Glutaminase in kidney

A

Releases NH3 from glutamine to help regulate urine pH

78
Q

Glutaminase in the brain

A

The formation of glutamate from glutamine via glutaminase is a pathway used to form the excitatory neurotransmitter (glutamate)

79
Q

Glutamate DH

A

Deaminates glutamate to form alpha-ketoglutarate/NAD(P)H/NH3

Reversible rx’n that is used to fix free ammonia to form glutamate

80
Q

Why is glutamate unique?

A

Only AA that undergoes rapid oxidative deamination

81
Q

In the liver, what enzymes release ammonia to enter the urea cycle?

A

Glutaminase and glutamate DH

82
Q

Carbomyl Phosphate Synthetase I

A

Step 1 of urea cycle

Rate-limiting step

N-acetyl glutamate is essential allosteric activator of CPS-I (formed by NAG synthetase which is activated by R)

Mitochondrial enzyme

83
Q

Why does adding arginine dietary intake help Tx Pt’s with some urea cycle disorders?

A

Arginine activates N-acetyl glutamate synthetase, which allosterically activates CPS-I

84
Q

Ornithine Transcarbamoylase (OTC)

A

Step two of urea cycle

carbamoyl phosphate + ornithine -> citrulline

Mitochondrial enzyme

85
Q

Argininosuccinate Synthetase (AS)

A

Step three or urea cycle

citrulline + aspartate -> argininosuccinate

AST supplies aspartate for this step

86
Q

Argininosuccinate lyase

A

Step four of urea cycle

argininosuccinate -> arginine + fumarate

86
Q
A
87
Q

Arginase

A

Step five of urea cycle

arginine -> urea + ornithine

88
Q

Hyperammonenmia

A

Causes:

Liver dysfunction
Urea cycle disorders (UCD)

Sxs: asterixis (flapping tremor), vomiting, confusion, blurred vision, slurred speech, seizures

89
Q

Only effective means to rapidly reduce level of circulating ammonia

A

Hemodialysis

90
Q

Ammonia scavengers

A

Form water soluble products with gly or glu that are excreted by the kidneys, providing alternate pathway for removal of NH3

Sodium benzoate - combines with gly in liver to form hippuric acid which is excreted

Sodium phenylbutyrate - metabolized to phenylacetate which reacts with gln to form phenylacetylglutamine which is excreted

91
Q

Lactulose

A

Non-absorbable disaccharide used in context of liver diseases. Fermentation of lactulose by gut bacteria lowers colonic pH.

Lower colonic pH promotes conversion of ammonia to ammonium, which do not easily diffuse across gut epithelium

NH3 is then able to be excreted in feces

92
Q

Rifaximin

A

Abx used to reduce the population of ammonia-producing bacteria in the gut

93
Q

Long-term management of hyperammonemia

A

Low-protein diet

Ammonia scavenger meds

Liver transplantation

94
Q

UCD’s

A

A complete lack of any enzyme of the urea cycle results in death shortly after birth

Deficiencies present after first feeding (first protein rich meal)

Deficiency of urea cycle enzyme:

Increased serum levels of gln

95
Q

CPS-I (CPSD)

A

Aka hyperammonemia-I

Most severe UCD

96
Q

A 30-year-old woman is concerned about her pregnancy after learning that her brother has a urea cycle disorder. She is currently 10 weeks pregnant and asymptomatic. Which of the following tests would be most appropriate to screen for the carrier status of ornithine transcarbamylase deficiency in this patient?

  1. Serum ammonia level
  2. Urinary orotic acid after protein load
  3. Plasma citrulline level
  4. Liver biopsy
  5. Serum urea nitrogen level
A

Urinary orotic acid after protein load.

Rationale: This test is most appropriate for screening for carrier status of ornithine transcarbamylase (OTC) deficiency. OTC deficiency is an X-linked disorder, and female carriers can be asymptomatic. The protein load test stimulates the urea cycle, and in OTC deficiency carriers, this leads to increased orotic acid excretion due to the accumulation of carbamoyl phosphate, which is then shunted into the pyrimidine synthesis pathway.

97
Q

A 28-year-old man presents to the clinic with a history of recurrent skin rashes, particularly on sun-exposed areas. He also complains of intermittent diarrhea and occasional confusion. Physical examination reveals a rough, scaly rash on face and hands. Which of the following amino acids is most likely affected in this condition?

  1. Phenylalanine
  2. Tryptophan
  3. Leucine
  4. Methionine
  5. Arginine
A

Tryptophan

Rationale: The clinical presentation of recurrent skin rashes on sun-exposed areas, intermittent diarrhea, and occasional confusion is consistent with Hartnup disease. Hartnup disease is a disorder of neutral amino acid transport, particularly affecting tryptophan absorption. Tryptophan is a precursor for niacin (vitamin B3), and its deficiency leads to pellagra-like symptoms, which include dermatitis, diarrhea, and dementia (the “3 D’s” of pellagra).

98
Q

A newborn presents with lethargy, poor feeding, and respiratory distress within 48 hours of birth. Laboratory tests reveal elevated plasma ammonia and trace amounts of citrulline. Urinary orotic acid levels are normal. Which of the following is the most likely diagnosis?

  1. Ornithine transcarbamylase deficiency
  2. Argininosuccinate synthetase deficiency
  3. Carbomoyl phosphate synthetase I deficiency
  4. Argininosuccinate lyase deficiency
  5. N-acetylglutamate synthase deficiency
A

Carbamoyl phosphate synthetase I deficiency

Rationale: The presentation of hyperammonemia within 48 hours of birth, along with trace amounts of citrulline and normal urinary orotic acid levels, is consistent with carbamoyl phosphate synthetase I (CPS-I) deficiency. CPS-I catalyzes the first step of the urea cycle. Its deficiency leads to ammonia accumulation and very low or absent citrulline. Normal orotic acid levels distinguish it from ornithine transcarbamylase deficiency, which would show elevated orotic acid.

99
Q

A 45-year-old man with a history of chronic alcoholism presents with confusion, asterixis, and a “sweet” odor on his breath. His blood ammonia level is 180 μmol/L. Which of the following medications would be most appropriate for immediate management?

  1. Sodium benzoate
  2. Rifaximin
  3. Lactulose
  4. Carbaglue (carglumic acid)
  5. Penicillamine
A

** Lactulose**

Rationale: The patient presents with signs of hepatic encephalopathy secondary to chronic alcoholism. Lactulose is the first-line treatment for acute management of hepatic encephalopathy. It works by lowering colonic pH, which promotes the conversion of NH3 to NH4+ ions, reducing ammonia absorption from the gut. The “sweet” odor on the breath is likely fetor hepaticus, often associated with severe liver disease.

100
Q

A patient with recurrent kidney stones is diagnosed with cystinuria. Which of the following is the primary defect in this condition?

A

Impaired reabsorption of dibasic amino acids in the kidneys

Rationale: Cystinuria is characterized by impaired reabsorption of dibasic amino acids (cystine, ornithine, arginine, and lysine) in the kidneys. This leads to excessive excretion of these amino acids, particularly cystine, which has low solubility and tends to form kidney stones. The primary defect is in the transport system for these amino acids in the renal tubules, not in their metabolism or production.

101
Q

Drug company develops a therapy to treat a cell membrane protein misfolding disorder. This mutation leads to abnormal protein folding and subsequent intracellular degradation of the protein before it can reach the cell membrane. With the new combination of drug therapy, the first drug corrects the processing and trafficking of the protein, enabling it to reach the cell surface membrane. Once the protein has reached the cell surface, its function is enhanced by the second drug. This therapy is most likely to be helpful in which of the following conditions?

A

Cystic fibrosis

102
Q

Atrophy of CNS is common in many pathologies. What type of CNS atrophy is unique to Creutzfeldt-Jakob disease?

A

Atrophy of the cerebellum

103
Q

Steps of the urea cycle

A

Remember enzymes by: COAAA

104
Q

Specific sxs of osteogenesis imperfecta

A

Transulcent skin showing visible underlying veins
Frequent bone fractures

Col I deficiency

105
Q

Specfic sxs of scurvy

A

Bleeding from gums

106
Q

Activator of NAG

A

Arginine

NAG is an obligate activator of CPS I

107
Q

OTC deficiency inheritance pattern

A

X-linked recessive

Only x-linked disease in the urea cycle

Female carriers report aversion to high-protein foods (due to lionization of x-chromosome)

M1 (30 decks)

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