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Biochemistry 2019 > Lecture 31 > Flashcards

Lecture 31 Flashcards

1
Q

Describe the 2 things that the low pH of the stomach causes that contribute to the breakdown of proteins in food.

A

The low pH denatures proteins (unfolds them)

Low pH also activates Pepsin

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2
Q

State the 3 enzymes in the small intestine that help break down proteins and state their functions.

A

Dipeptidase: breaks apart dipeptides

Enteropeptidase: cleaves Trypsinogen into it’s active form, Trypsin, in the duodenum

Aminopeptidase: Exopeptidases that chew from the N terminal on peptides

(“DEA” mnemonic)

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3
Q

AA’s, dipeptides, and tripeptides all have what in common?

A

they can all be transported into cells

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4
Q

What are the 2 structures within cells that degrade proteins? which of these does most of the work?

A

The proteasome (does most of the work) and lysosome

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5
Q

Describe the “N-end Rule”

A

N-end Rule: the N-terminal AA identity determines the rate of ubiquitination

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6
Q

Degradation is a form of ______.

A

Regulation

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7
Q

True or False:

Ubiquitin is Reusable. explain

A

True

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8
Q

What is the function of ubiquitin?

A

ubiquitin is a protein that binds to proteins to signal for the proteasome to come degrade them.

When the proteasome is interacting with a ubiquitinated protein, the ubiquitin molecule binds to the proteasome, feeds the protein into the proteasome, and is then released

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9
Q

Describe how ubiquitin is NOT just a degradation signal

A

It can play roles in the cell cycle by either recruiting factors or adding to a protein in disrupting interactions it may have otherwise had with other proteins

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10
Q

The proteasome is an _____, which used ATP to degrade proteins.

A

ATPase

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11
Q

The proteasome has a 20S subunit that is the_______ domain and a 19S subunit that is the _______ domain. Describe how these subunits can fit together to form different types of proteasomes

A

catalytic/proteolytic

Regulatory

Basically, several of the 20S and 19S subunits can come together in forming a proteasome
“The more subunits, the larger the proteasome, however the math does not add up correctly”

(ex. 20S + 19S = 26S proteasome ; 20S + 19S + 19S = 30S proteasome)

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12
Q

Compare the functions of Proteasomes and Cytosolic proteases

A

Proteasome: create AA fragments from proteins

Cytosolic proteases: create INDIVIDUAL AA’s from AA fragments

(these work in a sort of assembly line to fully degrade a protein completely into AA’s)

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13
Q

Describe the specific cellular function that occurs via protein degradation as they pertain to the following “3 R’s”

Reduce:

Reuse:

Recycle:

A

Reduce: dispose of nitrogen through the urea cycle

Reuse: Make new proteins out of AA’s created from old/ingested proteins

Recycle: Repurpose the carbon skeletons of old AA’s that used to compose proteins

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14
Q

State and describe the process by which AA’s are reduced to their “carbon skeleton”. Also include how PLP fits into this process.

A

Deamination: separating the NH3 group from the alpha Carbon, to leave behind a “carbon skeleton”

PLP (pyridoxal phosphate) is ALWAYS the coenzyme for this process
(Pyridoxine aka Vitamin B6 is also a common coenzyme for this process)

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15
Q

Describe the 2-enzyme process by which nearly all AA’s are deaminated. Then describe the 2 AA’s that are deaminated in a different manner.

A
  1. Aminotransferase
  2. Glutamate Dehydrogenase

Serine and Threonine are the 2 AA’s that are deaminated by the action of the single enzyme, Dehydratase

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16
Q

Which AA’s are deaminated by the dehydrogenase and which are deaminated by the dehydratase?

A

Most AA’s = dehydrogenase (glutamate dehydrogenase to be specific)

Serine and Threonine = Dehydratase

17
Q

What 2 enzymes are uniquely specific to each AA so that they will only deaminate their specific AA for which they fit?

A

Aminotransferase and Dehydratase (NOT dehydrogenase)

18
Q

State the 2 step process by which Serine and Threonine are DIRECTLY deaminated by Dehydratase (direct deamination). Then state the molecules that each of these AA’s re deaminated to become.

A
  1. Remove H2O (dehydration)
  2. Add H2O back in order to remove NH4+ (Deamination)

Serine becomes Pyruvate
Threonine becomes alpha-ketobutyrate

19
Q

Describe the 2 steps of Deamination of an AA via the Glutamate reaction.

A
  1. Aminotransferase (either AST/SGOT or ALT/SGPT) uses Alpha-ketoglutarate to split an AA and make glutamate in the following reaction
    (AA + alpha-ketoglutarate = Alpha-keto acid + Glutamate)
  2. Glutamate Dehydrogenase Releases an Ammonium Ion (NH4+) from Glutamate
    (Glutamate to Schiff-base intermediate to (NH4+ leaves here) Alpha-ketoglutarate)
20
Q

Compare AST/SGOT and ALT/SGPT Transaminase)

A

AST/SGOT: Aspartate to OAA
Catalyzes the interconversion of Aspartate and OAA
(Aspartate Aminotransferase/Serum Glutamate-Oxaloacetate Transaminase)

ALT/SGPT: Alanine to Pyruvate
Catalyzes the interconversion of Alanine and Pyruvate
(Alanine Aminotransferase/ Serum Glutamate-Pyruvate

21
Q

What is a toxic byproduct of AA catabolism that can be converted to urea in the liver? where does this urea then go once it is formed in the liver?

A

NH4+ (Ammonium)

Once NH4+ is converted to urea in the liver, it is transported to the kidneys to be excreted

22
Q

Explain the pathway that the NH4+ takes to eventually be excreted when it is formed in AA catabolism in most body tissues (include it’s different forms)

A

NH4+ is added to Glutamate (via glutamate synthetase) to form Glutamine, which can then travel to the liver

Glutaminase then uses water to cleave the NH4+ off of the glutamine, converting it back to glutamate

NH4+ is then excreted as urea

23
Q

Briefly describe the pathway NH4+ takes to be excreted when it is formed in muscle

A

NH4+ is added to pyruvate, forming Alanine, which can then be transported to the liver

Once in the liver, the NH4+ is added to alpha-ketoglutarate to form Glu, which reverts Alanine back to pyruvate

24
Q

Describe the glucose-alanine cycle and where in the body it occurs

A

glucose in the muscle is converted to Pyruvate via glycolysis

Pyruvate becomes Alanine when an NH4+ is added to it so that it can take the NH4+ to the liver.

Once in the liver, the Alanine reverts back to pyruvate after delivering the Nh4+

The Pyruvate now in the liver is converted to glucose via gluconeogenesis and that glucose moves back into the muscles to be used as fuel.

25
Q

Name the 4 “pieces” that compose urea

A

Bicarbonate (HCO3-)

Ammonia

NH2 from Aspartate

O2 from Water

26
Q

What is the “committed step” of the urea cycle? include the enzyme that conducts this step (including what it combines), the allosteric activator of this enzyme, and what supplies the energy needed for this step in the urea cycle.

A

The creation of Carbamoyl Phosphate is the “committed step” of the urea cycle and REQUIRES 2 ATP to provide energy for this step

CPSI (Carbamoyl Phosphate Synthetase I) is the enzyme that make Carbamoyl Phosphate from CO2 + NH3

NAG (N-acetyl glutamate) is the allosteric activator of CPSI

27
Q

State the 2 Non Proteinogenic AA’s involved in the urea cycle and where in the cell they move

A

Ornithine: moves into the mito to combine to become part of carbamoyl phosphate

Citrulline: created from the reaction between Ornithine and Carbamoyl Phosphate and then is exported to the cytoplasm

28
Q

Describe the role of aspartate in the urea cycle

A

Aspartate interacts with citrulline after it exits the mito

Aspartate donates an NH3+ to Citrulline, briefly creating Argininosuccinate

Then Fumarate and Arginine are formed and go their separate ways (arginine stays in the cytoplasm while fumarate enters the mito)

(Citrulline + Aspartate = Argininosuccinate = Arginine + Fumarate)

29
Q

Explain how Fumarate gets converted into OAA after it completes the cytosolic reaction that yields arginine. What is fumarate considered a “derivative” of? How does this process come full circle?

A

After forming Arginine, Fumarate reenters the mito and is converted to OAA via the TCA cycle

Fumarate is considered a derivative of Aspartate

Full Circle: Aspartate to Fumarate (moves to mito) to OAA back to Aspartate (moves to cytosol)

30
Q

What enzyme performs the OAA to Aspartate conversion?

A

SGOT aminotransferase

31
Q

Starting with Arginine in the Urea cycle, Explain how the cycle is completed and Urea is synthesized.

A

Arginine is cleaved by water (hydrolase reaction) into ornithine and this reaction gives off Urea

Ornithine then reenters the mito to become Carbamoyl Phosphate and conduct the urea cycle again.

32
Q

Conduction of the Urea cycle accounts for ___% of the ATP consumption in the liver. How many ATP are used per round of the Urea cycle?

A

50%

4 ATP per round

33
Q

State the 5 AA’s that are converted into Pyruvate when they are catabolized

A

Serine

Threonine

Glycine

Alanine

Cysteine

34
Q

State the 2 AA’s that are converted to Oxaloacetate and the 5 AA’s that are converted to Alpha-ketoglutarate when catabolized

A

Converted to OAA:
Asparagine
Aspartate

Converted to Alpha-ketoglutarate:
Glutamine

Proline (glutamate first)
Arginine (glutamate first)
Histidine (glutamate first)

“(PHAGG)”

35
Q

State the 3 AA’s that are catabolized into Propionyl-CoA in a B12 dependent reaction

A

Methionine

Valine

Isoleucine

36
Q

State the 7 overall “fates” of AA’s when they are catabolized

A
  1. Pyruvate
  2. OAA
  3. Alpha-ketoglutarate
  4. Succinyl-CoA
  5. Fumarate
  6. Acetyl-CoA
  7. Acetoacetate

“(SOAP FAA)”

37
Q

State all of the glucogenic AA’s

A 
Alanine
Arginine
Asparagine
Aspartate
Cysteine
Glycine
Glutamate
Glutamine
Histidine
Methionine
Serine 
Proline
Valine

“(Allen Andersen Always Asks, Can George Go Get His Metal Suit Polished Vigorously?)”

38
Q

State all of the ketogenic AA’s and then all of the AA’s that are both ketogenic and glucogenic.

A

Ketogenic: Lysine and Leucine

Both:
Threonine
Phenylalanine
Isoleucine
Tryptophan
Tyrosine

“(T. PITT)”

39
Q

What does the s in the 20s and 19 s subunits of a proteasome stand for?

A

Sedimentation units (or Svedberg)

Biochemistry 2019 (32 decks)

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