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

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83 Terms

1

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

Phenylketonuria

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2

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

Phenylalanine Hydroxylase

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3

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

Ubiquitin

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4

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

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5

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+

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6

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

Polyubiquitin

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7

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

Lysine, Lysine 48

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8

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

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9

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

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10

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

Degrons

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11

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

N Terminal rule

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12

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

Arginine, Leucine

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13

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

Cyclin destruction Boxes, PEST

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14

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

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15

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

19S, Polyubiquitin

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16

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

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17

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

ATPases

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18

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

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19

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

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20

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

Liver

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21

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+

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22

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

Aminotransferases, transaminases

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23

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

Glutamate

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24

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

Urea

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25

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

Glutamate Dehydrogenase

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26

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

Compartmentalization

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27

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

Serine, Threonine

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28

__________ precedes deamination

Dehydration

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29

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

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30

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-

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31

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

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32

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

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33

The urea cycle is linked to ___________ via fumarate

Gluconeogenesis

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34

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

Fumarate

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35

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

Oxaloacetate

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36

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

Ornithine, Citruline

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37

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

Fumarate, Aspartate

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38

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

Metabolic Intermediates

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39

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

7

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40

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

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41

____-_____________ 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

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42

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

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43

_______________ is an entry point into metabolism for aspartate and asparagine

Oxaloacetate

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44

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

Aspartate, Asparagine

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45

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

Asparaginase, Oxaloacetate

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46

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

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47

_____________ 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

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48

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

1. ____________

2. __________

3. __________

4. __________

Glutamine, Proline, Arginine, Histidine

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49

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

Succinyl CoA

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50

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

Methionine, Leucine, Valine

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51

The degradation of aromatic amino acids requires _____________.

Oxygenases

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52

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

Acetoacetate, Fumarate, Pyruvate

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53

The aromatic amino acids require ________________ for degradation.

monooxygenases

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54

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

O2, O

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55

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

Phenylalanine

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56

____________ is metabolized to fumarate and acetoacetate.

Tyrosine

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57

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

Tryptophan

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58

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

Dioxygenases

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59

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

aromatic rings

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60

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

Hyperammonemia

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61

___________________ deficiency is treated by supplementing the diet with arginine.

Argininosuccinate

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62

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

Nitrogen

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63

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

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64

______________ 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

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65

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

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66

In Phenylketonuria, _____________ hydroxylase activity is missing or deficient.

Therefore, no ___________ is produced.

Phenylalanine, Tyrosine

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67

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

Bortezomib

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68

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

HT1171

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69

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

Proteins

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70

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

Ubiquitination, E1

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71

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

Nitrogen

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72

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

Urea

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73

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

Metabolic intermediates

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74

____________ errors of metabolism can disrupt amino acid degradation.

Inborn

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75

What two amino acids are essential for blood transport?

Alanine (Ala) and Glutamine (Gln)

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76

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

Glycine, Glutamine

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77

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

Carbamoyl Phosphate Synthase

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78

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

19S, 20S

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79

The 2 stages of Amino Acid Degradation:

1. ________________

2. Oxidative deamination of __________ to ammonia

Aminotransferases, Glutamate

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80

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

Aspartate, NH4

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81

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

Leucine, Lysine

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82

Alcaptonuria is caused by the absence of ___________ ___________.

Homogentisate Oxidase

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83

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

Alpha Ketoacids

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