Chapter 21: Amino Acid Metabolism Flashcards
How is the chemical transformations of amino acids distinct from those of carbohydrates or lipids?
in that they involve the element nitrogen.We must therefore examine the origin of nitrogen in biological systems as well as its disposal. The bulk of the cell’s amino acids are incorporated into proteins, which are continuously being synthesized and degraded for energy.
Cells continuously synthesize proteins from and degrade them to amino acids. This seemingly wasteful process has what three functions?
(1) to store nutrients in the form of proteins and to break them down in times of metabolic need, processes that are most significant in muscle tissue;
(2) to eliminate abnormal proteins whose accumulation would be harmful to the cell;
(3) to permit the regulation of cellular metabolism by eliminating superfluous enzymes and regulatory proteins.
**Controlling a protein’s rate of degradation is therefore as important to the cellular and organismal economy as is controlling its rate of synthesis.
What enzymes degrade proteins?
Lysosomes/Lysosomal degradation
contain around 50 hydrolytic enzymes, a number of proteases known as cathepsins
- has an internal pH of ~ 5; many lysosomal enzymes inactive at cytosolic pH
and its enzymes have acidic pH optima. This situation presumably protects the cell against accidental lysosomal leakage - examples of lysosomal activity – regression of uterus after childbirth, rheumatoid arthritis
Extracellular and intracellular proteins may be digested by lysosomal proteases.
Is lysosomal degradation selective in well- nourished cells and starving cells?
In well-nourished cells, lysosomal protein degradation is nonselective.
In starving cells, however, KFERQ proteins degraded preferentially
exp: such degradation would deplete essential enzymes and regulatory proteins. Lysosomes therefore also have a selective pathway, which is activated only after a prolonged fast, that imports and degrades cytosolic proteins containing the pentapeptide Lys-PheGlu-Arg-Gln (KFERQ) or a closely related sequence./ degrades KFERQ proteins
How and under what conditions are certain proteins targeted to the lysosome?
- Lysosomes degrade substances (intracellular and extracellular proteins) that the cell takes up via endocytosis.
- They also recycle intracellular constituents that are enclosed within vesicles that fuse with lysosomes, a process called autophagy (Greek: autos, self + phagein, to eat).
Instead of lysosomes, what other way is protein degraded?
Ubiquitin-dependent degradation
marks proteins for degradation by covalent attachment
Protein breakdown in eukaryotic cells also occurs in an ATP-requiring process that is independent of lysosomes. This process involves ubiquitin (Fig. 21-1), a 76-residue monomeric protein named for its ubiquity and abundance.
Proteins are marked for degradation by covalently linking them to ubiquitin.
- 76 residue protein
- ubiquitous, abundant
- strongly conserved
For a protein to be efficiently degraded with ubiquitin what must occur?
chain of ubiquitins (n ≥ 4) required
For a protein to be efficiently degraded, it must be linked to a chain of at least four tandemly linked ubiquitin molecules in which Lys 48 of each ubiquitin forms an isopeptide bond with the C-terminal carboxyl group of the following ubiquitin. These polyubiquitin chains may contain 50 or more ubiquitin units. Ubiquitinated proteins are dynamic entities, with ubiquitin molecules being rapidly attached and removed (the latter by ubiquitin isopeptidases).
What is the N-end rule?
half-lives of many cytoplasmic proteins vary with the identities of their N-terminal residues
“destabilizing” N-terminal residues have low half lives and those with the “stabilizing” N-terminal residues have long half lives
The N-end rule relates the regulation of the in vivo half-life of a protein to the identity of its N-terminal residue.
What is the function and structure of the Proteasome ?
The Proteasome Unfolds and Hydrolyzes Ubiquitinated Polypeptides
Ubiquitinated proteins are proteolytically degraded in an ATP-dependent process mediated by a large (∼2500 kD, 26S) multiprotein complex named the 26S proteasome
- ubiquitinated proteins are degraded inside the 20S proteasome, by the b-type subunits
then digested into 8 residue fragments
Where do free amino acids originate from?
Free amino acids originate from the degradation of cellular proteins and from the digestion of dietary proteins. The gastric (stomach) protease pepsin, the pancreatic enzymes trypsin, chymotrypsin, and elastase, and a host of other endo- and exopeptidases degrade polypeptides to oligopeptides and amino acids. These substances are absorbed by the intestinal mucosa and transported via the bloodstream to be absorbed by other tissues.
The degradation of an amino acid almost always begins with?
Deamination, the removal of its amino group in a PLP-Facilitated transamination reaction.
This is one of the major degradation pathways which convert essential amino acids to non-essential amino acids (amino acids that can be synthesized de novo by the organism).
Transamination interconverts an amino acid and an α-keto acid.
What happens to the amino group and the remaining carbon skeleton after it is removed?
The amino group is removed and In many cases, the amino group is converted to ammonia then incorporated into urea for disposal/excretion. The remaining carbon skeleton (α-keto acid) can be broken down to CO 2 and H2 O or converted to glucose, acetyl-CoA, or ketone bodies.
In what mechanism are the amino groups of amino acids transferred?/How are amino acids deaminated?
Transaminases Use PLP to Transfer Amino Groups
-AA’s transfer their NH2 groups to an ἄ ketoglutarate to yield Glu & ἄ keto acid
Most amino acids are deaminated by transamination, the transfer of their amino group to an α-keto acid to yield the α-keto acid of the original amino acid and a new amino acid.
The predominant amino group acceptor is α-ketoglutarate, producing glutamate and the new α-keto acid
Glutamate’s amino group, in turn, can be transferred to oxaloacetate in a second transamination reaction, yielding aspartate and re-forming α-ketoglutarate:
- amino groups from most amino acids are funneled into glutamate or aspartate
- coenzyme of aminotransferases is pyridoxal-5’phosphate
The mechanism of PLP-dependent enzyme-catalyzed transamination.
The first stage of the reaction, in which the α-amino group of an amino acid is transferred to PLP yielding an α-keto acid and PMP, consists of three steps: (1) transimination, (2) tautomerization, in which the Lys released during the transimination reaction acts as a general acid–base catalyst, and (3) hydrolysis.
The second stage of the reaction, in which the amino group of PMP
is transferred to a different α-keto acid to yield a new α-amino acid and PLP, is essentially the reverse of the first stage: Steps 3′, 2′, and 1′ are, respectively, the reverse of Steps 3, 2, and 1.
-two stages: 1st half reaction: amino acid → keto acid & E-PLP complex → E-PMP
2 nd half reaction: keto acid → amino acid & E-PMP complex → PLP
Transamination is accomplished by what enzymes? What do they require? What is its derivative?
The enzymes that catalyze transamination, called aminotransferases or transaminases, require the coenzyme pyridoxal-5′-phosphate (PLP; Fig. 21-7a). PLP is a derivative of pyridoxine (vitamin B)
Transamination does not result in net deamination; products are glutamate or (to a lesser extent) aspartate. What happens to glutamate? What does it release and accept?
Glutamate, however, can be oxidatively deaminated by glutamate dehydrogenase (GDH), yielding ammonia and regenerating α-ketoglutarate for use in additional transamination reactions.
Releases ammonia for disposal
Glutamate dehydrogenase, a mitochondrial enzyme, is the only known enzyme that can accept either NAD +or NADP +as its redox coenzyme.
- net deamination of glutamate by glutamate dehydrogenase
- glutamate dehydrogenase accepts NAD +and NADP
What eventually happens to the ammonia liberated in the GDH reaction?
It is excreted in the form of urea. Thus, the glutamate dehydrogenase reaction functions to eliminate amino groups from amino acids that undergo transamination reactions with α-ketoglutarate.
Living organisms excrete the excess nitrogen arising from the metabolic breakdown of amino acids in one of three ways:
Many aquatic animals simply excrete ammonia. Where water is less plentiful, however, processes have evolved that convert ammonia to less toxic waste products that require less water for excretion. One such product is urea, which is produced by most terrestrial vertebrates; another is uric acid, which is excreted by birds and terrestrial reptiles.
We focus our attention on urea formation.
What occurs in the urea cycle? How many reactions take place?
Urea is synthesized in the liver by the enzymes of the urea cycle. It is then secreted into the bloodstream and sequestered by the kidneys for excretion in the urine.
What occurs in the urea cycle? How many reactions take place?
Urea is synthesized in the liver by the enzymes of the urea cycle. It is then secreted into the bloodstream and sequestered by the kidneys for excretion in the urine.
Five enzymatic reactions are involved in the urea cycle, two of which are mitochondrial and three cytosolic
- A nitrogen atom from ammonia (a product of the oxidative deamination of glutamate) and bicarbonate are incorporated into carbamoyl phosphate for entry into the urea cycle.
- A second nitrogen atom introduced from aspartate enters the cycle to produce urea for excretion.
What is the first reaction of the Urea Cycle?
- Carbamoyl Phosphate Synthetase Acquires the First Urea Nitrogen Atom.
Carbamoyl phosphate synthetase (CPS) is technically not a member of the urea cycle. It catalyzes the condensation and activation of NH 3 and HCO 3 − to form carbamoyl phosphate, the first of the cycle’s two nitrogen-containing substrates, with the concomitant cleavage of 2 ATP. Eukaryotes have two forms of CPS: Mitochondrial CPS I uses ammonia as its nitrogen donor and participates in urea biosynthesis, whereas cytosolic CPS II uses glutamine as its nitrogen donor and is involved in pyrimidine biosynthesis (Section 23-2A). CPS I catalyzes an essentially irreversible reaction that is the rate-limiting step of the urea cycle.
What reaction occurs after the first urea nitrogen atom is acquired of the Urea cycle?
- Carbamoylation of Ornithine Produces Citrulline. Ornithine transcarbamoylase transfers the carbamoyl group of carbamoyl phosphate to ornithine, yielding citrulline (Fig. 21-9, Reaction 2). Note that both of the latter compounds are “nonstandard” α-amino acids that do not occur in proteins. The transcarbamoylase reaction occurs in the mitochondrion, so ornithine, which is produced in the cytosol, must enter the mitochondrion via a specific transport system. Likewise, since the remaining urea cycle reactions occur in the cytosol, citrulline must be exported from the mitochondrion.
In the urea cycle, what reaction occurs after the formation of Citrulline?
- Argininosuccinate Synthetase Acquires the Second Urea Nitrogen Atom.
Urea’s second nitrogen atom is introduced by the condensation of citrulline’s ureido group with an aspartate amino group by argininosuccinate synthetase (Fig. 21-12). ATP activates the ureido oxygen atom as a leaving group through formation of a citrullyl–AMP intermediate, and AMP is subsequently displaced by the aspartate amino group. The PP i formed in the reaction is hydrolyzed to 2 Pi , so the reaction consumes two ATP equivalents.
In the Urea cycle what reaction occurs after the second urea nitrogen atom is acquired?
- Argininosuccinase Produces Fumarate and Arginine. With the formation of argininosuccinate, all of the urea molecule components have been assembled. However, the amino group donated by aspartate is still attached to the aspartate carbon skeleton. This situation is remedied by the argininosuccinasecatalyzed elimination of fumarate, leaving arginine (Fig. 21-9, Reaction 4). Arginine is urea’s immediate precursor. The fumarate produced in the argininosuccinase reaction is converted to oxaloacetate by the action of fumarase and malate dehydrogenase. These two reactions are the same as those that occur in the citric acid cycle, although they take place in the cytosol rather than in the mitochondrion. The oxaloacetate is then used for gluconeogenesis.
