Protein and Amino Acid Metabolism Flashcards
LO 1 proptein and AA metabolism
a. In order to understand the bioavailability of amino acids and the consequences of proteolysis, you should be able to:
a. Summarize the mechanisms for the maintenance of amino acid pool (Fig. 15.1)
i. Understand from the correlation box:
1. Hartnup disease and cystinuria (orange, p.255)
b. Compare and contrast mechanisms of intracellular proteolytic control:
i. Lysosomal degradation/Autophagy
ii. Proteasomal degradation and the role of ubiquitination (Fig. 15.3)
c. Summarize mechanisms of extracellular proteolytic control (Fig. 15.4)
d. Compare and contrast essential and non-essential amino acids (Tables 15.1-2)
e. Describe amino acid synthesis by grouping amino acid families that share common biosynthetic precursors (Fig. 15.5)
What are the essential amino acids?
Essential : Phe, Cal, Thr, Met, Leu, Ile, His, Lys
Conditionally essential: Arg (prematurity), Cys, Gly, Gln, Pro, Tyr
The population of free amino acids is supplied by:
- Protein turnover
- Digested food
- De novo synthesis (nonessential amino acids)
The population of free amino acids is DEPLETED by:
- Production of body protein
- Synthesis of nitrogen-containing compounds
- Degradation
Major source of nitrogen:
Major source of nitrogen: dietary protein
Major nitrogen excretory compounds:
Major nitrogen excretory compounds: Urea, Ammonia, Creatinine (muscle), uric acid (purine breakdown product), urobilinogen (heme metabolism)
Where does amino acid breakdown occur?
•Only occurs in the liver; generates an alpha-keto acid from the amino acid
Why do ketogenic dieters have to be careful about eating TOO MUCH protein?
•Carbon skeletons shuffled into different pathways, even to the formation of glucose (which is why ketogenic diets have to be careful about eating TOO MUCH protein à goes to glucose formation in amounts excessive for RBC function)
Hartnup disease and cystinuria (correlation box)
Hartnup disease and cystinuria (pg. 255): protein transporters mediate transport of amino acids in and out of cells.
- Hartnup disease and cystinuria are autosomal recessive conditions that are associated with defects in these transporters,
- Hartnup disease:
- Defective transport of nonpolar or neutral amino acids (e.g. Tryptophan) leads to elevated concentration in the urine.
- Ala, Ser, Thr, Val, Leu, Ile, Phe, Tyr, Trp, Gln, Asn, His excreted 5-10 times the normal level.
- Trp is a precursor for serotonin, melatonin, and niacin (which is a precursor for NAD), therefore niacin deficiency is also noted
- Transporter located in kidney and small intestine
- Manifests in infancy with failure to thrive, nystagmus, tremor, intermittent ataxia and photosensitivity.
- Also known as pellagra-like dermatosis. Pellagra: peeling, redness, scaling, thickening of sun-exposed areas
- Triggered by sunlight, fever, drugs, or emotional or physical stress.
- Treatment is directed at niacin repletion and includes a high-protein diet and daily nicotinamide supplementation (50–250 mg)
- A high protein diet can overcome the deficient transport of neutral amino acids in most patients.
- Thus, a period of poor nutrition nearly always precedes an attack
•Cystinuria:
- Defective transport of dimeric cystine and dibasic amino acids Arg, Lys, and ornithine (COAL).
- Formation of cystine crystals in the kidneys (renal calculi).
- Patients present with renal colic, which is abdominal pain that comes in waves and is liked to the formation of kidney stones.
Hartnup clinical case (not a question just read it)
•A seven-year-old boy with history of convulsion, cutaneous hyperpigmentation in sun-exposed areas and recurrent episodes of cerebellar ataxia is presented. Once established the clinical diagnosis of Hartnup disease, treatment with nicotinamide was started, with improvement. Laboratorial results did not confirm aminoaciduria nor other identified metabolic changes. In Hartnup disease, defective renal and intestinal transport of neutral amino acids occurs, resulting in reduction of tryptophan to produce to nicotinamide. Symptomatic cases present with intermittent episodes of cerebellar ataxia, pellagra-like skin rash and mental disturbances. Urinary chromatographic amino acid pattern confirms diagnosis; however, cases compatible with Hartnup disease, but without aminoaciduria, have been reported.
How are the aromatic essential amino acids (Trp, Tyr) synthesized?
Aromatic = Trp, Tyr
Phe —> Tyr
Ribose 5-P —> His
How are the serine essential amino acids (Ser, Cys, Gly) synthesized?
Serine = Ser, Cys, Gly
3-Phophoglycerate —> Ser —> Cys or Gly
How are the aspartate essential amino acids (Asp, Asn) synthesized?
Aspartate = Asp, Asn
Oxaloacetate —> Asp —> Asn
How are the pyruvate essential amino acids (Ala) synthesized?
Pyruvate = Ala
Pyruvate —> Ala
How are the glutamate essential amino acids (Glu, Gln, Pro, Arg) synthesized?
Glutamate = Glu, Gln, Pro, Arg
A-Ketoglutarate —> Glu —> Gln, Pro, Arg
What is Exopeptidase’s site of attack?
- Proteolysis = degradation of proteins for reabsorption
- Proteolytic enzymes are classified based on their site of attack (Table 15.3)
–Exopeptidase: attacks at C- (carboxypeptidase) or N-terminus (aminopeptidase) ends
What is Endopeptidase’s site of attack?
- Proteolysis = degradation of proteins for reabsorption
- Proteolytic enzymes are classified based on their site of attack (Table 15.3)
–Endopeptidase: attacks within the protein at a specific site (digests internal peptide bonds). These are described more specifically by their mechanism of action which is dependent on the catalytic enzyme in the active site
How is intracellular proteolytic control achieved?
•3 protein degradation pathways:
–Proteasome, lysosome and autophagosome
•Lysosomal /Autophagy: lysosomes sequester >50 hydrolase-type intracellular proteolytic enzymes.
–Active at pH 5 (in lysozyme), inactive at pH 7 (cytoplasmic)
–Non-selective
–3 types: macroautophagy, microautophagy and chaperone-mediated autophagy (CMA)
- CMA is mediated by chaperones that specifically recognize substrates (thus, is selective)
- Microautophagy has been proposed to occur based on morphological change of lysosome, but its molecular mechanism remains unknown.
- The molecular mechanism and physiologic significance of macroautophagy have been best studied. Thus, autophagy refers to macroautophagy.
- Uses multivesicular bodies (MVBs) to selectively deliver ubiquitinated membrane proteins together with extracellular components into lysosomes.
- Microautophagy (MA) and chaperone-mediated autophagy (CMA) additionally contribute to the selective delivery of cargo into lysosomes.
- Ubiquitin the common denominator in the targeting of substrates to all three protein degradation pathways
Describe the proteosomal degradation phase of intracellular proteolytic control.
- Proteasomal degradation: large proteasome cytoplasmic complexes that cleave polyubiquinated proteins —> ubiquitin pathway
- main take-away is ubiquination is signal for proteolysis, protesome
- The catalytic core of Proteasome or 20S, each ring consists of 7 subunits and they’re stacked on top of one another to form a barrel. Active sites are hidden inside the barrel. You have to be ushered into the catalytic core.
19S regulatory subunit attached to both ends of the catalytic subunit, a monster at 700 kDa each
(1) Ubq receptors in the 19S regulatory unit! Specifically to multi-Ubq chains
(2) isopeptidase in the regulatory unit cleave of Ubq for reuse. You’re not having to constantly make Ubq because there are mechanisms in place to re-use Ubq!
(3) Ubiquinated protein is unfolded and directed into the catalytic core
OH of Threonine acts as a nucleophile to attacks Carbonyl of peptide bonds, degraded to peptides ranging from 7-9 residues
Describe Extracellular Proteolytic Control.
- Proteolytic enzymes secreted as needed
- Secreted as inactive zymogens, activated by proteolytic cleavage
–Inactive trypsinogen and chymotrypsinogen are released into the SI lumen
– Trypsinogen is activated by an enterokinase, enteropeptidase
–Trypsin activates chymotrypsinogen and other molecules of trypsinogen
Enterokinase: are embedded in the intestinal mucosa
What role do enteropeptidases play in protein digestion?
Convert the zymogen trypsinogen to active trypsin
Learning Objective #2 proterin and amino acid metabolism
- In order to understand the general mechanisms and clinical relevance of amino acid metabolism (pp. 258-264, Fig. 15.6B) you should be able to:
a. Compare and contrast ketogenic and glucogenic amino acids (Fig. 15.6A)
b. Describe notable deficiencies in the Met metabolic pathway: hyperhomocysteinemia and homocystinuria (Figs. 15.9)
c. Describe the catabolism of branched chain amino acids: Val, Leu, Ile (Fig 15.9)
d. Recall clinical relevance to deficiencies in the Phe metabolic pathway (Fig. 15.10)
e. Understand from the correlation boxes:
i. Consequences of hyperhomocysteinemia and homocystinuria (blue, p. 267)
ii. Maple syrup urine disease (blue, p. 267)
iii. Phenylketonuria (blue, p. 268)
Metabolism of Amino Acids: Ketogenic vs. Glucogenic- Compare and contrast.
- Amino acids can be classified by what they are metabolized to.
- KETOGENIC —> alpha keto acids and ketone bodies, cannot be metabolized into glucose (both carbonyl carbons are ultimately metabolized to CO2 in the TCA cycle).
- GLUCOGENIC —> eventually converted into glucose
- What is this representative of? Amine – carboxylic acid è AMINO ACID
- KETO ACID (specifically alpha keto acids important in TCA cycle and glycolysis)
- Deep, deep recesses of your brain way back in o chem I
- KETONE
- CARBOXYLIC ACID
- Ketogenic amino acids can be deaminated to produce alpha keto acids and ketone bodies → fatty acids
overview of AA metabolism
- ROADMAP of METABOLISM
- The “roundabout of metabolism” == The TCA cycle (with central importance in both energy production and biosynthesis).
- Shows the ketogenic arm feeding into the TCA cycle through the formation of Acetyl CoA
AA metabolism ‘big picture’
- Aminotransferase/Transaminase
- Glutamate Dehydrogenase (oxidative deamination)
- Urea Cycle
- The key to amino acid metabolism: the “BIG PICTURE”
- Deficiencies in these enzymes is what leads to IEM.
- Kinda like acid-base chemistry in that every acid has a conjugate base? Well, every amino acid has a conjugate keto acid.
- Amine is eventually shuffled into the liver as other amino acids, then repackaged as urea in the urea cycle and excreted
What are the transamination reactions?
•Shuffling amine groups —> TRANSAMINATION
- Amino group is transferred to an α-ketoacid
- Coupled reactions
- Enzymes called transaminases/aminotransferases
- Oxaloacetate is the keto acid of aspartate
- Amine is eventually shuffled into the liver as other amino acids, then repackaged as urea in the urea cycle and excreted
Describe Metabolism of Gln, His, Arg, Pro and Glu
- Essential (His)
- Conditional (Gln, Arg, Pro)
- Direct your attention to this circle: why is this relevant?
- This is going to be relevant when we talk about the Urea cycle in about ten minutes. Why??
- Hyperammonemina —> primary cause of neurological disorders
- GLUTAMATE vs. GLUTAMINE —> nitrogen trap mechanism
- Glutamine SYNTHETASE —> nitrogen trap via energy consumption
- Glutaminase —> hydrolase
- Reversible reaction whose direction will be dependent on nitrogen levels
Describe Metabolism of: Met, Thr, Ile, Leu
- interested in the clinical implications of deficiencies in these pathways
- So let’s take a closer look:
- Methionine pathway —> homocystinuria
- Cystathionine beta-synthase (needs PLP coenzyme)
Describe the Metabolism of Met
- Clinical manifestation of deficiencies in the methionine cycle include homocystineuria
- Also the folate cycle (THF as a methyl carrier)
- Homoecysteine is more chemically similar to methionine than cysteine
- HomocystINE vs. HomocystEINE
- Mutations in CBS are the most common cause of homocystinuria
- Pyridoxal phosphate (PLP), COENZYME (WHERE DOES PLP COME FROM????)
- Active form of VitB6
- Cysteine has one fewer methyl groups than homocysteine
What are the consequences of hyperhomocysteinemia and homocystinuria?
[[[[[BLUE BOX ALERT]]]]]
Consequences of hyperhomocysteinemia and homocystinuria (pg. 267): Vitamin deficiencies (B6, B12, folic acid) or genetic defects in enzymes (cystathionine β-synthase) cause defective metabolism of homocysteine
- Hyperhomocysteinemia is a risk factor in atherosclerotic heart disease and stroke and can result in neuropsychiatric illness (vascular dementia, Alzheimer’s disease).
- Also in eye lens dislocation, osteoporosis and mental retardation.
- Vitamin supplementation can normalize plasma homocysteine levels in some cases.
Four organ systems: eye, skeletal, CNS, vascular
- Ocular: ectopia lentis and high myopia
- Skeletal: limbs grow out of proportion with trunk, anterior chest wall deformities, osteoporosis, altered facial appearance
- CNS: dementia
- Vasculature: stroke, thrombosis
- Homocystineuria? —> METHIONINE
- tetrahydrofolic acid (THF)
- WHAT VITAMIN SUPPLEMENTATION?
Describe metabolism of BCAs
- Metabolism produces both ketogenic and glucogenic intermediates
- What about Leucine is special? (KETOGENIC!)
- branched chain a-keto acid dehydrogenase (oxidative decarboxylation)
- Deficiencies in these pathways lead to Maple Syrup Urine Disease (MSUD)
- Needs CoA, FAD (B2), lipoic acid, NAD (B3), TPP (B1)
Describe metabolism of Phe and Asn
- Asparagine metabolizes to aspartate (removal of amine group) by asparaginase (liken to glutaminase)
- Phe has the asterisk again because it metabolizes to both ketogenic and glucogenic intermediates
- What’s the best known clinical presentation of deficiencies in the metabolism of Phe?
- Phenylketonuria is such a debilitating inborn error of metabolism (IEM) that is now screened for at birth. Along with galactosemia, tyrosinemia
- Controlled dietary
Describe Phenylketonuria.
[[[[[BLUE BOX]]]]]
Phenylketonuria (pg. 268): PKU is caused by defects in the activity of phenylalanine hydroxylase (PAH)
- Most common IEM; first IEM to be included in newborn screening.
- Phe instead converted to phenylpyruvte and then to phenyllactate (causes musty odor in urine) and phenylacetate.
- The later two disrupts neurotransmission and block amino acid transport in the brain as well as myelin formation, resulting in severe impairment of brain function.
- Dietary limit Phe, protein supplied with synthetic formula supplemented with Tyr.
- Secondary PKU resulting from tetrahydrobiopterin deficiency (a cofactor of phenylalanine hydroxlyase). Defects in synthesis or regeneration of BH4.
- Post-parturition Guthrie Test
- Over 300 distinct pathological mutants identified
- majority missense mutations in catalytic domain
- Recombinant expression showed altered kinetics and decreased stability
- THB/BH4 cycle, cofactor for hydroxylase enzymes: metabolism of Phe; biosynthesis of serotonin, melatonin, dopamine, norepinephrine, epinephrine
Describe amino acid derivatives
- deficiencies in Tryptophan uptake causing Hartnup disease and clinical manifestations of decreased NAD bioavailability
- Tyrosine bioavailability is critical to production of thyroid hormones and endocrine regulation
- GABA = chief inhibitory neurotransmitter in the mammailian CNS
- ACh = neurotransmitter in mammalian CNS (a7, a4b2 nAChR)
Describe tryptophan derivatives
Same THB/DHB cycle in Phe —-> Tyrosine metabolism
Serotonin is the p-hydroxylated and decarboxylated form of Tryptophan
Describe tyrosine derivatives
- Thyroglobulin (660 kDa protein) made by follicular cells of thyroid
- ~120 Tyr residues
- Iodinated (mono or diodinated)
- T4 = coupling two diiodotyrosine
- T3 = monoiodotyrosine + diiodotyrosine
- Hypothyroidism = high TSH, low T4
- Hyperthyroidism = low TSH, High T4/T3
describe arginine derivatives
•Made from Arg, Gly and Met
–1-2% is creatine phosphate (CP)
–Non-enzymatically converted from CP
–Excreted in urine
–Kidney dysfunction and muscle degradation à Elevated serum levels
•CP serves as energy storage in muscle, brain and sperm
–Quickly generates ATP; used as our immediate energy source
•Cardiac isoform creatine kinase (CK-MB) diagnostic for MI
Describe Thyroglobulin and thyroid hormones
[[[[[ORANGE BOX]]]]]
Thyroglobulin and thyroid hormones (pg. 269): Thyroglobulin is a 660 kDa protein made by the thyroid and is used to produce T4 and T3
- Thyroglobulin has ~120 Tyr residues, some of which can be labeled with iodine (mono- and diiodinated Tyr)
- T4 is the combination of 2 diiodinated Tyr
- T3 is the combination of 1 monoiodinated and 1 diiodinated Tyr; more potent than T4 but shorter half-life
- Patients with hyperthyroidism are treated with agents (carbimazole and propylthiouracil) which block iodination of thyroglobulin to decrease the production of T4 and T3
- Tyrosine peroxidase oxidizes iodine ions to iodine atoms for addition to Tyrosine residues on thyroglobulin
- Autoimmune thyroid disease in which anti-thyroid peroxidase antibodies are produced?
How is excess NH4+ removed from the brain?
- What happens if there’s too much ammonium?
- Glutamate dehydrogenase keeps on keeping on and keeps churning out glutamate to use up the NH4. Which in turn depletes the pool of alpha-ketoglutatrate, lowers the level of ATP and leads to unconsciousness
How is excess NH4+ removed from muscle?
- Glutamate and Alanine from the glycolysis pathway in the muscles
- Pyruvate is just the alpha-keto acid of Alanine
- Help of ALT (ALANINE AMINOTRANSFERASE)
Describe Transamination vs. Oxidative deamination
- Pyruvate is the alpha-keto acid
- Glutamate undergoes oxidative deamination to produce ammonia and a-ketoglutarate (Glutamate dehydrogenase)
Describe the Urea cycle?
- Producing urea from ammonia (ammonia trapping mechanism)
- Primarily occurs in the liver, kidneys to a lesser extent
- Two major sources of urea cycle deficiencies —> liver disease, IEM
- Defects in any of the 6 enzymes that contribute to the urea cycle can result in hyperammonemia
- Including NAG synthase which produces N-Acetylglutame (NAG) from glutamate and acetyl-CoA
- The lack of the NAGS enzyme results in excessive accumulation of nitrogen, in the form of ammonia, in the blood (hyperammonemia). Excess ammonia, which is a neurotoxin, travels to the central nervous system through the blood, resulting in the symptoms and physical findings of NAGS deficiency. Symptoms include vomiting, refusal to eat, progressive lethargy, and coma. NAGS deficiency is inherited as an autosomal recessive trait.
What are the [6] Defective Urea Cycle Enzymes and Their Associated Disorders?
Describe Urea cycle and the high protein diet
[[[[[green box??]]]]]
Urea cycle and the high protein diet (pg. 273): urea production is increased by a high protein diet and decreased by high carb diet.
- Insulin and glucagon play a role in urea production
- About 20-30% of urea produced is hydrolyzed in the GI tract by bacterial urease
- Provides a source of ammonia nitrogen for gut bacteria, salvage and reuse
- High protein diets enhances this production and hydrolysis
How is creatine synthesized?
[[[[[BLUE BOX]]]]]
Creatine (pg. 272)
- Synthesized from Arg, Gly, Met
- Phosphocreatine serves as a storage form of energy in muscle, brain, and sperm. It can quickly generate ATP
- Cardioselective isoform of creatine kinase (CK-MB) can serve as a diagnostic for myocardial infarction
- Creatinine
– Small fraction (1-2%) of creatine phosphate
–Non-enzymatically converted from creatine phosphate to creatinine
–Excreted in urine
–Elevated levels in serum are indicative for kidney dysfunction and muscle degeneration
Synthesis of creatine and creatine phosphate: The synthesis of creatine begins from arginine and glycine via the renal enzyme glycine amidinotransferase (GATM). The product, guanidinoacetate, is transported to the liver where it is methylated via the action of guanidinoacetate N-methyltransferase (GAMT) forming creatine. The methyl group is donated from S-adenosylmethionine (SAM). Creatine is released to the blood and picked up by the brain and skeletal muscle cells via the action of the SLC6A8 transporter. Creatine kinase (creatine phosphokinase) transfers a phosphate from ATP generating the high-energy intermediate, creatine phosphate
