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Biochem Test 2 > Protein Biochemistry > Flashcards

Protein Biochemistry Flashcards

1
Q

Describe the steps of the urea cycle

A
  1. Ornithine&raquo_space; Citrulline (catalzyed by Carbomoyl phosphate synthetase I)
  2. Citrulline + Aspartate&raquo_space; Argininosuccinate (catalyzed by Arginonosuccinate synthase)
  3. Argininosuccinate&raquo_space; Arginine (catalyzed by Argininosuccinate lyase)
  4. Arginine&raquo_space; Ornithine + Urea (catalyzed by Arginase)
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2
Q

List the means of ammonia transport in the blood

A
  • Ammonia cannot be transported in the blood
  • Glutamine “holds” two ammonia groups and transports them
  • Most tissues use glutamine synthetase to convert glutamate to glutamine for transport to the liver to enter the urea cycle
  • Muslce uses ALANINE instead of glutamine.
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3
Q

Understand the difference between ketogenic and gluconeogenic amino acids

A

Ketogenic: Produces no net production of glucose. Ex: Lysine and leucine give Acetyl CoA when broken down

Glucogenic: Produces pyruvate or Kreb Cycle intermediates. Ex: Oxaloacetate in Kreb cycle comes from aspartate transamination

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4
Q

Hyperammonemia

A

Hyperammonemia is a metabolic disturbance characterized by an excess of ammonia in the blood. It is a dangerous condition that may lead to encephalopathy and death. It may be primary or secondary.

Symptoms of hyperammonemia include:

  • Altered mental status
  • Vomiting
  • Seizures
  • Lethargy
  • Progressive obdundation → coma → death
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5
Q

Maple Syrup Disease

A

Dehydrogenase complex is deficient, causing a buildup of a-keto acids in urine

Branched chain amino acids (Leucine, Valine, Isoleucine) are deaminated by branched chain aminotransferase to produce a-keto acids. Then, they are decarboxylated by branched-chain a-keoacid dehydrogenase complex. If this dehydrogenase complex is deficient, then the a-keto acids will build up

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6
Q

Describe thyroid chemistry

A

Tyrosine is used to make T4 (prohormone) that is converted to T3 (hormone)

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7
Q

How is thyroxin produced?

A

T4 is thyroxine.

T4 is made from Tyrosine in the thyroid.
•Starts as a huge protein called Thyroglobulin that contains ~140 tyrosine residues that stick out
•Free iodide (I-) is oxidized to iodine (I2) in the thyroid by thyroid peroxidase
•2-5 of the tyrosines on thyroglobulin are iodinated and undergo proteolysis to be released as Thyroxin
•Thyroxin Binding Globulin carries T3,T4 in the blood

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8
Q

Describe heme metabolism

A

Heme is a porphyrin. Produced in liver. Binds iron.

Degraded to bilirubin&raquo_space; bilirubin diglucuronide&raquo_space; urobilinogen&raquo_space; stercobilin

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9
Q

Describe porphyrias

A

Disease of porphyrin synthesis.
Ex:
1. Lead inhibits two enzymes in porphyrin synthesis (lead poisoning)
2.

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10
Q

How is the initial step of Urea Cycle entry regulated?

A

*Enzyme is Carbamoyl phosphate synthetase I
*Found in Mitochondria
*Bicarb + ammonia&raquo_space; carbamoyl phosphate uses 2 of the 3 ATPs in the urea cycle
*N-acetylglutamate is an allosteric activator of Carbamoyl phophate synthetase I
*Arginine is an activator of N-acetylgluamate synthase, which catalyzes the reaction:
acetyl CoA + glutamate&raquo_space; N-acetylglutamate

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11
Q

What is the Alanine-Glucose Cycle?

A

In the muscle there is a buildup of pyruvate from glycolysis and pyruvate can be converted to alanine for pyruvate for transport tot he liver (transamination).
The liver then uses the alanine to convert back to pyruvate (transamination) and glucose remade (gluconeogenesis) can then be delivered back to the muscle

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12
Q

What is scurvy?

A

Scurvy is the disease that occurs as a result of Vitamin C deficiency. Active vitamin C, ascorbic acid, is a crucial coenzyme in hydroxylation of Pro and Lys residues. Deficiency in this vitamin leads to reduced strength of collagen because loss of hydroxyproline and hydroxylysine which form hydrogen bonds and strand cross links that stabilize the triple helix. Thus, vitamin C is required for maintaining normal connective tissue and wound healing.

Scurvy is characterized by: 
•	Sore and spongy gums
•	Loose teeth
•	Fragile blood vessels (reduced endothelium)
•	Hemorrhages
•	Swollen joints
•	Anemia
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13
Q

Use of cofactor Vitamin C

A

Vitamin C is required for Prolyl hydroxylase and lysyl hydroxylase to create Hyp and Hyl. These are necessary in forming normal, stable collagen. Deficiency results in Scurvy.

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14
Q

Use of cofactor Vitamin K

A

Vitamin K is required for production of clotting factors II, VII, IX and X by glutamyl carboxylase. The reaction results in carboxylated Glutamic acid or carboxyglutamate (Gla) that is capable of chelating calcium and targeting proteins to the membrane.

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15
Q

Use of cofactor Vitamin B6 (PLP)

A

Pyridoxal Phosphate (PLP) is a derivative of vitamin B6 which is required for aminotransferases to function normally. This moiety temporarily “holds” the amino group once it has been removed from an amino acid and before it is attached to glutamate. When the enzyme is not active, PLP forms a Schiff base with the aminotranferase to maintain the PLP in the resting enzyme.

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16
Q

Describe cellular aspects of protein degradation

A
  1. Ubiquitin – Proteasome
    • This pathway is ATP dependent
    • A poly-ubiquitin chain is added to a protein, targeting it for destruction in the proteasome
    • This uses several enzymes (E1-E3)
    • Ubiquitins are attached at lysines
    • The proteasome is a barrel-shaped proteolytic complex which unfolds the protein, removes the ubiquitin (for recycling) and cuts the protein into fragments
    •This pathway degrades mostly endogenous proteins that were synthesized within the cell
  2. Lysosome
    • This pathway is ATP independent
    • The lysosome is an intracellular organelle which engulfs proteins
    • In the lysosome, proteins are broken down by hydrolytic enzymes and proteases
    • This pathway degrades mostly exogenous proteins that are taken into the cell via endocytosis
17
Q

Describe transamination and list liver damage markers

A
  • Aminotransferases “move nitrogen”
  • Convert one a-keto acid to its corresponding amino acid and in the process converts another amino acids to its corresponding a-keto acid
  • For protein degradation, aminotransferases move nitrogen to Asp and ammonia for Urea Cycle
Liver damage markers:
Alanine aminotransferase (Alt)
Aspartate aminotransferase (Ast)
18
Q

Describe the general goal of the Urea Cycle

A

The main goal of the Urea Cycle is remove toxic NH3 by forming less toxic nitrogen-containing compounds that can be excreted (i.e. urea). The body has no way of storing amino acids or NH3 due to its toxic nature. Hyperammonemia is dangerous and can cause cerebral edema, coma and death. The urea cycle is a series of 5 reactions that occur in both the cytosol and mitochondria with the overall reaction:

3ATP + HCO3- + NH4+ + aspartate → 2ADP + AMP + 2Pi + PPi + fumarate + urea

There are 2 sources of nitrogen: aspartate and NH4+ (incorporated by carbamoyl phosphate). Ornithine is recycled in the urea cycle

19
Q

Examples of post-translational modification of amino acids

A

Collagen forms a triple-stranded helix, comprised of hydroxyproline (Hyp) and hydroxylysine (Hyl)
Hpy: Used in H-bonding (strength)
Hyl: used for interchain crossing

20
Q

Describe the proteases involved in protein degradation

A

•Pepsinogen is activated by HCl in the stomach to Pepsin
Pepsin is an endopeptidase
Pepsin is an aspartic protease – it hydrolyzes the N-terminal side of aromatic residues (Phe, Tyr, Trp)

•Enteropeptidase is on the brush border of the intestines and cleaves to Trypsin
Trypsin in a serine protease, which hydrolyzes the C-terminal side of basic residues (Arg, Lys)

•Trypsin activates the other enzymes
Chymotrypsin – a serine protease which hydrolyzes the C-terminal side of aromatic and some hydrophobic residues (Phe, Trp, Tyr, Leu, Met)
Carboxypeptidase A – a metallocarboxypeptidase which hydrolyzes at the C-terminal of hydrophobic amino acids (Ala, Ile, Leu, Val)
Carboxypeptidase B – a metallocarboxypeptidase which hydrolyzes at C-terminal of basic residues (Arg, Lys)

21
Q

List the sulfur containing amino acids

A

Methionine and Cysteine

22
Q

Describe the bio utility of Cys in regard to its oxidative state (alone of with GSH)

A

Cysteine: unessential amino acid that can form disulfides with another Cys using its –SH. This is really important for providing a structural matrix for many proteins, especially extracellular, hormones, cytokines, and receptors.

  • Glutathione: GSH, tripeptide controlling redox potential through conversion between GSH and GSSG. Cystine is the central amino acid that does the work!
  • Cystine is an integral part of protein structure because these disulfide bonds are covalent bonds.
  • Usually extracellular because intracellular have high reducing potential (so no disulfide bonds).
23
Q

Describe Met, its relation to SAM, and the energy provided in SAM

A

Methionine: (Met), essential amino acid that produces S-adenosylmethionine using an ATP molecule (transfer energy of phosphate). Can form succinyl-CoA

•S-adenosylmethionine (SAM) = intermediate in cysteine production
•SAM: produced in 1st step of methionine degradation, is a major carbon donor and high energy storage unit that can be converted to SAH (SA-homocysteine).
Major methyl-group donor in 1-C metabolism.
Formation driven by hydrolysis of all three P bonds in ATP.
Methyl group can be transferred to O or N atoms or C atoms.

24
Q

Hyperhomocysteinemia

A

homocysteine levels are elevated causing cardiovascular disease.
Results from low levels of folate, B6 and B12.
Cysteine becomes an essential amino acid and you have to treat it with folate, B6 and B12 supplementation

25
Q

Homocystinura

A

Defects in homocysteine metabolism.

  • Commonly from defect in enzyme cystathionine beta-synthase (converts homocysteine to cystathioine).
  • These patients can’t convert homocysteine to cystathionine (then cysteine).
  • If homozygous, have cystathionine Beta-synthase deficiency and show ectopia lentis (eye lens displacement), skeletal abnormalities, premature arterial disease, osteoporosis, and mental retardation.
  • B6 oral administration can help because it is the coenzyme of cystathionine Beta-synthase.
  • Treatment: restriction of methionine intake and B6, B12, and folate supplementation.
26
Q

Cysteinuria

A

kidney stones (renal failure) due to defective cysteine transporter along with that for ornithine, lysine, and arginine causing urea crystallization. Treat these pts w/ acetazolamide to make cysteine more soluble.

27
Q

Vascular disease

A

homocysteine is a metabolite associate w/ atherosclerotic vascular disease.
•Elevations in plasma homocysteine levels promote oxidative damage, inflammation, and endothelial dysfunction.
•Elevated plasma homocysteine = independent occlusive vascular disease risk.
•Plasma homocysteine levels are inversely related to plasma folate levels, B12, and B6.
•Supplementing these vitamins helps lower homocystine.

28
Q

Where is folate used in Cys Met Metabolism

A

Folate: necessary in order to carry carbon units. Can be reduced to dihydrofolate reductase in a two-step reaction using 2 NADPH.
• THF is used as N5-Methyltetrahydrofolate to combine with Homocysteine in the resynthesis of methionine.
• Note that THF here is carrying the CH3 (carbon group) necessary to regenerate Methionine.

29
Q

Where is B6 used in Cys Met Metabolism

A

B6: used in the conversion of homocysteine to cysteine. This is a transulfuration process.

30
Q

Where is B12 used in Cys Met Metabolism

A

B12: coenzme is derived from it, methylcobalamin, for the resynthesis of methionine.
• Used by methionine synthase.

31
Q

List biologically important molecules derived from Trp metabolism

A

Trp metabolism: metabolized to pyruvate or acetyl-CoA. Trp is first hydroxylated by tryptophan hydroxylase using BH4 (tetrahydrobiopterin) as cofactor. Trp produces:

1) . Serotonin (neurotransmitter)
2) . Melatonin (hormone)
3) . Niacin (energy
32
Q

Phenylketonuria

A

PKU, deficiency of phenylalanine hydroxylase (PAH).
Most common clinically encountered amino acid metabolism error.
Get accumulation of phenylalanine + deficiency of tyrosine.
Phe and phenylpyruvate accumulate in the blood.
Phenylacetate is reduced and decarboxylated.

Also has characteristic smell
Excreted in urine.

33
Q

Tyrosinemia

A

Tyrosinemia: defects in multi-step tyrosine degradation categorized as types I, II, and III referring to particular dysfunctional enzyme involved.

  • Symptoms lead to liver and kidney failure as well as mental retardation.
  • These lead to really high levels of tyrosine in the blood.
  • Often dermatologic manifestations of these diseases.
34
Q

What is the relation of Parkinson’s Disease and MAOIs to Tyr metabolism

A

The conversion of tyrosine to catecholamines and melanin is dysregulated

Biochem Test 2 (3 decks)

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