Lecture #16: Protein catabolism

Core concept: Amino acids are ______ with many metabolites in core energy metabolism (pyruvate and TCA pathways)

Interchangeable

Amino acids are interconverted with?

Carboxylic acid intermediates

What needs to be removed from an amino acid in order to be catabolized?

Amino group

When is amino acids consumed/used?

When organismal carbohydrate levels are low or there is an excess of amino acids (amino acids are oxidized for energy)

What are the two rxns that can be utilized to remove the nitrogen from amino acids?

• Transamination: movement of amino group from once carbon skeleton to another

• Deamination: Removal of free ammonium 

What is transamination?

Movement of amino group from one carbon skeleton to another

What is deamination?

Removal of free ammonium

What ae the two fates amino acids are catabolized into?

• Glucogenic: enters a pathway that can lead to formation of glucose 

• Both: enter pathways that can either glucose or ketones

• Ketogenic: enters a pathway that can lead to the formation of ketones 

What can glucogenic amino acids become?

Become glucose

Glucogenic

Enters a pathway that can lead to formation of glucose

• Yields pyruvate or oxaloacetate (reverse rxns in glycogenesis=glucose)

• Can all enter the TCA cycle

When gluconeogenic amino acids become glucose, what does it yield?

Pyruvate or oxaloacetate

What can gluconeogenic amino acids do in the TCA cycle?

They can all enter the TCA cycle

What can ketogenic amino acids cannot become?

CAN NOT be glucose

Ketogenic

Enters a pathway that can lead to the formation of ketones

• Yields acetyl-CoA or acetoacetyl-CoA

• Still requires a ≥4 carbon intermediate to enter TCA

What do ketogenic amino acids yield?

• Acetyl-CoA 

• Acetoacetyl-CoA

What do ketogenic amino acids require for the TCA cycle?

They still require ≥4 carbon intermediate to enter

Why does ketogenic amino acids need a ≥4 carbon intermediate to enter the TCA? 

Acetyl-CoA requires a molecules of oxaloacetate to enter TCA cycle

• Two carbons are fully oxidized and lost as CO2 during reactions 3 and 4 (not acetyl-CoA carbons in the first cycle)

• Net addition(2)/loss(2) of carbon each cycle = 0 

• Acetyl-CoA can never become oxaloacetate without a ≥4 carbon intermediate to bring it into the cycle

What does Acetyl-CoA require to enter the TCA cycle?

Oxaloacetate

What is oxidized and lost in the TCA cycle?

2 carbons are fully oxidized and lost as CO2 during rxns 3 and 4

(not acetyl-CoA carbons in the first cycle)

What is the net addition and loss of carbon in each cycle of the TCA?

Net additions: +2

Loss: -2 

Total carbon: 0

What allows acetyl-CoA to become oxaloacetate?

It needs a ≥4 carbon intermediate to bring it into the cycle

What happens if there is no  ≥4 carbon intermediate?

Acetyl-CoA will never become oxaloacetate and won’t be able to enter the TCA cycle

Amino acids that are glucogenic

Aspartate

Glutamate

Asparagine

Glutamine

Alanine

Arginine

Glycine

Proline

Serine

Histidine

Threonine

Valine

Cysteine

Methionine

Amino acids that are both glucogenic and ketogenic

Phenylalanine

Tyrosine

Tryptophan

Isoleucine

Amino acids that are ketogenic 

Leucine

Lysine 

How does the body deal with nitrogenous waste?

When pH<pka, molecules become protonated to NH4 (ammonium)

What happens deamination occurs at high rates?

Metabolic alkalosis 

What does high ammonium (NH4) push forward?

Glutamate and glutamine synthesis rxn

Glutamate: works as a stimulatory neurotransmitter (this is why we get increased heart rates bc of muscle contraction)

• Removes alpha-ketoglutarate from TCA (this stalls the TCA) 

Glutamate works as what?

Functions as a stimulatory neurotransmitter (this is why we get increased heart rates bc of muscle contraction)

How do mammals excrete nitrogen?

Urea (urea cycle)

Alpha-ketoglutarate (AKG)

A crucial intermediate in the urea cycle, linking amino acid breakdown to nitrogen detoxification. It acts as a "nitrogen scavenger," accepting amino groups from amino acids to form glutamate, which then releases toxic ammonia into the urea cycle for conversion into less harmful urea. AKG is also vital because if the urea cycle fails, it can be depleted by high ammonia levels, which impairs the citric acid cycle in the brain and can cause neurological damage. 

What is the main pathway of nitrogen elimination?

Urea cycle

Where does the urea cycle take place in the cell?

Mitochondria and cytosol

Where do the two nitrogen in urea come from?

1. First nitrogen is from carbamoyl-P

• Synthesized in mitochondria

• Carbamoyl-Phosphate is formed via condensation of free ammonium (from deamination) and CO2

• Requires two ATP per carbamoyl-P formed (carbamoyl-phosphate synthetase)

• Ornithine reacts with carbamoyl-P to form citrulline

• Citrulline (carries the 1 nitrogen) exported to the cytosol

2. Second nitrogen is from aspartate

• Aspartate reacts with citrulline (ATP→ AMP, which = 2 ATP) to form arginosuccinate

• Arginosuccinate split to form arginine and fumarate

• Arginine is hydrolyzed to form Urea (2 nitrogens) and regenerates ornithine

• Ornithine transported back into mitochondria

Where is the first nitrogen coming from in the urea cycle? 

carbamoyl-P

Where does the second nitrogen come from in the urea cycle?

Aspartate

First nitrogen is from carbamoyl-P

• Synthesized in mitochondria

• Carbamoyl-Phosphate is formed via condensation of free ammonium (from deamination) and CO2

• Requires two ATP per carbamoyl-P formed (carbamoyl-phosphate synthetase)

• Ornithine reacts with carbamoyl-P to form citrulline

• Citrulline (carries the 1 nitrogen) exported to the cytosol

Second nitrogen is from aspartate

• Aspartate reacts with citrulline (ATP→ AMP, which = 2 ATP) to form arginosuccinate

• Arginosuccinate split to form arginine and fumarate

• Arginine is hydrolyzed to form Urea (2 nitrogens) and regenerates ornithine

• Ornithine transported back into mitochondria

What is the net cost of the urea cycle?

4 ATP

• 2 ATP to form carbamoyl-P

• 2 ATP to form arginosuccinate (ATP to AMP)

Fumarate can enter where?

Can enter the TCA cycle 

When Fumarate enters the TCA cycle what can it become?

Fumarate can become oxaloacetate

What happens when fumarate enter the TCA cycle and becomes oxaloacetate? 

• Produces one NADH 

• Yields ~2.5 ATP in ETC, ~half of the energy needed for Urea Cycle

Oxaloacetate can be transaminated to what?

Aspartate (nitrogen from glucose)

What can aspartate do in the urea cycle?

It can bring it’s nitrogen back and produce another fumarate molecule.

Which two reactions prepare the carbon skeletons of amino acids for oxidation?

• Transamination 

• Deamination

What is a gluconeogenic intermediate of TCA cycle?

Oxaloacetate (intermediate)

What is a ketogenic intermediate of TCA cycle?

Acetyl-CoA (intermediate)

Which metabolites link the Urea and TCA cycles?

Fumarate, aspartate, NADH