Chapter 21 Flashcards
Excess dietary amino acids are not simply excreted but are converted to… that are precursors of glucose, fatty acids, and ketone bodies and are therefore metabolic fuels.
common metabolites
…: amino group removal
deamination
cells continuously synthesize proteins from and degrade them to …
amino acids
. Controlling a protein’s rate of ..is therefore as important to the cellular and organismal economy as is controlling its rate of ….
degradation ; synthesis
the most rapidly degraded enzymes all occupy…, whereas the relatively stable enzymes have nearly constant catalytic activities under..
important metabolic control points; all physiological conditions.
Lysosomes contain ∼50 hydrolytic enzymes, including a variety of proteases known as …
cathepsins
Lysosomes degrade substances that the cell takes up via endocytosis. They also recycle intracellular constituents that are enclosed within vesicles that fuse with lysosomes, a process called … In well-nourished cells, lysosomal protein degradation is …
autophagy; nonselective
Protein breakdown in eukaryotic cells also occurs in an ATP-requiring process that is independent of lysosomes. This process involves .., a 76-residue monomeric protein named for its ubiquity and abundance
ubiquitin
Proteins are marked for degradation by covalently …
linking them to ubiquitin.
linking a protein to ubiquitin:
- In an ATP-requiring reaction, ubiquitin’s terminal carboxyl group is conjugated, via a thioester bond, to… (E1).
- The ubiquitin is then transferred to a specific Cys sulfhydryl group on one of numerous homologous proteins named … (E2s
ubiquitin-activating enzyme
ubiquitin-conjugating enzymes
linking a protein to ubiquitin contd:
3. …(E3) transfers the activated ubiquitin from E2 to a Lys ε-amino group of a previously bound protein, thereby forming an isopeptide bond.
Ubiquitin-protein ligase
the half-lives of many cytoplasmic proteins vary with the identities of their … via the so-called …: Proteins with the “destabilizing” N-terminal residues Asp, Arg, Leu, Lys, and Phe have half-lives of only 2 to 3 minutes, whereas those with the “stabilizing” N -terminal residues Ala, Gly, Met, Ser, Thr, and Val have half-lives of >10 hours in prokaryotes and >20 hours in eukaryotes.
N-terminal residues; N-end rule
, it has long been known that proteins with segments rich in Pro (P), Glu (E), Ser (S), and Thr (T), the so-called … are rapidly degraded. It is now realized that this is because these PEST elements often contain phosphorylation sites that target their proteins for ubiquitination.
PEST proteins,
proteins known as …that control the progression of the cell cycle are selectively degraded through their ubiquitination at specific stages of the cell cycle
cyclins
reversible …controls the activities of certain proteins rather than their degradation, in much the same way that phosphorylation and dephosphorylation alter protein activity
monoubiquitination
all cells appear to contain proteases whose active sites are only available from the …to which access is controlled–> …
inner cavity of a hollow particle; self-compartmentalized proteases
Most amino acids are deaminated by …, 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…, producing glutamate and the new α-keto acid
transamination; α-ketoglutarate
the aminotransferase reaction occurs via a …
Ping Pong mechanism
(aminotransferase rxn) Stage I Converts an Amino Acid to an 𝛂-Keto Acid
The amino acid’s nucleophilic amino group attacks the enzyme–PLP Schiff base carbon atom in a …reaction to form an amino acid–PLP Schiff base (an aldimine), with concomitant release of the enzyme’s Lys amino group. This Lys is then free to act as a general …at the active site.
transamination; base
(aminotransferase rxn) Stage I Converts an Amino Acid to an 𝛂-Keto Acid
The amino acid–PLP Schiff base tautomerizes to an α-keto acid–PMP Schiff base (a ketimine) by the active site Lys–catalyzed removal of the amino acid …and protonation of PLP atom C4′ via a resonance stabilized ….intermediate. This resonance stabilization facilitates the cleavage of the Cα—H bond
α-hydrogen; carbanion
(aminotransferase rxn) Stage I Converts an Amino Acid to an 𝛂-Keto Acid
3. The α-keto acid–PMP Schiff base is ….to PMP and an α-keto acid.
hydrolyzed
(aminotransferase rxn) Stage II Converts an 𝛂-Keto Acid to an Amino Acid.
3′. PMP reacts with an α-keto acid to form a …
Schiff base.
(aminotransferase rxn) Stage II Converts an 𝛂-Keto Acid to an Amino Acid.
2′. The α-keto acid–PMP Schiff base …to form an amino acid– PLP Schiff base
tautomerizes
(aminotransferase rxn) Stage II Converts an 𝛂-Keto Acid to an Amino Acid.
1′. The ε-amino group of the active site Lys residue attacks the amino acid– PLP Schiff base in a …reaction to regenerate the active enzyme–PLP Schiff base and release the newly formed…
transamination; amino acid
Note that removal of the substrate amino acid’s α-proton produces a resonance-stabilized Cα carbanion whose electrons are delocalized all the way to the coenzyme’s protonated pyridinium nitrogen atom; that is, PLP functions as an …
electron sink
The amino groups from most amino acids are consequently funneled into the formation of …and ….
glutamate; aspartate
…is the only amino acid that is not transaminated.
Lysine
Transamination, of course, does not result in any net … Glutamate, however, can be oxidatively deaminated by … (GDH), yielding ammonia and regenerating α-ketoglutarate for use in additional transamination reactions.
.deamination; glutamate dehydrogenase
the glutamate dehydrogenase reaction functions to eliminate amino groups from amino acids that undergo …reactions with …
transamination; α -ketoglutarate.
Urea is synthesized in the liver by the enzymes of the … It is then secreted into the bloodstream and sequestered by the kidneys for excretion in the urine.
urea cycle.
urea’s two nitrogen atoms are contributed by …and …, whereas its carbon atom comes from …
ammonia; aspartate; HCO3-
(five rxns of urea cycle) … acquires the first urea nitrogen atom
carbamoyl phosphate synthetase
(five rxns of urea cycle) carbamoyl phosphate synthetase catalyzes the condensation and activation of ammonia and HCO3- to form …, the first of the cycle’s two nitrogen-containing substrates, with the concomitant cleavage of 2 ATP
carbamoyl phosphate
(five rxns of urea cycle) Mitochondrial… uses ammonia as its nitrogen donor and participates in urea biosynthesis, whereas cytosolic …uses glutamine as its nitrogen donor and is involved in pyrimidine biosynthesis
CPS I; CPS II
(five rxns of urea cycle) CPS I catalyzes irreversible rate limiting step of cycle:
- ATP activates HCO3- to form … and ADP
- Ammonia attacks carboxyphosphate, displacing phosphate to form … and Pi
- A second ATP phosphorylates carbamate to form … and ADP
carboxyphosphate
carbamate
carbamoyl phosphate
(five rxns of urea cycle) This phenomenon, in which the intermediate of two reactions is directly transferred from one enzyme active site to another, is called …. It increases the rate of a metabolic pathway by preventing the loss of its … as well as protecting them from degradation
channeling; intermediates
(five rxns of urea cycle) . Ornithine transcarbamoylase transfers the carbamoyl group of carbamoyl phosphate to …, yielding …
ornithine; citrulline
(five rxns of urea cycle) Urea’s second nitrogen atom is introduced by the condensation of citrulline’s ureido group with an aspartate amino group by … The PPi formed in the reaction is hydrolyzed to 2 Pi, so the reaction consumes …ATP equivalents
argininosuccinate synthetase; two
(five rxns of urea cycle) 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 …catalyzed elimination of fumarate, leaving arginine
argininosuccinase
(five rxns of urea cycle) …is urea’s immediate precursor
Arginine
(five rxns of urea cycle) The urea cycle’s final reaction is the …catalyzed hydrolysis of arginine to yield urea and regenerate …, which is then returned to the mitochondrion for another round of the cycle.
arginase; ornithine
(five rxns of urea cycle) The urea cycle thus converts two amino groups, one from ammonia and one from aspartate, and a carbon atom from HCO− 3 to the relatively nontoxic product, urea, at the cost of four … The energy spent is more than recovered, however, by the oxidation of the carbon skeletons of the amino acids that have donated their amino groups, via transamination, to glutamate and aspartate
“high-energy” phosphate bonds.
Carbamoyl phosphate synthetase I, which catalyzes the first committed step of the urea cycle, is allosterically activated by …
N-acetylglutamate
…:, which are degraded to pyruvate, α-ketoglutarate, succinyl-CoA, fumarate, or oxaloacetate and are therefore glucose precursors
Glucogenic amino acids
…, which are broken down to acetyl-CoA or acetoacetate and can thus be converted to fatty acids or ketone bodies
Ketogenic amino acids