Biochemistry Unit 3, Lecture 5: Protein Turnover & Amino Acid Catabolism

_____________ is one of the most common metabolic disorders. It results in severely impaired mental ability.

Phenylketonuria

Phenylketonuria is caused by absent or deficient ___________ __________ activity, which causes excess phenylalanine to be converted into phenylpyruvate.

Phenylalanine Hydroxylase

Proteins tagged with __________, a small (76 aa), highly conserved protein, are targeted for destruction.

Ubiquitin

Degradation of Cellular Proteins:

1. Removal of __________ from amino acids

2. Conversion of ammonia to ______

3. Generation of _______ atoms as major metabolic intermediates.

Ammonia, Urea, Carbon

Degradation of Ingested Proteins:

1. Ingested proteins are denatured in acidic environments and cleaved by ________ at pH 2

2. Beginning in the small intestine, secretion of NAHCO3 and pancreatic _________ enzymes degrade substates into free amino acids, dipeptides, and tripeptides.

3. Amino acids are transported into the intestinal cells and released into the blood by _____ amino acid antiporters.

Pepsin, Proteolytic, Na+

Multiple copies of ubiquitin, known as __________, are attached to proteins by an isopeptide bond and are effective destruction signals

Polyubiquitin

_________ residues, including ___________ _____, are the major site for linking addition ubiquitin molecules

Lysine, Lysine 48

Ubiquitin has an extended _____________ terminus, which is activated and linked to proteins targeted for destruction.

The carboxyl-terminal ___________ residue of ubiquitin becomes covalently attached to the ε-amino groups of several ___________ residues on a protein destined to be degrade

Carboxyl, Glycine, Lysine

Mechanisms of Ubiquitin Conjugation:

1. Ubiquitin ___________ enzyme (_____) adenylate Ub and transfers it to a cysteine residue on E1.

2. Ubiquitin ________ enzyme (_____) then transfers Ub to one of its cysteine residues

3. Ubiquitin-________ _______ (_____) uses the E2-Ub complex as a substrate, transferring the Ub to the target protein.

Activating, E1, Conjugating, E2, Protein Ligase, E3

__________ are the specific amino acid sequences that determine the half-life of proteins.

Degrons

The ____-__________ ______ is that the N-terminal amino acid is an important degradation signal in a protein.

N Terminal rule

N-terminal _________ or ________ residues favor rapid ubiquitination, whereas methionine or proline does not

Arginine, Leucine

Aside from certain amino acid residues, degrons include _______ _______ ________ and ___________ sequences

Cyclin destruction Boxes, PEST

The __________ is the organelle responsible for the degradation of ubiquitinated proteins. It consists of two components:

1. The ________ regulatory subunit

2. The _______ catalytic subunit

Proteasome, 19S, 20S

The _______ subunit of the proteasome is made up of 19 smaller subunits. It can recognize ubiquitin, and its receptors bind to _____________ chains

19S, Polyubiquitin

Three Functions of 19S Regulatory Subunit:

1. Its receptors bind to __________ chains

2. An __________ cleaves intact ubiquitin from the target protein for reuse.

3. The doomed protein is unfolded and directed into the catalytic core, ______ subunit.

Polyubiquitin, Isopeptidase, 20S

The 19S complex has six AAA class __________. ATP hydrolysis assists the 19S complex in unfolding the substrate and inducing conformational changes.

ATPases

The proteasome's _______ catalytic subunit is composed of 28 smaller subunits arranged into 4 ____________ rings forming a sealed barrel.

The peptide fragments are further digested to yield free amino acids, which will be used for _____________. Or, the amino group can be removed and processed to _________.

20S, Heteroheptameric Biosynthesis, Urea

The amino acids produced by the proteasome and proteolysis have multiple possible fates:

1. They can be left intact for __________

2. Their _______ ________ can be used for nitrogen disposal by the urea cycle

3. Their ______ _______ can be used in metabolism.

Biosynthesis, Amino Groups, Carbon Skeletons

The major site of amino acid degradation in mammals is the _________

Liver

The first step of amino acid degradation is the removal of ___________.

Amino groups from many amino acids are transferred to ___-___________ to form glutamate, which is then deaminated to form ________

Removal of Nitrogen, a ketoglutarate, NH4+

_______________ (____________) transfer amino groups from an amino acid to α-ketoglutarate to generate glutamate

Aminotransferases, transaminases

Aminotransferases (transaminases) transfer amino groups from an amino acid to α-ketoglutarate to generate ___________

Glutamate

In terrestrial vertebrates (ureotelic organisms), the ultimate fate of the NH4+ is the formation of __________.

Urea

____________ _________ is an enzyme that releases NH4+ by oxidative deamination using NAD+/NADH or NAP+/NADPH.

Glutamate Dehydrogenase

___________ by the help of liver-specific mitochondrial enzymes helps to sequester toxic NH4+

Compartmentalization

________ and ________ are two residues that have dehydratase enzymes that directly deaminate their their respective amino acids.

Serine, Threonine

__________ precedes deamination

Dehydration

Some of the NH4+ formed in the breakdown of amino acids is consumed in the ______________ of nitrogen compounds.

Excess NH4+ is converted into _______ in the liver.

Biosynthesis, Urea

In the formation of urea, one of the nitrogen atoms comes from ___________, while the other nitrogen atom comes from free ________ .

The carbon atom comes from ________ (derived by the hydration of CO2).

Aspartate, NH4+, HCO3-

Urea Cycle:

1. ___________, produced from the breakdown of amino acids, enters the cycle.

2. Ammonia combines with carbon dioxide (CO₂) and ATP to form __________ _________

3. The previous product combines with ornithine to produce ___________, which moves out of the mitochondria.

4. The previous product combines with aspartate to form _______________.

5. The previous product splits into arginine and fumarate. Arginine is then converted to _______ (excreted) and __________ (recycled).

Ammonia, Carbamoyl Phosphate, Citrulline, Argininosuccinate, Urea, Ornithine

Muscle uses branched-chain amino acids as fuel. The first step is NH4+ generation, but the muscle lacks the enzymes of the urea cycle. The nitrogen from these amino acids is transported to the liver by either __________ or _________

Glutamine, Alanine

The urea cycle is linked to ___________ via fumarate

Gluconeogenesis

_____________ can be converted into oxaloacetate by the citric acid cycle and then into glucose by the gluconeogenic pathway.

Fumarate

Fumarate can be converted into ______________ by the citric acid cycle and then into glucose by the gluconeogenic pathway

Oxaloacetate

____________ and ________ are amino acids, but they are not used as building blocks of proteins.

Ornithine, Citruline

(BIG QUESTION) The urea cycle, gluconeogenesis, and the transamination of oxaloacetate are linked by ___________ and _________

Fumarate, Aspartate

The carbon atoms of degraded amino acids emerge as major _____________ ____________.

Metabolic Intermediates

The carbon skeletons of the amino acids are metabolized to ___ major metabolic intermediates

7

Amino acids metabolized to acetyl CoA and acetoacetyl CoA are called ____________ amino acids because they can form fats but not glucose.


Amino acids degraded to the remaining major intermediates are called __________ amino acids because they can be used to synthesize glucose.

Ketogenic, Glucogenic

____-_____________ is an entry point into metabolism for five-carbon amino acids

___________ is an entry point into metabolism for three-carbon amino acids

a ketoglutarate, Pyruvate

Pyruvate is an entry point into metabolism for many (3-carbon) amino acids

Alanine is converted into pyruvate by the action of _________ _______________

___________ is subsequently oxidatively deaminated.

Serine is easily converted into pyruvate by the action of __________ ___________

Other amino acids require more complicated pathways to form pyruvate.

Alanine Aminotransferase, Glutamate, Serine Dehydratase

_______________ is an entry point into metabolism for aspartate and asparagine

Oxaloacetate

Oxaloactate is an entry point into metabolism for ___________ and __________.

Aspartate, Asparagine

Asparagine is hydrolyzed by ____________ to NH4+ and aspartate, which is converted into _____________.

Asparaginase, Oxaloacetate

a-ketoglutarate is an entry point into metabolism for five-carbon amino acids

Step 1: The 5-carbon amino acids are first converted into ____________.

Step 2: This product is deaminated to form ___-_____________.

Glutamate, a ketoglutarate

_____________ is converted into α-ketoglutarate in a reaction sequence that requires the coenzyme tetrahydrofolate.

Glutamine is hydrolyzed by glutaminase to form ____________.

Proline and arginine are converted into glutamate γ-semialdehyde and then to __________

Histidine, Glutamate, Glutamate

Four amino acids are converted into glutamate and eventually a-ketoglutarate:

1. ____________

2. __________

3. __________

4. __________

Glutamine, Proline, Arginine, Histidine

_____________ ________ is a point of entry for several nonpolar amino acids.

Succinyl CoA

_________, ________, and ________ are all amino acids that are ultimately converted to Succinyl CoA in a vitamin B12 dependent reaction

Methionine, Leucine, Valine

The degradation of aromatic amino acids requires _____________.

Oxygenases

The degradation of the aromatic amino acids yields the common intermediates _______________, __________, and __________.

Acetoacetate, Fumarate, Pyruvate

The aromatic amino acids require ________________ for degradation.

monooxygenases

Monooxygenases use ______ as a substrate and incorporate one ___ atom into the product and one into the water

O2, O

Degradation of ________________ begins with hydroxylation to tyrosine. The monooxygenase (phenylalanine hydroxylase) requires the cofactor tetrahydrobiopterin

Phenylalanine

____________ is metabolized to fumarate and acetoacetate.

Tyrosine

____________ degradation requires both monooxygenase and dioxygenase enzymes to metabolize the amino acid to acetoacetate

Tryptophan

_________________ incorporates both atoms of O2 into the product, are used to cleave aromatic rings. Helps with tryptophan cleavage

Dioxygenases

Dioxygenases incorporate both atoms of O2 into the product and are used to cleave __________ ________

aromatic rings

Inherited defects of the urea cycle cause _______________ due to elevated NH4+ in the blood and can lead to brain damage

Hyperammonemia

___________________ deficiency is treated by supplementing the diet with arginine.

Argininosuccinate

Carbamoyl phosphate synthetase deficiency and ornithine transcarbamoylase deficiency lead to the accumulation of __________ in glycine and glutamine

Nitrogen

The addition of ____________ to the diet leads to the excretion of glycine-nitrogen as hippurate, whereas the addition of phenylacetate results in the excretion of phenylacetylglutamine.

Benzoate

______________ is a disease that results from the absence of homogentisate oxidase, an enzyme in the tryptophan degradation pathway.

Homogentisate accumulates and upon excretion, turns the urine dark

Alcaptonuria

In _________ _________ _________ disease, the oxidative decarboxylation of α-ketoacids derived from valine, isoleucine, and leucine is blocked because the branched-chain dehydrogenase is missing or defective. Leads to mental and physical retardation.

Maple Syrup Urine

In Phenylketonuria, _____________ hydroxylase activity is missing or deficient.

Therefore, no ___________ is produced.

Phenylalanine, Tyrosine

________________ is a chemical inhibitor of the proteasome that is used to treat multiple myeloma

Bortezomib

_____________, an inhibitor of the proteasome of M. tuberculosis, shows promise as a treatment for tuberculosis.

HT1171

_____________ (dietary and cellular) are degraded to amino acids.

Proteins

Protein turnover is tightly regulated by mechanisms such as ____________ (______)

Ubiquitination, E1

The first step in amino acid degradation is the removal of ___________.

Nitrogen

In the second step of amino acid degradation, ammonium is converted into _________ in most terrestrial vertebrates

Urea

In the third step of amino acid degradation, the degradation of amino acids generates carbon atoms that become ____________ __________

Metabolic intermediates

____________ errors of metabolism can disrupt amino acid degradation.

Inborn

What two amino acids are essential for blood transport?

Alanine (Ala) and Glutamine (Gln)

Carbamoyl phosphate synthetase deficiency and ornithine transcarbamoylase deficiency lead to the accumulation of nitrogen in _______ and ________

Glycine, Glutamine

___________ __________ _________ deficiency and ornithine transcarbamoylase deficiency lead to the accumulation of nitrogen in glycine and glutamine.

Carbamoyl Phosphate Synthase

The two types of subunits for the proteasome that digests the ubiquitin-tagged proteins are the _______ __________ subunit and the _____ _________ subunit.

19S, 20S

The 2 stages of Amino Acid Degradation:

1. ________________

2. Oxidative deamination of __________ to ammonia

Aminotransferases, Glutamate

In the conversion of ammonium to urea, one of the nitrogen atoms comes from _________ while the other comes from _________

Aspartate, NH4

___________ and _________ are the only purely ketogenic amino acids. All others are either glucogenic or both

Leucine, Lysine

Alcaptonuria is caused by the absence of ___________ ___________.

Homogentisate Oxidase

Maple syrup urine disease is caused by the decarboxylation of _________-___________.

Alpha Ketoacids